Starting phenix.real_space_refine on Thu Aug 6 14:29:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s7g_54641/08_2026/9s7g_54641.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s7g_54641/08_2026/9s7g_54641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9s7g_54641/08_2026/9s7g_54641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s7g_54641/08_2026/9s7g_54641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9s7g_54641/08_2026/9s7g_54641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s7g_54641/08_2026/9s7g_54641.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 109 5.16 5 C 9645 2.51 5 N 2625 2.21 5 O 2932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15323 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3346 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3349 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain breaks: 1 Chain: "D" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3346 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "C" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3349 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain breaks: 1 Chain: "E" Number of atoms: 1290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1290 Classifications: {'peptide': 159} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 153} Chain: "F" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 7, 'TRANS': 56} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.70, per 1000 atoms: 0.24 Number of scatterers: 15323 At special positions: 0 Unit cell: (99, 121.44, 161.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 109 16.00 P 10 15.00 Mg 2 11.99 O 2932 8.00 N 2625 7.00 C 9645 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 57 " distance=2.04 Simple disulfide: pdb=" SG CYS E 80 " - pdb=" SG CYS E 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 753.8 milliseconds 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3582 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 11 sheets defined 52.4% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 40 through 46 removed outlier: 4.145A pdb=" N LEU B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARG B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 50 Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 109 through 126 removed outlier: 4.464A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.781A pdb=" N THR B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 193 Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 221 through 235 Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.595A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 removed outlier: 4.041A pdb=" N GLN B 334 " --> pdb=" O MET B 330 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN B 337 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.563A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.871A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 removed outlier: 3.701A pdb=" N GLY B 400 " --> pdb=" O HIS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.657A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.752A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 removed outlier: 4.550A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 85 removed outlier: 4.571A pdb=" N GLN A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 114 through 129 removed outlier: 4.064A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.335A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.626A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.729A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 4.065A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 297 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 338 removed outlier: 3.618A pdb=" N LYS A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.937A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.975A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 437 removed outlier: 3.521A pdb=" N PHE A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 29 Processing helix chain 'D' and resid 41 through 46 removed outlier: 4.251A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 70 through 79 removed outlier: 3.848A pdb=" N ASP D 74 " --> pdb=" O PRO D 70 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER D 75 " --> pdb=" O GLY D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 109 through 126 removed outlier: 4.333A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 removed outlier: 3.788A pdb=" N THR D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.778A pdb=" N LEU D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 211 Processing helix chain 'D' and resid 221 through 235 Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 276 through 280 removed outlier: 3.568A pdb=" N GLN D 279 " --> pdb=" O ARG D 276 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 280 " --> pdb=" O GLY D 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 276 through 280' Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.878A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.619A pdb=" N MET D 330 " --> pdb=" O VAL D 326 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.662A pdb=" N PHE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 374 through 391 removed outlier: 3.800A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 425 removed outlier: 3.827A pdb=" N ALA D 411 " --> pdb=" O GLU D 407 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU D 412 " --> pdb=" O PHE D 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 48 through 51 removed outlier: 4.140A pdb=" N THR C 51 " --> pdb=" O SER C 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 51' Processing helix chain 'C' and resid 72 through 81 removed outlier: 3.898A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 102 through 108 Processing helix chain 'C' and resid 110 through 113 Processing helix chain 'C' and resid 114 through 129 removed outlier: 3.953A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N CYS C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.507A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 Processing helix chain 'C' and resid 206 through 216 Processing helix chain 'C' and resid 223 through 244 removed outlier: 3.588A pdb=" N LEU C 227 " --> pdb=" O THR C 223 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 removed outlier: 4.450A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.954A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 297 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.510A pdb=" N VAL C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.941A pdb=" N ALA C 387 " --> pdb=" O ALA C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 414 through 437 removed outlier: 3.689A pdb=" N PHE C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 Processing helix chain 'E' and resid 21 through 36 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.644A pdb=" N VAL E 49 " --> pdb=" O SER E 45 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR E 56 " --> pdb=" O TYR E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 87 removed outlier: 3.991A pdb=" N HIS E 87 " --> pdb=" O PHE E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 104 Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 139 through 157 Processing helix chain 'F' and resid 119 through 121 No H-bonds generated for 'chain 'F' and resid 119 through 121' Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 92 removed outlier: 7.759A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N VAL B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N HIS B 6 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL B 5 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 134 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET B 164 " --> pdb=" O GLU B 198 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 268 through 271 removed outlier: 3.636A pdb=" N SER B 364 " --> pdb=" O ARG B 318 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR B 312 " --> pdb=" O ASN B 370 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 93 through 94 removed outlier: 7.860A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N SER A 140 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 137 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N HIS A 139 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.620A pdb=" N ALA A 273 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N CYS A 376 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 90 through 92 removed outlier: 7.861A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N VAL D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS D 6 " --> pdb=" O VAL D 64 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 134 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HIS D 137 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 51 through 53 removed outlier: 3.547A pdb=" N VAL D 60 " --> pdb=" O ASN D 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'C' and resid 93 through 94 removed outlier: 7.762A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER C 140 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N PHE C 135 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N PHE C 169 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL C 137 " --> pdb=" O PHE C 169 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ILE C 171 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N HIS C 139 " --> pdb=" O ILE C 171 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N LYS C 166 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N PHE C 202 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLU C 168 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL C 204 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N SER C 170 " --> pdb=" O VAL C 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 55 removed outlier: 3.534A pdb=" N VAL C 62 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.637A pdb=" N ALA C 273 " --> pdb=" O VAL C 375 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 69 through 71 removed outlier: 5.731A pdb=" N VAL F 94 " --> pdb=" O GLU F 108 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU F 108 " --> pdb=" O VAL F 94 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY F 114 " --> pdb=" O GLY F 107 " (cutoff:3.500A) 698 hydrogen bonds defined for protein. 