Starting phenix.real_space_refine on Mon Jan 20 16:56:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bru_44844/01_2025/9bru_44844.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bru_44844/01_2025/9bru_44844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bru_44844/01_2025/9bru_44844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bru_44844/01_2025/9bru_44844.map" model { file = "/net/cci-nas-00/data/ceres_data/9bru_44844/01_2025/9bru_44844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bru_44844/01_2025/9bru_44844.cif" } resolution = 4.4 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= 0.001 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: 4 Type Number sf(0) Gaussians S 387 5.16 5 C 41941 2.51 5 N 11101 2.21 5 O 12119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 206 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 65548 Number of models: 1 Model: "" Number of chains: 32 Chain: "7" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1676 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain: "8" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "9" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "Q" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "R" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "T" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "V" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "6" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2931 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 9, 'TRANS': 351} Chain breaks: 1 Chain: "U" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3501 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 8, 'TRANS': 417} Chain breaks: 1 Chain: "a" Number of atoms: 6117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 752, 6117 Classifications: {'peptide': 752} Link IDs: {'PTRANS': 31, 'TRANS': 720} Chain breaks: 2 Chain: "e" Number of atoms: 623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 623 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 6, 'TRANS': 70} Chain: "f" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 658 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "b" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1484 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 194} Chain: "g" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1069 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "X" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "d" Number of atoms: 2842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2842 Classifications: {'peptide': 351} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 337} Chain: "c" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1642 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "p" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 407 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} Chain: "1" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "0" Number of atoms: 4671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4671 Classifications: {'peptide': 602} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 571} Chain: "2" Number of atoms: 4656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4656 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 569} Chain: "3" Number of atoms: 3610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3610 Classifications: {'peptide': 461} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 433} Chain breaks: 1 Chain: "4" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3667 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Chain: "5" Number of atoms: 3667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3667 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 440} Time building chain proxies: 27.82, per 1000 atoms: 0.42 Number of scatterers: 65548 At special positions: 0 Unit cell: (161.534, 182.556, 300.941, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 387 16.00 O 12119 8.00 N 11101 7.00 C 41941 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.13 Conformation dependent library (CDL) restraints added in 6.6 seconds 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15510 Finding SS restraints... Secondary structure from input PDB file: 312 helices and 42 sheets defined 61.2% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.64 Creating SS restraints... Processing helix chain '7' and resid 12 through 48 Processing helix chain '7' and resid 50 through 77 Processing helix chain '7' and resid 79 through 86 Processing helix chain '7' and resid 128 through 175 removed outlier: 3.518A pdb=" N GLU 7 143 " --> pdb=" O ALA 7 139 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP 7 159 " --> pdb=" O PHE 7 155 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLU 7 160 " --> pdb=" O VAL 7 156 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA 7 161 " --> pdb=" O THR 7 157 " (cutoff:3.500A) Processing helix chain '7' and resid 175 through 210 removed outlier: 3.578A pdb=" N ARG 7 179 " --> pdb=" O VAL 7 175 " (cutoff:3.500A) Processing helix chain '8' and resid 3 through 106 removed outlier: 4.104A pdb=" N LYS 8 52 " --> pdb=" O THR 8 48 " (cutoff:3.500A) Processing helix chain '8' and resid 108 through 128 removed outlier: 3.657A pdb=" N VAL 8 