Starting phenix.real_space_refine on Tue Jun 24 19:34:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b0j_15785/06_2025/8b0j_15785.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b0j_15785/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8b0j_15785/06_2025/8b0j_15785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b0j_15785/06_2025/8b0j_15785.map" model { file = "/net/cci-nas-00/data/ceres_data/8b0j_15785/06_2025/8b0j_15785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b0j_15785/06_2025/8b0j_15785.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 10} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 10, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 15} 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: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 3, 'ASN:plan1': 8, 'TRP:plan': 1, 'HIS:plan': 4, 'PHE:plan': 5, 'GLU:plan': 8, 'ARG:plan': 18} 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: {'GLN:plan1': 2, 'HIS:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 19} 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, 'ASP:plan': 11, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 2, 'HIS:plan': 10, 'PHE:plan': 4, 'GLU:plan': 28, 'ARG:plan': 32} 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: {'GLN:plan1': 10, 'ASP:plan': 11, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 5, 'PHE:plan': 5, 'GLU:plan': 18, 'ARG:plan': 24} 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: 16.76, per 1000 atoms: 0.59 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: 7.79 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 12.04 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: 11.10 Time building geometry restraints manager: 9.42 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: 9.040 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: 0.500 Extract box with map and model: 1.290 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 72.050 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.200 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: 0.020 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.740 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (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 TRP 0.021 0.002 TRP A 229 HIS 0.007 0.002 HIS B 252 PHE 0.016 0.002 PHE C 218 TYR 0.023 0.002 TYR D 96 ARG 0.005 0.001 ARG A 184 Details of bonding type rmsd hydrogen bonds : bond 0.21264 ( 616) hydrogen bonds : angle 9.60525 ( 1732) covalent geometry : bond 0.00927 (16776) covalent geometry : angle 1.30405 (23691) *********************** 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 : 2.255 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: symmetry clash REVERT: A 123 LEU cc_start: 0.9504 (mp) cc_final: 0.9278 (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: 0.8812 (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: 0.8505 (mt) REVERT: D 53 VAL cc_start: 0.9061 (p) cc_final: 0.8849 (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: 0.8866 (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: 0.6080 time to fit residues: 439.4406 Evaluate side-chains 382 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN N 321 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.128358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.095621 restraints weight = 163813.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.099024 restraints weight = 70615.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.101153 restraints weight = 41978.766| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3556 r_free = 0.3556 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16776 Z= 0.223 Angle : 0.709 6.376 23691 Z= 0.384 Chirality : 0.043 0.306 3041 Planarity : 0.005 0.052 2530 Dihedral : 24.407 178.220 4465 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 2.90 % Allowed : 19.61 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.18), residues: 1893 helix: -0.70 (0.17), residues: 797 sheet: -1.82 (0.27), residues: 330 loop : -1.39 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 229 HIS 0.006 0.002 HIS C 212 PHE 0.015 0.002 PHE C 218 TYR 0.014 0.001 TYR A 179 ARG 0.005 0.001 ARG A 266 Details of bonding type rmsd hydrogen bonds : bond 0.05475 ( 616) hydrogen bonds : angle 6.87260 ( 1732) covalent geometry : bond 0.00427 (16776) covalent geometry : angle 0.70850 (23691) *********************** 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 443 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 413 time to evaluate : 2.035 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: A 123 LEU cc_start: 0.9457 (mp) cc_final: 0.9232 (tt) REVERT: A 175 ILE cc_start: 0.8455 (pt) cc_final: 0.8135 (tp) REVERT: A 214 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8319 (mm-30) REVERT: A 234 GLU cc_start: 0.9024 (tp30) cc_final: 0.8754 (tp30) REVERT: B 39 ASP cc_start: 0.9133 (m-30) cc_final: 0.8683 (p0) REVERT: B 96 TYR cc_start: 0.9201 (t80) cc_final: 0.8862 (t80) REVERT: B 251 LYS cc_start: 0.8599 (mttt) cc_final: 0.8396 (mttt) REVERT: D 3 LEU cc_start: 0.8982 (tp) cc_final: 0.8770 (mt) REVERT: D 44 LEU cc_start: 0.9470 (tp) cc_final: 0.9240 (tt) REVERT: D 67 PHE cc_start: 0.8321 (p90) cc_final: 0.8019 (p90) REVERT: D 88 ASP cc_start: 0.8908 (p0) cc_final: 0.8698 (p0) REVERT: C 186 LEU cc_start: 0.9288 (mt) cc_final: 0.9087 (mp) REVERT: C 192 ASP cc_start: 0.8971 (t0) cc_final: 0.8603 (t0) REVERT: C 220 TYR cc_start: 0.8787 (t80) cc_final: 0.8533 (t80) REVERT: L 59 ASP cc_start: 0.8035 (t0) cc_final: 0.7742 (t0) REVERT: N 1 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8892 (tmm) REVERT: N 183 ASP cc_start: 0.8358 (t70) cc_final: 0.7925 (m-30) REVERT: N 478 GLN cc_start: 0.9030 (mt0) cc_final: 0.8744 (tt0) outliers start: 30 outliers final: 24 residues processed: 422 average time/residue: 0.6138 time to fit residues: 371.7979 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 : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 43 THR 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 222 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain D residue 102 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 183 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 73 ILE Chi-restraints excluded: chain L residue 92 ASP 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 Chi-restraints excluded: chain N residue 384 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 191 optimal weight: 9.9990 chunk 160 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 127 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 155 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.125489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.092546 restraints weight = 163769.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.095849 restraints weight = 70356.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.097894 restraints weight = 42145.511| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16776 Z= 0.207 Angle : 0.636 6.198 23691 Z= 0.344 Chirality : 0.041 0.286 3041 Planarity : 0.005 0.053 2530 Dihedral : 24.269 177.399 4465 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.67 % Allowed : 21.64 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.19), residues: 1893 helix: -0.15 (0.18), residues: 810 sheet: -1.72 (0.27), residues: 325 loop : -1.34 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 229 HIS 0.006 0.001 HIS B 171 PHE 0.020 0.002 PHE C 164 TYR 0.011 0.001 TYR C 264 ARG 0.007 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.04770 ( 616) hydrogen bonds : angle 6.23816 ( 1732) covalent geometry : bond 0.00400 (16776) covalent geometry : angle 0.63644 (23691) *********************** 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 420 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 382 time to evaluate : 2.129 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: A 123 LEU cc_start: 0.9451 (mp) cc_final: 0.9235 (tt) REVERT: A 175 ILE cc_start: 0.8696 (pt) cc_final: 0.8433 (tp) REVERT: A 234 GLU cc_start: 0.8965 (tp30) cc_final: 0.8745 (tp30) REVERT: B 39 ASP cc_start: 0.9127 (m-30) cc_final: 0.8671 (p0) REVERT: B 96 TYR cc_start: 0.9340 (t80) cc_final: 0.9051 (t80) REVERT: B 176 ASP cc_start: 0.8871 (p0) cc_final: 0.8591 (p0) REVERT: D 3 LEU cc_start: 0.9017 (tp) cc_final: 0.8750 (mt) REVERT: D 22 GLU cc_start: 0.8947 (pp20) cc_final: 0.8362 (pp20) REVERT: D 44 LEU cc_start: 0.9473 (tp) cc_final: 0.9234 (tt) REVERT: C 186 LEU cc_start: 0.9271 (mt) cc_final: 0.9031 (mp) REVERT: C 220 TYR cc_start: 0.8908 (t80) cc_final: 0.8614 (t80) REVERT: L 59 ASP cc_start: 0.8110 (t0) cc_final: 0.7794 (t0) REVERT: L 109 ARG cc_start: 0.8727 (tmm160) cc_final: 0.8359 (tmm-80) REVERT: N 183 ASP cc_start: 0.8390 (t70) cc_final: 0.7959 (m-30) REVERT: N 430 GLU cc_start: 0.9205 (tp30) cc_final: 0.8897 (tm-30) REVERT: N 478 GLN cc_start: 0.8944 (mt0) cc_final: 0.8631 (tt0) outliers start: 38 outliers final: 34 residues processed: 398 average time/residue: 0.6071 time to fit residues: 346.4330 Evaluate side-chains 393 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 359 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 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 215 VAL Chi-restraints excluded: chain A residue 243 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 148 LEU 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 173 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain C residue 67 PHE 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 295 SER 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 323 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 165 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 132 optimal weight: 0.2980 chunk 8 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 323 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.124189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.090653 restraints weight = 163232.