2028 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 1.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5092 1.34 - 1.47: 3684 1.47 - 1.59: 6710 1.59 - 1.71: 16 1.71 - 1.84: 170 Bond restraints: 15672 Sorted by residual: bond pdb=" C5 GDP D 501 " pdb=" C4 GDP D 501 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" C5 GDP B 501 " pdb=" C4 GDP B 501 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" CB GLN D 83 " pdb=" CG GLN D 83 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CG LEU C 152 " pdb=" CD2 LEU C 152 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.36e+00 bond pdb=" CB GLU B 111 " pdb=" CG GLU B 111 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.20e+00 ... (remaining 15667 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 20745 1.89 - 3.77: 438 3.77 - 5.66: 68 5.66 - 7.55: 17 7.55 - 9.43: 6 Bond angle restraints: 21274 Sorted by residual: angle pdb=" CA GLN D 83 " pdb=" CB GLN D 83 " pdb=" CG GLN D 83 " ideal model delta sigma weight residual 114.10 121.12 -7.02 2.00e+00 2.50e-01 1.23e+01 angle pdb=" C ASP F 118 " pdb=" N ASN F 119 " pdb=" CA ASN F 119 " ideal model delta sigma weight residual 122.31 115.55 6.76 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CB GLN D 83 " pdb=" CG GLN D 83 " pdb=" CD GLN D 83 " ideal model delta sigma weight residual 112.60 118.03 -5.43 1.70e+00 3.46e-01 1.02e+01 angle pdb=" CA GLU C 168 " pdb=" CB GLU C 168 " pdb=" CG GLU C 168 " ideal model delta sigma weight residual 114.10 120.03 -5.93 2.00e+00 2.50e-01 8.79e+00 angle pdb=" CA GLU D 383 " pdb=" CB GLU D 383 " pdb=" CG GLU D 383 " ideal model delta sigma weight residual 114.10 119.98 -5.88 2.00e+00 2.50e-01 8.63e+00 ... (remaining 21269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.08: 8737 31.08 - 62.17: 577 62.17 - 93.25: 33 93.25 - 124.33: 3 124.33 - 155.41: 4 Dihedral angle restraints: 9354 sinusoidal: 3777 harmonic: 5577 Sorted by residual: dihedral pdb=" O5' GTP C 501 " pdb=" O3A GTP C 501 " pdb=" PA GTP C 501 " pdb=" PB GTP C 501 " ideal model delta sinusoidal sigma weight residual -85.88 69.54 -155.41 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -154.52 -136.21 1 2.00e+01 2.50e-03 4.13e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -28.54 133.13 1 2.00e+01 2.50e-03 4.04e+01 ... (remaining 9351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1352 0.032 - 0.065: 648 0.065 - 0.097: 220 0.097 - 0.130: 97 0.130 - 0.162: 10 Chirality restraints: 2327 Sorted by residual: chirality pdb=" CG LEU C 152 " pdb=" CB LEU C 152 " pdb=" CD1 LEU C 152 " pdb=" CD2 LEU C 152 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CB THR C 334 " pdb=" CA THR C 334 " pdb=" OG1 THR C 334 " pdb=" CG2 THR C 334 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CB ILE D 345 " pdb=" CA ILE D 345 " pdb=" CG1 ILE D 345 " pdb=" CG2 ILE D 345 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 2324 not shown) Planarity restraints: 2766 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 286 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO B 287 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 103 " 0.011 2.00e-02 2.50e+03 1.47e-02 4.33e+00 pdb=" CG TYR C 103 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR C 103 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR C 103 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR C 103 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR C 103 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 103 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 103 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 286 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO D 287 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 287 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 287 " 0.026 5.00e-02 4.00e+02 ... (remaining 2763 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 12 2.48 - 3.09: 10675 3.09 - 3.69: 24696 3.69 - 4.30: 35509 4.30 - 4.90: 59041 Nonbonded interactions: 129933 Sorted by model distance: nonbonded pdb=" O1G GTP A 501 " pdb="MG MG A 502 " model vdw 1.876 2.170 nonbonded pdb=" O1G GTP C 501 " pdb="MG MG C 502 " model vdw 1.946 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 1.962 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.976 2.170 nonbonded pdb=" O3B GTP C 501 " pdb="MG MG C 502 " model vdw 2.194 2.170 ... (remaining 129928 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 6.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.360 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 0.041 15674 Z= 0.164 Angle : 0.690 9.435 21278 Z= 0.354 Chirality : 0.045 0.162 2327 Planarity : 0.005 0.053 2766 Dihedral : 18.848 155.412 5766 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.95 % Allowed : 28.80 % Favored : 66.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.19), residues: 1913 helix: 0.90 (0.18), residues: 867 sheet: -1.21 (0.32), residues: 285 loop : -1.02 (0.22), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 320 TYR 0.035 0.001 TYR C 103 PHE 0.029 0.002 PHE C 49 TRP 0.012 0.002 TRP D 344 HIS 0.019 0.001 HIS E 154 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (15672) covalent geometry : angle 0.68789 / 0.35 (21274) SS BOND : bond 0.00465 / 0.24 ( 2) SS BOND : angle 3.57760 / 1.78 ( 4) hydrogen bonds : bond 0.15357 / 9.84 ( 698) hydrogen bonds : angle 6.74394 / 4.96 ( 2028) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 476 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 ARG cc_start: 0.6496 (mmt180) cc_final: 0.6032 (mmt-90) REVERT: B 108 GLU cc_start: 0.6502 (tp30) cc_final: 0.6229 (tp30) REVERT: B 121 ARG cc_start: 0.7944 (mtm180) cc_final: 0.7602 (mtm180) REVERT: B 255 VAL cc_start: 0.8686 (OUTLIER) cc_final: 0.8368 (t) REVERT: B 343 GLU cc_start: 0.7140 (tt0) cc_final: 0.6874 (tt0) REVERT: B 374 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.7994 (tp) REVERT: B 405 GLU cc_start: 0.7109 (mp0) cc_final: 0.6685 (mp0) REVERT: B 416 ASN cc_start: 0.6661 (OUTLIER) cc_final: 0.6443 (t0) REVERT: B 423 GLN cc_start: 0.6896 (mm110) cc_final: 0.6687 (mm110) REVERT: A 50 ASN cc_start: 0.8349 (t0) cc_final: 0.8073 (t0) REVERT: A 74 VAL cc_start: 0.8714 (p) cc_final: 0.8451 (m) REVERT: A 77 GLU cc_start: 0.6156 (mp0) cc_final: 0.5794 (mp0) REVERT: A 90 GLU cc_start: 0.7586 (tp30) cc_final: 0.7376 (tp30) REVERT: A 141 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: A 149 PHE cc_start: 0.7451 (t80) cc_final: 0.7068 (t80) REVERT: A 154 MET cc_start: 0.7816 (mmm) cc_final: 0.7123 (mmt) REVERT: A 164 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7708 (mttp) REVERT: A 170 SER cc_start: 0.7386 (OUTLIER) cc_final: 0.7161 (p) REVERT: A 172 TYR cc_start: 0.7942 (t80) cc_final: 0.7410 (t80) REVERT: A 258 ASN cc_start: 0.7099 (m-40) cc_final: 0.6725 (m-40) REVERT: A 288 VAL cc_start: 0.8030 (m) cc_final: 0.7622 (t) REVERT: A 326 LYS cc_start: 0.7607 (tmmt) cc_final: 0.7291 (tptt) REVERT: A 418 PHE cc_start: 0.7375 (m-80) cc_final: 0.7111 (m-80) REVERT: D 3 GLU cc_start: 0.6439 (mp0) cc_final: 0.6209 (pm20) REVERT: D 14 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7610 (m-40) REVERT: D 25 SER cc_start: 0.8080 (OUTLIER) cc_final: 0.7705 (m) REVERT: D 41 ASP cc_start: 0.7307 (t0) cc_final: 0.6947 (t0) REVERT: D 83 GLN cc_start: 0.7112 (pm20) cc_final: 0.6890 (pm20) REVERT: D 92 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7273 (p90) REVERT: D 128 ASP cc_start: 0.5824 (p0) cc_final: 0.5576 (p0) REVERT: D 147 MET cc_start: 0.7665 (ptm) cc_final: 0.7320 (ttp) REVERT: D 205 GLU cc_start: 0.7109 (tp30) cc_final: 0.6846 (mp0) REVERT: D 209 ASP cc_start: 0.7579 (t0) cc_final: 0.7218 (t0) REVERT: D 228 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7451 (mm) REVERT: D 233 MET cc_start: 0.5623 (ptt) cc_final: 0.5185 (ttp) REVERT: D 256 ASN cc_start: 0.7025 (m-40) cc_final: 0.6644 (m-40) REVERT: D 267 MET cc_start: 0.5920 (ttt) cc_final: 0.5576 (ttt) REVERT: D 299 MET cc_start: 0.7517 (mmm) cc_final: 0.7155 (mmm) REVERT: D 389 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6655 (m-80) REVERT: C 80 THR cc_start: 0.8105 (t) cc_final: 0.7868 (t) REVERT: C 150 THR cc_start: 0.7332 (m) cc_final: 0.6917 (m) REVERT: C 154 MET cc_start: 0.7451 (mmt) cc_final: 0.7149 (mmm) REVERT: C 158 SER cc_start: 0.8509 (m) cc_final: 0.8166 (p) REVERT: C 172 TYR cc_start: 0.7095 (t80) cc_final: 0.6694 (t80) REVERT: C 214 ARG cc_start: 0.7539 (ttp80) cc_final: 0.7308 (ttp80) REVERT: C 234 ILE cc_start: 0.7879 (mm) cc_final: 0.7633 (mt) REVERT: C 329 ASN cc_start: 0.6742 (t0) cc_final: 0.6453 (t0) REVERT: E 10 SER cc_start: 0.8508 (m) cc_final: 0.8116 (t) REVERT: E 47 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7115 (pm20) outliers start: 82 outliers final: 58 residues processed: 517 average time/residue: 0.1476 time to fit residues: 108.8937 Evaluate side-chains 528 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 458 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 379 LYS Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 11 GLN Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 172 SER Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 435 VAL Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 15 GLN A 18 ASN A 61 HIS D 11 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 11 GLN C 356 ASN ** E 35 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 = 0.3971 r_free = 0.3971 target = 