114 " --> pdb=" O THR 8 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU 8 128 " --> pdb=" O LEU 8 124 " (cutoff:3.500A) Processing helix chain '8' and resid 140 through 160 removed outlier: 3.571A pdb=" N ALA 8 146 " --> pdb=" O PRO 8 142 " (cutoff:3.500A) Proline residue: 8 153 - end of helix Processing helix chain '8' and resid 196 through 207 Processing helix chain '8' and resid 207 through 217 Processing helix chain '9' and resid 6 through 107 removed outlier: 4.142A pdb=" N LYS 9 107 " --> pdb=" O SER 9 103 " (cutoff:3.500A) Processing helix chain '9' and resid 108 through 128 removed outlier: 3.988A pdb=" N VAL 9 114 " --> pdb=" O THR 9 110 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU 9 128 " --> pdb=" O LEU 9 124 " (cutoff:3.500A) Processing helix chain '9' and resid 137 through 139 No H-bonds generated for 'chain '9' and resid 137 through 139' Processing helix chain '9' and resid 140 through 160 Proline residue: 9 153 - end of helix Processing helix chain '9' and resid 196 through 207 Processing helix chain '9' and resid 207 through 217 Processing helix chain 'Q' and resid 4 through 44 removed outlier: 4.450A pdb=" N VAL Q 8 " --> pdb=" O SER Q 4 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE Q 18 " --> pdb=" O HIS Q 14 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLN Q 21 " --> pdb=" O ALA Q 17 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA Q 23 " --> pdb=" O ILE Q 19 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 107 removed outlier: 4.151A pdb=" N LYS Q 107 " --> pdb=" O SER Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 128 removed outlier: 4.209A pdb=" N GLN Q 113 " --> pdb=" O THR Q 109 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL Q 114 " --> pdb=" O THR Q 110 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU Q 128 " --> pdb=" O LEU Q 124 " (cutoff:3.500A) Processing helix chain 'Q' and resid 137 through 139 No H-bonds generated for 'chain 'Q' and resid 137 through 139' Processing helix chain 'Q' and resid 140 through 160 Proline residue: Q 153 - end of helix Processing helix chain 'Q' and resid 195 through 207 Processing helix chain 'Q' and resid 207 through 217 Processing helix chain 'R' and resid 5 through 103 removed outlier: 3.661A pdb=" N LEU R 11 " --> pdb=" O GLY R 7 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY R 64 " --> pdb=" O GLN R 60 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASN R 91 " --> pdb=" O SER R 87 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N GLU R 93 " --> pdb=" O GLN R 89 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ARG R 94 " --> pdb=" O ARG R 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 91 removed outlier: 3.719A pdb=" N ASN T 91 " --> pdb=" O SER T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 105 removed outlier: 3.536A pdb=" N LEU T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) Processing helix chain 'V' and resid 7 through 91 removed outlier: 3.874A pdb=" N ARG V 90 " --> pdb=" O SER V 86 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASN V 91 " --> pdb=" O SER V 87 " (cutoff:3.500A) Processing helix chain 'V' and resid 91 through 105 removed outlier: 3.927A pdb=" N VAL V 95 " --> pdb=" O ASN V 91 " (cutoff:3.500A) Processing helix chain '6' and resid 15 through 23 removed outlier: 4.336A pdb=" N LYS 6 21 " --> pdb=" O GLN 6 17 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N HIS 6 23 " --> pdb=" O TRP 6 19 " (cutoff:3.500A) Processing helix chain '6' and resid 50 through 79 Processing helix chain '6' and resid 92 through 96 removed outlier: 3.876A pdb=" N GLY 6 95 " --> pdb=" O LEU 6 92 " (cutoff:3.500A) Processing helix chain '6' and resid 97 through 103 Processing helix chain '6' and resid 117 through 157 Processing helix chain '6' and resid 171 through 175 removed outlier: 3.980A pdb=" N PHE 6 175 " --> pdb=" O LYS 6 172 " (cutoff:3.500A) Processing helix chain '6' and resid 193 through 205 removed outlier: 3.724A pdb=" N TRP 6 197 " --> pdb=" O ASN 6 193 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE 6 198 " --> pdb=" O HIS 6 194 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS 6 199 " --> pdb=" O ASN 6 195 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU 6 202 " --> pdb=" O ILE 6 198 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N THR 6 203 " --> pdb=" O LYS 6 199 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA 6 205 " --> pdb=" O TYR 6 201 " (cutoff:3.500A) Processing helix chain '6' and resid 232 through 242 removed outlier: 4.067A pdb=" N ASP 6 236 " --> pdb=" O LYS 6 232 " (cutoff:3.500A) Processing helix chain '6' and resid 243 through 245 No H-bonds generated for 'chain '6' and resid 243 through 245' Processing helix chain '6' and resid 254 through 310 Proline residue: 6 278 - end of helix Processing helix chain '6' and resid 327 through 344 removed outlier: 4.261A pdb=" N HIS 6 341 " --> pdb=" O GLU 6 337 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU 6 342 " --> pdb=" O LEU 6 338 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASP 6 343 " --> pdb=" O TYR 6 339 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 27 Processing helix chain 'U' and resid 33 through 37 Processing helix chain 'U' and resid 45 through 