Starting phenix.real_space_refine on Mon Aug 25 14:38:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b0j_15785/08_2025/8b0j_15785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b0j_15785/08_2025/8b0j_15785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8b0j_15785/08_2025/8b0j_15785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b0j_15785/08_2025/8b0j_15785.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b0j_15785/08_2025/8b0j_15785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b0j_15785/08_2025/8b0j_15785.map" } resolution = 3.99 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= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 160 5.49 5 S 17 5.16 5 C 9573 2.51 5 N 2853 2.21 5 O 3599 1.98 5 H 12434 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28636 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 3695 Classifications: {'peptide': 268} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 205 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 11, 'ASP:plan': 10, 'ASN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 2, 'HIS:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 176 Chain: "B" Number of atoms: 3571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 3571 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 15, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 410 Unresolved non-hydrogen dihedrals: 272 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ARG:plan': 15, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 10, 'GLU:plan': 10, 'PHE:plan': 2, 'GLN:plan1': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 208 Chain: "D" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 3462 Classifications: {'peptide': 281} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 15, 'TRANS': 265} Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 492 Unresolved non-hydrogen dihedrals: 328 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ARG:plan': 18, 'PHE:plan': 5, 'ASN:plan1': 8, 'ASP:plan': 6, 'HIS:plan': 4, 'GLU:plan': 8, 'TYR:plan': 3, 'GLN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 252 Chain: "C" Number of atoms: 3239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 3239 Classifications: {'peptide': 266} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 393 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 333 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'ARG:plan': 19, 'GLU:plan': 12, 'ASP:plan': 9, 'TYR:plan': 4, 'ASN:plan1': 4, 'PHE:plan': 2, 'HIS:plan': 4, 'TRP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 259 Chain: "L" Number of atoms: 5605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 5605 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 20, 'TRANS': 460} Chain breaks: 3 Unresolved non-hydrogen bonds: 771 Unresolved non-hydrogen angles: 964 Unresolved non-hydrogen dihedrals: 641 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 13, 'GLU:plan': 28, 'ARG:plan': 32, 'ASP:plan': 11, 'TYR:plan': 7, 'HIS:plan': 10, 'ASN:plan1': 6, 'PHE:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 516 Chain: "N" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 4220 Classifications: {'peptide': 356} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 343} Chain breaks: 7 Unresolved non-hydrogen bonds: 558 Unresolved non-hydrogen angles: 700 Unresolved non-hydrogen dihedrals: 458 Unresolved non-hydrogen chiralities: 34 Planarities with less than four sites: {'ARG:plan': 24, 'ASP:plan': 11, 'GLN:plan1': 10, 'TYR:plan': 5, 'GLU:plan': 18, 'HIS:plan': 5, 'ASN:plan1': 5, 'PHE:plan': 5, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 376 Chain: "K" Number of atoms: 4844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 4844 Classifications: {'RNA': 160} Modifications used: {'3*END': 1, 'rna2p_pur': 22, 'rna2p_pyr': 23, 'rna3p_pur': 49, 'rna3p_pyr': 66} Link IDs: {'rna2p': 45, 'rna3p': 114} Chain breaks: 6 Time building chain proxies: 5.99, per 1000 atoms: 0.21 Number of scatterers: 28636 At special positions: 0 Unit cell: (127.14, 131.052, 180.604, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 17 16.00 P 160 15.00 O 3599 8.00 N 2853 7.00 C 9573 6.00 H 12434 1.00 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: 2.66 Conformation dependent library (CDL) restraints added in 916.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 17 sheets defined 47.5% alpha, 10.5% beta 4 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 4.78 Creating SS restraints... Processing helix chain 'A' and resid 13 through 25 removed outlier: 3.512A pdb=" N ALA A 17 " --> pdb=" O GLY A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 36 through 48 removed outlier: 3.542A pdb=" N LEU A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 removed outlier: 3.846A pdb=" N PHE A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.710A pdb=" N ARG A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 130 Proline residue: A 125 - end of helix Processing helix chain 'A' and resid 140 through 154 Processing helix chain 'A' and resid 188 through 196 Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 202 through 212 removed outlier: 3.765A pdb=" N HIS A 212 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 235 removed outlier: 3.955A pdb=" N HIS A 216 " --> pdb=" O HIS A 212 " (cutoff:3.500A) Proline residue: A 231 - end of helix Processing helix chain 'A' and resid 252 through 268 removed outlier: 3.616A pdb=" N PHE A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'B' and resid 13 through 25 removed outlier: 3.791A pdb=" N ASP B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 35 No H-bonds generated for 'chain 'B' and resid 33 through 35' Processing helix chain 'B' and resid 36 through 48 removed outlier: 3.958A pdb=" N ASP B 46 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 47 " --> pdb=" O THR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 73 removed outlier: 3.663A pdb=" N PHE B 67 " --> pdb=" O SER B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 97 Processing helix chain 'B' and resid 104 through 109 removed outlier: 4.054A pdb=" N LYS B 108 " --> pdb=" O PRO B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 130 removed outlier: 3.804A pdb=" N ILE B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP B 121 " --> pdb=" O ASP B 117 " (cutoff:3.500A) Proline residue: B 125 - end of helix Processing helix chain 'B' and resid 140 through 153 removed outlier: 3.764A pdb=" N GLU B 146 " --> pdb=" O HIS B 142 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU B 153 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 188 through 192 Processing helix chain 'B' and resid 202 through 212 removed outlier: 3.525A pdb=" N ALA B 206 " --> pdb=" O ASP B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 236 removed outlier: 3.973A pdb=" N HIS B 216 " --> pdb=" O HIS B 212 " (cutoff:3.500A) Proline residue: B 231 - end of helix removed outlier: 3.713A pdb=" N ASN B 236 " --> pdb=" O MET B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 268 removed outlier: 3.612A pdb=" N TYR B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 280 No H-bonds generated for 'chain 'B' and resid 278 through 280' Processing helix chain 'D' and resid 13 through 25 Processing helix chain 'D' and resid 36 through 48 removed outlier: 3.923A pdb=" N ASP D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG D 47 " --> pdb=" O THR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 73 removed outlier: 3.829A pdb=" N GLU D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 97 Processing helix chain 'D' and resid 111 through 129 removed outlier: 3.500A pdb=" N SER D 120 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP D 121 " --> pdb=" O ASP D 117 " (cutoff:3.500A) Proline residue: D 125 - end of helix removed outlier: 3.780A pdb=" N SER D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG D 129 " --> pdb=" O PRO D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 151 removed outlier: 3.655A pdb=" N GLU D 146 " --> pdb=" O HIS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 192 removed outlier: 3.960A pdb=" N TRP D 191 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 211 Processing helix chain 'D' and resid 213 through 228 removed outlier: 3.568A pdb=" N LEU D 228 " --> pdb=" O SER D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 235 Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.936A pdb=" N ILE D 257 " --> pdb=" O ARG D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 281 removed outlier: 4.114A pdb=" N GLU D 280 " --> pdb=" O HIS D 276 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS D 281 " --> pdb=" O ARG D 277 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 276 through 281' Processing helix chain 'C' and resid 13 through 24 Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 36 through 48 removed outlier: 4.305A pdb=" N ASP C 46 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 63 through 74 removed outlier: 3.699A pdb=" N PHE C 67 " --> pdb=" O SER C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 95 removed outlier: 3.987A pdb=" N ARG C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 129 Proline residue: C 125 - end of helix Processing helix chain 'C' and resid 140 through 152 removed outlier: 3.561A pdb=" N GLU C 146 " --> pdb=" O HIS C 142 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG C 151 " --> pdb=" O MET C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 192 Processing helix chain 'C' and resid 202 through 211 Processing helix chain 'C' and resid 212 through 236 removed outlier: 3.687A pdb=" N HIS C 216 " --> pdb=" O HIS C 212 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TRP C 229 " --> pdb=" O TYR C 225 " (cutoff:3.500A) Proline residue: C 231 - end of helix removed outlier: 3.614A pdb=" N ASN C 236 " --> pdb=" O MET C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 267 Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'L' and resid 69 through 73 Processing helix chain 'L' and resid 89 through 94 Processing helix chain 'L' and resid 144 through 158 Processing helix chain 'L' and resid 176 through 199 Processing helix chain 'L' and resid 214 through 220 Processing helix chain 'L' and resid 233 