Starting phenix.real_space_refine on Fri Aug 7 19:44:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z0h_73706/08_2026/9z0h_73706.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z0h_73706/08_2026/9z0h_73706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9z0h_73706/08_2026/9z0h_73706.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z0h_73706/08_2026/9z0h_73706.map" model { file = "/net/cci-nas-00/data/ceres_data/9z0h_73706/08_2026/9z0h_73706.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z0h_73706/08_2026/9z0h_73706.cif" } resolution = 2.79 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= 1.016 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 77 5.49 5 Mg 2 5.21 5 S 129 5.16 5 C 14300 2.51 5 N 4118 2.21 5 O 4736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23367 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 2991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2991 Classifications: {'peptide': 374} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 351} Chain: "B" Number of atoms: 2859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2859 Classifications: {'peptide': 348} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 325} Chain breaks: 1 Chain: "C" Number of atoms: 2532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2532 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 11, 'TRANS': 297} Chain: "D" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2890 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain breaks: 1 Chain: "E" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 895 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "F" Number of atoms: 1040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1040 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 119} Chain: "G" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1342 Classifications: {'peptide': 178} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 167} Chain breaks: 1 Chain: "H" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 931 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "I" Number of atoms: 1487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1487 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 185} Chain breaks: 1 Chain: "J" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 936 Classifications: {'peptide': 119} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Chain: "K" Number of atoms: 1393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1393 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 173} Chain: "L" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1115 Classifications: {'peptide': 139} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 1 Chain: "O" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1105 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain breaks: 1 Chain: "R" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1645 Classifications: {'RNA': 77} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p_pur': 31, 'rna3p_pyr': 31} Link IDs: {'rna2p': 14, 'rna3p': 62} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3348 SG CYS B 58 77.846 126.180 31.513 1.00 11.42 S ATOM 3370 SG CYS B 61 75.384 123.873 33.531 1.00 3.33 S ATOM 6235 SG CYS C 122 30.520 137.716 44.341 1.00 20.74 S ATOM 6258 SG CYS C 125 33.913 136.402 45.708 1.00 10.66 S ATOM 8447 SG CYS D 51 79.108 126.932 99.046 1.00 0.00 S ATOM 8469 SG CYS D 54 77.917 123.656 97.282 1.00 0.00 S ATOM 17958 SG CYS K 410 116.681 71.002 38.019 1.00 4.77 S ATOM 17978 SG CYS K 413 113.149 69.415 38.151 1.00 4.79 S ATOM 20956 SG CYS O 499 65.677 115.217 109.786 1.00 33.37 S ATOM 20977 SG CYS O 502 66.258 115.677 113.487 1.00 37.20 S Time building chain proxies: 5.19, per 1000 atoms: 0.22 Number of scatterers: 23367 At special positions: 0 Unit cell: (159.5, 200.2, 148.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 129 16.00 P 77 15.00 Mg 2 11.99 O 4736 8.00 N 4118 7.00 C 14300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 501 " pdb="ZN ZN B 501 " - pdb=" NE2 HIS B 71 " pdb="ZN ZN B 501 " - pdb=" ND1 HIS B 77 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 61 " pdb="ZN ZN B 501 " - pdb=" SG CYS B 58 " pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" ND1 HIS C 141 " pdb="ZN ZN C 603 " - pdb=" NE2 HIS C 135 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 125 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 122 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 70 " pdb="ZN ZN D 501 " - pdb=" NE2 HIS D 64 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 54 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 51 " pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 431 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 426 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 410 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 413 " pdb=" ZN O 801 " pdb="ZN ZN O 801 " - pdb=" NE2 HIS O 542 " pdb="ZN ZN O 801 " - pdb=" NE2 HIS O 537 " pdb="ZN ZN O 801 " - pdb=" SG CYS O 499 " pdb="ZN ZN O 801 " - pdb=" SG CYS O 502 " Number of angles added : 9 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5106 Finding SS restraints... Secondary structure from input PDB file: 94 helices and 21 sheets defined 44.1% alpha, 12.0% beta 24 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 23 through 30 Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.760A pdb=" N HIS A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 137 removed outlier: 3.693A pdb=" N LEU A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 153 Processing helix chain 'A' and resid 154 through 165 Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.829A pdb=" N ALA A 169 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 171 " --> pdb=" O LYS A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 208 removed outlier: 3.627A pdb=" N LYS A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 257 Proline residue: A 239 - end of helix removed outlier: 4.347A pdb=" N VAL A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.579A pdb=" N GLN A 252 " --> pdb=" O GLU A 248 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 264 Processing helix chain 'A' and resid 265 through 270 removed outlier: 3.981A pdb=" N LEU A 269 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N HIS A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 265 through 270' Processing helix chain 'A' and resid 276 through 280 removed outlier: 3.659A pdb=" N LEU A 279 " --> pdb=" O ILE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 329 through 337 removed outlier: 6.121A pdb=" N ARG A 334 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ARG A 335 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 74 through 89 Processing helix chain 'B' and resid 95 through 108 removed outlier: 5.466A pdb=" N PHE B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP B 105 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 119 removed outlier: 3.955A pdb=" N TYR B 114 " --> pdb=" O PRO B 110 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B 119 " --> pdb=" O GLN B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 139 removed outlier: 3.579A pdb=" N ARG B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 124 " --> pdb=" O CYS B 120 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.590A pdb=" N THR B 150 " --> pdb=" O PRO B 147 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR B 151 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU B 152 " --> pdb=" O ASN B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 174 Processing helix chain 'B' and resid 174 through 182 Processing helix chain 'B' and resid 186 through 199 Processing helix chain 'B' and resid 199 through 211 removed outlier: 3.607A pdb=" N MET B 203 " --> pdb=" O CYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 215 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'B' and resid 278 through 293 removed outlier: 4.174A pdb=" N ALA B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.595A pdb=" N LEU B 299 " --> pdb=" O TRP B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 348 removed outlier: 3.514A pdb=" N MET B 315 " --> pdb=" O PRO B 311 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) Proline residue: B 343 - end of helix Processing helix chain 'B' and resid 356 through 364 Processing helix chain 'B' and resid 392 through 411 Processing helix chain 