0.148318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.131339 restraints weight = 22348.100| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.03 r_work: 0.3626 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15674 Z= 0.152 Angle : 0.611 10.936 21278 Z= 0.307 Chirality : 0.044 0.155 2327 Planarity : 0.004 0.058 2766 Dihedral : 11.646 156.464 2283 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 6.40 % Allowed : 26.21 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 1913 helix: 1.17 (0.18), residues: 861 sheet: -1.26 (0.33), residues: 262 loop : -0.96 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 123 TYR 0.021 0.001 TYR C 103 PHE 0.017 0.001 PHE D 367 TRP 0.013 0.002 TRP B 344 HIS 0.004 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (15672) covalent geometry : angle 0.61054 / 0.31 (21274) SS BOND : bond 0.00377 / 0.19 ( 2) SS BOND : angle 2.42052 / 1.20 ( 4) hydrogen bonds : bond 0.04575 / 3.05 ( 698) hydrogen bonds : angle 5.08931 / 3.70 ( 2028) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 457 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8216 (m) REVERT: B 86 ARG cc_start: 0.6796 (mmt180) cc_final: 0.6336 (mmt-90) REVERT: B 157 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8072 (mm-30) REVERT: B 255 VAL cc_start: 0.8820 (p) cc_final: 0.8535 (t) REVERT: B 273 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7166 (mp) REVERT: B 318 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7981 (mtt-85) REVERT: B 321 MET cc_start: 0.8525 (ptp) cc_final: 0.8266 (ptp) REVERT: B 343 GLU cc_start: 0.8311 (tt0) cc_final: 0.7981 (tt0) REVERT: B 405 GLU cc_start: 0.7638 (mp0) cc_final: 0.7155 (mp0) REVERT: A 1 MET cc_start: 0.7112 (pmm) cc_final: 0.6797 (pmm) REVERT: A 50 ASN cc_start: 0.8475 (t0) cc_final: 0.7957 (t0) REVERT: A 74 VAL cc_start: 0.8745 (p) cc_final: 0.8476 (m) REVERT: A 77 GLU cc_start: 0.6903 (mt-10) cc_final: 0.6544 (mp0) REVERT: A 90 GLU cc_start: 0.8475 (tp30) cc_final: 0.8228 (tp30) REVERT: A 141 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.7648 (m-80) REVERT: A 149 PHE cc_start: 0.7751 (t80) cc_final: 0.7351 (t80) REVERT: A 154 MET cc_start: 0.8098 (mmm) cc_final: 0.7492 (mmt) REVERT: A 172 TYR cc_start: 0.8278 (t80) cc_final: 0.7504 (t80) REVERT: A 243 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7566 (mtp180) REVERT: A 258 ASN cc_start: 0.7721 (m-40) cc_final: 0.7321 (m-40) REVERT: A 288 VAL cc_start: 0.8170 (m) cc_final: 0.7780 (t) REVERT: A 326 LYS cc_start: 0.7951 (tmmt) cc_final: 0.7296 (tppt) REVERT: A 386 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.5343 (pt0) REVERT: D 14 ASN cc_start: 0.8167 (OUTLIER) cc_final: 0.7966 (m-40) REVERT: D 25 SER cc_start: 0.8274 (t) cc_final: 0.8046 (m) REVERT: D 41 ASP cc_start: 0.7665 (t0) cc_final: 0.7154 (t0) REVERT: D 128 ASP cc_start: 0.6558 (p0) cc_final: 0.6295 (p0) REVERT: D 179 VAL cc_start: 0.7593 (p) cc_final: 0.7381 (t) REVERT: D 205 GLU cc_start: 0.7784 (tp30) cc_final: 0.7313 (mp0) REVERT: D 209 ASP cc_start: 0.8228 (t0) cc_final: 0.7883 (t0) REVERT: D 224 ASP cc_start: 0.7322 (m-30) cc_final: 0.6820 (m-30) REVERT: D 228 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7624 (mm) REVERT: D 233 MET cc_start: 0.6665 (ptt) cc_final: 0.6062 (ttp) REVERT: D 240 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8164 (tp) REVERT: D 267 MET cc_start: 0.7072 (ttt) cc_final: 0.6627 (ttt) REVERT: D 299 MET cc_start: 0.7823 (mmm) cc_final: 0.7201 (mmm) REVERT: D 336 LYS cc_start: 0.6746 (mmtp) cc_final: 0.6478 (mmtp) REVERT: D 389 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6880 (m-80) REVERT: C 80 THR cc_start: 0.8148 (t) cc_final: 0.7938 (t) REVERT: C 97 GLU cc_start: 0.6749 (tp30) cc_final: 0.6523 (tp30) REVERT: C 150 THR cc_start: 0.7555 (m) cc_final: 0.7206 (m) REVERT: C 158 SER cc_start: 0.8743 (m) cc_final: 0.8348 (p) REVERT: C 169 PHE cc_start: 0.7496 (t80) cc_final: 0.7268 (t80) REVERT: C 203 MET cc_start: 0.8102 (mmt) cc_final: 0.7774 (mmm) REVERT: C 214 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7534 (ttp80) REVERT: C 234 ILE cc_start: 0.8118 (mm) cc_final: 0.7841 (mt) REVERT: C 243 ARG cc_start: 0.7675 (mtm-85) cc_final: 0.7447 (mtm-85) REVERT: C 245 ASP cc_start: 0.7399 (p0) cc_final: 0.7122 (p0) REVERT: C 329 ASN cc_start: 0.7597 (t0) cc_final: 0.7292 (t0) REVERT: C 343 PHE cc_start: 0.8477 (m-10) cc_final: 0.8113 (m-80) REVERT: C 425 MET cc_start: 0.7449 (tpp) cc_final: 0.7061 (mmm) REVERT: E 10 SER cc_start: 0.8512 (m) cc_final: 0.8100 (t) REVERT: E 47 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7462 (pm20) outliers start: 106 outliers final: 54 residues processed: 522 average time/residue: 0.1450 time to fit residues: 108.7216 Evaluate side-chains 508 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 443 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain D residue 14 ASN Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 379 SER Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 152 ILE Chi-restraints excluded: chain E residue 154 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 81 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 ASN A 61 HIS A 256 GLN D 195 ASN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.145581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.128638 restraints weight = 22510.320| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.01 r_work: 0.3579 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15674 Z= 0.204 Angle : 0.628 10.357 21278 Z= 0.315 Chirality : 0.045 0.170 2327 Planarity : 0.004 0.060 2766 Dihedral : 10.847 156.054 2201 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 8.21 % Allowed : 23.79 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.19), residues: 1913 helix: 1.00 (0.17), residues: 875 sheet: -1.19 (0.33), residues: 262 loop : -1.01 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 123 TYR 0.017 0.002 TYR B 183 PHE 0.019 0.002 PHE C 395 TRP 0.014 0.002 TRP C 21 HIS 0.007 0.001 HIS B 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (15672) covalent geometry : angle 0.62727 / 0.31 (21274) SS BOND : bond 0.01010 / 0.53 ( 2) SS BOND : angle 2.74009 / 1.49 ( 4) hydrogen bonds : bond 0.04515 / 3.03 ( 698) hydrogen bonds : angle 4.96453 / 3.61 ( 2028) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 468 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8249 (m) REVERT: B 26 ASP cc_start: 0.8009 (t0) cc_final: 0.7806 (t0) REVERT: B 86 ARG cc_start: 0.6340 (mmt180) cc_final: 0.5838 (mmt-90) REVERT: B 108 GLU cc_start: 0.7522 (tp30) cc_final: 0.6849 (tp30) REVERT: B 143 THR cc_start: 0.7274 (m) cc_final: 0.6928 (m) REVERT: B 155 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8420 (mt) REVERT: B 157 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8057 (mm-30) REVERT: B 209 ASP cc_start: 0.8067 (t0) cc_final: 0.7099 (t0) REVERT: B 213 ARG cc_start: 0.7514 (mtm180) cc_final: 0.7302 (mtm-85) REVERT: B 255 VAL cc_start: 0.8811 (p) cc_final: 0.8557 (t) REVERT: B 262 ARG cc_start: 0.7923 (mtp85) cc_final: 0.7545 (mtp85) REVERT: B 273 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7300 (mp) REVERT: B 318 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7972 (mtt-85) REVERT: B 321 MET cc_start: 0.8579 (ptp) cc_final: 0.8305 (ptp) REVERT: B 343 GLU cc_start: 0.8317 (tt0) cc_final: 0.7983 (tt0) REVERT: B 405 GLU cc_start: 0.7597 (mp0) cc_final: 0.7149 (mp0) REVERT: A 50 ASN cc_start: 0.8522 (t0) cc_final: 0.7953 (t0) REVERT: A 74 VAL cc_start: 0.8756 (p) cc_final: 0.8462 (m) REVERT: A 77 GLU cc_start: 0.6794 (mt-10) cc_final: 0.6529 (mp0) REVERT: A 90 GLU cc_start: 0.8465 (tp30) cc_final: 0.8189 (tp30) REVERT: A 108 TYR cc_start: 0.8266 (m-80) cc_final: 0.7192 (m-80) REVERT: A 141 PHE cc_start: 0.8770 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: A 149 PHE cc_start: 0.7767 (t80) cc_final: 0.7441 (t80) REVERT: A 154 MET cc_start: 0.8094 (mmm) cc_final: 0.7615 (mmt) REVERT: A 164 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7918 (mttp) REVERT: A 170 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7616 (p) REVERT: A 172 TYR cc_start: 0.8279 (t80) cc_final: 0.7529 (t80) REVERT: A 254 GLU cc_start: 0.3506 (mm-30) cc_final: 0.2708 (mm-30) REVERT: A 258 ASN cc_start: 0.7853 (m-40) cc_final: 0.7469 (m-40) REVERT: A 288 VAL cc_start: 0.8153 (m) cc_final: 0.7794 (t) REVERT: A 326 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7869 (tptt) REVERT: D 2 ARG cc_start: 0.7319 (OUTLIER) cc_final: 0.6535 (pmt-80) REVERT: D 25 SER cc_start: 0.8271 (t) cc_final: 0.7950 (m) REVERT: D 26 ASP cc_start: 0.7768 (t70) cc_final: 0.7533 (t0) REVERT: D 41 ASP cc_start: 0.7622 (t0) cc_final: 0.7159 (t0) REVERT: D 128 ASP cc_start: 0.6633 (p0) cc_final: 0.6383 (p0) REVERT: D 205 GLU cc_start: 0.7677 (tp30) cc_final: 0.7216 (mp0) REVERT: D 209 ASP cc_start: 0.8334 (t0) cc_final: 0.8079 (t0) REVERT: D 224 ASP cc_start: 0.7359 (m-30) cc_final: 0.6840 (m-30) REVERT: D 228 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7574 (mm) REVERT: D 264 HIS cc_start: 0.8238 (p90) cc_final: 0.7936 (p90) REVERT: D 267 MET cc_start: 0.7205 (ttt) cc_final: 0.6612 (ttt) REVERT: D 280 GLN cc_start: 0.7819 (mm-40) cc_final: 0.7224 (mt0) REVERT: D 299 MET cc_start: 0.8045 (mmm) cc_final: 0.7272 (mmm) REVERT: D 336 LYS cc_start: 0.7032 (mmtp) cc_final: 0.6728 (mmtp) REVERT: D 347 ASN cc_start: 0.6869 (OUTLIER) cc_final: 0.6610 (t0) REVERT: D 389 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.6757 (m-80) REVERT: C 80 THR cc_start: 0.8200 (t) cc_final: 0.7987 (t) REVERT: C 97 GLU cc_start: 0.6928 (tp30) cc_final: 0.6703 (tp30) REVERT: C 150 THR cc_start: 0.7412 (m) cc_final: 0.7203 (m) REVERT: C 154 MET cc_start: 0.7932 (mmm) cc_final: 0.7722 (mmt) REVERT: C 158 SER cc_start: 0.8790 (m) cc_final: 0.8412 (p) REVERT: C 169 PHE cc_start: 0.7592 (t80) cc_final: 0.7343 (t80) REVERT: C 183 GLU cc_start: 0.7498 (tt0) cc_final: 0.7254 (tt0) REVERT: C 203 MET cc_start: 0.8134 (mmt) cc_final: 0.7800 (mmm) REVERT: C 214 ARG cc_start: 0.8187 (ttp80) cc_final: 0.7718 (ttp80) REVERT: C 221 ARG cc_start: 0.7835 (ptp90) cc_final: 0.7545 (mtm-85) REVERT: C 234 ILE cc_start: 0.8106 (mm) cc_final: 0.7842 (mt) REVERT: C 243 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.6854 (mtm-85) REVERT: C 245 ASP cc_start: 0.7460 (p0) cc_final: 0.7223 (p0) REVERT: C 329 ASN cc_start: 0.7713 (t0) cc_final: 0.7408 (t0) REVERT: C 343 PHE cc_start: 0.8554 (m-10) cc_final: 0.8249 (m-80) REVERT: C 425 MET cc_start: 0.7425 (tpp) cc_final: 0.7128 (tpp) REVERT: E 47 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7397 (pm20) outliers start: 136 outliers final: 81 residues processed: 545 average time/residue: 0.1405 time to fit residues: 110.5674 Evaluate side-chains 549 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 455 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 389 PHE Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 372 GLN Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 92 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 47 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 chunk 157 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN A 61 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN D 131 GLN ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.147334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.130258 restraints weight = 22508.821| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.05 r_work: 0.3609 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15674 Z= 0.140 Angle : 0.594 9.926 21278 Z= 0.298 Chirality : 0.043 0.186 2327 Planarity : 0.004 0.057 2766 Dihedral : 10.588 156.446 2196 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 6.94 % Allowed : 26.39 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.19), residues: 1913 helix: 1.14 (0.18), residues: 871 sheet: -1.16 (0.33), residues: 262 loop : -1.00 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 123 TYR 0.013 0.001 TYR B 183 PHE 0.017 0.001 PHE A 296 TRP 0.013 0.001 TRP C 21 HIS 0.004 0.001 HIS E 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (15672) covalent geometry : angle 0.59254 / 0.30 (21274) SS BOND : bond 0.00455 / 0.24 ( 2) SS BOND : angle 3.05568 / 1.69 ( 4) hydrogen bonds : bond 0.04055 / 2.73 ( 698) hydrogen bonds : angle 4.79730 / 3.47 ( 2028) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 469 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8243 (m) REVERT: B 86 ARG cc_start: 0.6870 (mmt180) cc_final: 0.6410 (mmt-90) REVERT: B 143 THR cc_start: 0.7359 (m) cc_final: 0.7044 (m) REVERT: B 157 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7991 (mm-30) REVERT: B 209 ASP cc_start: 0.8076 (t0) cc_final: 0.7039 (t0) REVERT: B 252 LYS cc_start: 0.7773 (mttt) cc_final: 0.7546 (mttt) REVERT: B 255 VAL cc_start: 0.8812 (p) cc_final: 0.8543 (t) REVERT: B 262 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7612 (mtp85) REVERT: B 318 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7974 (mtt-85) REVERT: B 343 GLU cc_start: 0.8330 (tt0) cc_final: 0.7996 (tt0) REVERT: B 405 GLU cc_start: 0.7520 (mp0) cc_final: 0.7120 (mp0) REVERT: A 50 ASN cc_start: 0.8574 (t0) cc_final: 0.8188 (t0) REVERT: A 74 VAL cc_start: 0.8764 (p) cc_final: 0.8534 (m) REVERT: A 90 GLU cc_start: 0.8494 (tp30) cc_final: 0.8232 (tp30) REVERT: A 108 TYR cc_start: 0.8287 (m-80) cc_final: 0.7310 (m-80) REVERT: A 141 PHE cc_start: 0.8783 (OUTLIER) cc_final: 0.7697 (m-80) REVERT: A 154 MET cc_start: 0.8078 (mmm) cc_final: 0.7524 (mmm) REVERT: A 164 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7936 (ttmm) REVERT: A 170 SER cc_start: 0.7950 (OUTLIER) cc_final: 0.7592 (p) REVERT: A 172 TYR cc_start: 0.8237 (t80) cc_final: 0.7450 (t80) REVERT: A 258 ASN cc_start: 0.7819 (m-40) cc_final: 0.7372 (m-40) REVERT: A 288 VAL cc_start: 0.8123 (m) cc_final: 0.7764 (t) REVERT: A 326 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7826 (tptt) REVERT: A 386 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.5164 (pt0) REVERT: A 393 HIS cc_start: 0.7397 (t70) cc_final: 0.6937 (t70) REVERT: D 2 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6576 (pmt-80) REVERT: D 25 SER cc_start: 0.8248 (t) cc_final: 0.7981 (m) REVERT: D 41 ASP cc_start: 0.7602 (t0) cc_final: 0.7141 (t0) REVERT: D 92 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7691 (p90) REVERT: D 111 GLU cc_start: 0.7377 (mt-10) cc_final: 0.6922 (mt-10) REVERT: D 205 GLU cc_start: 0.7675 (tp30) cc_final: 0.7247 (mp0) REVERT: D 209 ASP cc_start: 0.8332 (t0) cc_final: 0.8075 (t0) REVERT: D 224 ASP cc_start: 0.7362 (m-30) cc_final: 0.6888 (m-30) REVERT: D 228 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7597 (mm) REVERT: D 233 MET cc_start: 0.6947 (ptt) cc_final: 0.6739 (ttp) REVERT: D 267 MET cc_start: 0.7167 (ttt) cc_final: 0.6555 (ttt) REVERT: D 280 GLN cc_start: 0.7765 (mm-40) cc_final: 0.7278 (mt0) REVERT: D 285 THR cc_start: 0.7477 (OUTLIER) cc_final: 0.7145 (t) REVERT: D 287 PRO cc_start: 0.7834 (Cg_exo) cc_final: 0.7589 (Cg_endo) REVERT: D 293 MET cc_start: 0.7394 (mmm) cc_final: 0.6898 (mtt) REVERT: D 299 MET cc_start: 0.7943 (mmm) cc_final: 0.7319 (mmm) REVERT: D 336 LYS cc_start: 0.7245 (mmtp) cc_final: 0.6858 (mmtp) REVERT: D 350 LYS cc_start: 0.7481 (tptp) cc_final: 0.7123 (tptp) REVERT: D 426 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.5993 (tp-100) REVERT: C 22 GLU cc_start: 0.7883 (tt0) cc_final: 0.7612 (tt0) REVERT: C 80 THR cc_start: 0.8191 (t) cc_final: 0.7970 (t) REVERT: C 97 GLU cc_start: 0.6843 (tp30) cc_final: 0.6617 (tp30) REVERT: C 105 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7818 (mtp180) REVERT: C 154 MET cc_start: 0.7990 (mmm) cc_final: 0.7740 (mmt) REVERT: C 158 SER cc_start: 0.8790 (m) cc_final: 0.8424 (p) REVERT: C 194 THR cc_start: 0.7480 (p) cc_final: 0.7192 (t) REVERT: C 203 MET cc_start: 0.8103 (mmt) cc_final: 0.7818 (mmm) REVERT: C 214 ARG cc_start: 0.8129 (ttp80) cc_final: 0.7704 (ttp80) REVERT: C 221 ARG cc_start: 0.7879 (ptp90) cc_final: 0.7624 (mtm-85) REVERT: C 234 ILE cc_start: 0.8138 (mm) cc_final: 0.7860 (mt) REVERT: C 243 ARG cc_start: 0.7485 (mtm-85) cc_final: 0.6822 (mtm-85) REVERT: C 271 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8193 (m) REVERT: C 329 ASN cc_start: 0.7644 (t0) cc_final: 0.7346 (t0) REVERT: C 343 PHE cc_start: 0.8547 (m-10) cc_final: 0.8174 (m-80) REVERT: C 425 MET cc_start: 0.7374 (tpp) cc_final: 0.7012 (tpp) REVERT: E 35 ASN cc_start: 0.4543 (OUTLIER) cc_final: 0.4323 (t0) REVERT: E 47 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7496 (pm20) outliers start: 115 outliers final: 75 residues processed: 539 average time/residue: 0.1435 time to fit residues: 111.1052 Evaluate side-chains 554 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 463 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 GLN Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 426 GLN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 105 ARG Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 152 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 129 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 117 optimal weight: 0.2980 chunk 180 optimal weight: 3.9990 chunk 148 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN A 18 ASN A 61 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.146475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129935 restraints weight = 22496.142| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.99 r_work: 0.3616 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15674 Z= 0.139 Angle : 0.585 8.488 21278 Z= 0.291 Chirality : 0.043 0.194 2327 Planarity : 0.004 0.056 2766 Dihedral : 10.315 157.101 2189 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 7.37 % Allowed : 26.57 % Favored : 66.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.19), residues: 1913 helix: 1.11 (0.18), residues: 883 sheet: -1.23 (0.32), residues: 266 loop : -1.04 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 123 TYR 0.014 0.001 TYR D 208 PHE 0.017 0.001 PHE A 296 TRP 0.013 0.001 TRP C 21 HIS 0.009 0.001 HIS D 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (15672) covalent geometry : angle 0.58401 / 0.29 (21274) SS BOND : bond 0.00256 / 0.13 ( 2) SS BOND : angle 2.27152 / 1.24 ( 4) hydrogen bonds : bond 0.03941 / 2.65 ( 698) hydrogen bonds : angle 4.67532 / 3.37 ( 2028) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 473 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 SER cc_start: 0.8540 (OUTLIER) cc_final: 0.8207 (m) REVERT: B 86 ARG cc_start: 0.6834 (mmt180) cc_final: 0.6372 (mmt-90) REVERT: B 94 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8124 (mm-40) REVERT: B 143 THR cc_start: 0.7345 (m) cc_final: 0.7080 (m) REVERT: B 157 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7977 (mm-30) REVERT: B 209 ASP cc_start: 0.8120 (t0) cc_final: 0.7041 (t0) REVERT: B 213 ARG cc_start: 0.7612 (mtm180) cc_final: 0.7069 (mtm-85) REVERT: B 252 LYS cc_start: 0.7756 (mttt) cc_final: 0.7486 (mttt) REVERT: B 255 VAL cc_start: 0.8815 (p) cc_final: 0.8540 (t) REVERT: B 262 ARG cc_start: 0.7943 (mtp85) cc_final: 0.7651 (mtp85) REVERT: B 318 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8062 (mtt-85) REVERT: B 343 GLU cc_start: 0.8314 (tt0) cc_final: 0.7975 (tt0) REVERT: B 405 GLU cc_start: 0.7526 (mp0) cc_final: 0.7147 (mp0) REVERT: A 50 ASN cc_start: 0.8604 (t0) cc_final: 0.8182 (t0) REVERT: A 74 VAL cc_start: 0.8815 (OUTLIER) cc_final: 0.8548 (m) REVERT: A 90 GLU cc_start: 0.8457 (tp30) cc_final: 0.8195 (tp30) REVERT: A 108 TYR cc_start: 0.8279 (m-80) cc_final: 0.7197 (m-80) REVERT: A 141 PHE cc_start: 0.8777 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: A 154 MET cc_start: 0.8076 (mmm) cc_final: 0.7472 (mmm) REVERT: A 164 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7986 (ttmm) REVERT: A 170 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7584 (p) REVERT: A 172 TYR cc_start: 0.8231 (t80) cc_final: 0.7423 (t80) REVERT: A 243 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7582 (mtp180) REVERT: A 258 ASN cc_start: 0.7795 (m-40) cc_final: 0.7338 (m-40) REVERT: A 288 VAL cc_start: 0.8161 (m) cc_final: 0.7801 (t) REVERT: A 326 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7799 (tptt) REVERT: A 377 MET cc_start: 0.7995 (tpt) cc_final: 0.7668 (tpt) REVERT: A 386 GLU cc_start: 0.5772 (OUTLIER) cc_final: 0.5239 (pt0) REVERT: A 393 HIS cc_start: 0.7379 (t70) cc_final: 0.6928 (t70) REVERT: D 2 ARG cc_start: 0.7307 (OUTLIER) cc_final: 0.6558 (pmt-80) REVERT: D 25 SER cc_start: 0.8194 (t) cc_final: 0.7960 (m) REVERT: D 41 ASP cc_start: 0.7625 (t0) cc_final: 0.7161 (t0) REVERT: D 92 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.7763 (p90) REVERT: D 111 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6933 (mt-10) REVERT: D 205 GLU cc_start: 0.7633 (tp30) cc_final: 0.7198 (mp0) REVERT: D 209 ASP cc_start: 0.8294 (t70) cc_final: 0.8027 (t0) REVERT: D 224 ASP cc_start: 0.7339 (m-30) cc_final: 0.6865 (m-30) REVERT: D 228 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7529 (mm) REVERT: D 233 MET cc_start: 0.6929 (ptt) cc_final: 0.6715 (ttp) REVERT: D 267 MET cc_start: 0.7095 (ttt) cc_final: 0.6541 (ttt) REVERT: D 280 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7318 (mt0) REVERT: D 285 THR cc_start: 0.7475 (OUTLIER) cc_final: 0.7115 (t) REVERT: D 287 PRO cc_start: 0.7856 (Cg_exo) cc_final: 0.7636 (Cg_endo) REVERT: D 299 MET cc_start: 0.7959 (mmm) cc_final: 0.7319 (mmm) REVERT: D 300 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.7776 (mtt) REVERT: D 336 LYS cc_start: 0.7222 (mmtp) cc_final: 0.6813 (mmtp) REVERT: D 350 LYS cc_start: 0.7366 (tptp) cc_final: 0.7016 (tptp) REVERT: D 412 GLU cc_start: 0.6730 (mm-30) cc_final: 0.6525 (mm-30) REVERT: D 424 GLN cc_start: 0.6454 (pt0) cc_final: 0.6253 (pt0) REVERT: D 426 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6014 (tp-100) REVERT: C 22 GLU cc_start: 0.7852 (tt0) cc_final: 0.7642 (tt0) REVERT: C 97 GLU cc_start: 0.6877 (tp30) cc_final: 0.6628 (tp30) REVERT: C 154 MET cc_start: 0.7887 (mmm) cc_final: 0.7646 (mmt) REVERT: C 158 SER cc_start: 0.8800 (m) cc_final: 0.8440 (p) REVERT: C 168 GLU cc_start: 0.8009 (pm20) cc_final: 0.7451 (pm20) REVERT: C 203 MET cc_start: 0.8016 (mmt) cc_final: 0.7808 (mmm) REVERT: C 234 ILE cc_start: 0.8114 (mm) cc_final: 0.7830 (mt) REVERT: C 271 THR cc_start: 0.8392 (OUTLIER) cc_final: 0.8020 (m) REVERT: C 329 ASN cc_start: 0.7671 (t0) cc_final: 0.7372 (t0) REVERT: C 343 PHE cc_start: 0.8560 (m-10) cc_final: 0.8342 (m-80) REVERT: C 423 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6571 (mm-30) REVERT: C 425 MET cc_start: 0.7405 (tpp) cc_final: 0.6999 (tpp) REVERT: E 47 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7480 (pm20) outliers start: 122 outliers final: 81 residues processed: 552 average time/residue: 0.1378 time to fit residues: 110.8733 Evaluate side-chains 562 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 464 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 92 PHE Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 285 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 426 GLN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 152 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 38 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 172 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 HIS ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN A 18 ASN A 61 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 GLN ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 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 = 0.3952 r_free = 0.3952 target = 0.145942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129294 restraints weight = 22504.360| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.00 r_work: 0.3609 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15674 Z= 0.152 Angle : 0.604 9.623 21278 Z= 0.301 Chirality : 0.044 0.238 2327 Planarity : 0.004 0.055 2766 Dihedral : 10.312 157.164 2188 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 7.55 % Allowed : 26.87 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.19), residues: 1913 helix: 1.14 (0.18), residues: 870 sheet: -1.26 (0.32), residues: 266 loop : -1.02 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 390 TYR 0.019 0.001 TYR C 103 PHE 0.018 0.002 PHE A 296 TRP 0.013 0.001 TRP C 21 HIS 0.009 0.001 HIS D 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (15672) covalent geometry : angle 0.60245 / 0.30 (21274) SS BOND : bond 0.00566 / 0.30 ( 2) SS BOND : angle 3.18509 / 1.75 ( 4) hydrogen bonds : bond 0.03977 / 2.67 ( 698) hydrogen bonds : angle 4.63450 / 3.34 ( 2028) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 467 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8220 (m) REVERT: B 86 ARG cc_start: 0.6852 (mmt180) cc_final: 0.6385 (mmt-90) REVERT: B 108 GLU cc_start: 0.7277 (tp30) cc_final: 0.7021 (tp30) REVERT: B 143 THR cc_start: 0.7384 (m) cc_final: 0.7143 (m) REVERT: B 155 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8431 (mt) REVERT: B 157 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8013 (mm-30) REVERT: B 209 ASP cc_start: 0.8202 (t0) cc_final: 0.7207 (t0) REVERT: B 213 ARG cc_start: 0.7661 (mtm180) cc_final: 0.7169 (mtm-85) REVERT: B 252 LYS cc_start: 0.7804 (mttt) cc_final: 0.7498 (mttt) REVERT: B 255 VAL cc_start: 0.8825 (p) cc_final: 0.8563 (t) REVERT: B 262 ARG cc_start: 0.7960 (mtp85) cc_final: 0.7656 (mtp85) REVERT: B 318 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8057 (mtt-85) REVERT: B 343 GLU cc_start: 0.8358 (tt0) cc_final: 0.8030 (tt0) REVERT: B 405 GLU cc_start: 0.7553 (mp0) cc_final: 0.7157 (mp0) REVERT: A 50 ASN cc_start: 0.8585 (t0) cc_final: 0.8152 (t0) REVERT: A 74 VAL cc_start: 0.8834 (OUTLIER) cc_final: 0.8584 (m) REVERT: A 90 GLU cc_start: 0.8462 (tp30) cc_final: 0.8206 (tp30) REVERT: A 108 TYR cc_start: 0.8305 (m-80) cc_final: 0.7437 (m-80) REVERT: A 119 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8301 (mp) REVERT: A 141 PHE cc_start: 0.8789 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: A 154 MET cc_start: 0.8054 (mmm) cc_final: 0.7424 (mmm) REVERT: A 164 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7962 (ttmm) REVERT: A 168 GLU cc_start: 0.8110 (pt0) cc_final: 0.7611 (pm20) REVERT: A 170 SER cc_start: 0.7947 (OUTLIER) cc_final: 0.7597 (p) REVERT: A 172 TYR cc_start: 0.8220 (t80) cc_final: 0.7459 (t80) REVERT: A 243 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7588 (mtp180) REVERT: A 254 GLU cc_start: 0.3793 (mm-30) cc_final: 0.3111 (mm-30) REVERT: A 258 ASN cc_start: 0.7828 (m-40) cc_final: 0.7441 (m-40) REVERT: A 288 VAL cc_start: 0.8152 (m) cc_final: 0.7801 (t) REVERT: A 326 LYS cc_start: 0.8108 (tmmt) cc_final: 0.7816 (tptt) REVERT: A 377 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7754 (tpt) REVERT: A 386 GLU cc_start: 0.5758 (OUTLIER) cc_final: 0.5249 (pt0) REVERT: A 393 HIS cc_start: 0.7396 (t70) cc_final: 0.6953 (t70) REVERT: D 2 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.6602 (pmt-80) REVERT: D 25 SER cc_start: 0.8234 (t) cc_final: 0.7944 (m) REVERT: D 41 ASP cc_start: 0.7575 (t0) cc_final: 0.7137 (t0) REVERT: D 92 PHE cc_start: 0.7998 (p90) cc_final: 0.7672 (p90) REVERT: D 111 GLU cc_start: 0.7455 (mt-10) cc_final: 0.6722 (mt-10) REVERT: D 205 GLU cc_start: 0.7607 (tp30) cc_final: 0.7179 (mp0) REVERT: D 209 ASP cc_start: 0.8337 (t70) cc_final: 0.8045 (t0) REVERT: D 224 ASP cc_start: 0.7351 (m-30) cc_final: 0.6892 (m-30) REVERT: D 228 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7539 (mm) REVERT: D 233 MET cc_start: 0.6907 (ptt) cc_final: 0.6682 (ttp) REVERT: D 251 ARG cc_start: 0.7997 (ttp-170) cc_final: 0.7647 (ttp-170) REVERT: D 267 MET cc_start: 0.7147 (ttt) cc_final: 0.6567 (ttt) REVERT: D 276 ARG cc_start: 0.8365 (tpp-160) cc_final: 0.8135 (mmt-90) REVERT: D 280 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7465 (mt0) REVERT: D 299 MET cc_start: 0.7972 (mmm) cc_final: 0.7339 (mmm) REVERT: D 300 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7762 (mtt) REVERT: D 336 LYS cc_start: 0.7218 (mmtp) cc_final: 0.6770 (mmtp) REVERT: D 343 GLU cc_start: 0.7999 (tt0) cc_final: 0.7763 (tt0) REVERT: D 350 LYS cc_start: 0.7550 (tptp) cc_final: 0.7240 (tptp) REVERT: D 412 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6558 (mm-30) REVERT: D 426 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6072 (tp-100) REVERT: C 22 GLU cc_start: 0.7840 (tt0) cc_final: 0.7550 (tt0) REVERT: C 97 GLU cc_start: 0.6912 (tp30) cc_final: 0.6255 (tp30) REVERT: C 158 SER cc_start: 0.8801 (m) cc_final: 0.8468 (p) REVERT: C 168 GLU cc_start: 0.8040 (pm20) cc_final: 0.7476 (pm20) REVERT: C 234 ILE cc_start: 0.8121 (mm) cc_final: 0.7858 (mt) REVERT: C 243 ARG cc_start: 0.7538 (mtm-85) cc_final: 0.6866 (mtm-85) REVERT: C 271 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8036 (m) REVERT: C 301 GLN cc_start: 0.8438 (tt0) cc_final: 0.8192 (tt0) REVERT: C 329 ASN cc_start: 0.7712 (t0) cc_final: 0.7417 (t0) REVERT: C 417 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6897 (tm-30) REVERT: C 423 GLU cc_start: 0.6904 (mm-30) cc_final: 0.6614 (mm-30) REVERT: C 425 MET cc_start: 0.7435 (tpp) cc_final: 0.6986 (tpp) REVERT: E 47 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7558 (pm20) outliers start: 125 outliers final: 80 residues processed: 548 average time/residue: 0.1399 time to fit residues: 110.4226 Evaluate side-chains 550 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 453 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 426 GLN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 152 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 27 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 