through 235 No H-bonds generated for 'chain 'L' and resid 233 through 235' Processing helix chain 'L' and resid 236 through 245 removed outlier: 4.574A pdb=" N HIS L 243 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ALA L 245 " --> pdb=" O ARG L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 254 removed outlier: 4.019A pdb=" N PHE L 252 " --> pdb=" O ARG L 249 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER L 254 " --> pdb=" O ASP L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 269 Processing helix chain 'L' and resid 271 through 278 Processing helix chain 'L' and resid 315 through 338 removed outlier: 3.829A pdb=" N ASP L 328 " --> pdb=" O LEU L 324 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU L 329 " --> pdb=" O GLU L 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 369 removed outlier: 3.559A pdb=" N ALA L 366 " --> pdb=" O ARG L 362 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN L 369 " --> pdb=" O GLU L 365 " (cutoff:3.500A) Processing helix chain 'L' and resid 415 through 432 Processing helix chain 'L' and resid 444 through 455 removed outlier: 3.544A pdb=" N TYR L 450 " --> pdb=" O PRO L 446 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU L 452 " --> pdb=" O ALA L 448 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ASN L 453 " --> pdb=" O SER L 449 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU L 454 " --> pdb=" O TYR L 450 " (cutoff:3.500A) Processing helix chain 'L' and resid 455 through 466 removed outlier: 3.732A pdb=" N GLN L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 154 removed outlier: 4.121A pdb=" N GLU N 153 " --> pdb=" O THR N 149 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA N 154 " --> pdb=" O GLU N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 176 through 190 removed outlier: 3.918A pdb=" N TRP N 182 " --> pdb=" O GLU N 178 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP N 183 " --> pdb=" O ALA N 179 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N PHE N 186 " --> pdb=" O TRP N 182 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG N 187 " --> pdb=" O ASP N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 214 through 221 removed outlier: 3.628A pdb=" N PHE N 218 " --> pdb=" O ILE N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 248 removed outlier: 3.541A pdb=" N ALA N 245 " --> pdb=" O ARG N 241 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA N 246 " --> pdb=" O GLN N 242 " (cutoff:3.500A) Processing helix chain 'N' and resid 251 through 256 removed outlier: 4.290A pdb=" N LYS N 255 " --> pdb=" O PHE N 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 261 through 266 removed outlier: 3.838A pdb=" N LEU N 265 " --> pdb=" O GLY N 261 " (cutoff:3.500A) Processing helix chain 'N' and resid 271 through 278 Processing helix chain 'N' and resid 314 through 338 removed outlier: 3.729A pdb=" N ALA N 331 " --> pdb=" O ALA N 327 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG N 332 " --> pdb=" O ASP N 328 " (cutoff:3.500A) Processing helix chain 'N' and resid 352 through 367 removed outlier: 3.958A pdb=" N VAL N 367 " --> pdb=" O LEU N 363 " (cutoff:3.500A) Processing helix chain 'N' and resid 406 through 410 removed outlier: 4.326A pdb=" N GLY N 409 " --> pdb=" O ARG N 406 " (cutoff:3.500A) Processing helix chain 'N' and resid 415 through 432 removed outlier: 3.817A pdb=" N LEU N 421 " --> pdb=" O GLU N 417 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU N 424 " --> pdb=" O SER N 420 " (cutoff:3.500A) Processing helix chain 'N' and resid 444 through 453 removed outlier: 3.597A pdb=" N TYR N 450 " --> pdb=" O PRO N 446 " (cutoff:3.500A) Processing helix chain 'N' and resid 455 through 466 Processing helix chain 'N' and resid 502 through 510 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 5.716A pdb=" N TYR A 27 " --> pdb=" O ALA A 52 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N VAL A 2 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 53 " --> pdb=" O VAL A 2 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N MET A 4 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN A 81 " --> pdb=" O LEU A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 182 removed outlier: 5.928A pdb=" N VAL A 163 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE A 245 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU A 165 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N CYS A 247 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A 167 " --> pdb=" O CYS A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 30 removed outlier: 6.374A pdb=" N MET B 4 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE B 5 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU B 85 " --> pdb=" O ILE B 5 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N SER B 7 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU B 82 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL B 134 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N PHE B 84 " --> pdb=" O VAL B 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 180 through 182 removed outlier: 3.819A pdb=" N GLY B 246 " --> pdb=" O PHE B 181 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N CYS B 247 " --> pdb=" O PHE B 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'D' and resid 165 through 168 removed outlier: 5.830A pdb=" N GLU D 165 " --> pdb=" O ILE D 245 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N CYS D 247 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE D 167 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N TYR D 179 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY D 246 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE D 181 " --> pdb=" O GLY D 246 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL D 180 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL C 180 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N TYR C 179 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N GLY C 246 " --> pdb=" O TYR C 179 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE C 181 " --> pdb=" O GLY C 246 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 241 " --> pdb=" O THR C 161 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS C 247 " --> pdb=" O PHE C 167 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N MET C 162 " --> pdb=" O GLN C 273 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ARG C 275 " --> pdb=" O MET C 162 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE C 164 " --> pdb=" O ARG C 275 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 29 through 30 removed outlier: 7.025A pdb=" N VAL C 29 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 53 " --> pdb=" O MET C 4 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE C 5 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N LEU C 85 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LEU C 82 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N VAL C 134 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE C 84 " --> pdb=" O VAL C 134 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 23 through 27 removed outlier: 6.380A pdb=" N LEU L 18 " --> pdb=" O TYR L 25 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N LEU L 27 " --> pdb=" O VAL L 16 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL L 16 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE L 6 " --> pdb=" O LEU L 230 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE L 229 " --> pdb=" O LYS L 257 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 41 through 42 removed outlier: 6.446A pdb=" N ILE L 104 " --> pdb=" O THR L 117 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR L 117 " --> pdb=" O ILE L 104 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA L 115 " --> pdb=" O LYS L 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 46 through 50 removed outlier: 3.546A pdb=" N ARG L 48 " --> pdb=" O PHE L 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 122 through 123 Processing sheet with id=AB3, first strand: chain 'L' and resid 282 through 283 removed outlier: 6.591A pdb=" N THR L 300 " --> pdb=" O VAL L 344 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 412 through 414 Processing sheet with id=AB5, first strand: chain 'L' and resid 441 through 442 Processing sheet with id=AB6, first strand: chain 'N' and resid 26 through 28 Processing sheet with id=AB7, first strand: chain 'N' and resid 282 through 283 removed outlier: 3.558A pdb=" N VAL N 283 " --> pdb=" O ILE N 291 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP N 303 " --> pdb=" O VAL N 292 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA N 301 " --> pdb=" O ASP N 294 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ILE N 302 " --> pdb=" O CYS N 346 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 474 through 475 608 hydrogen bonds defined for protein. 1716 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 8 hydrogen bonds 16 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 6.69 Time building geometry restraints manager: 3.