'C' and resid 106 through 113 removed outlier: 3.500A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 137 Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.501A pdb=" N GLU C 150 " --> pdb=" O ALA C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 172 Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 186 through 204 Processing helix chain 'C' and resid 223 through 249 removed outlier: 3.568A pdb=" N GLU C 227 " --> pdb=" O SER C 223 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR C 239 " --> pdb=" O ASN C 235 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 262 through 269 Processing helix chain 'C' and resid 269 through 281 Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'C' and resid 292 through 314 removed outlier: 3.684A pdb=" N LYS C 296 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 369 removed outlier: 3.932A pdb=" N PHE C 332 " --> pdb=" O THR C 328 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER C 333 " --> pdb=" O GLY C 329 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS C 353 " --> pdb=" O MET C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 376 through 382 Processing helix chain 'D' and resid 60 through 65 Processing helix chain 'D' and resid 67 through 81 Processing helix chain 'D' and resid 82 through 98 removed outlier: 3.630A pdb=" N HIS D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL D 89 " --> pdb=" O ARG D 85 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 129 removed outlier: 4.111A pdb=" N VAL D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 179 removed outlier: 3.533A pdb=" N TYR D 159 " --> pdb=" O SER D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 196 through 207 Processing helix chain 'D' and resid 209 through 214 removed outlier: 3.617A pdb=" N VAL D 213 " --> pdb=" O MET D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 258 removed outlier: 3.790A pdb=" N ARG D 257 " --> pdb=" O GLN D 253 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG D 258 " --> pdb=" O MET D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 303 removed outlier: 3.582A pdb=" N ALA D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR D 303 " --> pdb=" O VAL D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 313 Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 340 through 360 removed outlier: 4.483A pdb=" N ARG D 357 " --> pdb=" O VAL D 353 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LEU D 358 " --> pdb=" O ASP D 354 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR D 359 " --> pdb=" O LEU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 376 through 392 Processing helix chain 'E' and resid 77 through 87 Processing helix chain 'F' and resid 266 through 273 Processing helix chain 'F' and resid 339 through 350 Processing helix chain 'G' and resid 419 through 430 Processing helix chain 'G' and resid 477 through 480 removed outlier: 3.584A pdb=" N GLU G 480 " --> pdb=" O SER G 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 477 through 480' Processing helix chain 'G' and resid 532 through 543 Processing helix chain 'H' and resid 76 through 87 Processing helix chain 'I' and resid 15 through 25 Processing helix chain 'I' and resid 30 through 37 removed outlier: 4.132A pdb=" N SER I 34 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 39 through 44 removed outlier: 4.177A pdb=" N THR I 43 " --> pdb=" O HIS I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 47 No H-bonds generated for 'chain 'I' and resid 45 through 47' Processing helix chain 'I' and resid 67 through 88 Processing helix chain 'I' and resid 97 through 100 Processing helix chain 'I' and resid 153 through 168 removed outlier: 3.735A pdb=" N ASP I 161 " --> pdb=" O GLN I 157 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU I 162 " --> pdb=" O ASN I 158 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS I 165 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 169 through 171 No H-bonds generated for 'chain 'I' and resid 169 through 171' Processing helix chain 'J' and resid 76 through 87 Processing helix chain 'K' and resid 419 through 431 Processing helix chain 'K' and resid 532 through 543 Processing helix chain 'L' and resid 48 through 51 Processing helix chain 'L' and resid 77 through 80 No H-bonds generated for 'chain 'L' and resid 77 through 80' Processing helix chain 'L' and resid 93 through 104 Processing helix chain 'L' and resid 154 through 169 removed outlier: 4.134A pdb=" N LEU L 158 " --> pdb=" O ARG L 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 422 through 427 removed outlier: 4.490A pdb=" N GLU O 426 " --> pdb=" O GLN O 423 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 447 removed outlier: 4.533A pdb=" N ALA O 440 " --> pdb=" O GLU O 436 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ALA O 441 " --> pdb=" O GLU O 437 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS O 447 " --> pdb=" O LEU O 443 " (cutoff:3.500A) Processing helix chain 'O' and resid 467 through 471 Processing helix chain 'O' and resid 472 through 483 removed outlier: 4.013A pdb=" N GLY O 483 " --> pdb=" O GLU O 479 " (cutoff:3.500A) Processing helix chain 'O' and resid 487 through 492 removed outlier: 3.560A pdb=" N SER O 491 " --> pdb=" O SER O 487 " (cutoff:3.500A) Processing helix chain 'O' and resid 499 through 513 Processing helix chain 'O' and resid 514 through 523 Processing helix chain 'O' and resid 530 through 542 removed outlier: 3.551A pdb=" N LEU O 534 " --> pdb=" O LEU O 530 " (cutoff:3.500A) Processing helix chain 'O' and resid 547 through 559 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 removed outlier: 3.663A pdb=" N LYS A 19 " --> pdb=" O CYS A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.668A pdb=" N THR A 107 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.693A pdb=" N ARG A 325 " --> pdb=" O LEU G 483 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 31 Processing sheet with id=AA6, first strand: chain 'B' and resid 37 through 41 removed outlier: 6.777A pdb=" N ILE B 37 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG B 48 " --> pdb=" O ILE B 37 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER B 39 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 57 through 58 removed outlier: 3.614A pdb=" N GLU B 63 " --> pdb=" O CYS B 58 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 115 through 116 removed outlier: 3.776A pdb=" N GLU C 127 " --> pdb=" O CYS C 122 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 315 through 318 Processing sheet with id=AB1, first strand: chain 'D' and resid 49 through 51 removed outlier: 4.465A pdb=" N HIS D 49 " --> pdb=" O TYR D 58 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL D 56 " --> pdb=" O CYS D 51 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 138 through 142 removed outlier: 3.706A pdb=" N GLU D 146 " --> pdb=" O ASP D 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 22 through 39 removed outlier: 16.884A pdb=" N LEU E 27 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 15.950A pdb=" N ILE E 54 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N GLY E 29 " --> pdb=" O THR E 52 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N THR E 52 " --> pdb=" O GLY E 29 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL E 31 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N THR E 50 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASP E 33 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR E 48 " --> pdb=" O ASP E 33 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 64 through 75 current: chain 'E' and resid 111 through 120 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 111 through 120 current: chain 'F' and resid 309 through 319 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 330 through 337 current: chain 'F' and resid 374 through 383 Processing sheet with id=AB4, first strand: chain 'G' and resid 408 through 409 Processing sheet with id=AB5, first strand: chain 'G' and resid 488 through 489 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 488 through 489 current: chain 'G' and resid 509 through 516 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 525 through 531 current: chain 'G' and resid 567 through 576 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 567 through 576 current: chain 'H' and resid 42 through 55 