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093813 restraints weight = 71545.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.095790 restraints weight = 43524.071| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 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 = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16776 Z= 0.214 Angle : 0.619 6.151 23691 Z= 0.333 Chirality : 0.040 0.268 3041 Planarity : 0.005 0.053 2530 Dihedral : 24.046 179.411 4465 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 4.25 % Allowed : 23.00 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.19), residues: 1893 helix: -0.04 (0.18), residues: 796 sheet: -1.85 (0.27), residues: 334 loop : -1.24 (0.23), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 229 HIS 0.006 0.001 HIS B 171 PHE 0.018 0.002 PHE C 164 TYR 0.014 0.001 TYR B 220 ARG 0.007 0.000 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.04508 ( 616) hydrogen bonds : angle 6.10940 ( 1732) covalent geometry : bond 0.00415 (16776) covalent geometry : angle 0.61887 (23691) *********************** 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 409 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 365 time to evaluate : 2.037 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: 0.9448 (mp) cc_final: 0.9227 (tt) REVERT: A 234 GLU cc_start: 0.8914 (tp30) cc_final: 0.8618 (tp30) REVERT: B 39 ASP cc_start: 0.9137 (m-30) cc_final: 0.8677 (p0) REVERT: B 96 TYR cc_start: 0.9383 (t80) cc_final: 0.9083 (t80) REVERT: B 176 ASP cc_start: 0.8922 (p0) cc_final: 0.8617 (p0) REVERT: B 251 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8310 (mttt) REVERT: D 3 LEU cc_start: 0.9001 (tp) cc_final: 0.8727 (mt) REVERT: D 44 LEU cc_start: 0.9470 (tp) cc_final: 0.9233 (tt) REVERT: C 220 TYR cc_start: 0.8953 (t80) cc_final: 0.8707 (t80) REVERT: L 59 ASP cc_start: 0.8128 (t0) cc_final: 0.7833 (t0) REVERT: L 109 ARG cc_start: 0.8739 (tmm160) cc_final: 0.8245 (tmm-80) REVERT: N 183 ASP cc_start: 0.8420 (t70) cc_final: 0.7990 (m-30) REVERT: N 430 GLU cc_start: 0.9219 (tp30) cc_final: 0.8899 (tm-30) REVERT: N 478 GLN cc_start: 0.8938 (mt0) cc_final: 0.8603 (tt0) outliers start: 44 outliers final: 40 residues processed: 383 average time/residue: 0.5998 time to fit residues: 330.0993 Evaluate side-chains 391 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 350 time to evaluate : 2.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU 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 69 GLN 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 55 ILE 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 B residue 251 LYS 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 123 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 199 THR 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 100 VAL Chi-restraints excluded: chain L residue 105 ASP Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain L residue 295 SER 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 247 LEU Chi-restraints excluded: chain N residue 305 ASN 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 86 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 193 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 237 ASN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.125431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.091739 restraints weight = 164703.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095090 restraints weight = 70180.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097118 restraints weight = 42136.883| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 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 = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16776 Z= 0.140 Angle : 0.573 7.956 23691 Z= 0.300 Chirality : 0.039 0.262 3041 Planarity : 0.004 0.050 2530 Dihedral : 23.685 179.256 4465 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.67 % Allowed : 24.15 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1893 helix: 0.50 (0.18), residues: 810 sheet: -1.71 (0.28), residues: 315 loop : -1.12 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP C 229 HIS 0.008 0.001 HIS N 243 PHE 0.021 0.001 PHE C 218 TYR 0.019 0.001 TYR B 220 ARG 0.004 0.000 ARG N 373 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 616) hydrogen bonds : angle 5.59979 ( 1732) covalent geometry : bond 0.00281 (16776) covalent geometry : angle 0.57271 (23691) *********************** 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 415 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 377 time to evaluate : 2.079 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: 0.9453 (mp) cc_final: 0.9239 (tt) REVERT: A 234 GLU cc_start: 0.8915 (tp30) cc_final: 0.8638 (tp30) REVERT: B 39 ASP cc_start: 0.9124 (m-30) cc_final: 0.8675 (p0) REVERT: B 96 TYR cc_start: 0.9401 (t80) cc_final: 0.9067 (t80) REVERT: B 176 ASP cc_start: 0.8979 (p0) cc_final: 0.8652 (p0) REVERT: B 251 LYS cc_start: 0.8457 (mttt) cc_final: 0.8225 (mttt) REVERT: D 259 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8509 (tp30) REVERT: C 220 TYR cc_start: 0.8894 (t80) cc_final: 0.8585 (t80) REVERT: L 59 ASP cc_start: 0.8114 (t0) cc_final: 0.7824 (t0) REVERT: L 109 ARG cc_start: 0.8736 (tmm160) cc_final: 0.8258 (tmm-80) REVERT: N 4 MET cc_start: 0.8272 (tmm) cc_final: 0.7964 (tmm) REVERT: N 183 ASP cc_start: 0.8505 (t70) cc_final: 0.8098 (m-30) REVERT: N 506 HIS cc_start: 0.8825 (m90) cc_final: 0.8476 (m90) outliers start: 38 outliers final: 31 residues processed: 388 average time/residue: 0.5682 time to fit residues: 316.6954 Evaluate side-chains 399 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 368 time to evaluate : 2.078 ------------------------------------------------------------------------------- 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 180 VAL Chi-restraints excluded: chain A residue 215 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 37 LEU 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 183 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 299 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 224 GLN Chi-restraints excluded: chain N residue 321 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 452 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 53 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 196 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 158 optimal weight: 50.0000 chunk 128 optimal weight: 9.9990 chunk 185 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 268 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.121834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.088355 restraints weight = 168958.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.091509 restraints weight = 72512.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.093497 restraints weight = 43775.935| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.5416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16776 Z= 0.239 Angle : 0.635 6.751 23691 Z= 0.340 Chirality : 0.040 0.267 3041 Planarity : 0.005 0.051 2530 Dihedral : 23.829 177.002 4465 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 5.22 % Allowed : 24.93 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.19), residues: 1893 helix: 0.24 (0.18), residues: 788 sheet: -1.85 (0.27), residues: 333 loop : -1.08 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 229 HIS 0.007 0.002 HIS B 171 PHE 0.022 0.002 PHE C 218 TYR 0.017 0.002 TYR B 220 ARG 0.007 0.001 ARG N 389 Details of bonding type rmsd hydrogen bonds : bond 0.04349 ( 616) hydrogen bonds : angle 5.87385 ( 1732) covalent geometry : bond 0.00458 (16776) covalent geometry : angle 0.63534 (23691) *********************** 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 399 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 345 time to evaluate : 2.109 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: A 123 LEU cc_start: 0.9438 (mp) cc_final: 0.9226 (tt) REVERT: B 39 ASP cc_start: 0.9122 (m-30) cc_final: 0.8692 (p0) REVERT: B 54 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.8035 (p) REVERT: B 96 TYR cc_start: 0.9391 (t80) cc_final: 0.9151 (t80) REVERT: B 176 ASP cc_start: 0.9014 (p0) cc_final: 0.8656 (p0) REVERT: B 251 LYS cc_start: 0.8584 (mttt) cc_final: 0.8317 (mttt) REVERT: D 138 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7071 (tm-30) REVERT: L 59 ASP cc_start: 0.8041 (t0) cc_final: 0.7776 (t0) REVERT: L 109 ARG cc_start: 0.8754 (tmm160) cc_final: 0.8325 (tmm-80) REVERT: N 4 MET cc_start: 0.8447 (tmm) cc_final: 0.8123 (tmm) REVERT: N 183 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.8039 (m-30) REVERT: N 506 HIS cc_start: 0.8846 (m90) cc_final: 0.8478 (m90) outliers start: 54 outliers final: 51 residues processed: 368 average time/residue: 0.6813 time to fit residues: 366.5657 Evaluate side-chains 391 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 338 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain B residue 53 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 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 3 LEU Chi-restraints excluded: chain D residue 21 LEU 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 126 LEU Chi-restraints excluded: chain D residue 173 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain C residue 67 PHE 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 100 VAL 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 L residue 370 ASP Chi-restraints excluded: chain L residue 379 ILE Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 183 ASP Chi-restraints excluded: chain N residue 224 GLN Chi-restraints excluded: chain N residue 305 ASN Chi-restraints excluded: chain N residue 321 ASN Chi-restraints excluded: chain N residue 323 ASN Chi-restraints excluded: chain N residue 370 ASP Chi-restraints excluded: chain N residue 426 LEU Chi-restraints excluded: chain N residue 452 LEU 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 171 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 72 optimal weight: 0.2980 chunk 159 optimal weight: 0.5980 chunk 166 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.125243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.091661 restraints weight = 165792.