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11340 1.03 - 1.23: 1250 1.23 - 1.42: 6921 1.42 - 1.62: 9635 1.62 - 1.82: 64 Bond restraints: 29210 Sorted by residual: bond pdb=" N1 G K 193 " pdb=" H1 G K 193 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" N3 U K 138 " pdb=" H3 U K 138 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" N1 G K 152 " pdb=" H1 G K 152 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.15e+01 bond pdb=" N3 U K 22 " pdb=" H3 U K 22 " ideal model delta sigma weight residual 0.860 1.041 -0.181 2.00e-02 2.50e+03 8.15e+01 bond pdb=" N3 U K 27 " pdb=" H3 U K 27 " ideal model delta sigma weight residual 0.860 1.040 -0.180 2.00e-02 2.50e+03 8.14e+01 ... (remaining 29205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 51620 4.08 - 8.16: 538 8.16 - 12.24: 27 12.24 - 16.32: 4 16.32 - 20.39: 1 Bond angle restraints: 52190 Sorted by residual: angle pdb=" O2' C K 177 " pdb=" C2' C K 177 " pdb=" C1' C K 177 " ideal model delta sigma weight residual 111.80 98.43 13.37 1.50e+00 4.44e-01 7.94e+01 angle pdb=" N HIS C 190 " pdb=" CA HIS C 190 " pdb=" C HIS C 190 " ideal model delta sigma weight residual 112.38 101.77 10.61 1.22e+00 6.72e-01 7.56e+01 angle pdb=" O3' G K 185 " pdb=" C3' G K 185 " pdb=" C2' G K 185 " ideal model delta sigma weight residual 113.70 101.74 11.96 1.50e+00 4.44e-01 6.36e+01 angle pdb=" C ASN A 188 " pdb=" CA ASN A 188 " pdb=" CB ASN A 188 " ideal model delta sigma weight residual 109.85 100.87 8.98 1.14e+00 7.69e-01 6.21e+01 angle pdb=" C4' U K 150 " pdb=" C3' U K 150 " pdb=" O3' U K 150 " ideal model delta sigma weight residual 113.00 101.46 11.54 1.50e+00 4.44e-01 5.91e+01 ... (remaining 52185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 13413 36.00 - 72.00: 818 72.00 - 107.99: 195 107.99 - 143.99: 15 143.99 - 179.99: 41 Dihedral angle restraints: 14482 sinusoidal: 8384 harmonic: 6098 Sorted by residual: dihedral pdb=" C5' C K 177 " pdb=" C4' C K 177 " pdb=" C3' C K 177 " pdb=" O3' C K 177 " ideal model delta sinusoidal sigma weight residual 147.00 76.00 71.00 1 8.00e+00 1.56e-02 1.01e+02 dihedral pdb=" C4' A K 42 " pdb=" C3' A K 42 " pdb=" C2' A K 42 " pdb=" C1' A K 42 " ideal model delta sinusoidal sigma weight residual -35.00 30.31 -65.31 1 8.00e+00 1.56e-02 8.73e+01 dihedral pdb=" C5' A K 42 " pdb=" C4' A K 42 " pdb=" C3' A K 42 " pdb=" O3' A K 42 " ideal model delta sinusoidal sigma weight residual 147.00 82.42 64.58 1 8.00e+00 1.56e-02 8.56e+01 ... (remaining 14479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2606 0.108 - 0.216: 370 0.216 - 0.324: 60 0.324 - 0.432: 3 0.432 - 0.540: 2 Chirality restraints: 3041 Sorted by residual: chirality pdb=" C3' A K 87 " pdb=" C4' A K 87 " pdb=" O3' A K 87 " pdb=" C2' A K 87 " both_signs ideal model delta sigma weight residual False -2.74 -2.20 -0.54 2.00e-01 2.50e+01 7.29e+00 chirality pdb=" C3' C K 177 " pdb=" C4' C K 177 " pdb=" O3' C K 177 " pdb=" C2' C K 177 " both_signs ideal model delta sigma weight residual False -2.74 -2.27 -0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" C2' C K 77 " pdb=" C3' C K 77 " pdb=" O2' C K 77 " pdb=" C1' C K 77 " both_signs ideal model delta sigma weight residual False -2.52 -2.13 -0.39 2.00e-01 2.50e+01 3.87e+00 ... (remaining 3038 not shown) Planarity restraints: 4457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN L 323 " -0.016 2.00e-02 2.50e+03 4.41e-01 2.92e+03 pdb=" CG ASN L 323 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN L 323 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN L 323 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN L 323 " 0.765 2.00e-02 2.50e+03 pdb="HD22 ASN L 323 " -0.763 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 271 " -0.123 2.00e-02 2.50e+03 1.33e-01 2.67e+02 pdb=" CG ASN B 271 " 0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN B 271 " 0.120 2.00e-02 2.50e+03 pdb=" ND2 ASN B 271 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN B 271 " -0.200 2.00e-02 2.50e+03 pdb="HD22 ASN B 271 " 0.193 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN N 478 " -0.117 2.00e-02 2.50e+03 1.31e-01 2.56e+02 pdb=" CD GLN N 478 " 0.002 2.00e-02 2.50e+03 pdb=" OE1 GLN N 478 " 0.117 2.00e-02 2.50e+03 pdb=" NE2 GLN N 478 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN N 478 " 0.194 2.00e-02 2.50e+03 pdb="HE22 GLN N 478 " -0.193 2.00e-02 2.50e+03 ... (remaining 4454 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.07: 454 2.07 - 2.70: 40514 2.70 - 3.33: 74414 3.33 - 3.97: 89155 3.97 - 4.60: 132515 Nonbonded interactions: 337052 Sorted by model distance: nonbonded pdb=" O2 U K 179 " pdb=" H2' U K 179 " model vdw 1.437 2.620 nonbonded pdb=" O2 C K 110 " pdb=" H3' C K 110 " model vdw 1.497 2.620 nonbonded pdb=" OP1 G K 51 " pdb=" H21 G K 51 " model vdw 1.497 2.450 nonbonded pdb=" O2 U K 12 " pdb=" H3' U K 12 " model vdw 1.507 2.620 nonbonded pdb="HD12 LEU A 36 " pdb="HD23 LEU D 36 " model vdw 1.549 2.440 ... (remaining 337047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 5 or (resid 6 through 7 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 8 throu \ gh 11 or (resid 12 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 13 through 15 or (resid 16 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 17 through 18 or (re \ sid 19 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 20 or (resid 21 through 24 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 25 or (resid 27 through 32 and ( \ name N or name CA or name C or name O or name CB or name H or name HA )) or resi \ d 33 through 35 or (resid 36 through 37 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 38 or (resid 39 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 40 through \ 41 or (resid 42 through 44 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 45 or (resid 46 through 49 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 50 through \ 55 or (resid 56 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 57 or (resid 58 through 60 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 61 through 66 or (resid \ 67 through 68 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 69 through 72 or (resid 73 through 74 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 75 through 80 \ or (resid 81 through 84 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 85 through 87 or (resid 88 through 90 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 91 \ through 95 or (resid 112 through 113 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 114 through 119 or (resid 120 throug \ h 121 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 122 through 125 or (resid 126 through 127 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 128 or (resid 129 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 130 or (resid 131 through 133 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 134 through 135 or (resid 136 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 137 through 140 or (resid 141 through 144 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 145 through 147 or (resid 148 \ through 152 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 153 through 155 or (resid 156 through 160 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 161 or (resi \ d 162 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 163 through 165 or (resid 166 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 167 through 169 or (resid 170 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 171 through 178 or (resid 179 through 185 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 186 through 189 or (resi \ d 190 through 191 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 192 through 193 or (resid 194 through 196 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 197 th \ rough 198 or (resid 199 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 200 or (resid 201 through 203 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 204 through \ 207 or (resid 208 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 209 through 210 or (resid 211 through 214 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 215 or \ (resid 216 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 217 or (resid 218 through 223 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 224 or (resid 225 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 226 through 228 or (resid 229 through 230 and (name N or name CA or name C or n \ ame O or name CB or name H or name HA )) or resid 231 or (resid 232 through 243 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 244 or (resid 245 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 246 or (resid 247 through 248 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 249 through \ 250 or (resid 251 through 253 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 254 or (resid 255 through 256 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 257 t \ hrough 258 or (resid 259 through 260 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 261 through 262 or (resid 263 throug \ h 264 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 265 through 266 or (resid 267 through 268 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 269 or (resid 270 \ through 271 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 272 or (resid 273 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 274 or (resid 275 through 281 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )))) selection = (chain 'B' and (resid 3 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 8 or (resid 9 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 10 thr \ ough 15 or (resid 16 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 17 through 21 or (resid 22 through 24 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 25 thro \ ugh 27 or (resid 28 through 32 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 33 through 38 or (resid 39 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 40 throu \ gh 48 or (resid 49 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 50 through 64 or (resid 65 through 68 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 69 throug \ h 72 or (resid 73 through 74 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 75 through 83 or (resid 84 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 85 through \ 88 or (resid 89 through 90 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 91 through 94 or (resid 95 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 112 through \ 115 or (resid 116 through 121 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 122 through 123 or (resid 124 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 125 o \ r (resid 126 through 127 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 128 through 130 or (resid 131 through 133 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 134 through 135 or (resid 136 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 137 or (resid 138 through 139 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 140 t \ hrough 141 or (resid 142 through 144 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 145 through 147 or (resid 148 throug \ h 152 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 153 through 154 or (resid 155 through 160 and (name N or name CA or \ name C or name O or name CB or name H or name HA )) or resid 161 through 169 or \ (resid 170 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 171 through 