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 64 through 75 current: chain 'H' and resid 117 through 120 Processing sheet with id=AB6, first strand: chain 'H' and resid 103 through 105 Processing sheet with id=AB7, first strand: chain 'I' and resid 93 through 94 Processing sheet with id=AB8, first strand: chain 'I' and resid 102 through 118 removed outlier: 9.535A pdb=" N GLY I 108 " --> pdb=" O GLU I 131 " (cutoff:3.500A) removed outlier: 9.256A pdb=" N GLU I 131 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL I 110 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU I 129 " --> pdb=" O VAL I 110 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN I 112 " --> pdb=" O ILE I 127 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE I 127 " --> pdb=" O GLN I 112 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG I 122 " --> pdb=" O PRO I 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 141 through 151 current: chain 'I' and resid 194 through 205 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 194 through 205 current: chain 'J' and resid 42 through 55 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 64 through 75 current: chain 'J' and resid 117 through 120 Processing sheet with id=AB9, first strand: chain 'J' and resid 103 through 105 Processing sheet with id=AC1, first strand: chain 'K' and resid 408 through 409 Processing sheet with id=AC2, first strand: chain 'K' and resid 493 through 499 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 493 through 499 current: chain 'K' and resid 509 through 516 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 525 through 531 current: chain 'K' and resid 567 through 576 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 567 through 576 current: chain 'L' and resid 34 through 46 removed outlier: 3.941A pdb=" N PHE L 37 " --> pdb=" O CYS L 90 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS L 90 " --> pdb=" O PHE L 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 81 through 92 current: chain 'L' and resid 126 through 136 Processing sheet with id=AC3, first strand: chain 'O' and resid 497 through 498 896 hydrogen bonds defined for protein. 2550 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 100 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 4.43 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3681 1.31 - 1.44: 6759 1.44 - 1.57: 13044 1.57 - 1.69: 153 1.69 - 1.82: 189 Bond restraints: 23826 Sorted by residual: bond pdb=" C6 G R 1 " pdb=" O6 G R 1 " ideal model delta sigma weight residual 1.237 1.398 -0.161 9.00e-03 1.23e+04 3.20e+02 bond pdb=" N7 G R 1 " pdb=" C5 G R 1 " ideal model delta sigma weight residual 1.388 1.495 -0.107 6.00e-03 2.78e+04 3.20e+02 bond pdb=" C3' G R 1 " pdb=" O3' G R 1 " ideal model delta sigma weight residual 1.417 1.187 0.230 1.40e-02 5.10e+03 2.70e+02 bond pdb=" C2 G R 1 " pdb=" N3 G R 1 " ideal model delta sigma weight residual 1.323 1.415 -0.092 8.00e-03 1.56e+04 1.33e+02 bond pdb=" C2 G R 1 " pdb=" N2 G R 1 " ideal model delta sigma weight residual 1.341 1.456 -0.115 1.00e-02 1.00e+04 1.33e+02 ... (remaining 23821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 32592 3.67 - 7.33: 63 7.33 - 11.00: 5 11.00 - 14.67: 2 14.67 - 18.33: 1 Bond angle restraints: 32663 Sorted by residual: angle pdb=" C8 G R 1 " pdb=" N9 G R 1 " pdb=" C4 G R 1 " ideal model delta sigma weight residual 106.40 114.12 -7.72 4.00e-01 6.25e+00 3.72e+02 angle pdb=" C5 G R 1 " pdb=" C6 G R 1 " pdb=" N1 G R 1 " ideal model delta sigma weight residual 111.50 119.80 -8.30 5.00e-01 4.00e+00 2.75e+02 angle pdb=" C5 G R 1 " pdb=" C6 G R 1 " pdb=" O6 G R 1 " ideal model delta sigma weight residual 128.60 119.95 8.65 6.00e-01 2.78e+00 2.08e+02 angle pdb=" C6 G R 1 " pdb=" N1 G R 1 " pdb=" C2 G R 1 " ideal model delta sigma weight residual 125.10 119.14 5.96 6.00e-01 2.78e+00 9.88e+01 angle pdb=" C3' G R 1 " pdb=" C2' G R 1 " pdb=" C1' G R 1 " ideal model delta sigma weight residual 101.30 106.33 -5.03 7.00e-01 2.04e+00 5.15e+01 ... (remaining 32658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 13997 35.95 - 71.90: 461 71.90 - 107.84: 59 107.84 - 143.79: 1 143.79 - 179.74: 2 Dihedral angle restraints: 14520 sinusoidal: 6644 harmonic: 7876 Sorted by residual: dihedral pdb=" O4' C R 76 " pdb=" C1' C R 76 " pdb=" N1 C R 76 " pdb=" C2 C R 76 " ideal model delta sinusoidal sigma weight residual -128.00 51.74 -179.74 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U R 20 " pdb=" C1' U R 20 " pdb=" N1 U R 20 " pdb=" C2 U R 20 " ideal model delta sinusoidal sigma weight residual 232.00 107.60 124.40 1 1.70e+01 3.46e-03 5.20e+01 dihedral pdb=" CA HIS H 131 " pdb=" C HIS H 131 " pdb=" N GLY H 132 " pdb=" CA GLY H 132 " ideal model delta harmonic sigma weight residual -180.00 -147.64 -32.36 0 5.00e+00 4.00e-02 4.19e+01 ... (remaining 14517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 3402 0.090 - 0.180: 315 0.180 - 0.270: 0 0.270 - 0.360: 1 0.360 - 0.450: 1 Chirality restraints: 3719 Sorted by residual: chirality pdb=" P G R 1 " pdb=" OP1 G R 1 " pdb=" OP2 G R 1 " pdb=" O5' G R 1 " both_signs ideal model delta sigma weight residual True 2.41 2.86 -0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" C3' G R 1 " pdb=" C4' G R 1 " pdb=" O3' G R 1 " pdb=" C2' G R 1 " both_signs ideal model delta sigma weight residual False -2.48 -2.17 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C1' A R 35 " pdb=" O4' A R 35 " pdb=" C2' A R 35 " pdb=" N9 A R 35 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 3716 not shown) Planarity restraints: 3939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 325 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO C 326 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO C 326 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 326 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 286 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO A 287 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 287 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 287 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 261 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO A 262 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " 0.026 5.00e-02 4.00e+02 ... (remaining 3936 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 179 2.59 - 3.17: 18261 3.17 - 3.74: 35471 3.74 - 4.32: 48517 4.32 - 4.90: 80071 Nonbonded interactions: 182499 Sorted by model distance: nonbonded pdb=" OE1 GLU C 301 " pdb="MG MG C 602 " model vdw 2.012 2.170 nonbonded pdb=" OG SER D 325 " pdb=" OE1 GLN J 46 " model vdw 2.118 3.040 nonbonded pdb=" O2' G R 30 " pdb=" OP1 C R 31 " model vdw 2.190 3.040 nonbonded pdb=" O VAL K 490 " pdb=" OG1 THR K 580 " model vdw 2.203 3.040 nonbonded pdb=" OE2 GLU C 230 " pdb="MG MG C 602 " model vdw 2.218 2.170 ... (remaining 182494 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 'E' selection = (chain 'H' and resid 20 through 133) selection = (chain 'J' and resid 20 through 133) } ncs_group { reference = chain 'G' selection = (chain 'K' and (resid 404 through 439 or resid 446 through 587)) } 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: 4.