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.095016 restraints weight = 70366.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.097086 restraints weight = 42019.735| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 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 = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16776 Z= 0.108 Angle : 0.565 6.347 23691 Z= 0.290 Chirality : 0.039 0.238 3041 Planarity : 0.004 0.054 2530 Dihedral : 23.490 179.452 4465 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.00 % Allowed : 26.86 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.20), residues: 1893 helix: 0.90 (0.19), residues: 798 sheet: -1.59 (0.28), residues: 317 loop : -0.84 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 229 HIS 0.016 0.001 HIS N 243 PHE 0.015 0.001 PHE C 218 TYR 0.014 0.001 TYR B 220 ARG 0.004 0.000 ARG N 389 Details of bonding type rmsd hydrogen bonds : bond 0.03514 ( 616) hydrogen bonds : angle 5.28608 ( 1732) covalent geometry : bond 0.00226 (16776) covalent geometry : angle 0.56537 (23691) *********************** 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 394 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 363 time to evaluate : 2.109 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: A 123 LEU cc_start: 0.9448 (mp) cc_final: 0.9231 (tt) REVERT: A 214 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8303 (mm-30) REVERT: B 39 ASP cc_start: 0.9140 (m-30) cc_final: 0.8649 (p0) REVERT: B 96 TYR cc_start: 0.9405 (t80) cc_final: 0.9019 (t80) REVERT: B 176 ASP cc_start: 0.9024 (p0) cc_final: 0.8657 (p0) REVERT: B 251 LYS cc_start: 0.8638 (mttt) cc_final: 0.8383 (mttt) REVERT: D 44 LEU cc_start: 0.9453 (tp) cc_final: 0.9242 (tt) REVERT: D 138 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7069 (tm-30) REVERT: D 259 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8457 (tp30) REVERT: C 220 TYR cc_start: 0.8819 (t80) cc_final: 0.8583 (t80) REVERT: L 109 ARG cc_start: 0.8748 (tmm160) cc_final: 0.8286 (tmm-80) REVERT: N 4 MET cc_start: 0.8430 (tmm) cc_final: 0.8109 (tmm) REVERT: N 183 ASP cc_start: 0.8544 (t70) cc_final: 0.8165 (m-30) REVERT: N 506 HIS cc_start: 0.8776 (m90) cc_final: 0.8397 (m90) outliers start: 31 outliers final: 29 residues processed: 373 average time/residue: 0.6499 time to fit residues: 354.9546 Evaluate side-chains 383 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 354 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 PHE 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 215 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 272 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 173 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain C residue 67 PHE 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 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 323 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 74 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 72 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** L 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.124969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.091648 restraints weight = 167913.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.094977 restraints weight = 72165.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.096995 restraints weight = 43254.015| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 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 = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16776 Z= 0.116 Angle : 0.549 6.807 23691 Z= 0.282 Chirality : 0.038 0.228 3041 Planarity : 0.004 0.058 2530 Dihedral : 23.317 177.877 4465 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.38 % Allowed : 26.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.20), residues: 1893 helix: 1.14 (0.19), residues: 795 sheet: -1.60 (0.28), residues: 319 loop : -0.61 (0.24), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 229 HIS 0.003 0.001 HIS N 485 PHE 0.017 0.001 PHE C 218 TYR 0.020 0.001 TYR B 220 ARG 0.006 0.000 ARG N 389 Details of bonding type rmsd hydrogen bonds : bond 0.03354 ( 616) hydrogen bonds : angle 5.13675 ( 1732) covalent geometry : bond 0.00237 (16776) covalent geometry : angle 0.54867 (23691) *********************** 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 393 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 358 time to evaluate : 2.005 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 54 SER cc_start: 