177 or (resid 178 through 185 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 186 through \ 189 or (resid 190 through 191 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 192 through 194 or (resid 195 through 196 a \ nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 197 through 198 or (resid 199 and (name N or name CA or name C or name O o \ r name CB or name H or name HA )) or resid 200 or (resid 201 through 203 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 204 through 207 or (resid 208 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 209 or (resid 210 through 214 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 215 or \ (resid 216 and (name N or name CA or name C or name O or name CB or name H or n \ ame HA )) or resid 217 or (resid 218 through 223 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 224 or (resid 225 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 226 or (resid 227 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 228 through 229 or (resid 230 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 231 through 232 o \ r (resid 233 through 243 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 244 or (resid 245 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 246 through 250 or (res \ id 251 through 253 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 254 or (resid 255 through 256 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 257 through 258 o \ r (resid 259 through 260 and (name N or name CA or name C or name O or name CB o \ r name H or name HA )) or resid 261 through 263 or (resid 264 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 265 through \ 267 or (resid 268 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 269 through 270 or (resid 271 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 272 or (resid 273 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 274 or (resid 275 through 281 and (name N or name CA or name C or name O \ or name CB or name H or name HA )))) selection = (chain 'C' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 5 or (resid 6 through 7 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 8 throu \ gh 20 or (resid 21 through 24 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 25 or (resid 27 through 32 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 33 throug \ h 35 or (resid 36 through 37 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 38 or (resid 39 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 40 through 42 or (res \ id 43 through 44 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 45 or (resid 46 through 49 and (name N or name CA or nam \ e C or name O or name CB or name H or name HA )) or resid 50 through 55 or (resi \ d 56 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 57 or (resid 58 through 60 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 61 through 65 or (resid 66 through \ 68 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 69 through 70 or (resid 71 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 72 or (resid 73 through 74 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 7 \ 5 through 77 or (resid 78 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 79 through 80 or (resid 81 through 84 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 85 \ or (resid 86 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 87 or (resid 88 through 90 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 91 through 112 or (resid \ 113 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 114 through 115 or (resid 116 through 121 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 122 through 126 or ( \ resid 127 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 128 through 130 or (resid 131 through 133 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 134 or (resid \ 135 through 136 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 137 through 145 or (resid 146 through 152 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 153 thro \ ugh 182 or (resid 183 through 185 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 186 through 187 or (resid 188 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 18 \ 9 through 193 or (resid 194 through 196 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 197 through 198 or (resid 199 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or re \ sid 200 or (resid 201 through 203 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 204 through 207 or (resid 208 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or resid 20 \ 9 through 211 or (resid 212 through 214 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 215 or (resid 216 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 217 or ( \ resid 218 through 223 and (name N or name CA or name C or name O or name CB or n \ ame H or name HA )) or resid 224 through 226 or (resid 227 and (name N or name C \ A or name C or name O or name CB or name H or name HA )) or resid 228 or (resid \ 229 through 230 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 231 through 232 or (resid 233 through 243 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 244 or ( \ resid 245 and (name N or name CA or name C or name O or name CB or name H or nam \ e HA )) or resid 246 through 247 or (resid 248 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 249 through 255 or (resid \ 256 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 257 through 259 or (resid 260 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 261 through 263 or (resid 264 an \ d (name N or name CA or name C or name O or name CB or name H or name HA )) or r \ esid 265 through 267 or (resid 268 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 269 through 270 or (resid 271 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 2 \ 72 through 274 or (resid 275 through 281 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )))) selection = (chain 'D' and ((resid 3 through 4 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 5 or (resid 6 through 7 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 8 throu \ gh 11 or (resid 12 and (name N or name CA or name C or name O or name CB or name \ H or name HA )) or resid 13 or (resid 14 and (name N or name CA or name C or na \ me O or name CB or name H or name HA )) or resid 15 or (resid 16 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 17 throu \ gh 20 or (resid 21 through 24 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 25 or (resid 27 through 32 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 33 or (re \ sid 34 and (name N or name CA or name C or name O or name CB or name H or name H \ A )) or resid 35 or (resid 36 through 37 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 38 through 41 or (resid 42 throu \ gh 44 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 45 or (resid 46 through 49 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 50 through 57 or (resid 58 throug \ h 60 and (name N or name CA or name C or name O or name CB or name H or name HA \ )) or resid 61 or (resid 62 and (name N or name CA or name C or name O or name C \ B or name H or name HA )) or resid 63 through 64 or (resid 65 through 68 and (na \ me N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 69 through 75 or (resid 76 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 77 through 80 or (resid 81 through 84 and (nam \ e N or name CA or name C or name O or name CB or name H or name HA )) or resid 8 \ 5 through 87 or (resid 88 through 90 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 91 through 94 or (resid 95 and (name \ N or name CA or name C or name O or name CB or name H or name HA )) or (resid 1 \ 12 through 113 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 114 through 115 or (resid 116 through 121 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 122 throu \ gh 123 or (resid 124 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 125 or (resid 126 through 127 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 128 through 134 \ or (resid 135 through 136 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 137 or (resid 138 through 139 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 140 throu \ gh 147 or (resid 148 through 152 and (name N or name CA or name C or name O or n \ ame CB or name H or name HA )) or resid 153 through 154 or (resid 155 through 16 \ 0 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 161 through 165 or (resid 166 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 167 through 169 or (resid 170 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 171 through 178 or (resid 179 through 185 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 186 through 190 or (resid 19 \ 1 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 192 through 195 or (resid 196 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 197 or (resid 198 through 199 and \ (name N or name CA or name C or name O or name CB or name H or name HA )) or res \ id 200 through 201 or (resid 202 through 203 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 204 through 209 or (resid 21 \ 0 through 214 and (name N or name CA or name C or name O or name CB or name H or \ name HA )) or resid 215 through 221 or (resid 222 through 223 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 224 or (re \ sid 225 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 226 through 241 or (resid 242 through 243 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 244 through 251 \ or (resid 252 through 253 and (name N or name CA or name C or name O or name CB \ or name H or name HA )) or resid 254 or (resid 255 through 256 and (name N or na \ me CA or name C or name O or name CB or name H or name HA )) or resid 257 throug \ h 258 or (resid 259 through 260 and (name N or name CA or name C or name O or na \ me CB or name H or name HA )) or resid 261 through 262 or (resid 263 through 264 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) o \ r resid 265 through 266 or (resid 267 through 268 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 269 through 275 or (res \ id 276 through 281 and (name N or name CA or name C or name O or name CB or name \ H or name HA )))) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 8.