52 removed outlier: 3.674A pdb=" N PHE U 49 " --> pdb=" O GLU U 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 65 Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'U' and resid 79 through 84 removed outlier: 3.591A pdb=" N ILE U 84 " --> pdb=" O LEU U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 86 through 103 removed outlier: 3.793A pdb=" N GLN U 91 " --> pdb=" O GLU U 87 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR U 92 " --> pdb=" O GLN U 88 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU U 103 " --> pdb=" O ASP U 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 118 through 122 removed outlier: 3.822A pdb=" N THR U 121 " --> pdb=" O SER U 118 " (cutoff:3.500A) Processing helix chain 'U' and resid 136 through 146 Processing helix chain 'U' and resid 158 through 163 Processing helix chain 'U' and resid 164 through 169 removed outlier: 4.051A pdb=" N ILE U 168 " --> pdb=" O TYR U 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 170 through 172 No H-bonds generated for 'chain 'U' and resid 170 through 172' Processing helix chain 'U' and resid 196 through 209 Processing helix chain 'U' and resid 211 through 221 removed outlier: 3.993A pdb=" N ALA U 217 " --> pdb=" O GLU U 213 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA U 221 " --> pdb=" O ALA U 217 " (cutoff:3.500A) Processing helix chain 'U' and resid 222 through 233 Processing helix chain 'U' and resid 236 through 251 removed outlier: 3.704A pdb=" N GLN U 240 " --> pdb=" O GLY U 236 " (cutoff:3.500A) Processing helix chain 'U' and resid 253 through 261 Processing helix chain 'U' and resid 264 through 276 Processing helix chain 'U' and resid 279 through 296 Processing helix chain 'U' and resid 298 through 302 Processing helix chain 'U' and resid 303 through 311 removed outlier: 4.033A pdb=" N MET U 309 " --> pdb=" O TYR U 305 " (cutoff:3.500A) Processing helix chain 'U' and resid 313 through 322 removed outlier: 3.670A pdb=" N GLN U 317 " --> pdb=" O LYS U 313 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN U 320 " --> pdb=" O LYS U 316 " (cutoff:3.500A) Processing helix chain 'U' and resid 328 through 350 removed outlier: 3.838A pdb=" N SER U 332 " --> pdb=" O ASP U 328 " (cutoff:3.500A) Processing helix chain 'U' and resid 351 through 362 removed outlier: 3.687A pdb=" N GLY U 362 " --> pdb=" O GLU U 358 " (cutoff:3.500A) Processing helix chain 'U' and resid 367 through 371 Processing helix chain 'U' and resid 372 through 379 Processing helix chain 'U' and resid 380 through 384 Processing helix chain 'U' and resid 388 through 401 Processing helix chain 'U' and resid 403 through 419 Processing helix chain 'U' and resid 421 through 432 Processing helix chain 'U' and resid 432 through 441 removed outlier: 3.569A pdb=" N LEU U 436 " --> pdb=" O GLY U 432 " (cutoff:3.500A) Processing helix chain 'U' and resid 445 through 459 Processing helix chain 'a' and resid 19 through 33 removed outlier: 3.915A pdb=" N CYS a 24 " --> pdb=" O GLU a 20 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER a 27 " --> pdb=" O TYR a 23 " (cutoff:3.500A) Processing helix chain 'a' and resid 51 through 76 Processing helix chain 'a' and resid 92 through 132 removed outlier: 4.186A pdb=" N ASP a 96 " --> pdb=" O ARG a 92 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA a 117 " --> pdb=" O THR a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 199 removed outlier: 3.774A pdb=" N ARG a 192 " --> pdb=" O PRO a 188 " (cutoff:3.500A) Processing helix chain 'a' and resid 233 through 248 removed outlier: 4.239A pdb=" N LYS a 241 " --> pdb=" O LYS a 237 " (cutoff:3.500A) Processing helix chain 'a' and resid 258 through 316 removed outlier: 4.043A pdb=" N LYS a 262 " --> pdb=" O PRO a 258 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP a 273 " --> pdb=" O ASN a 269 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP a 274 " --> pdb=" O THR a 270 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU a 290 " --> pdb=" O ARG a 286 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLN a 291 " --> pdb=" O GLN a 287 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA a 292 " --> pdb=" O ARG a 288 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA a 293 " --> pdb=" O VAL a 289 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASN a 296 " --> pdb=" O ALA a 292 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG a 298 " --> pdb=" O ALA a 294 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N VAL a 299 " --> pdb=" O LYS a 295 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU a 316 " --> pdb=" O HIS a 312 " (cutoff:3.500A) Processing helix chain 'a' and resid 336 through 351 Processing helix chain 'a' and resid 378 through 389 removed outlier: 3.646A pdb=" N TYR a 388 " --> pdb=" O ILE a 384 " (cutoff:3.500A) Processing helix chain 'a' and resid 398 through 414 Proline residue: a 407 - end of helix Processing helix chain 'a' and resid 417 through 433 Processing helix chain 'a' and resid 433 through 440 removed outlier: 3.574A pdb=" N GLN a 440 " --> pdb=" O ARG a 436 " (cutoff:3.500A) Processing helix chain 'a' and resid 444 through 453 Processing helix chain 'a' and resid 453 through 472 removed outlier: 3.905A pdb=" N ASN a 472 " --> pdb=" O