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 26.220 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 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 0.230 23846 Z= 0.310 Angle : 0.609 18.334 32672 Z= 0.421 Chirality : 0.046 0.450 3719 Planarity : 0.005 0.053 3939 Dihedral : 17.038 179.740 9414 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.29 % Favored : 96.64 % Rotamer: Outliers : 1.55 % Allowed : 10.46 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.16), residues: 2676 helix: 1.56 (0.16), residues: 1027 sheet: 0.90 (0.21), residues: 539 loop : -0.80 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 73 TYR 0.012 0.001 TYR B 207 PHE 0.019 0.001 PHE C 327 TRP 0.016 0.002 TRP B 57 HIS 0.007 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.31 (23826) covalent geometry : angle 0.60548 / 0.42 (32663) hydrogen bonds : bond 0.17556 / 11.83 ( 958) hydrogen bonds : angle 5.47630 / 3.90 ( 2650) metal coordination : bond 0.01392 / 0.60 ( 20) metal coordination : angle 3.90663 / 2.57 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 379 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 333 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7529 (mmt180) REVERT: D 160 MET cc_start: 0.7846 (ttp) cc_final: 0.7352 (ttp) REVERT: G 500 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7316 (pp) REVERT: G 524 GLU cc_start: 0.7118 (mp0) cc_final: 0.6881 (mp0) REVERT: I 126 PHE cc_start: 0.7165 (m-80) cc_final: 0.6886 (m-80) outliers start: 37 outliers final: 30 residues processed: 415 average time/residue: 0.7535 time to fit residues: 352.8145 Evaluate side-chains 289 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 257 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain E residue 24 SER Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 292 CYS Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 500 LEU Chi-restraints excluded: chain G residue 513 THR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 464 SER Chi-restraints excluded: chain K residue 478 TRP Chi-restraints excluded: chain K residue 500 LEU Chi-restraints excluded: chain O residue 423 GLN Chi-restraints excluded: chain O residue 468 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 0.0040 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 HIS C 126 ASN G 504 GLN G 537 GLN G 546 ASN K 575 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.196681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.158690 restraints weight = 28202.868| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 2.30 r_work: 0.3627 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23846 Z= 0.147 Angle : 0.592 12.047 32672 Z= 0.322 Chirality : 0.044 0.284 3719 Planarity : 0.005 0.054 3939 Dihedral : 14.473 179.232 4250 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.44 % Favored : 96.49 % Rotamer: Outliers : 3.73 % Allowed : 16.28 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2676 helix: 1.58 (0.16), residues: 1049 sheet: 0.77 (0.21), residues: 545 loop : -0.86 (0.19), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 193 TYR 0.035 0.002 TYR K 561 PHE 0.030 0.002 PHE J 113 TRP 0.012 0.001 TRP D 61 HIS 0.009 0.001 HIS D 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (23826) covalent geometry : angle 0.58851 / 0.32 (32663) hydrogen bonds : bond 0.07038 / 4.77 ( 958) hydrogen bonds : angle 4.45057 / 3.15 ( 2650) metal coordination : bond 0.01238 / 0.66 ( 20) metal coordination : angle 3.82645 / 3.04 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 267 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.6771 (ttm) cc_final: 0.6258 (ttm) REVERT: A 286 LYS cc_start: 0.7679 (pttm) cc_final: 0.7019 (mptp) REVERT: B 46 GLN cc_start: 0.8101 (tt0) cc_final: 0.7330 (tp-100) REVERT: B 174 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7337 (mp) REVERT: C 264 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.6161 (tt0) REVERT: C 371 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: D 160 MET cc_start: 0.8018 (ttp) cc_final: 0.7500 (ttp) REVERT: D 181 ARG cc_start: 0.8430 (ptp-110) cc_final: 0.8128 (ptp90) REVERT: E 84 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7637 (tttp) REVERT: F 347 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8212 (tttt) REVERT: G 500 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7521 (pp) REVERT: G 524 GLU cc_start: 0.8025 (mp0) cc_final: 0.7551 (mp0) REVERT: G 537 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.6335 (mm-40) REVERT: H 33 ASP cc_start: 0.7673 (m-30) cc_final: 0.7468 (m-30) REVERT: I 20 ASP cc_start: 0.6014 (OUTLIER) cc_final: 0.5587 (m-30) REVERT: I 151 PRO cc_start: 0.7637 (Cg_endo) cc_final: 0.7322 (Cg_exo) REVERT: J 21 SER cc_start: 0.6864 (OUTLIER) cc_final: 0.6327 (t) REVERT: J 51 THR cc_start: 0.7636 (OUTLIER) cc_final: 0.7427 (t) outliers start: 89 outliers final: 34 residues processed: 330 average time/residue: 0.7210 time to fit residues: 269.4728 Evaluate side-chains 286 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 177 ASN Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 500 LEU Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 537 GLN Chi-restraints excluded: chain G residue 546 ASN Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 20 ASP Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 478 TRP Chi-restraints excluded: chain K residue 500 LEU Chi-restraints excluded: chain K residue 585 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain O residue 423 GLN Chi-restraints excluded: chain O residue 488 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 104 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 230 optimal weight: 20.0000 chunk 257 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 226 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 126 ASN D 134 HIS D 215 ASN D 281 HIS D 348 ASN F 300 ASN ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.194927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155008 restraints weight = 28082.730| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.44 r_work: 0.3588 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23846 Z= 0.167 Angle : 0.614 13.338 32672 Z= 0.331 Chirality : 0.045 0.285 3719 Planarity : 0.005 0.057 3939 Dihedral : 14.312 179.411 4228 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.55 % Favored : 96.38 % Rotamer: Outliers : 4.44 % Allowed : 16.95 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.16), residues: 2676 helix: 1.42 (0.16), residues: 1059 sheet: 0.68 (0.21), residues: 532 loop : -0.94 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 74 TYR 0.032 0.002 TYR I 23 PHE 0.024 0.002 PHE C 327 TRP 0.011 0.002 TRP I 149 HIS 0.008 0.001 HIS B 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (23826) covalent geometry : angle 0.60884 / 0.33 (32663) hydrogen bonds : bond 0.07633 / 5.17 ( 958) hydrogen bonds : angle 4.32412 / 3.08 ( 2650) metal coordination : bond 0.01728 / 0.85 ( 20) metal coordination : angle 4.68693 / 3.58 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 250 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.6843 (ttm) cc_final: 0.6317 (ttm) REVERT: A 236 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7592 (tm-30) REVERT: A 286 LYS cc_start: 0.7798 (pttm) cc_final: 0.7093 (mptp) REVERT: B 46 GLN cc_start: 0.8131 (tt0) cc_final: 0.7286 (tp-100) REVERT: B 174 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7483 (mp) REVERT: B 352 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7920 (ptt-90) REVERT: C 138 VAL cc_start: 0.7099 (OUTLIER) cc_final: 0.6867 (m) REVERT: C 371 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7983 (mt0) REVERT: D 147 VAL cc_start: 0.7737 (t) cc_final: 0.7515 (p) REVERT: D 160 MET cc_start: 0.7996 (ttp) cc_final: 0.7541 (ttp) REVERT: D 181 ARG cc_start: 0.8481 (ptp-110) cc_final: 0.8193 (ptp90) REVERT: D 283 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6665 (ttm) REVERT: D 402 PHE cc_start: 0.4201 (OUTLIER) cc_final: 0.3701 (m-80) REVERT: F 347 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8240 (tttt) REVERT: G 500 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7840 (pp) REVERT: G 524 GLU cc_start: 0.8074 (mp0) cc_final: 0.7581 (mp0) REVERT: H 33 ASP cc_start: 0.7822 (m-30) cc_final: 0.7598 (m-30) REVERT: H 62 GLU cc_start: 0.7896 (pt0) cc_final: 0.7600 (mm-30) REVERT: J 35 GLN cc_start: 0.6742 (mt0) cc_final: 0.6528 (mp10) REVERT: J 68 ASP cc_start: 0.7208 (t70) cc_final: 0.6854 (t70) REVERT: L 19 MET cc_start: 0.7283 (mpp) cc_final: 0.6920 (ttt) REVERT: L 156 TRP cc_start: 0.5094 (OUTLIER) cc_final: 0.4545 (p-90) outliers start: 106 outliers final: 49 residues processed: 332 average time/residue: 0.6945 time to fit residues: 261.9330 Evaluate side-chains 296 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 237 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 500 LEU Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 148 ARG Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain K residue 433 ILE Chi-restraints excluded: chain K residue 478 TRP Chi-restraints excluded: chain K residue 585 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 156 TRP Chi-restraints excluded: chain O residue 423 GLN Chi-restraints excluded: chain O residue 443 LEU Chi-restraints excluded: chain O residue 445 VAL Chi-restraints excluded: chain O residue 468 ILE Chi-restraints excluded: chain O residue 488 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 20 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 chunk 242 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 28 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 