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.660 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 31.900 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 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 : 0.009 0.081 16776 Z= 0.616 Angle : 1.304 13.370 23691 Z= 0.916 Chirality : 0.078 0.540 3041 Planarity : 0.007 0.053 2530 Dihedral : 22.578 178.023 6627 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.18), residues: 1893 helix: -1.24 (0.17), residues: 757 sheet: -2.19 (0.26), residues: 338 loop : -1.50 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 184 TYR 0.023 0.002 TYR D 96 PHE 0.016 0.002 PHE C 218 TRP 0.021 0.002 TRP A 229 HIS 0.007 0.002 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00927 (16776) covalent geometry : angle 1.30405 (23691) hydrogen bonds : bond 0.21264 ( 616) hydrogen bonds : angle 9.60525 ( 1732) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 512 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 0.836 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.9504 (mp) cc_final: 0.9279 (tt) REVERT: A 175 ILE cc_start: 0.8165 (pt) cc_final: 0.7940 (tp) REVERT: B 39 ASP cc_start: 0.9246 (m-30) cc_final: 0.8811 (p0) REVERT: B 122 LEU cc_start: 0.9585 (tp) cc_final: 0.9349 (mp) REVERT: B 148 LEU cc_start: 0.9303 (mt) cc_final: 0.9077 (mt) REVERT: B 176 ASP cc_start: 0.8341 (p0) cc_final: 0.7973 (t0) REVERT: B 220 TYR cc_start: 0.8606 (t80) cc_final: 0.8339 (t80) REVERT: D 3 LEU cc_start: 0.9176 (tp) cc_final: 0.8506 (mt) REVERT: D 53 VAL cc_start: 0.9061 (p) cc_final: 0.8850 (p) REVERT: D 67 PHE cc_start: 0.9016 (p90) cc_final: 0.7589 (p90) REVERT: D 118 LYS cc_start: 0.9153 (ptmt) cc_final: 0.8867 (ptpt) REVERT: D 265 PHE cc_start: 0.9017 (m-80) cc_final: 0.8794 (m-80) REVERT: C 192 ASP cc_start: 0.8887 (t0) cc_final: 0.8242 (t0) REVERT: C 220 TYR cc_start: 0.8879 (t80) cc_final: 0.8563 (t80) REVERT: L 96 GLU cc_start: 0.9250 (pt0) cc_final: 0.9040 (pt0) REVERT: N 183 ASP cc_start: 0.8643 (t70) cc_final: 0.8263 (m-30) REVERT: N 365 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8914 (mm-30) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.3124 time to fit residues: 224.6885 Evaluate side-chains 381 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 GLN C 260 GLN N 321 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.131339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098158 restraints weight = 161983.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.101734 restraints weight = 69285.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.103982 restraints weight = 40924.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105343 restraints weight = 29579.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.106116 restraints weight = 24450.570| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3648 r_free = 0.3648 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3649 r_free = 0.3649 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16776 Z= 0.156 Angle : 0.673 6.302 23691 Z= 0.359 Chirality : 0.042 0.302 3041 Planarity : 0.005 0.044 2530 Dihedral : 24.249 179.232 4465 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.22 % Allowed : 19.52 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.60 (0.18), residues: 1893 helix: -0.38 (0.17), residues: 803 sheet: -1.77 (0.27), residues: 330 loop : -1.29 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 266 TYR 0.012 0.001 TYR A 179 PHE 0.015 0.001 PHE C 218 TRP 0.012 0.001 TRP A 229 HIS 0.006 0.001 HIS C 212 Details of bonding type rmsd covalent geometry : bond 0.00305 (16776) covalent geometry : angle 0.67283 (23691) hydrogen bonds : bond 0.05227 ( 616) hydrogen bonds : angle 6.59306 ( 1732) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 442 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 419 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.9418 (mp) cc_final: 0.9189 (tt) REVERT: A 175 ILE cc_start: 0.8241 (pt) cc_final: 0.7813 (tp) REVERT: A 214 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8340 (mm-30) REVERT: A 234 GLU cc_start: 0.8898 (tp30) cc_final: 0.8645 (tp30) REVERT: B 39 ASP cc_start: 0.9077 (m-30) cc_final: 0.8630 (p0) REVERT: B 96 TYR cc_start: 0.9097 (t80) cc_final: 0.8789 (t80) REVERT: B 148 LEU cc_start: 0.9383 (mt) cc_final: 0.9179 (mt) REVERT: B 176 ASP cc_start: 0.8646 (p0) cc_final: 0.8230 (t0) REVERT: D 3 LEU cc_start: 0.8970 (tp) cc_final: 0.8726 (mt) REVERT: D 22 GLU cc_start: 0.9072 (pt0) cc_final: 0.8838 (pp20) REVERT: D 44 LEU cc_start: 0.9424 (tp) cc_final: 0.9168 (tt) REVERT: D 67 PHE cc_start: 0.8156 (p90) cc_final: 0.7808 (p90) REVERT: C 192 ASP cc_start: 0.8948 (t0) cc_final: 0.8564 (t0) REVERT: C 220 TYR cc_start: 0.8702 (t80) cc_final: 0.8380 (t80) REVERT: N 183 ASP cc_start: 0.8347 (t70) cc_final: 0.7927 (m-30) outliers start: 23 outliers final: 22 residues processed: 426 average time/residue: 0.2919 time to fit residues: 177.6733 Evaluate side-chains 394 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 372 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 179 TYR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 370 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 186 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 179 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 146 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 268 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.125997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.092201 restraints weight = 162367.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095575 restraints weight = 69740.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097631 restraints weight = 41658.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.098892 restraints weight = 30617.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099618 restraints weight = 25535.447| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16776 Z= 0.226 Angle : 0.665 6.253 23691 Z= 0.359 Chirality : 0.041 0.310 3041 Planarity : 0.005 0.076 2530 Dihedral : 24.293 176.463 4465 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.06 % Allowed : 21.45 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.19), residues: 1893 helix: -0.18 (0.18), residues: 807 sheet: -1.70 (0.27), residues: 339 loop : -1.29 (0.23), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 42 TYR 0.013 0.001 TYR C 264 PHE 0.027 0.002 PHE N 320 TRP 0.004 0.001 TRP A 229 HIS 0.009 0.002 HIS N 355 Details of bonding type rmsd covalent geometry : bond 0.00440 (16776) covalent geometry : angle 0.66545 (23691) hydrogen bonds : bond 0.04960 ( 616) hydrogen bonds : angle 6.33186 ( 1732) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 417 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 375 time to evaluate : 0.753 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.9438 (mp) cc_final: 0.9222 (tt) REVERT: A 175 ILE cc_start: 0.8618 (pt) cc_final: 0.8341 (tp) REVERT: B 39 ASP cc_start: 0.9140 (m-30) cc_final: 0.8690 (p0) REVERT: B 96 TYR cc_start: 0.9384 (t80) cc_final: 0.9085 (t80) REVERT: B 176 ASP cc_start: 0.9078 (p0) cc_final: 0.8868 (p0) REVERT: D 3 LEU cc_start: 0.9017 (tp) cc_final: 0.8756 (mt) REVERT: D 44 LEU cc_start: 0.9461 (tp) cc_final: 0.9222 (tt) REVERT: C 220 TYR cc_start: 0.8939 (t80) cc_final: 0.8693 (t80) REVERT: L 59 ASP cc_start: 0.8196 (t0) cc_final: 0.7878 (t0) REVERT: N 1 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8817 (tmm) REVERT: N 183 ASP cc_start: 0.8385 (t70) cc_final: 0.7962 (m-30) REVERT: N 430 GLU cc_start: 0.9232 (tp30) cc_final: 0.8928 (tm-30) outliers start: 42 outliers final: 33 residues processed: 392 average time/residue: 0.2964 time to fit residues: 165.0104 Evaluate side-chains 391 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 357 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 69 GLN Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 176 ASP Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 370 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 184 optimal weight: 8.9990 chunk 120 optimal weight: 0.2980 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 69 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.126762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.093174 restraints weight = 160495.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096566 restraints weight = 68509.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.098682 restraints weight = 40839.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.099959 restraints weight = 29840.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.100692 restraints weight = 24839.053| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16776 Z= 0.152 Angle : 0.589 11.643 23691 Z= 0.312 Chirality : 0.039 0.263 3041 Planarity : 0.005 0.085 2530 Dihedral : 23.914 178.986 4465 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 3.86 % Allowed : 22.90 % Favored : 73.