GLY a 468 " (cutoff:3.500A) Processing helix chain 'a' and resid 527 through 532 removed outlier: 3.546A pdb=" N ILE a 532 " --> pdb=" O ILE a 529 " (cutoff:3.500A) Processing helix chain 'a' and resid 533 through 534 No H-bonds generated for 'chain 'a' and resid 533 through 534' Processing helix chain 'a' and resid 535 through 562 Processing helix chain 'a' and resid 562 through 570 removed outlier: 4.439A pdb=" N ASN a 566 " --> pdb=" O LEU a 562 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE a 570 " --> pdb=" O ASN a 566 " (cutoff:3.500A) Processing helix chain 'a' and resid 573 through 578 removed outlier: 4.181A pdb=" N PHE a 578 " --> pdb=" O LEU a 574 " (cutoff:3.500A) Processing helix chain 'a' and resid 579 through 605 removed outlier: 4.962A pdb=" N TYR a 593 " --> pdb=" O SER a 589 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU a 594 " --> pdb=" O LEU a 590 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR a 603 " --> pdb=" O PHE a 599 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR a 605 " --> pdb=" O LYS a 601 " (cutoff:3.500A) Processing helix chain 'a' and resid 606 through 613 removed outlier: 5.682A pdb=" N ARG a 611 " --> pdb=" O HIS a 608 " (cutoff:3.500A) Processing helix chain 'a' and resid 617 through 625 Processing helix chain 'a' and resid 639 through 653 removed outlier: 3.512A pdb=" N PHE a 646 " --> pdb=" O GLY a 642 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL a 649 " --> pdb=" O CYS a 645 " (cutoff:3.500A) Processing helix chain 'a' and resid 661 through 674 Processing helix chain 'a' and resid 716 through 739 removed outlier: 4.400A pdb=" N ILE a 734 " --> pdb=" O CYS a 730 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER a 735 " --> pdb=" O LEU a 731 " (cutoff:3.500A) Processing helix chain 'a' and resid 740 through 762 removed outlier: 4.211A pdb=" N TRP a 744 " --> pdb=" O TYR a 740 " (cutoff:3.500A) Processing helix chain 'a' and resid 769 through 791 removed outlier: 4.165A pdb=" N LEU a 775 " --> pdb=" O LEU a 771 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY a 776 " --> pdb=" O ALA a 772 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N PHE a 779 " --> pdb=" O LEU a 775 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA a 782 " --> pdb=" O PHE a 778 " (cutoff:3.500A) Processing helix chain 'a' and resid 793 through 817 removed outlier: 3.744A pdb=" N GLN a 813 " --> pdb=" O TRP a 809 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN a 814 " --> pdb=" O VAL a 810 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE a 816 " --> pdb=" O PHE a 812 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 23 Processing helix chain 'e' and resid 23 through 28 Processing helix chain 'e' and resid 33 through 59 removed outlier: 4.106A pdb=" N GLN e 59 " --> pdb=" O ALA e 55 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 78 Processing helix chain 'f' and resid 8 through 36 removed outlier: 4.255A pdb=" N ILE f 24 " --> pdb=" O ALA f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 44 Processing helix chain 'f' and resid 59 through 90 removed outlier: 3.725A pdb=" N ASN f 90 " --> pdb=" O GLN f 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 29 removed outlier: 4.005A pdb=" N PHE b 29 " --> pdb=" O CYS b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 35 Processing helix chain 'b' and resid 36 through 44 removed outlier: 4.141A pdb=" N THR b 44 " --> pdb=" O PHE b 40 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 81 removed outlier: 3.676A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL b 81 " --> pdb=" O ILE b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 86 through 91 Processing helix chain 'b' and resid 91 through 114 removed outlier: 3.898A pdb=" N MET b 107 " --> pdb=" O TYR b 103 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 169 removed outlier: 3.690A pdb=" N GLY b 161 " --> pdb=" O ILE b 157 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N LEU b 164 " --> pdb=" O SER b 160 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ALA b 167 " --> pdb=" O ALA b 163 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN b 169 " --> pdb=" O ALA b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 176 removed outlier: 4.437A pdb=" N VAL b 174 " --> pdb=" O SER b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 177 through 200 removed outlier: 3.726A pdb=" N ARG b 200 " --> pdb=" O LEU b 196 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 48 removed outlier: 4.227A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA g 43 " --> pdb=" O THR g 39 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL g 46 " --> pdb=" O ALA g 42 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N MET g 47 " --> pdb=" O ALA g 43 " (cutoff:3.500A) Processing helix chain 'g' and resid 53 through 55 No H-bonds generated for 'chain 'g' and resid 53 through 55' Processing helix chain 'g' and resid 56 through 62 Processing helix chain 'g' and resid 63 through 79 Processing helix chain 'g' and resid 88 through 121 Processing helix chain 'g' and resid 124 through 126 No H-bonds generated for 'chain 'g' and resid 124 through 126' Processing helix chain 'g' and resid 127 through 155 removed outlier: 3.579A pdb=" N ALA g 138 " --> pdb=" O ILE g 134 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL g 148 " --> pdb=" O TYR g 144 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS g 155 " --> pdb=" O ILE g 151 " (cutoff:3.500A) Processing helix chain 'h' and resid 11 through 46 removed outlier: 4.444A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL h 16 " --> pdb=" O SER h 12 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL h 46 " --> pdb=" O ALA h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 51 through 63 Proline residue: h 58 - end of helix removed outlier: 3.893A pdb=" N GLY h 63 " --> pdb=" O VAL h 59 " (cutoff:3.500A) Processing helix chain 'h' and resid 63 through 80 Processing helix chain 'h' and resid 88 through 122 removed outlier: 3.689A pdb=" N PHE h 108 " --> pdb=" O LEU h 104 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA h 109 " --> pdb=" O ALA h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 126 through 139 removed outlier: 4.632A pdb=" N GLY h 130 " --> pdb=" O ARG h 126 " (cutoff:3.500A) Processing helix chain 'h' and resid 139 through 154 Processing helix chain 'i' and resid 13 through 45 Processing helix chain 'i' and resid 46 through 47 No H-bonds generated for 'chain 'i' and resid 46 through 47' Processing helix chain 'i' and resid 48 through 50 No H-bonds generated for 'chain 'i' and resid 48 through 50' Processing helix chain 'i' and resid 51 through 62 removed outlier: 4.535A pdb=" N ILE i 57 " --> pdb=" O MET i 53 " (cutoff:3.500A) Proline residue: i 58 - end of helix Processing helix chain 'i' and resid 63 through 80 Processing helix chain 'i' and resid 87 through 121 removed outlier: 4.120A pdb=" N LEU i 91 " --> pdb=" O TYR i 87 " (cutoff:3.500A) Processing helix chain 'i' and resid 122 through 123 No H-bonds generated for 'chain 'i' and resid 122 through 123' Processing helix chain 'i' and resid 124 through 125 No H-bonds generated for 'chain 'i' and resid 124 through 125' Processing helix chain 'i' and resid 126 through 155 removed outlier: 4.416A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) Processing helix chain 'j' and resid 12 through 48 removed outlier: 3.743A pdb=" N MET j 23 " --> pdb=" O ALA j 19 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 62 Processing helix chain 'j' and resid 63 through 80 Processing helix chain 'j' and resid 88 through 122 Processing helix chain 'j' and resid 124 through 126 No H-bonds generated for 'chain 'j' and resid 124 through 126' Processing helix chain 'j' and resid 127 through 139 Processing helix chain 'j' and resid 139 through 155 removed outlier: 4.064A pdb=" N LEU j 143 " --> pdb=" O GLU j 139 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 43 removed outlier: 3.787A pdb=" N THR k 39 " --> pdb=" O ALA k 35 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE k 41 " --> pdb=" O SER k 37 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA k 42 " --> pdb=" O GLY k 38 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA k 43 " --> pdb=" O THR k 39 " (cutoff:3.500A) Processing helix chain 'k' and resid 48 through 55 removed outlier: 3.935A pdb=" N LEU k 51 " --> pdb=" O ARG k 48 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE k 52 " --> pdb=" O PRO k 49 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N MET k 53 " --> pdb=" O GLU k 50 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER k 55 " --> pdb=" O ILE k 52 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 80 Processing helix chain 'k' and resid 88 through 121 removed outlier: 3.695A pdb=" N ALA k 116 " --> pdb=" O ILE k 112 " (cutoff:3.500A) Processing helix chain 'k' and resid 124 through 126 No H-bonds generated for 'chain 'k' and resid 124 through 126' Processing helix chain 'k' and resid 127 through 155 removed outlier: 3.636A pdb=" N VAL k 140 " --> pdb=" O ILE k 136 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU k 141 " --> pdb=" O PHE k 137 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLY k 142 " --> pdb=" O ALA k 138 " (cutoff:3.500A) Processing helix chain 'l' and resid 11 through 43 removed outlier: 4.080A pdb=" N GLY l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 79 removed outlier: 4.885A pdb=" N GLY l 63 " --> pdb=" O VAL l 59 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE l 64 " --> pdb=" O VAL l 60 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE l 65 " --> pdb=" O MET l 61 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA l 66 " --> pdb=" O ALA l 62 " (cutoff:3.500A) Processing helix chain 'l' and resid 88 through 120 removed outlier: 4.232A pdb=" N VAL l 118 " --> pdb=" O GLY l 114 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 126 No H-bonds generated for 'chain 'l' and resid 124 through 126' Processing helix chain 'l' and resid 127 through 152 removed outlier: 3.672A pdb=" N GLY l 145 " --> pdb=" O LEU l 141 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU l 146 " --> pdb=" O GLY l 142 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU l 152 " --> pdb=" O VAL l 148 " (cutoff:3.500A) Processing helix chain 'm' and resid 11 through 45 Processing helix chain 'm' and resid 46 through 47 No H-bonds generated for 'chain 'm' and resid 46 through 47' Processing helix chain 'm' and resid 48 through 