0.8880 (t) cc_final: 0.8520 (p) REVERT: A 123 LEU cc_start: 0.9441 (mp) cc_final: 0.9223 (tt) REVERT: A 179 TYR cc_start: 0.9316 (m-80) cc_final: 0.9042 (m-10) REVERT: B 39 ASP cc_start: 0.9120 (m-30) cc_final: 0.8635 (p0) REVERT: B 54 SER cc_start: 0.8341 (OUTLIER) cc_final: 0.8072 (p) REVERT: B 96 TYR cc_start: 0.9390 (t80) cc_final: 0.9064 (t80) REVERT: B 176 ASP cc_start: 0.9054 (p0) cc_final: 0.8692 (p0) REVERT: B 251 LYS cc_start: 0.8600 (mttt) cc_final: 0.8366 (mttt) REVERT: D 44 LEU cc_start: 0.9464 (tp) cc_final: 0.9242 (tt) REVERT: C 260 GLN cc_start: 0.8958 (mm-40) cc_final: 0.8743 (mm-40) REVERT: L 109 ARG cc_start: 0.8738 (tmm160) cc_final: 0.8286 (tmm-80) REVERT: N 4 MET cc_start: 0.8471 (tmm) cc_final: 0.8102 (tmm) REVERT: N 183 ASP cc_start: 0.8556 (t70) cc_final: 0.8182 (m-30) REVERT: N 506 HIS cc_start: 0.8755 (m90) cc_final: 0.8359 (m90) outliers start: 35 outliers final: 31 residues processed: 369 average time/residue: 0.5925 time to fit residues: 316.3335 Evaluate side-chains 380 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 348 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG 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 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 B residue 272 VAL Chi-restraints excluded: chain D residue 10 SER 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 180 VAL Chi-restraints excluded: chain C residue 67 PHE 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 C residue 274 SER 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 299 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 224 GLN Chi-restraints excluded: chain N residue 243 HIS Chi-restraints excluded: chain N residue 323 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 452 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 90 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.123376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.089993 restraints weight = 168181.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.093279 restraints weight = 71805.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.095301 restraints weight = 42974.983| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.5955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16776 Z= 0.167 Angle : 0.575 7.263 23691 Z= 0.302 Chirality : 0.038 0.224 3041 Planarity : 0.005 0.094 2530 Dihedral : 23.365 176.390 4465 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.67 % Allowed : 26.67 % Favored : 69.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.20), residues: 1893 helix: 0.90 (0.19), residues: 804 sheet: -1.70 (0.28), residues: 323 loop : -0.71 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 229 HIS 0.007 0.001 HIS N 355 PHE 0.018 0.001 PHE C 218 TYR 0.019 0.001 TYR B 220 ARG 0.006 0.000 ARG D 266 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 616) hydrogen bonds : angle 5.27488 ( 1732) covalent geometry : bond 0.00331 (16776) covalent geometry : angle 0.57481 (23691) *********************** 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 381 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 343 time to evaluate : 2.164 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 54 SER cc_start: 0.8848 (t) cc_final: 0.8505 (p) REVERT: A 123 LEU cc_start: 0.9459 (mp) cc_final: 0.9246 (tt) REVERT: A 214 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8342 (mm-30) REVERT: B 54 SER cc_start: 0.8387 (OUTLIER) cc_final: 0.8113 (p) REVERT: B 96 TYR cc_start: 0.9423 (t80) cc_final: 0.9076 (t80) REVERT: B 176 ASP cc_start: 0.9068 (p0) cc_final: 0.8685 (p0) REVERT: B 251 LYS cc_start: 0.8669 (mttt) cc_final: 0.8446 (mttt) REVERT: D 138 GLU cc_start: 0.7388 (mm-30) cc_final: 0.7005 (tm-30) REVERT: D 259 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8414 (tp30) REVERT: L 59 ASP cc_start: 0.7868 (t0) cc_final: 0.7656 (t0) REVERT: L 109 ARG cc_start: 0.8789 (tmm160) cc_final: 0.8339 (tmm-80) REVERT: N 4 MET cc_start: 0.8500 (tmm) cc_final: 0.8132 (tmm) REVERT: N 183 ASP cc_start: 0.8576 (t70) cc_final: 0.8200 (m-30) REVERT: N 506 HIS cc_start: 0.8764 (m90) cc_final: 0.8368 (m90) outliers start: 38 outliers final: 37 residues processed: 355 average time/residue: 0.6158 time to fit residues: 319.9201 Evaluate side-chains 378 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 340 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 PHE 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 161 THR Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain C residue 67 PHE 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 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 188 LEU Chi-restraints excluded: chain L residue 299 LEU Chi-restraints excluded: chain L residue 370 ASP Chi-restraints excluded: chain L residue 421 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 224 GLN Chi-restraints excluded: chain N residue 243 HIS Chi-restraints excluded: chain N residue 323 ASN Chi-restraints excluded: chain N residue 355 HIS Chi-restraints excluded: chain N residue 359 VAL 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 452 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 13 optimal weight: 0.2980 chunk 114 optimal weight: 0.8980 chunk 200 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 124 optimal weight: 0.0470 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 45 optimal weight: 0.0970 chunk 35 optimal weight: 5.9990 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.126622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.093377 restraints weight = 164221.