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.19), residues: 1893 helix: 0.31 (0.18), residues: 807 sheet: -1.76 (0.27), residues: 347 loop : -1.14 (0.23), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 127 TYR 0.010 0.001 TYR C 264 PHE 0.019 0.001 PHE C 164 TRP 0.004 0.000 TRP C 229 HIS 0.006 0.001 HIS N 243 Details of bonding type rmsd covalent geometry : bond 0.00297 (16776) covalent geometry : angle 0.58933 (23691) hydrogen bonds : bond 0.04202 ( 616) hydrogen bonds : angle 5.86689 ( 1732) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 414 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 374 time to evaluate : 0.781 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: 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: 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: 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: 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: 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 123 LEU cc_start: 0.9428 (mp) cc_final: 0.9208 (tt) REVERT: A 175 ILE cc_start: 0.8672 (pt) cc_final: 0.8384 (tp) REVERT: B 39 ASP cc_start: 0.9128 (m-30) cc_final: 0.8667 (p0) REVERT: B 96 TYR cc_start: 0.9379 (t80) cc_final: 0.9032 (t80) REVERT: B 176 ASP cc_start: 0.9122 (p0) cc_final: 0.8880 (p0) REVERT: D 3 LEU cc_start: 0.8989 (tp) cc_final: 0.8764 (mt) REVERT: D 44 LEU cc_start: 0.9454 (tp) cc_final: 0.9196 (tt) REVERT: D 164 PHE cc_start: 0.8378 (m-80) cc_final: 0.8084 (m-10) REVERT: C 220 TYR cc_start: 0.8895 (t80) cc_final: 0.8581 (t80) REVERT: L 59 ASP cc_start: 0.8069 (t0) cc_final: 0.7784 (t0) REVERT: L 73 ILE cc_start: 0.9526 (pt) cc_final: 0.9149 (mm) REVERT: N 183 ASP cc_start: 0.8417 (t70) cc_final: 0.8007 (m-30) REVERT: N 430 GLU cc_start: 0.9204 (tp30) cc_final: 0.8871 (tm-30) outliers start: 40 outliers final: 37 residues processed: 388 average time/residue: 0.2900 time to fit residues: 161.8254 Evaluate side-chains 398 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 361 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 224 GLN Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 359 VAL Chi-restraints excluded: chain N residue 370 ASP Chi-restraints excluded: chain N residue 427 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 31 optimal weight: 0.0030 chunk 98 optimal weight: 0.1980 chunk 48 optimal weight: 0.6980 chunk 158 optimal weight: 50.0000 chunk 13 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 202 optimal weight: 20.0000 chunk 188 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.128960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094952 restraints weight = 158582.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098444 restraints weight = 67450.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.100637 restraints weight = 40244.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.101973 restraints weight = 29294.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.102784 restraints weight = 24289.451| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16776 Z= 0.110 Angle : 0.554 6.175 23691 Z= 0.286 Chirality : 0.039 0.263 3041 Planarity : 0.004 0.047 2530 Dihedral : 23.496 176.794 4465 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.80 % Allowed : 23.86 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.20), residues: 1893 helix: 0.98 (0.19), residues: 811 sheet: -1.44 (0.28), residues: 325 loop : -0.82 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 266 TYR 0.009 0.001 TYR D 225 PHE 0.013 0.001 PHE C 218 TRP 0.004 0.000 TRP C 229 HIS 0.006 0.001 HIS N 243 Details of bonding type rmsd covalent geometry : bond 0.00222 (16776) covalent geometry : angle 0.55362 (23691) hydrogen bonds : bond 0.03640 ( 616) hydrogen bonds : angle 5.31401 ( 1732) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 417 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 388 time to evaluate : 0.862 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: 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: 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: 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: 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: 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 123 LEU cc_start: 0.9430 (mp) cc_final: 0.9207 (tt) REVERT: B 39 ASP cc_start: 0.9119 (m-30) cc_final: 0.8651 (p0) REVERT: B 96 TYR cc_start: 0.9371 (t80) cc_final: 0.8998 (t80) REVERT: B 176 ASP cc_start: 0.9126 (p0) cc_final: 0.8872 (p0) REVERT: D 89 ARG cc_start: 0.8327 (ptm-80) cc_final: 0.8019 (ptm-80) REVERT: C 220 TYR cc_start: 0.8801 (t80) cc_final: 0.8455 (t80) REVERT: L 59 ASP cc_start: 0.8099 (t0) cc_final: 0.7825 (t0) REVERT: L 73 ILE cc_start: 0.9504 (pt) cc_final: 0.9171 (mm) REVERT: N 183 ASP cc_start: 0.8466 (t70) cc_final: 0.8078 (m-30) REVERT: N 430 GLU cc_start: 0.9174 (tp30) cc_final: 0.8855 (tm-30) outliers start: 29 outliers final: 25 residues processed: 395 average time/residue: 0.2927 time to fit residues: 167.4812 Evaluate side-chains 391 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 366 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 224 GLN Chi-restraints excluded: chain N residue 370 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 144 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 154 optimal weight: 20.0000 chunk 48 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 chunk 163 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN L 11 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.122499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088640 restraints weight = 163834.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.091888 restraints weight = 70880.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.093901 restraints weight = 42686.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095141 restraints weight = 31480.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095860 restraints weight = 26410.726| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16776 Z= 0.272 Angle : 0.660 7.256 23691 Z= 0.354 Chirality : 0.040 0.267 3041 Planarity : 0.005 0.061 2530 Dihedral : 23.757 177.983 4465 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.54 % Allowed : 24.64 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.00 (0.19), residues: 1893 helix: 0.31 (0.18), residues: 790 sheet: -1.70 (0.28), residues: 328 loop : -1.07 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 373 TYR 0.016 0.002 TYR C 264 PHE 0.021 0.002 PHE C 218 TRP 0.007 0.001 TRP C 229 HIS 0.008 0.002 HIS C 216 Details of bonding type rmsd covalent geometry : bond 0.00521 (16776) covalent geometry : angle 0.66004 (23691) hydrogen bonds : bond 0.04477 ( 616) hydrogen bonds : angle 5.89263 ( 1732) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 394 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 347 time to evaluate : 0.581 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.9438 (mp) cc_final: 0.9230 (tt) REVERT: A 194 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8790 (mttp) REVERT: B 39 ASP cc_start: 0.9160 (m-30) cc_final: 0.8701 (p0) REVERT: B 96 TYR cc_start: 0.9447 (t80) cc_final: 0.9175 (t80) REVERT: B 176 ASP cc_start: 0.9198 (p0) cc_final: 0.8921 (p0) REVERT: D 44 LEU cc_start: 0.9413 (tp) cc_final: 0.9207 (tt) REVERT: D 89 ARG cc_start: 0.8382 (ptm-80) cc_final: 0.8176 (ptm-80) REVERT: D 259 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8491 (tp30) REVERT: L 59 ASP cc_start: 0.8136 (t0) cc_final: 0.7847 (t0) REVERT: N 183 ASP cc_start: 0.8438 (t70) cc_final: 0.8029 (m-30) outliers start: 47 outliers final: 44 residues processed: 363 average time/residue: 0.2652 time to fit residues: 140.5324 Evaluate side-chains 385 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 341 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain C residue 28 CYS Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 184 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 330 ILE Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 370 ASP Chi-restraints excluded: chain N residue 426 LEU Chi-restraints excluded: chain N residue 427 ILE Chi-restraints excluded: chain N residue 504 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 31 optimal weight: 3.9990 chunk 184 optimal weight: 0.4980 chunk 117 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 169 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 143 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.125197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091464 restraints weight = 160378.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.094905 restraints weight = 68248.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.096999 restraints weight = 40540.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.098285 restraints weight = 29736.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099044 restraints weight = 24703.688| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.5524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16776 Z= 0.127 Angle : 0.567 7.924 23691 Z= 0.293 Chirality : 0.039 0.244 3041 Planarity : 0.004 0.046 2530 Dihedral : 23.486 179.010 4465 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.09 % Allowed : 25.99 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.20), residues: 1893 helix: 0.83 (0.19), residues: 807 sheet: -1.62 (0.28), residues: 329 loop : -0.85 (0.23), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 268 TYR 0.011 0.001 TYR C 264 PHE 0.014 0.001 PHE C 218 TRP 0.007 0.001 TRP C 229 HIS 0.013 0.001 HIS N 243 Details of bonding type rmsd covalent geometry : bond 0.00257 (16776) covalent geometry : angle 0.56668 (23691) hydrogen bonds : bond 0.03594 ( 616) hydrogen bonds : angle 5.37018 ( 1732) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 389 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 357 time to evaluate : 0.820 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.9430 (mp) cc_final: 0.9220 (tt) REVERT: A 179 TYR cc_start: 0.9389 (m-10) cc_final: 0.9168 (m-10) REVERT: A 214 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8387 (mm-30) REVERT: B 39 ASP cc_start: 0.9160 (m-30) cc_final: 0.8684 (p0) REVERT: B 54 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.8035 (p) REVERT: B 96 TYR cc_start: 0.9426 (t80) cc_final: 0.9075 (t80) REVERT: D 138 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7147 (tm-30) REVERT: D 259 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8430 (tp30) REVERT: C 220 TYR cc_start: 0.8857 (t80) cc_final: 0.8627 (t80) REVERT: N 183 ASP cc_start: 0.8458 (t70) cc_final: 0.8066 (m-30) REVERT: N 243 HIS cc_start: 0.8238 (m-70) cc_final: 0.7986 (m-70) REVERT: N 389 ARG cc_start: 0.8143 (tmm160) cc_final: 0.7840 (tmm160) REVERT: N 430 GLU cc_start: 0.9244 (tp30) cc_final: 0.8885 (tm-30) outliers start: 32 outliers final: 29 residues processed: 366 average time/residue: 0.2612 time to fit residues: 140.7300 Evaluate side-chains 371 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 341 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 224 GLN Chi-restraints excluded: chain N residue 370 ASP Chi-restraints excluded: chain N residue 426 LEU Chi-restraints excluded: chain N residue 427 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 98 optimal weight: 4.9990 chunk 196 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 149 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.125989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.092204 restraints weight = 159626.