94 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 197 HIS ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.145587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.129150 restraints weight = 22340.516| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.98 r_work: 0.3605 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15674 Z= 0.155 Angle : 0.612 9.200 21278 Z= 0.304 Chirality : 0.045 0.270 2327 Planarity : 0.004 0.057 2766 Dihedral : 10.288 156.807 2186 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 7.31 % Allowed : 27.48 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.19), residues: 1913 helix: 1.14 (0.18), residues: 869 sheet: -1.19 (0.33), residues: 266 loop : -1.01 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 390 TYR 0.015 0.001 TYR D 208 PHE 0.020 0.002 PHE C 351 TRP 0.013 0.001 TRP C 21 HIS 0.009 0.001 HIS D 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (15672) covalent geometry : angle 0.61022 / 0.30 (21274) SS BOND : bond 0.00659 / 0.33 ( 2) SS BOND : angle 3.00736 / 1.58 ( 4) hydrogen bonds : bond 0.03964 / 2.67 ( 698) hydrogen bonds : angle 4.61437 / 3.32 ( 2028) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 468 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 SER cc_start: 0.8523 (OUTLIER) cc_final: 0.8209 (m) REVERT: B 86 ARG cc_start: 0.6806 (mmt180) cc_final: 0.6335 (mmt-90) REVERT: B 108 GLU cc_start: 0.7240 (tp30) cc_final: 0.7008 (tp30) REVERT: B 143 THR cc_start: 0.7350 (m) cc_final: 0.7120 (m) REVERT: B 155 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8408 (mt) REVERT: B 157 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8004 (mm-30) REVERT: B 209 ASP cc_start: 0.8116 (t0) cc_final: 0.7118 (t0) REVERT: B 213 ARG cc_start: 0.7572 (mtm180) cc_final: 0.7082 (mtm-85) REVERT: B 252 LYS cc_start: 0.7771 (mttt) cc_final: 0.7440 (mttt) REVERT: B 255 VAL cc_start: 0.8822 (p) cc_final: 0.8554 (t) REVERT: B 262 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7625 (mtp85) REVERT: B 318 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8067 (mtt-85) REVERT: B 343 GLU cc_start: 0.8325 (tt0) cc_final: 0.7993 (tt0) REVERT: B 405 GLU cc_start: 0.7536 (mp0) cc_final: 0.7151 (mp0) REVERT: A 50 ASN cc_start: 0.8594 (t0) cc_final: 0.8146 (t0) REVERT: A 74 VAL cc_start: 0.8872 (OUTLIER) cc_final: 0.8609 (m) REVERT: A 76 ASP cc_start: 0.7968 (t0) cc_final: 0.7531 (t0) REVERT: A 90 GLU cc_start: 0.8459 (tp30) cc_final: 0.8201 (tp30) REVERT: A 108 TYR cc_start: 0.8320 (m-80) cc_final: 0.7326 (m-80) REVERT: A 119 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8319 (mp) REVERT: A 141 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: A 149 PHE cc_start: 0.7750 (t80) cc_final: 0.7536 (t80) REVERT: A 154 MET cc_start: 0.8089 (mmm) cc_final: 0.7542 (mmm) REVERT: A 164 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7938 (ttmm) REVERT: A 170 SER cc_start: 0.7966 (OUTLIER) cc_final: 0.7565 (p) REVERT: A 172 TYR cc_start: 0.8228 (t80) cc_final: 0.7460 (t80) REVERT: A 243 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.7597 (mtp180) REVERT: A 254 GLU cc_start: 0.3787 (mm-30) cc_final: 0.3191 (mm-30) REVERT: A 258 ASN cc_start: 0.7832 (m-40) cc_final: 0.7508 (m-40) REVERT: A 288 VAL cc_start: 0.8166 (m) cc_final: 0.7801 (t) REVERT: A 326 LYS cc_start: 0.8113 (tmmt) cc_final: 0.7820 (tptt) REVERT: A 358 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6367 (pt0) REVERT: A 377 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7808 (tpt) REVERT: A 386 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.5220 (pt0) REVERT: A 393 HIS cc_start: 0.7402 (t70) cc_final: 0.6949 (t70) REVERT: D 2 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6675 (pmt-80) REVERT: D 25 SER cc_start: 0.8224 (t) cc_final: 0.7950 (m) REVERT: D 41 ASP cc_start: 0.7646 (t0) cc_final: 0.7187 (t0) REVERT: D 92 PHE cc_start: 0.8018 (p90) cc_final: 0.7699 (p90) REVERT: D 111 GLU cc_start: 0.7474 (mt-10) cc_final: 0.6747 (mt-10) REVERT: D 205 GLU cc_start: 0.7588 (tp30) cc_final: 0.7159 (mp0) REVERT: D 209 ASP cc_start: 0.8317 (t70) cc_final: 0.8029 (t0) REVERT: D 224 ASP cc_start: 0.7338 (m-30) cc_final: 0.7105 (m-30) REVERT: D 233 MET cc_start: 0.6731 (ptt) cc_final: 0.6513 (ttp) REVERT: D 251 ARG cc_start: 0.7998 (ttp-170) cc_final: 0.7621 (ttp-170) REVERT: D 267 MET cc_start: 0.7150 (ttt) cc_final: 0.6595 (ttt) REVERT: D 276 ARG cc_start: 0.8312 (tpp-160) cc_final: 0.8077 (mmt-90) REVERT: D 280 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7527 (mt0) REVERT: D 299 MET cc_start: 0.7961 (mmm) cc_final: 0.7361 (mmm) REVERT: D 300 MET cc_start: 0.8038 (OUTLIER) cc_final: 0.7750 (mtt) REVERT: D 336 LYS cc_start: 0.7192 (mmtp) cc_final: 0.6746 (mmtp) REVERT: D 343 GLU cc_start: 0.7965 (tt0) cc_final: 0.7716 (tt0) REVERT: D 370 ASN cc_start: 0.7753 (m-40) cc_final: 0.7500 (m-40) REVERT: D 426 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.6026 (tp-100) REVERT: C 97 GLU cc_start: 0.6860 (tp30) cc_final: 0.6292 (tp30) REVERT: C 158 SER cc_start: 0.8752 (m) cc_final: 0.8396 (p) REVERT: C 194 THR cc_start: 0.7525 (p) cc_final: 0.7265 (t) REVERT: C 234 ILE cc_start: 0.8086 (mm) cc_final: 0.7823 (mt) REVERT: C 243 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.6870 (mtm-85) REVERT: C 271 THR cc_start: 0.8365 (OUTLIER) cc_final: 0.7978 (m) REVERT: C 301 GLN cc_start: 0.8451 (tt0) cc_final: 0.8191 (tt0) REVERT: C 329 ASN cc_start: 0.7739 (t0) cc_final: 0.7431 (t0) REVERT: C 423 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6621 (mm-30) REVERT: C 425 MET cc_start: 0.7480 (tpp) cc_final: 0.7022 (tpp) REVERT: E 1 MET cc_start: 0.7631 (OUTLIER) cc_final: 0.7376 (mmm) REVERT: E 47 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7496 (pm20) REVERT: E 67 LEU cc_start: 0.7800 (tp) cc_final: 0.7531 (tt) REVERT: E 148 MET cc_start: 0.7017 (mmt) cc_final: 0.6734 (mmt) outliers start: 121 outliers final: 84 residues processed: 543 average time/residue: 0.1329 time to fit residues: 104.6130 Evaluate side-chains 557 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 455 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 426 GLN Chi-restraints excluded: chain C residue 4 CYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 152 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN B 375 GLN A 61 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN D 370 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN ** E 35 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 = 0.3935 r_free = 0.3935 target = 0.144682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.128173 restraints weight = 22652.832| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.00 r_work: 0.3585 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15674 Z= 0.175 Angle : 0.621 9.203 21278 Z= 0.309 Chirality : 0.045 0.263 2327 Planarity : 0.004 0.058 2766 Dihedral : 10.349 156.558 2186 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 7.37 % Allowed : 27.66 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.19), residues: 1913 helix: 1.10 (0.18), residues: 867 sheet: -1.19 (0.34), residues: 252 loop : -0.99 (0.21), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 123 TYR 0.012 0.001 TYR B 183 PHE 0.021 0.002 PHE A 296 TRP 0.013 0.002 TRP C 21 HIS 0.008 0.001 HIS D 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.17 (15672) covalent geometry : angle 0.61959 / 0.31 (21274) SS BOND : bond 0.00364 / 0.19 ( 2) SS BOND : angle 2.67794 / 1.44 ( 4) hydrogen bonds : bond 0.04013 / 2.70 ( 698) hydrogen bonds : angle 4.62898 / 3.33 ( 2028) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 466 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8229 (m) REVERT: B 26 ASP cc_start: 0.7991 (t0) cc_final: 0.7780 (t0) REVERT: B 86 ARG cc_start: 0.6377 (mmt180) cc_final: 0.5862 (mmt-90) REVERT: B 108 GLU cc_start: 0.7337 (tp30) cc_final: 0.7068 (tp30) REVERT: B 143 THR cc_start: 0.7392 (m) cc_final: 0.7162 (m) REVERT: B 155 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8426 (mt) REVERT: B 157 GLU cc_start: 0.8284 (mm-30) cc_final: 0.8058 (mm-30) REVERT: B 191 GLN cc_start: 0.7681 (tt0) cc_final: 0.7459 (tt0) REVERT: B 209 ASP cc_start: 0.8120 (t0) cc_final: 0.7080 (t0) REVERT: B 213 ARG cc_start: 0.7649 (mtm180) cc_final: 0.7143 (mtm-85) REVERT: B 252 LYS cc_start: 0.7779 (mttt) cc_final: 0.7463 (mttt) REVERT: B 255 VAL cc_start: 0.8834 (p) cc_final: 0.8574 (t) REVERT: B 262 ARG cc_start: 0.7947 (mtp85) cc_final: 0.7642 (mtp85) REVERT: B 318 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8076 (mtt-85) REVERT: B 343 GLU cc_start: 0.8376 (tt0) cc_final: 0.8051 (tt0) REVERT: B 405 GLU cc_start: 0.7482 (mp0) cc_final: 0.7089 (mp0) REVERT: A 50 ASN cc_start: 0.8621 (t0) cc_final: 0.8171 (t0) REVERT: A 74 VAL cc_start: 0.8878 (OUTLIER) cc_final: 0.8059 (m) REVERT: A 76 ASP cc_start: 0.7975 (t0) cc_final: 0.7571 (t0) REVERT: A 108 TYR cc_start: 0.8339 (m-80) cc_final: 0.7202 (m-80) REVERT: A 119 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8332 (mp) REVERT: A 141 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.7778 (m-80) REVERT: A 154 MET cc_start: 0.8106 (mmm) cc_final: 0.7530 (mmm) REVERT: A 164 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7918 (ttmm) REVERT: A 168 GLU cc_start: 0.8075 (pt0) cc_final: 0.7580 (pm20) REVERT: A 170 SER cc_start: 0.7958 (OUTLIER) cc_final: 0.7575 (p) REVERT: A 172 TYR cc_start: 0.8225 (t80) cc_final: 0.7439 (t80) REVERT: A 243 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7604 (mtp180) REVERT: A 254 GLU cc_start: 0.3858 (mm-30) cc_final: 0.3235 (mm-30) REVERT: A 258 ASN cc_start: 0.7856 (m-40) cc_final: 0.7535 (m-40) REVERT: A 288 VAL cc_start: 0.8167 (m) cc_final: 0.7829 (t) REVERT: A 326 LYS cc_start: 0.8138 (tmmt) cc_final: 0.7410 (mptt) REVERT: A 358 GLN cc_start: 0.6874 (OUTLIER) cc_final: 0.6360 (pt0) REVERT: A 377 