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.096774 restraints weight = 70489.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.098881 restraints weight = 42049.364| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 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 = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.6134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16776 Z= 0.103 Angle : 0.558 6.927 23691 Z= 0.283 Chirality : 0.038 0.192 3041 Planarity : 0.004 0.049 2530 Dihedral : 23.085 177.310 4465 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.22 % Allowed : 28.50 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.20), residues: 1893 helix: 1.31 (0.19), residues: 809 sheet: -1.55 (0.28), residues: 330 loop : -0.52 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 191 HIS 0.004 0.001 HIS N 485 PHE 0.023 0.001 PHE C 218 TYR 0.022 0.001 TYR B 220 ARG 0.005 0.000 ARG N 389 Details of bonding type rmsd hydrogen bonds : bond 0.03097 ( 616) hydrogen bonds : angle 4.84098 ( 1732) covalent geometry : bond 0.00220 (16776) covalent geometry : angle 0.55814 (23691) ********************** 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 384 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 361 time to evaluate : 3.180 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: A 54 SER cc_start: 0.8840 (t) cc_final: 0.8477 (p) REVERT: A 123 LEU cc_start: 0.9445 (mp) cc_final: 0.9232 (tt) REVERT: B 54 SER cc_start: 0.8360 (OUTLIER) cc_final: 0.8077 (p) REVERT: B 96 TYR cc_start: 0.9355 (t80) cc_final: 0.9029 (t80) REVERT: B 124 GLU cc_start: 0.9014 (tp30) cc_final: 0.8791 (tp30) REVERT: B 251 LYS cc_start: 0.8651 (mttt) cc_final: 0.8422 (mttt) REVERT: D 44 LEU cc_start: 0.9435 (tp) cc_final: 0.9212 (tt) REVERT: D 138 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6897 (tm-30) REVERT: L 109 ARG cc_start: 0.8679 (tmm160) cc_final: 0.8216 (tmm-80) REVERT: N 4 MET cc_start: 0.8477 (tmm) cc_final: 0.8196 (tmm) REVERT: N 183 ASP cc_start: 0.8586 (t70) cc_final: 0.8234 (m-30) REVERT: N 506 HIS cc_start: 0.8704 (m90) cc_final: 0.8306 (m90) outliers start: 23 outliers final: 18 residues processed: 368 average time/residue: 0.6211 time to fit residues: 332.5792 Evaluate side-chains 372 residues out of total 1691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 353 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain B residue 54 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain C residue 67 PHE 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 L residue 100 VAL Chi-restraints excluded: chain L residue 127 LEU Chi-restraints excluded: chain N residue 1 MET Chi-restraints excluded: chain N residue 323 ASN Chi-restraints excluded: chain N residue 359 VAL 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 173 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 137 optimal weight: 0.0470 chunk 175 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 overall best weight: 3.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.122195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.088668 restraints weight = 168912.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.091896 restraints weight = 72521.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.093879 restraints weight = 43559.194| |-----------------------------------------------------------------------------| r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16776 Z= 0.218 Angle : 0.607 8.441 23691 Z= 0.321 Chirality : 0.039 0.210 3041 Planarity : 0.005 0.046 2530 Dihedral : 23.344 174.108 4465 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.71 % Allowed : 28.60 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.20), residues: 1893 helix: 0.89 (0.19), residues: 802 sheet: -1.68 (0.28), residues: 324 loop : -0.56 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 191 HIS 0.014 0.002 HIS N 243 PHE 0.023 0.002 PHE C 218 TYR 0.019 0.002 TYR C 220 ARG 0.005 0.001 ARG L 364 Details of bonding type rmsd hydrogen bonds : bond 0.03733 ( 616) hydrogen bonds : angle 5.34083 ( 1732) covalent geometry : bond 0.00425 (16776) covalent geometry : angle 0.60678 (23691) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14255.69 seconds wall clock time: 243 minutes 54.25 seconds (14634.25 seconds total)