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095625 restraints weight = 68202.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.097755 restraints weight = 40665.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099071 restraints weight = 29748.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.099831 restraints weight = 24692.764| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16776 Z= 0.115 Angle : 0.553 8.489 23691 Z= 0.283 Chirality : 0.038 0.230 3041 Planarity : 0.004 0.043 2530 Dihedral : 23.267 178.222 4465 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.90 % Allowed : 25.80 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.20), residues: 1893 helix: 1.17 (0.19), residues: 810 sheet: -1.58 (0.28), residues: 333 loop : -0.67 (0.24), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 373 TYR 0.012 0.001 TYR D 225 PHE 0.021 0.001 PHE C 218 TRP 0.004 0.000 TRP C 229 HIS 0.013 0.001 HIS N 243 Details of bonding type rmsd covalent geometry : bond 0.00241 (16776) covalent geometry : angle 0.55343 (23691) hydrogen bonds : bond 0.03322 ( 616) hydrogen bonds : angle 5.07105 ( 1732) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 389 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 359 time to evaluate : 0.717 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: 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: 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: 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: 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: 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 123 LEU cc_start: 0.9428 (mp) cc_final: 0.9208 (tt) REVERT: A 179 TYR cc_start: 0.9393 (m-10) cc_final: 0.9157 (m-10) REVERT: A 214 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8330 (mm-30) REVERT: B 39 ASP cc_start: 0.9130 (m-30) cc_final: 0.8647 (p0) REVERT: B 54 SER cc_start: 0.8334 (OUTLIER) cc_final: 0.8068 (p) REVERT: B 96 TYR cc_start: 0.9428 (t80) cc_final: 0.9019 (t80) REVERT: D 138 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7119 (tm-30) REVERT: D 259 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8399 (tp30) REVERT: C 220 TYR cc_start: 0.8855 (t80) cc_final: 0.8644 (t80) REVERT: C 260 GLN cc_start: 0.8928 (mm-40) cc_final: 0.8081 (mp10) REVERT: N 183 ASP cc_start: 0.8486 (t70) cc_final: 0.8105 (m-30) REVERT: N 243 HIS cc_start: 0.8222 (m-70) cc_final: 0.7900 (m-70) REVERT: N 373 ARG cc_start: 0.7592 (ttp80) cc_final: 0.7288 (ttp80) outliers start: 30 outliers final: 27 residues processed: 368 average time/residue: 0.2469 time to fit residues: 133.6186 Evaluate side-chains 372 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 344 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 421 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 370 ASP Chi-restraints excluded: chain N residue 426 LEU Chi-restraints excluded: chain N residue 427 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 72 optimal weight: 0.0070 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 183 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 overall best weight: 1.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.126254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.092536 restraints weight = 166600.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.095984 restraints weight = 71146.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.098128 restraints weight = 42590.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099415 restraints weight = 31292.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.100127 restraints weight = 26233.365| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3540 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3540 r_free = 0.3540 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3540 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.5961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16776 Z= 0.109 Angle : 0.551 8.286 23691 Z= 0.280 Chirality : 0.038 0.209 3041 Planarity : 0.004 0.043 2530 Dihedral : 23.109 177.275 4465 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.42 % Allowed : 26.96 % Favored : 70.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.20), residues: 1893 helix: 1.26 (0.19), residues: 812 sheet: -1.55 (0.28), residues: 341 loop : -0.51 (0.24), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 389 TYR 0.026 0.001 TYR B 220 PHE 0.019 0.001 PHE C 218 TRP 0.005 0.001 TRP C 229 HIS 0.012 0.001 HIS N 243 Details of bonding type rmsd covalent geometry : bond 0.00232 (16776) covalent geometry : angle 0.55075 (23691) hydrogen bonds : bond 0.03183 ( 616) hydrogen bonds : angle 4.92491 ( 1732) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 380 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 355 time to evaluate : 0.942 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: 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: 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: 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: 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: 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 123 LEU cc_start: 0.9411 (mp) cc_final: 0.9210 (tt) REVERT: A 179 TYR cc_start: 0.9338 (m-80) cc_final: 0.9099 (m-10) REVERT: A 214 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8195 (mm-30) REVERT: B 54 SER cc_start: 0.8375 (OUTLIER) cc_final: 0.8107 (p) REVERT: B 96 TYR cc_start: 0.9381 (t80) cc_final: 0.9010 (t80) REVERT: D 259 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8382 (tp30) REVERT: C 3 LEU cc_start: 0.9499 (tp) cc_final: 0.9151 (tp) REVERT: C 260 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8735 (mm-40) REVERT: L 59 ASP cc_start: 0.8272 (t0) cc_final: 0.8067 (t0) REVERT: N 183 ASP cc_start: 0.8501 (t70) cc_final: 0.8121 (m-30) REVERT: N 243 HIS cc_start: 0.8217 (m-70) cc_final: 0.7880 (m-70) REVERT: N 373 ARG cc_start: 0.7479 (ttp80) cc_final: 0.7103 (ttp80) outliers start: 25 outliers final: 22 residues processed: 362 average time/residue: 0.2657 time to fit residues: 140.5620 Evaluate side-chains 371 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 348 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 421 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 370 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 186 optimal weight: 0.6980 chunk 178 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 145 optimal weight: 8.9990 chunk 196 optimal weight: 7.9990 chunk 33 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.123854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.090515 restraints weight = 168188.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.093837 restraints weight = 71818.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095852 restraints weight = 42956.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097040 restraints weight = 31738.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097618 restraints weight = 26759.688| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16776 Z= 0.173 Angle : 0.578 8.441 23691 Z= 0.301 Chirality : 0.039 0.207 3041 Planarity : 0.005 0.075 2530 Dihedral : 23.271 174.404 4465 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.71 % Allowed : 27.05 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.20), residues: 1893 helix: 1.02 (0.19), residues: 802 sheet: -1.62 (0.28), residues: 322 loop : -0.58 (0.24), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG N 389 TYR 0.015 0.001 TYR B 220 PHE 0.021 0.002 PHE C 218 TRP 0.006 0.001 TRP C 229 HIS 0.011 0.002 HIS N 243 Details of bonding type rmsd covalent geometry : bond 0.00341 (16776) covalent geometry : angle 0.57781 (23691) hydrogen bonds : bond 0.03621 ( 616) hydrogen bonds : angle 5.18718 ( 1732) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3786 Ramachandran restraints generated. 1893 Oldfield, 0 Emsley, 1893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 29 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue ILE 66 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue TYR 96 is missing expected H atoms. Skipping. Residue ILE 116 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 264 is missing expected H atoms. Skipping. Residue LEU 3 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue VAL 6 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue LEU 21 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 36 is missing expected H atoms. Skipping. Residue LEU 37 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 82 is missing expected H atoms. Skipping. Residue LEU 83 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LEU 102 is missing expected H atoms. Skipping. Residue LEU 105 is missing expected H atoms. Skipping. Residue LYS 108 is missing expected H atoms. Skipping. Residue LEU 110 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 152 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 213 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue VAL 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 7 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue LEU 32 is missing expected H atoms. Skipping. Residue THR 43 is missing expected H atoms. Skipping. Residue ILE 49 is missing expected H atoms. Skipping. Residue MET 71 is missing expected H atoms. Skipping. Residue LEU 74 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue SER 111 is missing expected H atoms. Skipping. Residue SER 120 is missing expected H atoms. Skipping. Residue LEU 132 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue THR 136 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue THR 150 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LYS 194 is missing expected H atoms. Skipping. Residue LEU 195 is missing expected H atoms. Skipping. Residue THR 199 is missing expected H atoms. Skipping. Residue LEU 201 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue ILE 219 is missing expected H atoms. Skipping. Residue TYR 220 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue LEU 233 is missing expected H atoms. Skipping. Residue THR 235 is missing expected H atoms. Skipping. Residue SER 239 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue ILE 245 is missing expected H atoms. Skipping. Residue THR 248 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue TYR 256 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue SER 12 is missing expected H atoms. Skipping. Residue LYS 14 is missing expected H atoms. Skipping. Residue VAL 16 is missing expected H atoms. Skipping. Residue MET 24 is missing expected H atoms. Skipping. Residue TYR 27 is missing expected H atoms. Skipping. Residue VAL 34 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue MET 60 is missing expected H atoms. Skipping. Residue LEU 112 is missing expected H atoms. Skipping. Residue LYS 118 is missing expected H atoms. Skipping. Residue LEU 126 is missing expected H atoms. Skipping. Residue MET 139 is missing expected H atoms. Skipping. Residue VAL 141 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue MET 147 is missing expected H atoms. Skipping. Residue LEU 148 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 162 is missing expected H atoms. Skipping. Residue SER 166 is missing expected H atoms. Skipping. Residue LYS 170 is missing expected H atoms. Skipping. Residue TYR 179 is missing expected H atoms. Skipping. Residue VAL 180 is missing expected H atoms. Skipping. Residue MET 198 is missing expected H atoms. Skipping. Residue LYS 203 is missing expected H atoms. Skipping. Residue THR 222 is missing expected H atoms. Skipping. Residue TYR 225 is missing expected H atoms. Skipping. Residue MET 232 is missing expected H atoms. Skipping. Residue TYR 240 is missing expected H atoms. Skipping. Residue LEU 241 is missing expected H atoms. Skipping. Residue THR 242 is missing expected H atoms. Skipping. Residue VAL 243 is missing expected H atoms. Skipping. Residue LYS 251 is missing expected H atoms. Skipping. Residue VAL 255 is missing expected H atoms. Skipping. Residue SER 267 is missing expected H atoms. Skipping. Residue LYS 270 is missing expected H atoms. Skipping. Residue LEU 279 is missing expected H atoms. Skipping. Residue LYS 281 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue MET 4 is missing expected H atoms. Skipping. Residue LEU 14 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue ILE 29 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue LYS 45 is missing expected H atoms. Skipping. Residue LEU 70 is missing expected H atoms. Skipping. Residue TYR 77 is missing expected H atoms. Skipping. Residue TYR 82 is missing expected H atoms. Skipping. Residue ILE 90 is missing expected H atoms. Skipping. Residue LYS 91 is missing expected H atoms. Skipping. Residue LEU 94 is missing expected H atoms. Skipping. Residue ILE 104 is missing expected H atoms. Skipping. Residue LYS 112 is missing expected H atoms. Skipping. Residue VAL 128 is missing expected H atoms. Skipping. Residue MET 130 is missing expected H atoms. Skipping. Residue ILE 143 is missing expected H atoms. Skipping. Residue LYS 152 is missing expected H atoms. Skipping. Residue LEU 158 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue MET 164 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 194 is missing expected H atoms. Skipping. Residue LYS 195 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue ILE 229 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 255 is missing expected H atoms. Skipping. Residue LYS 257 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue TYR 259 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue LEU 285 is missing expected H atoms. Skipping. Residue SER 290 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue LEU 324 is missing expected H atoms. Skipping. Residue LEU 336 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue LEU 363 is missing expected H atoms. Skipping. Residue VAL 367 is missing expected H atoms. Skipping. Residue ILE 376 is missing expected H atoms. Skipping. Residue LEU 384 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue VAL 403 is missing expected H atoms. Skipping. Residue THR 410 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 420 is missing expected H atoms. Skipping. Residue ILE 423 is missing expected H atoms. Skipping. Residue LEU 426 is missing expected H atoms. Skipping. Residue ILE 427 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 447 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue THR 481 is missing expected H atoms. Skipping. Residue TYR 484 is missing expected H atoms. Skipping. Residue VAL 486 is missing expected H atoms. Skipping. Residue LEU 487 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 5 is missing expected H atoms. Skipping. Residue LEU 24 is missing expected H atoms. Skipping. Residue TYR 25 is missing expected H atoms. Skipping. Residue LEU 27 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 38 is missing expected H atoms. Skipping. Residue ILE 41 is missing expected H atoms. Skipping. Residue TYR 42 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue VAL 58 is missing expected H atoms. Skipping. Residue LYS 175 is missing expected H atoms. Skipping. Residue LYS 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue VAL 215 is missing expected H atoms. Skipping. Residue TYR 221 is missing expected H atoms. Skipping. Residue LEU 230 is missing expected H atoms. Skipping. Residue LYS 235 is missing expected H atoms. Skipping. Residue LEU 258 is missing expected H atoms. Skipping. Residue ILE 263 is missing expected H atoms. Skipping. Residue TYR 269 is missing expected H atoms. Skipping. Residue ILE 291 is missing expected H atoms. Skipping. Residue ILE 293 is missing expected H atoms. Skipping. Residue SER 295 is missing expected H atoms. Skipping. Residue THR 296 is missing expected H atoms. Skipping. Residue LEU 299 is missing expected H atoms. Skipping. Residue ILE 302 is missing expected H atoms. Skipping. Residue THR 310 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue LEU 334 is missing expected H atoms. Skipping. Residue LEU 339 is missing expected H atoms. Skipping. Residue ILE 343 is missing expected H atoms. Skipping. Residue ILE 345 is missing expected H atoms. Skipping. Residue ILE 348 is missing expected H atoms. Skipping. Residue MET 350 is missing expected H atoms. Skipping. Residue VAL 353 is missing expected H atoms. Skipping. Residue SER 380 is missing expected H atoms. Skipping. Residue MET 387 is missing expected H atoms. Skipping. Residue THR 412 is missing expected H atoms. Skipping. Residue VAL 413 is missing expected H atoms. Skipping. Residue SER 418 is missing expected H atoms. Skipping. Residue LEU 421 is missing expected H atoms. Skipping. Residue LYS 433 is missing expected H atoms. Skipping. Residue VAL 439 is missing expected H atoms. Skipping. Residue ILE 442 is missing expected H atoms. Skipping. Residue VAL 445 is missing expected H atoms. Skipping. Residue TYR 450 is missing expected H atoms. Skipping. Residue LEU 451 is missing expected H atoms. Skipping. Residue LYS 455 is missing expected H atoms. Skipping. Residue ILE 462 is missing expected H atoms. Skipping. Residue ILE 473 is missing expected H atoms. Skipping. Residue VAL 474 is missing expected H atoms. Skipping. Residue MET 479 is missing expected H atoms. Skipping. Residue MET 501 is missing expected H atoms. Skipping. Residue LEU 502 is missing expected H atoms. Skipping. Evaluate side-chains 363 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 335 time to evaluate : 0.627 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 LEU cc_start: 0.9424 (mp) cc_final: 0.9223 (tt) REVERT: A 214 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8336 (mm-30) REVERT: B 54 SER cc_start: 0.8425 (OUTLIER) cc_final: 0.8144 (p) REVERT: B 96 TYR cc_start: 0.9411 (t80) cc_final: 0.9110 (t80) REVERT: D 138 GLU cc_start: 0.7347 (mm-30) cc_final: 0.6975 (tm-30) REVERT: D 259 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8406 (tp30) REVERT: C 260 GLN cc_start: 0.8909 (mm-40) cc_final: 0.8697 (mm-40) REVERT: N 183 ASP cc_start: 0.8541 (t70) cc_final: 0.8178 (m-30) REVERT: N 243 HIS cc_start: 0.8242 (m-70) cc_final: 0.7905 (m-70) outliers start: 28 outliers final: 25 residues processed: 347 average time/residue: 0.2430 time to fit residues: 123.7207 Evaluate side-chains 358 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 332 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 229 TRP Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 163 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 188 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 344 VAL Chi-restraints excluded: chain L residue 421 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 370 ASP Chi-restraints excluded: chain N residue 426 LEU Chi-restraints excluded: chain N residue 427 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 100 optimal weight: 0.7980 chunk 199 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 153 optimal weight: 20.0000 chunk 175 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.124304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.090555 restraints weight = 168075.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.093919 restraints weight = 71725.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.096003 restraints weight = 42964.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097259 restraints weight = 31594.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.097956 restraints weight = 26536.786| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.6350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16776 Z= 0.138 Angle : 0.561 8.577 23691 Z= 0.288 Chirality : 0.038 0.192 3041 Planarity : 0.004 0.043 2530 Dihedral : 23.214 174.054 4465 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.42 % Allowed : 27.63 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.20), residues: 1893 helix: 1.13 (0.19), residues: 802 sheet: -1.69 (0.27), residues: 335 loop : -0.50 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 389 TYR 0.011 0.001 TYR C 264 PHE 0.024 0.001 PHE C 218 TRP 0.006 0.001 TRP C 229 HIS 0.011 0.001 HIS N 243 Details of bonding type rmsd covalent geometry : bond 0.00277 (16776) covalent geometry : angle 0.56053 (23691) hydrogen bonds : bond 0.03326 ( 616) hydrogen bonds : angle 5.04395 ( 1732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7332.87 seconds wall clock time: 125 minutes 11.86 seconds (7511.86 seconds total)