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7819 (tpt) REVERT: A 386 GLU cc_start: 0.5701 (OUTLIER) cc_final: 0.5162 (pt0) REVERT: A 393 HIS cc_start: 0.7402 (t70) cc_final: 0.6963 (t70) REVERT: D 2 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6668 (pmt-80) REVERT: D 7 LEU cc_start: 0.8044 (mt) cc_final: 0.7793 (mp) REVERT: D 25 SER cc_start: 0.8263 (t) cc_final: 0.7966 (m) REVERT: D 41 ASP cc_start: 0.7686 (t0) cc_final: 0.7233 (t0) REVERT: D 92 PHE cc_start: 0.8089 (p90) cc_final: 0.7749 (p90) REVERT: D 108 GLU cc_start: 0.7940 (tp30) cc_final: 0.7157 (tp30) REVERT: D 111 GLU cc_start: 0.7536 (mt-10) cc_final: 0.6695 (mt-10) REVERT: D 205 GLU cc_start: 0.7510 (tp30) cc_final: 0.7095 (mp0) REVERT: D 209 ASP cc_start: 0.8378 (t70) cc_final: 0.8099 (t0) REVERT: D 224 ASP cc_start: 0.7326 (m-30) cc_final: 0.7116 (m-30) REVERT: D 233 MET cc_start: 0.6752 (ptt) cc_final: 0.6549 (ttp) REVERT: D 251 ARG cc_start: 0.8038 (ttp-170) cc_final: 0.7624 (ttp-170) REVERT: D 276 ARG cc_start: 0.8330 (tpp-160) cc_final: 0.8101 (mmt-90) REVERT: D 300 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7720 (mtt) REVERT: D 336 LYS cc_start: 0.7217 (mmtp) cc_final: 0.6766 (mmtp) REVERT: D 343 GLU cc_start: 0.7949 (tt0) cc_final: 0.7700 (tt0) REVERT: D 370 ASN cc_start: 0.7806 (OUTLIER) cc_final: 0.7393 (m110) REVERT: D 426 GLN cc_start: 0.7532 (OUTLIER) cc_final: 0.6084 (tp-100) REVERT: C 97 GLU cc_start: 0.6862 (tp30) cc_final: 0.6354 (tp30) REVERT: C 158 SER cc_start: 0.8764 (m) cc_final: 0.8421 (p) REVERT: C 194 THR cc_start: 0.7541 (p) cc_final: 0.7276 (t) REVERT: C 234 ILE cc_start: 0.8112 (mm) cc_final: 0.7847 (mt) REVERT: C 243 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.6902 (mtm-85) REVERT: C 271 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8013 (m) REVERT: C 301 GLN cc_start: 0.8492 (tt0) cc_final: 0.8216 (tt0) REVERT: C 329 ASN cc_start: 0.7795 (t0) cc_final: 0.7489 (t0) REVERT: C 386 GLU cc_start: 0.7075 (pt0) cc_final: 0.6579 (pt0) REVERT: C 423 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6659 (mm-30) REVERT: C 425 MET cc_start: 0.7468 (tpp) cc_final: 0.7020 (tpp) REVERT: E 1 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7482 (mmm) REVERT: E 47 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7488 (pm20) REVERT: E 67 LEU cc_start: 0.7807 (tp) cc_final: 0.7529 (tt) outliers start: 122 outliers final: 89 residues processed: 540 average time/residue: 0.1284 time to fit residues: 100.2773 Evaluate side-chains 564 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 456 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 325 GLU Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 43 GLN Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 383 GLU Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 426 GLN Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 335 ILE Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 152 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 149 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN A 61 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN D 370 ASN ** E 35 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 = 0.3936 r_free = 0.3936 target = 0.145567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.128799 restraints weight = 22468.812| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.01 r_work: 0.3582 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15674 Z= 0.172 Angle : 0.638 9.234 21278 Z= 0.316 Chirality : 0.045 0.286 2327 Planarity : 0.004 0.058 2766 Dihedral : 10.370 156.516 2186 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 7.07 % Allowed : 27.84 % Favored : 65.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.19), residues: 1913 helix: 1.11 (0.17), residues: 869 sheet: -1.18 (0.33), residues: 266 loop : -1.01 (0.22), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 390 TYR 0.016 0.001 TYR D 208 PHE 0.022 0.002 PHE A 296 TRP 0.013 0.002 TRP C 21 HIS 0.008 0.001 HIS D 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (15672) covalent geometry : angle 0.63620 / 0.32 (21274) SS BOND : bond 0.00579 / 0.30 ( 2) SS BOND : angle 3.63870 / 2.00 ( 4) hydrogen bonds : bond 0.04052 / 2.74 ( 698) hydrogen bonds : angle 4.63804 / 3.33 ( 2028) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 466 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 SER cc_start: 0.8614 (OUTLIER) cc_final: 0.8225 (m) REVERT: B 26 ASP cc_start: 0.7979 (t0) cc_final: 0.7765 (t0) REVERT: B 86 ARG cc_start: 0.6364 (mmt180) cc_final: 0.5846 (mmt-90) REVERT: B 108 GLU cc_start: 0.7328 (tp30) cc_final: 0.7092 (tp30) REVERT: B 143 THR cc_start: 0.7391 (m) cc_final: 0.7162 (m) REVERT: B 155 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8420 (mt) REVERT: B 157 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8053 (mm-30) REVERT: B 209 ASP cc_start: 0.8120 (t0) cc_final: 0.6961 (t0) REVERT: B 213 ARG cc_start: 0.7608 (mtm180) cc_final: 0.7063 (mtm-85) REVERT: B 252 LYS cc_start: 0.7756 (mttt) cc_final: 0.7443 (mttt) REVERT: B 255 VAL cc_start: 0.8841 (p) cc_final: 0.8566 (t) REVERT: B 262 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7613 (mtp85) REVERT: B 318 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.8060 (mtt-85) REVERT: B 343 GLU cc_start: 0.8335 (tt0) cc_final: 0.8006 (tt0) REVERT: B 405 GLU cc_start: 0.7481 (mp0) cc_final: 0.7114 (mp0) REVERT: B 423 GLN cc_start: 0.7618 (mm110) cc_final: 0.7351 (mm110) REVERT: A 50 ASN cc_start: 0.8621 (t0) cc_final: 0.8170 (t0) REVERT: A 77 GLU cc_start: 0.6669 (mp0) cc_final: 0.6447 (mp0) REVERT: A 90 GLU cc_start: 0.8442 (tp30) cc_final: 0.8113 (tp30) REVERT: A 108 TYR cc_start: 0.8344 (m-80) cc_final: 0.7202 (m-80) REVERT: A 119 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8285 (mp) REVERT: A 141 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: A 154 MET cc_start: 0.8093 (mmm) cc_final: 0.7440 (mmm) REVERT: A 164 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7915 (ttmm) REVERT: A 168 GLU cc_start: 0.8074 (pt0) cc_final: 0.7573 (pm20) REVERT: A 170 SER cc_start: 0.7949 (OUTLIER) cc_final: 0.7561 (p) REVERT: A 172 TYR cc_start: 0.8224 (t80) cc_final: 0.7434 (t80) REVERT: A 243 ARG cc_start: 0.8000 (OUTLIER) cc_final: 0.7626 (mtp180) REVERT: A 254 GLU cc_start: 0.3856 (mm-30) cc_final: 0.3228 (mm-30) REVERT: A 258 ASN cc_start: 0.7873 (m-40) cc_final: 0.7557 (m-40) REVERT: A 288 VAL cc_start: 0.8187 (m) cc_final: 0.7822 (t) REVERT: A 326 LYS cc_start: 0.8140 (tmmt) cc_final: 0.7415 (mptt) REVERT: A 358 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6361 (pt0) REVERT: A 377 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7756 (tpt) REVERT: A 386 GLU cc_start: 0.5680 (OUTLIER) cc_final: 0.5139 (pt0) REVERT: A 393 HIS cc_start: 0.7385 (t70) cc_final: 0.6941 (t70) REVERT: D 2 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6734 (pmt-80) REVERT: D 7 LEU cc_start: 0.8035 (mt) cc_final: 0.7817 (mp) REVERT: D 25 SER cc_start: 0.8265 (t) cc_final: 0.7955 (m) REVERT: D 41 ASP cc_start: 0.7657 (t0) cc_final: 0.7211 (t0) REVERT: D 108 GLU cc_start: 0.7889 (tp30) cc_final: 0.7141 (tp30) REVERT: D 111 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6739 (mt-10) REVERT: D 162 ARG cc_start: 0.7192 (mmt-90) cc_final: 0.6836 (mmt-90) REVERT: D 205 GLU cc_start: 0.7492 (tp30) cc_final: 0.7073 (mp0) REVERT: D 209 ASP cc_start: 0.8348 (t70) cc_final: 0.8054 (t0) REVERT: D 233 MET cc_start: 0.6853 (ptt) cc_final: 0.6641 (ttp) REVERT: D 251 ARG cc_start: 0.8033 (ttp-170) cc_final: 0.7627 (ttp-170) REVERT: D 276 ARG cc_start: 0.8288 (tpp-160) cc_final: 0.8069 (mmt-90) REVERT: D 300 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7685 (mtt) REVERT: D 336 LYS cc_start: 0.7211 (mmtp) cc_final: 0.6766 (mmtp) REVERT: D 343 GLU cc_start: 0.7917 (tt0) cc_final: 0.7662 (tt0) REVERT: D 347 ASN cc_start: 0.6859 (OUTLIER) cc_final: 0.6420 (t0) REVERT: D 370 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7373 (m110) REVERT: D 379 LYS cc_start: 0.8491 (mtpp) cc_final: 0.8023 (ttmm) REVERT: D 426 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.5997 (tp-100) REVERT: C 97 GLU cc_start: 0.6884 (tp30) cc_final: 0.6371 (tp30) REVERT: C 158 SER cc_start: 0.8775 (m) cc_final: 0.8471 (t) REVERT: C 172 TYR cc_start: 0.8037 (t80) cc_final: 0.7677 (t80) REVERT: C 194 THR cc_start: 0.7541 (p) cc_final: 0.7271 (t) REVERT: C 234 ILE cc_start: 0.8124 (mm) cc_final: 0.7851 (mt) REVERT: C 243 ARG cc_start: 0.7559 (mtm-85) cc_final: 0.6917 (mtm-85) REVERT: C 271 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8023 (m) REVERT: C 301 GLN cc_start: 0.8504 (tt0) cc_final: 0.8209 (tt0) REVERT: C 329 ASN cc_start: 0.7816 (t0) cc_final: 0.7509 (t0) REVERT: C 386 GLU cc_start: 0.7134 (pt0) cc_final: 0.6591 (pt0) REVERT: C 423 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6675 (mm-30) REVERT: C 425 MET cc_start: 0.7472 (tpp) cc_final: 0.7036 (tpp) REVERT: C 429 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7251 (mm-30) REVERT: E 1 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7310 (mmm) REVERT: E 47 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: E 67 LEU cc_start: 0.7820 (tp) cc_final: 0.7551 (tt) REVERT: E 148 MET cc_start: 0.7069 (mmt) cc_final: 0.6767 (mmt) outliers start: 117 outliers final: 86 residues processed: 538 average time/residue: 0.1345 time to fit residues: 103.8355 Evaluate side-chains 561 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 456 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 243 ARG Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 426 GLN Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 53 MET Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 152 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 188 optimal weight: 0.0050 chunk 116 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 195 ASN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN A 61 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN D 370 ASN ** C 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 35 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 = 0.3939 r_free = 0.3939 target = 0.145894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.129156 restraints weight = 22463.638| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.01 r_work: 0.3592 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15674 Z= 0.157 Angle : 0.634 9.184 21278 Z= 0.316 Chirality : 0.045 0.295 2327 Planarity : 0.004 0.057 2766 Dihedral : 10.347 157.017 2186 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 6.52 % Allowed : 28.93 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.19), residues: 1913 helix: 1.13 (0.17), residues: 869 sheet: -1.16 (0.34), residues: 252 loop : -0.99 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 390 TYR 0.013 0.001 TYR B 183 PHE 0.022 0.002 PHE A 296 TRP 0.013 0.001 TRP C 21 HIS 0.009 0.001 HIS D 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (15672) covalent geometry : angle 0.63228 / 0.31 (21274) SS BOND : bond 0.00467 / 0.24 ( 2) SS BOND : angle 3.47475 / 1.92 ( 4) hydrogen bonds : bond 0.03970 / 2.69 ( 698) hydrogen bonds : angle 4.61447 / 3.32 ( 2028) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3826 Ramachandran restraints generated. 