50 No H-bonds generated for 'chain 'm' and resid 48 through 50' Processing helix chain 'm' and resid 51 through 56 Processing helix chain 'm' and resid 58 through 80 removed outlier: 4.465A pdb=" N ILE m 65 " --> pdb=" O MET m 61 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA m 66 " --> pdb=" O ALA m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 86 through 120 removed outlier: 4.328A pdb=" N PHE m 90 " --> pdb=" O LEU m 86 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY m 120 " --> pdb=" O ALA m 116 " (cutoff:3.500A) Processing helix chain 'm' and resid 127 through 154 removed outlier: 4.428A pdb=" N MET m 131 " --> pdb=" O LEU m 127 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR m 154 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 45 Processing helix chain 'n' and resid 53 through 55 No H-bonds generated for 'chain 'n' and resid 53 through 55' Processing helix chain 'n' and resid 56 through 80 removed outlier: 4.075A pdb=" N ALA n 62 " --> pdb=" O PRO n 58 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY n 63 " --> pdb=" O VAL n 59 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE n 64 " --> pdb=" O VAL n 60 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE n 65 " --> pdb=" O MET n 61 " (cutoff:3.500A) Processing helix chain 'n' and resid 88 through 122 Processing helix chain 'n' and resid 123 through 126 removed outlier: 6.915A pdb=" N ARG n 126 " --> pdb=" O GLN n 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 123 through 126' Processing helix chain 'n' and resid 127 through 154 removed outlier: 3.607A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 46 removed outlier: 4.630A pdb=" N VAL o 46 " --> pdb=" O ALA o 42 " (cutoff:3.500A) Processing helix chain 'o' and resid 56 through 80 removed outlier: 3.705A pdb=" N ILE o 65 " --> pdb=" O MET o 61 " (cutoff:3.500A) Processing helix chain 'o' and resid 88 through 122 removed outlier: 3.804A pdb=" N ALA o 109 " --> pdb=" O ALA o 105 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA o 122 " --> pdb=" O VAL o 118 " (cutoff:3.500A) Processing helix chain 'o' and resid 123 through 126 removed outlier: 6.543A pdb=" N ARG o 126 " --> pdb=" O GLN o 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 123 through 126' Processing helix chain 'o' and resid 127 through 155 removed outlier: 4.096A pdb=" N ILE o 132 " --> pdb=" O PHE o 128 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU o 133 " --> pdb=" O VAL o 129 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ILE o 134 " --> pdb=" O GLY o 130 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU o 135 " --> pdb=" O MET o 131 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY o 145 " --> pdb=" O LEU o 141 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 23 Processing helix chain 'X' and resid 44 through 58 Processing helix chain 'X' and resid 68 through 74 removed outlier: 3.550A pdb=" N VAL X 74 " --> pdb=" O ILE X 70 " (cutoff:3.500A) Processing helix chain 'X' and resid 74 through 80 Processing helix chain 'X' and resid 103 through 109 Processing helix chain 'd' and resid 8 through 24 removed outlier: 5.474A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU d 16 " --> pdb=" O ASP d 12 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU d 19 " --> pdb=" O TYR d 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 27 No H-bonds generated for 'chain 'd' and resid 25 through 27' Processing helix chain 'd' and resid 29 through 37 removed outlier: 3.867A pdb=" N ASN d 35 " --> pdb=" O ALA d 31 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 51 Processing helix chain 'd' and resid 67 through 87 Processing helix chain 'd' and resid 90 through 113 removed outlier: 4.155A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 119 Processing helix chain 'd' and resid 121 through 126 removed outlier: 3.802A pdb=" N LEU d 125 " --> pdb=" O SER d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 134 Processing helix chain 'd' and resid 146 through 158 removed outlier: 4.256A pdb=" N ASP d 157 " --> pdb=" O ALA d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 165 Processing helix chain 'd' and resid 169 through 174 removed outlier: 3.660A pdb=" N ASP d 174 " --> pdb=" O GLU d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 177 through 200 Processing helix chain 'd' and resid 202 through 228 Proline residue: d 210 - end of helix Processing helix chain 'd' and resid 233 through 241 Processing helix chain 'd' and resid 251 through 258 removed outlier: 3.658A pdb=" N ARG d 257 " --> pdb=" O ALA d 253 " (cutoff:3.500A) Processing helix chain 'd' and resid 260 through 269 Processing helix chain 'd' and resid 271 through 281 removed outlier: 4.171A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 308 removed outlier: 4.094A pdb=" N ASN d 308 " --> pdb=" O LEU d 304 " (cutoff:3.500A) Processing helix chain 'd' and resid 311 through 315 removed outlier: 3.769A pdb=" N VAL d 314 " --> pdb=" O HIS d 311 " (cutoff:3.500A) Processing helix chain 'd' and resid 316 through 339 Processing helix chain 'c' and resid 278 through 283 removed outlier: 3.673A pdb=" N THR c 283 " --> pdb=" O THR c 280 " (cutoff:3.500A) Processing helix chain 'c' and resid 419 through 441 removed