199 optimal weight: 0.9990 chunk 234 optimal weight: 7.9990 chunk 253 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN D 91 GLN D 215 ASN G 566 ASN ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 82 ASN O 423 GLN O 431 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.194971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.154229 restraints weight = 28095.169| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 2.42 r_work: 0.3595 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23846 Z= 0.150 Angle : 0.585 12.488 32672 Z= 0.316 Chirality : 0.044 0.282 3719 Planarity : 0.005 0.051 3939 Dihedral : 14.267 179.314 4223 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Rotamer: Outliers : 4.14 % Allowed : 17.87 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 2676 helix: 1.50 (0.16), residues: 1052 sheet: 0.69 (0.21), residues: 523 loop : -0.90 (0.19), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 74 TYR 0.025 0.002 TYR I 23 PHE 0.029 0.002 PHE J 79 TRP 0.016 0.002 TRP I 149 HIS 0.007 0.001 HIS B 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (23826) covalent geometry : angle 0.58167 / 0.32 (32663) hydrogen bonds : bond 0.07250 / 4.90 ( 958) hydrogen bonds : angle 4.23717 / 3.03 ( 2650) metal coordination : bond 0.01526 / 0.73 ( 20) metal coordination : angle 3.69814 / 2.70 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 242 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.6833 (ttm) cc_final: 0.6299 (ttm) REVERT: A 236 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7618 (tm-30) REVERT: A 286 LYS cc_start: 0.7763 (pttm) cc_final: 0.7048 (mptp) REVERT: B 46 GLN cc_start: 0.8078 (tt0) cc_final: 0.7259 (tp-100) REVERT: B 116 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7607 (ttp-110) REVERT: B 174 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7536 (mp) REVERT: B 352 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7866 (ptt90) REVERT: C 138 VAL cc_start: 0.7112 (OUTLIER) cc_final: 0.6879 (m) REVERT: C 285 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7906 (mm) REVERT: C 371 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7921 (mt0) REVERT: D 152 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6312 (mp0) REVERT: D 181 ARG cc_start: 0.8449 (ptp-110) cc_final: 0.8169 (ptp90) REVERT: D 283 MET cc_start: 0.7045 (OUTLIER) cc_final: 0.6646 (ttm) REVERT: D 402 PHE cc_start: 0.4142 (OUTLIER) cc_final: 0.3422 (m-80) REVERT: E 84 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7597 (tttp) REVERT: F 347 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8208 (tttt) REVERT: G 500 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7881 (pp) REVERT: G 524 GLU cc_start: 0.7941 (mp0) cc_final: 0.7521 (mp0) REVERT: H 33 ASP cc_start: 0.7714 (m-30) cc_final: 0.7481 (m-30) REVERT: I 149 TRP cc_start: 0.5398 (t60) cc_final: 0.5086 (t60) REVERT: J 35 GLN cc_start: 0.6773 (mt0) cc_final: 0.6468 (mp10) REVERT: J 66 GLU cc_start: 0.5541 (mp0) cc_final: 0.5295 (mp0) REVERT: L 19 MET cc_start: 0.7380 (mpp) cc_final: 0.6921 (ttt) REVERT: L 83 LYS cc_start: 0.7506 (mppt) cc_final: 0.6599 (tptt) REVERT: L 156 TRP cc_start: 0.5546 (OUTLIER) cc_final: 0.4988 (p-90) REVERT: O 488 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.7237 (mtt) outliers start: 99 outliers final: 54 residues processed: 317 average time/residue: 0.6984 time to fit residues: 251.0799 Evaluate side-chains 301 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 233 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 303 GLU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 500 LEU Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 148 ARG Chi-restraints excluded: chain I residue 160 MET Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 470 THR Chi-restraints excluded: chain K residue 478 TRP Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 585 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 156 TRP Chi-restraints excluded: chain O residue 443 LEU Chi-restraints excluded: chain O residue 468 ILE Chi-restraints excluded: chain O residue 488 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 190 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 249 optimal weight: 5.9990 chunk 242 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 176 optimal weight: 4.9990 chunk 172 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 264 GLN C 353 HIS ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN D 215 ASN E 61 GLN G 566 ASN ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 15 ASN O 442 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.192182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.152793 restraints weight = 28110.089| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.54 r_work: 0.3518 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 23846 Z= 0.214 Angle : 0.680 15.491 32672 Z= 0.363 Chirality : 0.048 0.284 3719 Planarity : 0.006 0.055 3939 Dihedral : 14.327 177.620 4220 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 4.90 % Allowed : 18.04 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.16), residues: 2676 helix: 1.17 (0.16), residues: 1052 sheet: 0.56 (0.21), residues: 526 loop : -1.09 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 330 TYR 0.024 0.003 TYR H 114 PHE 0.030 0.002 PHE J 79 TRP 0.014 0.002 TRP C 231 HIS 0.006 0.002 HIS H 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (23826) covalent geometry : angle 0.67426 / 0.36 (32663) hydrogen bonds : bond 0.08739 / 5.91 ( 958) hydrogen bonds : angle 4.38724 / 3.15 ( 2650) metal coordination : bond 0.02153 / 1.06 ( 20) metal coordination : angle 5.29507 / 3.82 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 243 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ARG cc_start: 0.6243 (tpm170) cc_final: 0.6037 (tpm170) REVERT: A 76 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7429 (mtm-85) REVERT: A 179 MET cc_start: 0.6826 (ttm) cc_final: 0.6278 (ttm) REVERT: A 236 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7670 (tm-30) REVERT: A 286 LYS cc_start: 0.7831 (pttm) cc_final: 0.7122 (mptp) REVERT: B 74 ARG cc_start: 0.7111 (mtt90) cc_final: 0.6400 (mtp-110) REVERT: B 174 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7519 (mp) REVERT: C 138 VAL cc_start: 0.7558 (OUTLIER) cc_final: 0.7283 (m) REVERT: C 225 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: C 264 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: C 285 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.7928 (mm) REVERT: C 371 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: D 147 VAL cc_start: 0.7817 (t) cc_final: 0.7587 (p) REVERT: D 181 ARG cc_start: 0.8567 (ptp-110) cc_final: 0.8308 (ptp90) REVERT: D 283 MET cc_start: 0.7176 (OUTLIER) cc_final: 0.6838 (ttm) REVERT: D 402 PHE cc_start: 0.4017 (OUTLIER) cc_final: 0.3390 (m-80) REVERT: F 347 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8173 (tttt) REVERT: G 493 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7297 (tt) REVERT: G 524 GLU cc_start: 0.8108 (mp0) cc_final: 0.7615 (mp0) REVERT: G 537 GLN cc_start: 0.6721 (mm-40) cc_final: 0.6392 (mm-40) REVERT: H 33 ASP cc_start: 0.8098 (m-30) cc_final: 0.7759 (m-30) REVERT: I 210 MET cc_start: 0.4135 (mtm) cc_final: 0.3835 (mmm) REVERT: J 35 GLN cc_start: 0.6829 (mt0) cc_final: 0.6559 (mp10) REVERT: J 68 ASP cc_start: 0.7111 (t70) cc_final: 0.6802 (t70) REVERT: K 500 LEU cc_start: 0.3619 (OUTLIER) cc_final: 0.3294 (pp) REVERT: L 19 MET cc_start: 0.7359 (mpp) cc_final: 0.6975 (ttt) REVERT: L 156 TRP cc_start: 0.5469 (OUTLIER) cc_final: 0.4879 (p-90) REVERT: O 488 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7478 (mmt) outliers start: 117 outliers final: 67 residues processed: 331 average time/residue: 0.6587 time to fit residues: 248.1122 Evaluate side-chains 309 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 227 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 176 PHE Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 264 GLN Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 347 LYS Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 513 THR Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 148 ARG Chi-restraints excluded: chain I residue 160 MET Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 433 ILE Chi-restraints excluded: chain K residue 470 THR Chi-restraints excluded: chain K residue 478 TRP Chi-restraints excluded: chain K residue 500 LEU Chi-restraints excluded: chain K residue 585 VAL Chi-restraints excluded: chain L residue 11 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 156 TRP Chi-restraints excluded: chain O residue 442 GLN Chi-restraints excluded: chain O residue 443 LEU Chi-restraints excluded: chain O residue 445 VAL Chi-restraints excluded: chain O residue 468 ILE Chi-restraints excluded: chain O residue 488 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 176 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 57 optimal weight: 4.9990 chunk 204 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 210 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 239 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 241 optimal weight: 8.