1913 Oldfield, 0 Emsley, 1913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 455 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 SER cc_start: 0.8599 (OUTLIER) cc_final: 0.8225 (m) REVERT: B 26 ASP cc_start: 0.7986 (t0) cc_final: 0.7772 (t0) REVERT: B 86 ARG cc_start: 0.6380 (mmt180) cc_final: 0.5909 (mmt-90) REVERT: B 108 GLU cc_start: 0.7365 (tp30) cc_final: 0.7093 (tp30) REVERT: B 143 THR cc_start: 0.7384 (m) cc_final: 0.7169 (m) REVERT: B 155 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8427 (mt) REVERT: B 191 GLN cc_start: 0.7601 (tt0) cc_final: 0.7397 (tt0) REVERT: B 209 ASP cc_start: 0.8236 (t0) cc_final: 0.7076 (t0) REVERT: B 213 ARG cc_start: 0.7649 (mtm180) cc_final: 0.7092 (mtm-85) REVERT: B 252 LYS cc_start: 0.7730 (mttt) cc_final: 0.7425 (mttt) REVERT: B 255 VAL cc_start: 0.8848 (p) cc_final: 0.8563 (t) REVERT: B 262 ARG cc_start: 0.7904 (mtp85) cc_final: 0.7628 (mtp85) REVERT: B 318 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.8052 (mtt-85) REVERT: B 343 GLU cc_start: 0.8358 (tt0) cc_final: 0.8035 (tt0) REVERT: B 405 GLU cc_start: 0.7500 (mp0) cc_final: 0.7133 (mp0) REVERT: B 423 GLN cc_start: 0.7578 (mm110) cc_final: 0.7299 (mm110) REVERT: A 50 ASN cc_start: 0.8624 (t0) cc_final: 0.8165 (t0) REVERT: A 77 GLU cc_start: 0.6601 (mp0) cc_final: 0.6303 (mp0) REVERT: A 90 GLU cc_start: 0.8456 (tp30) cc_final: 0.8117 (tp30) REVERT: A 108 TYR cc_start: 0.8301 (m-80) cc_final: 0.7092 (m-80) REVERT: A 119 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8339 (mp) REVERT: A 141 PHE cc_start: 0.8799 (OUTLIER) cc_final: 0.7707 (m-80) REVERT: A 154 MET cc_start: 0.8091 (mmm) cc_final: 0.7445 (mmm) REVERT: A 164 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7921 (ttmm) REVERT: A 168 GLU cc_start: 0.8082 (pt0) cc_final: 0.7586 (pm20) REVERT: A 170 SER cc_start: 0.7946 (OUTLIER) cc_final: 0.7552 (p) REVERT: A 172 TYR cc_start: 0.8223 (t80) cc_final: 0.7432 (t80) REVERT: A 254 GLU cc_start: 0.3812 (mm-30) cc_final: 0.3193 (mm-30) REVERT: A 258 ASN cc_start: 0.7858 (m-40) cc_final: 0.7543 (m-40) REVERT: A 288 VAL cc_start: 0.8157 (m) cc_final: 0.7797 (t) REVERT: A 326 LYS cc_start: 0.8155 (tmmt) cc_final: 0.7425 (mptt) REVERT: A 358 GLN cc_start: 0.6853 (OUTLIER) cc_final: 0.6405 (pt0) REVERT: A 377 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7701 (tpt) REVERT: A 386 GLU cc_start: 0.5788 (OUTLIER) cc_final: 0.5294 (pt0) REVERT: A 393 HIS cc_start: 0.7384 (t70) cc_final: 0.6953 (t70) REVERT: D 2 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6700 (pmt-80) REVERT: D 25 SER cc_start: 0.8257 (t) cc_final: 0.7950 (m) REVERT: D 41 ASP cc_start: 0.7583 (t0) cc_final: 0.7158 (t0) REVERT: D 73 MET cc_start: 0.8308 (mmm) cc_final: 0.7966 (mmt) REVERT: D 108 GLU cc_start: 0.7799 (tp30) cc_final: 0.7569 (tp30) REVERT: D 111 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7254 (mp0) REVERT: D 162 ARG cc_start: 0.7185 (mmt-90) cc_final: 0.6821 (mmt-90) REVERT: D 205 GLU cc_start: 0.7481 (tp30) cc_final: 0.7073 (mp0) REVERT: D 209 ASP cc_start: 0.8345 (t70) cc_final: 0.8057 (t0) REVERT: D 233 MET cc_start: 0.6875 (ptt) cc_final: 0.6661 (ttp) REVERT: D 251 ARG cc_start: 0.8034 (ttp-170) cc_final: 0.7620 (ttp-170) REVERT: D 276 ARG cc_start: 0.8318 (tpp-160) cc_final: 0.8106 (mmt-90) REVERT: D 300 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7692 (mtt) REVERT: D 336 LYS cc_start: 0.7270 (mmtp) cc_final: 0.6832 (mmtp) REVERT: D 343 GLU cc_start: 0.7939 (tt0) cc_final: 0.7686 (tt0) REVERT: D 347 ASN cc_start: 0.6810 (OUTLIER) cc_final: 0.6521 (t0) REVERT: D 350 LYS cc_start: 0.7662 (tptp) cc_final: 0.7368 (tptp) REVERT: D 426 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6065 (tp-100) REVERT: C 97 GLU cc_start: 0.6797 (tp30) cc_final: 0.6307 (tp30) REVERT: C 158 SER cc_start: 0.8771 (m) cc_final: 0.8466 (t) REVERT: C 172 TYR cc_start: 0.8049 (t80) cc_final: 0.7676 (t80) REVERT: C 194 THR cc_start: 0.7510 (p) cc_final: 0.7254 (t) REVERT: C 234 ILE cc_start: 0.8127 (mm) cc_final: 0.7848 (mt) REVERT: C 243 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.6899 (mtm-85) REVERT: C 271 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8010 (m) REVERT: C 301 GLN cc_start: 0.8499 (tt0) cc_final: 0.8195 (tt0) REVERT: C 329 ASN cc_start: 0.7814 (t0) cc_final: 0.7497 (t0) REVERT: C 386 GLU cc_start: 0.7095 (pt0) cc_final: 0.6513 (pt0) REVERT: C 423 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6669 (mm-30) REVERT: C 425 MET cc_start: 0.7459 (tpp) cc_final: 0.7024 (tpp) REVERT: E 1 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7337 (mmm) REVERT: E 47 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: E 67 LEU cc_start: 0.7841 (tp) cc_final: 0.7574 (tt) REVERT: E 148 MET cc_start: 0.7078 (mmt) cc_final: 0.6783 (mmt) outliers start: 108 outliers final: 83 residues processed: 522 average time/residue: 0.1317 time to fit residues: 99.1015 Evaluate side-chains 550 residues out of total 1656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 450 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 ARG Chi-restraints excluded: chain B residue 12 CYS Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 155 ILE Chi-restraints excluded: chain B residue 165 ASN Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 172 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 GLU Chi-restraints excluded: chain B residue 232 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 318 ARG Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 GLN Chi-restraints excluded: chain A residue 137 VAL Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 141 PHE Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 200 CYS Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 358 GLN Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 417 GLU Chi-restraints excluded: chain D residue 2 ARG Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 274 THR Chi-restraints excluded: chain D residue 291 GLN Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 321 MET Chi-restraints excluded: chain D residue 347 ASN Chi-restraints excluded: chain D residue 370 ASN Chi-restraints excluded: chain D residue 375 GLN Chi-restraints excluded: chain D residue 418 LEU Chi-restraints excluded: chain D residue 426 GLN Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 76 ASP Chi-restraints excluded: chain C residue 121 ARG Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 266 HIS Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 341 ILE Chi-restraints excluded: chain C residue 355 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 376 CYS Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 17 LEU Chi-restraints excluded: chain E residue 20 GLN Chi-restraints excluded: chain E residue 24 THR Chi-restraints excluded: chain E residue 31 HIS Chi-restraints excluded: chain E residue 47 GLU Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 66 LEU Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 92 VAL Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain E residue 152 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 132 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 167 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 292 GLN A 61 HIS ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** D 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 ASN C 11 GLN ** E 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.145421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.128763 restraints weight = 22351.956| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.00 r_work: 0.3585 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15674 Z= 0.178 Angle : 0.643 9.418 21278 Z= 0.320 Chirality : 0.046 0.330 2327 Planarity : 0.005 0.057 2766 Dihedral : 10.364 157.225 2186 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 6.34 % Allowed : 29.17 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.19), residues: 1913 helix: 1.10 (0.17), residues: 871 sheet: -1.14 (0.34), residues: 252 loop : -1.01 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 390 TYR 0.022 0.001 TYR C 103 PHE 0.022 0.002 PHE A 296 TRP 0.013 0.002 TRP B 344 HIS 0.008 0.001 HIS D 264 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (15672) covalent geometry : angle 0.64186 / 0.32 (21274) SS BOND : bond 0.00481 / 0.25 ( 2) SS BOND : angle 3.33091 / 1.84 ( 4) hydrogen bonds : bond 0.04022 / 2.72 ( 698) hydrogen bonds : angle 4.63869 / 3.34 ( 2028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4528.04 seconds wall clock time: 78 minutes 19.55 seconds (4699.55 seconds total)