outlier: 3.882A pdb=" N PHE c 428 " --> pdb=" O LEU c 424 " (cutoff:3.500A) Processing helix chain 'p' and resid 300 through 330 removed outlier: 4.119A pdb=" N SER p 304 " --> pdb=" O ASN p 300 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL p 305 " --> pdb=" O LEU p 301 " (cutoff:3.500A) Processing helix chain '1' and resid 105 through 114 Processing helix chain '1' and resid 255 through 266 removed outlier: 4.000A pdb=" N ILE 1 259 " --> pdb=" O GLY 1 255 " (cutoff:3.500A) Processing helix chain '1' and resid 280 through 291 removed outlier: 3.856A pdb=" N MET 1 284 " --> pdb=" O ARG 1 280 " (cutoff:3.500A) Processing helix chain '1' and resid 321 through 339 removed outlier: 3.523A pdb=" N ILE 1 327 " --> pdb=" O ARG 1 323 " (cutoff:3.500A) Processing helix chain '1' and resid 350 through 365 removed outlier: 3.933A pdb=" N TRP 1 354 " --> pdb=" O SER 1 350 " (cutoff:3.500A) Processing helix chain '1' and resid 377 through 388 removed outlier: 3.823A pdb=" N ARG 1 388 " --> pdb=" O SER 1 384 " (cutoff:3.500A) Processing helix chain '1' and resid 419 through 427 removed outlier: 3.943A pdb=" N GLY 1 427 " --> pdb=" O SER 1 423 " (cutoff:3.500A) Processing helix chain '1' and resid 436 through 443 Processing helix chain '1' and resid 461 through 467 Processing helix chain '1' and resid 471 through 497 removed outlier: 4.200A pdb=" N LEU 1 475 " --> pdb=" O GLU 1 471 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU 1 491 " --> pdb=" O GLU 1 487 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE 1 492 " --> pdb=" O ASP 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 502 through 519 Processing helix chain '1' and resid 533 through 560 removed outlier: 3.878A pdb=" N THR 1 537 " --> pdb=" O PRO 1 533 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N GLN 1 560 " --> pdb=" O GLU 1 556 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 584 removed outlier: 6.903A pdb=" N GLU 1 576 " --> pdb=" O GLU 1 572 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N ILE 1 577 " --> pdb=" O HIS 1 573 " (cutoff:3.500A) Processing helix chain '1' and resid 593 through 616 Processing helix chain '0' and resid 106 through 114 Processing helix chain '0' and resid 255 through 267 Processing helix chain '0' and resid 280 through 294 removed outlier: 3.643A pdb=" N MET 0 284 " --> pdb=" O ARG 0 280 " (cutoff:3.500A) Proline residue: 0 292 - end of helix Processing helix chain '0' and resid 319 through 340 removed outlier: 3.723A pdb=" N ARG 0 323 " --> pdb=" O PRO 0 319 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ILE 0 327 " --> pdb=" O ARG 0 323 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N TYR 0 328 " --> pdb=" O GLU 0 324 " (cutoff:3.500A) Processing helix chain '0' and resid 350 through 365 removed outlier: 3.720A pdb=" N TRP 0 354 " --> pdb=" O SER 0 350 " (cutoff:3.500A) Processing helix chain '0' and resid 377 through 387 Processing helix chain '0' and resid 412 through 416 removed outlier: 3.781A pdb=" N ASP 0 416 " --> pdb=" O PRO 0 413 " (cutoff:3.500A) Processing helix chain '0' and resid 419 through 427 Processing helix chain '0' and resid 436 through 442 Processing helix chain '0' and resid 457 through 469 removed outlier: 4.025A pdb=" N GLU 0 463 " --> pdb=" O ARG 0 459 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TYR 0 464 " --> pdb=" O ALA 0 460 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS 0 467 " --> pdb=" O GLU 0 463 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N HIS 0 468 " --> pdb=" O TYR 0 464 " (cutoff:3.500A) Processing helix chain '0' and resid 471 through 496 removed outlier: 4.042A pdb=" N LEU 0 475 " --> pdb=" O GLU 0 471 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU 0 491 " --> pdb=" O GLU 0 487 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE 0 492 " --> pdb=" O ASP 0 488 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL 0 496 " --> pdb=" O ILE 0 492 " (cutoff:3.500A) Processing helix chain '0' and resid 502 through 519 Processing helix chain '0' and resid 533 through 561 removed outlier: 3.602A pdb=" N THR 0 558 " --> pdb=" O ALA 0 554 " (cutoff:3.500A) Processing helix chain '0' and resid 566 through 583 removed outlier: 3.878A pdb=" N ILE 0 570 " --> pdb=" O THR 0 566 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N GLU 0 576 " --> pdb=" O GLU 0 572 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE 0 577 " --> pdb=" O HIS 0 573 " (cutoff:3.500A) Processing helix chain '0' and resid 584 through 587 Processing helix chain '0' and resid 593 through 616 Processing helix chain '2' and resid 105 through 114 Processing helix chain '2' and resid 256 through 266 removed outlier: 3.571A pdb=" N SER 2 260 " --> pdb=" O LYS 2 256 " (cutoff:3.500A) Processing helix chain '2' and resid 280 through 294 removed outlier: 3.768A pdb=" N MET 2 284 " --> pdb=" O ARG 2 280 " (cutoff:3.500A) Proline residue: 2 292 - end of helix Processing helix chain '2' and resid 304 through 309 Processing helix chain '2' and resid 319 through 339 removed outlier: 4.670A pdb=" N ILE 2 327 " --> pdb=" O ARG 2 323 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TYR 2 328 " --> pdb=" O GLU 2 324 " (cutoff:3.500A) Processing helix chain '2' and resid 350 through 364 removed