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 345 GLN ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN D 215 ASN G 566 ASN J 61 GLN ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.193957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155249 restraints weight = 28319.459| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 2.49 r_work: 0.3565 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23846 Z= 0.148 Angle : 0.590 12.730 32672 Z= 0.318 Chirality : 0.044 0.274 3719 Planarity : 0.005 0.053 3939 Dihedral : 14.289 178.882 4216 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.85 % Favored : 96.08 % Rotamer: Outliers : 4.44 % Allowed : 18.67 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.16), residues: 2676 helix: 1.43 (0.16), residues: 1052 sheet: 0.60 (0.22), residues: 527 loop : -1.02 (0.19), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 556 TYR 0.023 0.002 TYR O 564 PHE 0.032 0.002 PHE J 79 TRP 0.017 0.002 TRP I 149 HIS 0.007 0.001 HIS B 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (23826) covalent geometry : angle 0.58605 / 0.32 (32663) hydrogen bonds : bond 0.07430 / 5.01 ( 958) hydrogen bonds : angle 4.23874 / 3.03 ( 2650) metal coordination : bond 0.01500 / 0.72 ( 20) metal coordination : angle 4.07631 / 2.90 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 235 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.6839 (ttm) cc_final: 0.6310 (ttm) REVERT: A 313 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6981 (mtp85) REVERT: B 116 ARG cc_start: 0.7961 (ttm110) cc_final: 0.7711 (ttp-110) REVERT: B 174 ILE cc_start: 0.7744 (OUTLIER) cc_final: 0.7484 (mp) REVERT: B 352 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7931 (ptt-90) REVERT: C 138 VAL cc_start: 0.7530 (OUTLIER) cc_final: 0.7272 (m) REVERT: C 285 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7939 (mm) REVERT: C 371 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: D 152 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6421 (mp0) REVERT: D 181 ARG cc_start: 0.8498 (ptp-110) cc_final: 0.8227 (ptp90) REVERT: D 402 PHE cc_start: 0.3972 (OUTLIER) cc_final: 0.3352 (m-80) REVERT: G 524 GLU cc_start: 0.8073 (mp0) cc_final: 0.7633 (mp0) REVERT: G 537 GLN cc_start: 0.6623 (mm-40) cc_final: 0.6291 (mm-40) REVERT: H 33 ASP cc_start: 0.7847 (m-30) cc_final: 0.7543 (m-30) REVERT: I 149 TRP cc_start: 0.5479 (t60) cc_final: 0.5153 (t60) REVERT: I 210 MET cc_start: 0.4219 (mtm) cc_final: 0.3909 (mmm) REVERT: J 35 GLN cc_start: 0.6775 (mt0) cc_final: 0.6522 (mp10) REVERT: J 66 GLU cc_start: 0.5350 (mp0) cc_final: 0.4935 (mp0) REVERT: J 68 ASP cc_start: 0.7108 (t70) cc_final: 0.6798 (t70) REVERT: L 19 MET cc_start: 0.7305 (mpp) cc_final: 0.6975 (ttt) REVERT: L 83 LYS cc_start: 0.7686 (mppt) cc_final: 0.6693 (tptt) REVERT: L 156 TRP cc_start: 0.5578 (OUTLIER) cc_final: 0.4931 (p-90) REVERT: O 444 GLN cc_start: 0.7901 (tt0) cc_final: 0.7684 (tt0) REVERT: O 488 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.7366 (mtt) outliers start: 106 outliers final: 64 residues processed: 315 average time/residue: 0.6901 time to fit residues: 247.5805 Evaluate side-chains 302 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 228 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain B residue 106 GLU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 500 LEU Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 535 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 148 ARG Chi-restraints excluded: chain I residue 160 MET Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 470 THR Chi-restraints excluded: chain K residue 478 TRP Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 585 VAL Chi-restraints excluded: chain K residue 586 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 156 TRP Chi-restraints excluded: chain O residue 443 LEU Chi-restraints excluded: chain O residue 445 VAL Chi-restraints excluded: chain O residue 468 ILE Chi-restraints excluded: chain O residue 488 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 71 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 176 optimal weight: 0.0060 chunk 15 optimal weight: 0.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN D 215 ASN G 504 GLN ** K 575 HIS ** 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 = 0.4400 r_free = 0.4400 target = 0.194581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.157302 restraints weight = 28167.155| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.32 r_work: 0.3577 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23846 Z= 0.141 Angle : 0.583 12.367 32672 Z= 0.313 Chirality : 0.044 0.269 3719 Planarity : 0.005 0.053 3939 Dihedral : 14.263 179.349 4216 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 4.19 % Allowed : 19.38 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.16), residues: 2676 helix: 1.52 (0.16), residues: 1054 sheet: 0.61 (0.22), residues: 508 loop : -0.95 (0.19), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 74 TYR 0.022 0.002 TYR H 114 PHE 0.035 0.002 PHE J 79 TRP 0.012 0.002 TRP I 149 HIS 0.007 0.001 HIS B 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (23826) covalent geometry : angle 0.57917 / 0.31 (32663) hydrogen bonds : bond 0.07083 / 4.78 ( 958) hydrogen bonds : angle 4.18632 / 2.99 ( 2650) metal coordination : bond 0.01532 / 0.72 ( 20) metal coordination : angle 3.95757 / 3.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 239 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.7514 (mtm-85) REVERT: A 179 MET cc_start: 0.6815 (ttm) cc_final: 0.6293 (ttm) REVERT: A 313 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6919 (mtp85) REVERT: B 74 ARG cc_start: 0.6906 (mtt90) cc_final: 0.6220 (mtp-110) REVERT: B 116 ARG cc_start: 0.7951 (ttm110) cc_final: 0.7707 (ttp-110) REVERT: B 155 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8173 (mtm) REVERT: B 174 ILE cc_start: 0.7745 (OUTLIER) cc_final: 0.7475 (mp) REVERT: B 352 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7836 (ptt90) REVERT: C 138 VAL cc_start: 0.7486 (OUTLIER) cc_final: 0.7220 (m) REVERT: C 225 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: C 285 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.7908 (mm) REVERT: C 371 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7993 (mt0) REVERT: D 152 GLU cc_start: 0.6771 (OUTLIER) cc_final: 0.6405 (mt-10) REVERT: D 181 ARG cc_start: 0.8483 (ptp-110) cc_final: 0.8206 (ptp90) REVERT: D 283 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6634 (ttm) REVERT: D 402 PHE cc_start: 0.4196 (OUTLIER) cc_final: 0.3472 (m-80) REVERT: E 105 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8142 (tp) REVERT: G 493 ILE cc_start: 0.7515 (OUTLIER) cc_final: 0.7198 (tt) REVERT: G 524 GLU cc_start: 0.8055 (mp0) cc_final: 0.7612 (mp0) REVERT: G 537 GLN cc_start: 0.6631 (mm-40) cc_final: 0.6298 (mm-40) REVERT: H 33 ASP cc_start: 0.7755 (m-30) cc_final: 0.7448 (m-30) REVERT: I 149 TRP cc_start: 0.5495 (t60) cc_final: 0.5154 (t60) REVERT: I 210 MET cc_start: 0.4190 (mtm) cc_final: 0.3858 (mmm) REVERT: J 35 GLN cc_start: 0.6777 (mt0) cc_final: 0.6478 (mp10) REVERT: J 68 ASP cc_start: 0.7077 (t70) cc_final: 0.6745 (t70) REVERT: K 488 GLN cc_start: 0.7572 (mp10) cc_final: 0.6838 (tt0) REVERT: L 19 MET cc_start: 0.7355 (mpp) cc_final: 0.6996 (ttt) REVERT: L 83 LYS cc_start: 0.7576 (mppt) cc_final: 0.6651 (tptt) REVERT: L 156 TRP cc_start: 0.5527 (OUTLIER) cc_final: 0.4921 (p-90) REVERT: O 444 GLN cc_start: 0.7925 (tt0) cc_final: 0.7707 (tt0) REVERT: O 488 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7369 (mmt) outliers start: 100 outliers final: 63 residues processed: 315 average time/residue: 0.6892 time to fit residues: 247.3756 Evaluate side-chains 309 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 230 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 57 TRP Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 176 PHE Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 ILE Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain F residue 372 MET Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 535 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 148 ARG Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 433 ILE Chi-restraints excluded: chain K residue 470 THR Chi-restraints excluded: chain K residue 478 TRP Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 585 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 156 TRP Chi-restraints excluded: chain O residue 443 LEU Chi-restraints excluded: chain O residue 445 VAL Chi-restraints excluded: chain O residue 468 ILE Chi-restraints excluded: chain O residue 488 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 244 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 188 optimal weight: 0.1980 chunk 51 optimal weight: 0.0030 chunk 43 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 250 optimal weight: 0.0370 chunk 223 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.6472 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN D 215 ASN G 566 ASN ** K 575 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 = 0.4413 r_free = 0.4413 target = 0.195943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.157747 restraints weight = 28228.965| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.44 r_work: 0.3608 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23846 Z= 0.127 Angle : 0.557 11.150 32672 Z= 0.300 Chirality : 0.042 0.263 3719 Planarity : 0.005 0.053 3939 Dihedral : 14.221 179.872 4216 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.74 % Favored : 96.19 % Rotamer: Outliers : 4.19 % Allowed : 19.51 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.16), residues: 2676 helix: 1.70 (0.16), residues: 1054 sheet: 0.71 (0.22), residues: 503 loop : -0.90 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 556 TYR 0.022 0.002 TYR O 564 PHE 0.026 0.001 PHE J 79 TRP 0.012 0.001 TRP C 167 HIS 0.006 0.001 HIS H 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (23826) covalent geometry : angle 0.55329 / 0.30 (32663) hydrogen bonds : bond 0.06409 / 4.32 ( 958) hydrogen bonds : angle 4.09273 / 2.93 ( 2650) metal coordination : bond 0.01373 / 0.65 ( 20) metal coordination : angle 3.63803 / 2.86 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 234 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7408 (mtm-85) REVERT: B 46 GLN cc_start: 0.8158 (tt0) cc_final: 0.7265 (tp-100) REVERT: B 116 ARG cc_start: 0.7914 (ttm110) cc_final: 0.7705 (ttp-110) REVERT: B 155 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7850 (mtp) REVERT: B 174 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7416 (mp) REVERT: B 352 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7867 (ptt90) REVERT: C 138 VAL cc_start: 0.7453 (OUTLIER) cc_final: 0.7185 (m) REVERT: C 285 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7898 (mm) REVERT: C 371 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7992 (mt0) REVERT: D 152 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6400 (mt-10) REVERT: D 181 ARG cc_start: 0.8470 (ptp-110) cc_final: 0.8191 (ptp90) REVERT: D 402 PHE cc_start: 0.4250 (OUTLIER) cc_final: 0.3392 (m-80) REVERT: E 101 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7038 (pp) REVERT: E 105 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8160 (tp) REVERT: G 480 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7089 (tm-30) REVERT: G 493 ILE cc_start: 0.7502 (OUTLIER) cc_final: 0.7164 (tt) REVERT: G 524 GLU cc_start: 0.8008 (mp0) cc_final: 0.7596 (mp0) REVERT: G 537 GLN cc_start: 0.6738 (mm-40) cc_final: 0.6392 (mm-40) REVERT: H 33 ASP cc_start: 0.7630 (m-30) cc_final: 0.7321 (m-30) REVERT: I 210 MET cc_start: 0.4257 (mtm) cc_final: 0.3986 (mmm) REVERT: J 68 ASP cc_start: 0.7095 (t70) cc_final: 0.6770 (t70) REVERT: K 488 GLN cc_start: 0.7513 (mp10) cc_final: 0.6829 (tt0) REVERT: L 83 LYS cc_start: 0.7490 (mppt) cc_final: 0.6701 (tptt) REVERT: L 156 TRP cc_start: 0.5341 (OUTLIER) cc_final: 0.4716 (p-90) REVERT: O 444 GLN cc_start: 0.7920 (tt0) cc_final: 0.7713 (tt0) REVERT: O 488 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7257 (mtt) outliers start: 100 outliers final: 56 residues processed: 308 average time/residue: 0.6508 time to fit residues: 228.8335 Evaluate side-chains 292 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 222 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 535 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 148 ARG Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 99 LEU Chi-restraints excluded: chain K residue 470 THR Chi-restraints excluded: chain K residue 478 TRP Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 585 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 156 TRP Chi-restraints excluded: chain O residue 443 LEU Chi-restraints excluded: chain O residue 468 ILE Chi-restraints excluded: chain O residue 488 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 266 optimal weight: 50.0000 chunk 105 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 242 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 218 optimal weight: 8.9990 chunk 170 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 HIS A 345 GLN ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN D 215 ASN J 35 GLN ** K 575 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 = 0.4380 r_free = 0.4380 target = 0.193186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.153114 restraints weight = 28190.994| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.34 r_work: 0.3553 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23846 Z= 0.144 Angle : 0.587 12.335 32672 Z= 0.314 Chirality : 0.044 0.258 3719 Planarity : 0.005 0.054 3939 Dihedral : 14.216 179.768 4215 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 3.22 % Allowed : 20.51 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.16), residues: 2676 helix: 1.63 (0.16), residues: 1055 sheet: 0.73 (0.22), residues: 501 loop : -0.91 (0.19), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 74 TYR 0.022 0.002 TYR H 114 PHE 0.033 0.002 PHE J 79 TRP 0.025 0.002 TRP I 149 HIS 0.007 0.001 HIS B 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (23826) covalent geometry : angle 0.58354 / 0.31 (32663) hydrogen bonds : bond 0.06836 / 4.61 ( 958) hydrogen bonds : angle 4.11084 / 2.95 ( 2650) metal coordination : bond 0.01494 / 0.72 ( 20) metal coordination : angle 3.75727 / 2.85 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 230 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7399 (mtm-85) REVERT: A 236 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7595 (tm-30) REVERT: A 286 LYS cc_start: 0.7761 (pttm) cc_final: 0.7066 (mptp) REVERT: B 46 GLN cc_start: 0.8147 (tt0) cc_final: 0.7274 (tp-100) REVERT: B 74 ARG cc_start: 0.6817 (mtt90) cc_final: 0.6161 (mtp-110) REVERT: B 155 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8115 (mtm) REVERT: B 174 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7450 (mp) REVERT: B 352 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7838 (ptt90) REVERT: C 138 VAL cc_start: 0.7468 (OUTLIER) cc_final: 0.7218 (m) REVERT: C 285 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.7878 (mm) REVERT: C 371 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7886 (mt0) REVERT: D 152 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6422 (mt-10) REVERT: D 181 ARG cc_start: 0.8495 (ptp-110) cc_final: 0.8232 (ptp90) REVERT: D 402 PHE cc_start: 0.4280 (OUTLIER) cc_final: 0.3414 (m-80) REVERT: E 101 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7079 (pp) REVERT: G 480 GLU cc_start: 0.7347 (tm-30) cc_final: 0.7107 (tm-30) REVERT: G 493 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7182 (tt) REVERT: G 524 GLU cc_start: 0.8001 (mp0) cc_final: 0.7566 (mp0) REVERT: G 537 GLN cc_start: 0.6571 (mm-40) cc_final: 0.6242 (mm-40) REVERT: H 33 ASP cc_start: 0.7701 (m-30) cc_final: 0.7382 (m-30) REVERT: I 210 MET cc_start: 0.4260 (mtm) cc_final: 0.3859 (mmm) REVERT: J 68 ASP cc_start: 0.7061 (t70) cc_final: 0.6745 (t70) REVERT: J 100 ARG cc_start: 0.7299 (mmm-85) cc_final: 0.6490 (mmp-170) REVERT: K 488 GLN cc_start: 0.7468 (mp10) cc_final: 0.6770 (tt0) REVERT: L 83 LYS cc_start: 0.7492 (mppt) cc_final: 0.6710 (tptt) REVERT: L 156 TRP cc_start: 0.5391 (OUTLIER) cc_final: 0.4780 (p-90) REVERT: O 444 GLN cc_start: 0.7891 (tt0) cc_final: 0.7685 (tt0) REVERT: O 488 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7358 (mmt) outliers start: 77 outliers final: 51 residues processed: 293 average time/residue: 0.6730 time to fit residues: 224.6698 Evaluate side-chains 286 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 221 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 101 LEU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 535 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 148 ARG Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 470 THR Chi-restraints excluded: chain K residue 478 TRP Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 585 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 156 TRP Chi-restraints excluded: chain O residue 443 LEU Chi-restraints excluded: chain O residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 161 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 146 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 160 optimal weight: 0.2980 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 337 HIS A 345 GLN ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN E 61 GLN ** K 575 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 = 0.4362 r_free = 0.4362 target = 0.191423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.152725 restraints weight = 28107.964| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.38 r_work: 0.3526 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 23846 Z= 0.183 Angle : 0.642 14.061 32672 Z= 0.344 Chirality : 0.046 0.254 3719 Planarity : 0.006 0.056 3939 Dihedral : 14.262 178.667 4215 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 3.22 % Allowed : 20.76 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.16), residues: 2676 helix: 1.42 (0.16), residues: 1053 sheet: 0.71 (0.22), residues: 508 loop : -0.99 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 74 TYR 0.029 0.002 TYR I 195 PHE 0.031 0.002 PHE J 79 TRP 0.038 0.002 TRP I 149 HIS 0.007 0.001 HIS B 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (23826) covalent geometry : angle 0.63842 / 0.34 (32663) hydrogen bonds : bond 0.07799 / 5.26 ( 958) hydrogen bonds : angle 4.20698 / 3.02 ( 2650) metal coordination : bond 0.01874 / 0.91 ( 20) metal coordination : angle 4.40032 / 3.28 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5352 Ramachandran restraints generated. 2676 Oldfield, 0 Emsley, 2676 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 230 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7494 (mtm-85) REVERT: A 236 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7593 (tm-30) REVERT: A 286 LYS cc_start: 0.7801 (pttm) cc_final: 0.7114 (mptp) REVERT: A 313 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6878 (mtp85) REVERT: B 46 GLN cc_start: 0.8199 (tt0) cc_final: 0.7259 (tp-100) REVERT: B 74 ARG cc_start: 0.6958 (mtt90) cc_final: 0.6262 (mtp-110) REVERT: B 155 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8156 (mtm) REVERT: B 352 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7921 (ptt-90) REVERT: C 138 VAL cc_start: 0.7562 (OUTLIER) cc_final: 0.7309 (m) REVERT: C 285 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7907 (mm) REVERT: C 371 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: D 152 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6398 (mt-10) REVERT: D 181 ARG cc_start: 0.8601 (ptp-110) cc_final: 0.8260 (ptp90) REVERT: D 402 PHE cc_start: 0.3893 (OUTLIER) cc_final: 0.3348 (m-80) REVERT: G 480 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7177 (tm-30) REVERT: G 493 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7238 (tt) REVERT: G 524 GLU cc_start: 0.7996 (mp0) cc_final: 0.7581 (mp0) REVERT: G 537 GLN cc_start: 0.6631 (mm-40) cc_final: 0.6263 (mm-40) REVERT: H 33 ASP cc_start: 0.7977 (m-30) cc_final: 0.7641 (m-30) REVERT: I 149 TRP cc_start: 0.5400 (t60) cc_final: 0.5105 (t60) REVERT: J 55 ASP cc_start: 0.7170 (m-30) cc_final: 0.6736 (m-30) REVERT: J 66 GLU cc_start: 0.5501 (mp0) cc_final: 0.5033 (mp0) REVERT: J 100 ARG cc_start: 0.7283 (mmm-85) cc_final: 0.6530 (mmp-170) REVERT: J 114 TYR cc_start: 0.6508 (m-10) cc_final: 0.6283 (m-80) REVERT: K 488 GLN cc_start: 0.7449 (mp10) cc_final: 0.6836 (tt0) REVERT: L 19 MET cc_start: 0.7162 (mpp) cc_final: 0.6800 (ttt) REVERT: L 83 LYS cc_start: 0.7562 (mppt) cc_final: 0.6742 (tptt) REVERT: L 156 TRP cc_start: 0.5392 (OUTLIER) cc_final: 0.4853 (p-90) REVERT: O 488 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7376 (mmt) outliers start: 77 outliers final: 54 residues processed: 292 average time/residue: 0.6714 time to fit residues: 222.9882 Evaluate side-chains 291 residues out of total 2389 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 224 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 PHE Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 308 SER Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 345 GLN Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 155 MET Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 352 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 256 ILE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 371 GLN Chi-restraints excluded: chain D residue 152 GLU Chi-restraints excluded: chain D residue 153 SER Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 382 VAL Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain F residue 287 ARG Chi-restraints excluded: chain F residue 298 VAL Chi-restraints excluded: chain F residue 359 THR Chi-restraints excluded: chain G residue 462 LEU Chi-restraints excluded: chain G residue 493 ILE Chi-restraints excluded: chain G residue 521 SER Chi-restraints excluded: chain G residue 535 VAL Chi-restraints excluded: chain G residue 570 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 94 VAL Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 148 ARG Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 44 VAL Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain K residue 463 SER Chi-restraints excluded: chain K residue 470 THR Chi-restraints excluded: chain K residue 478 TRP Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 585 VAL Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 156 TRP Chi-restraints excluded: chain O residue 443 LEU Chi-restraints excluded: chain O residue 488 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 189 optimal weight: 2.9990 chunk 264 optimal weight: 30.0000 chunk 50 optimal weight: 0.7980 chunk 220 optimal weight: 0.6980 chunk 255 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 235 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 111 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN D 215 ASN J 112 HIS ** K 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 442 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.192419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.149808 restraints weight = 27978.428| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.70 r_work: 0.3515 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23846 Z= 0.150 Angle : 0.603 12.668 32672 Z= 0.324 Chirality : 0.044 0.251 3719 Planarity : 0.005 0.058 3939 Dihedral : 14.256 179.225 4215 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.15 % Favored : 95.78 % Rotamer: Outliers : 3.52 % Allowed : 20.64 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.16), residues: 2676 helix: 1.55 (0.16), residues: 1047 sheet: 0.72 (0.22), residues: 508 loop : -0.93 (0.19), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 74 TYR 0.025 0.002 TYR O 564 PHE 0.029 0.002 PHE J 79 TRP 0.032 0.002 TRP I 149 HIS 0.007 0.001 HIS B 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (23826) covalent geometry : angle 0.59922 / 0.32 (32663) hydrogen bonds : bond 0.07219 / 4.87 ( 958) hydrogen bonds : angle 4.17229 / 2.99 ( 2650) metal coordination : bond 0.01558 / 0.74 ( 20) metal coordination : angle 3.96838 / 2.92 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8545.18 seconds wall clock time: 146 minutes 13.58 seconds (8773.58 seconds total)