outlier: 3.996A pdb=" N ARG 2 364 " --> pdb=" O GLU 2 360 " (cutoff:3.500A) Processing helix chain '2' and resid 377 through 387 Processing helix chain '2' and resid 419 through 427 Processing helix chain '2' and resid 436 through 442 Processing helix chain '2' and resid 457 through 469 removed outlier: 4.342A pdb=" N GLU 2 463 " --> pdb=" O ARG 2 459 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR 2 464 " --> pdb=" O ALA 2 460 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS 2 468 " --> pdb=" O TYR 2 464 " (cutoff:3.500A) Processing helix chain '2' and resid 471 through 497 removed outlier: 3.503A pdb=" N LEU 2 475 " --> pdb=" O GLU 2 471 " (cutoff:3.500A) Processing helix chain '2' and resid 502 through 519 removed outlier: 4.107A pdb=" N THR 2 508 " --> pdb=" O THR 2 504 " (cutoff:3.500A) Processing helix chain '2' and resid 533 through 559 Processing helix chain '2' and resid 566 through 574 Processing helix chain '2' and resid 574 through 583 Processing helix chain '2' and resid 593 through 616 Processing helix chain '3' and resid 124 through 128 removed outlier: 3.548A pdb=" N LEU 3 128 " --> pdb=" O GLU 3 125 " (cutoff:3.500A) Processing helix chain '3' and resid 198 through 209 removed outlier: 3.936A pdb=" N ILE 3 202 " --> pdb=" O PRO 3 198 " (cutoff:3.500A) Processing helix chain '3' and resid 237 through 251 removed outlier: 3.507A pdb=" N ALA 3 241 " --> pdb=" O ASN 3 237 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASN 3 251 " --> pdb=" O ASP 3 247 " (cutoff:3.500A) Processing helix chain '3' and resid 252 through 255 removed outlier: 3.952A pdb=" N ASP 3 255 " --> pdb=" O GLY 3 252 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 252 through 255' Processing helix chain '3' and resid 267 through 272 Processing helix chain '3' and resid 273 through 288 Processing helix chain '3' and resid 299 through 314 removed outlier: 3.588A pdb=" N TYR 3 303 " --> pdb=" O ASP 3 299 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG 3 314 " --> pdb=" O VAL 3 310 " (cutoff:3.500A) Processing helix chain '3' and resid 319 through 323 removed outlier: 4.157A pdb=" N GLY 3 322 " --> pdb=" O GLY 3 319 " (cutoff:3.500A) Processing helix chain '3' and resid 324 through 325 No H-bonds generated for 'chain '3' and resid 324 through 325' Processing helix chain '3' and resid 326 through 336 Processing helix chain '3' and resid 357 through 360 Processing helix chain '3' and resid 363 through 373 Processing helix chain '3' and resid 380 through 386 removed outlier: 3.607A pdb=" N HIS 3 384 " --> pdb=" O ASP 3 380 " (cutoff:3.500A) Processing helix chain '3' and resid 401 through 406 Processing helix chain '3' and resid 414 through 440 removed outlier: 3.838A pdb=" N VAL 3 438 " --> pdb=" O ALA 3 434 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY 3 440 " --> pdb=" O LYS 3 436 " (cutoff:3.500A) Processing helix chain '3' and resid 441 through 444 Processing helix chain '3' and resid 445 through 462 Processing helix chain '3' and resid 472 through 485 Processing helix chain '3' and resid 486 through 487 No H-bonds generated for 'chain '3' and resid 486 through 487' Processing helix chain '3' and resid 488 through 492 Processing helix chain '3' and resid 496 through 504 removed outlier: 3.640A pdb=" N LEU 3 500 " --> pdb=" O PRO 3 496 " (cutoff:3.500A) Processing helix chain '4' and resid 124 through 128 removed outlier: 3.518A pdb=" N MET 4 127 " --> pdb=" O SER 4 124 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU 4 128 " --> pdb=" O GLU 4 125 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 124 through 128' Processing helix chain '4' and resid 159 through 161 No H-bonds generated for 'chain '4' and resid 159 through 161' Processing helix chain '4' and resid 198 through 209 Processing helix chain '4' and resid 218 through 223 Processing helix chain '4' and resid 237 through 251 removed outlier: 3.773A pdb=" N ASN 4 251 " --> pdb=" O ASP 4 247 " (cutoff:3.500A) Processing helix chain '4' and resid 252 through 255 removed outlier: 4.198A pdb=" N ASP 4 255 " --> pdb=" O GLY 4 252 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 252 through 255' Processing helix chain '4' and resid 268 through 272 removed outlier: 3.813A pdb=" N ILE 4 272 " --> pdb=" O ILE 4 269 " (cutoff:3.500A) Processing helix chain '4' and resid 273 through 290 Processing helix chain '4' and resid 299 through 314 removed outlier: 3.633A pdb=" N TYR 4 303 " --> pdb=" O ASP 4 299 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG 4 314 " --> pdb=" O VAL 4 310 " (cutoff:3.500A) Processing helix chain '4' and resid 319 through 323 removed outlier: 3.691A pdb=" N GLY 4 322 " --> pdb=" O GLY 4 319 " (cutoff:3.500A) Processing helix chain '4' and resid 324 through 325 No H-bonds generated for 'chain '4' and resid 324 through 325' Processing helix chain '4' and resid 326 through 336 Processing helix chain '4' and resid 357 through 360 Processing helix chain '4' and resid 363 through 373 Processing helix chain '4' and resid 381 through 386 Processing helix chain '4' and resid 401 through 406 removed outlier: 3.541A pdb=" N ILE 4 406 " --> pdb=" O MET 4 402 " (cutoff:3.500A) Processing helix chain '4' and resid 415 through 440 Processing helix chain '4' and resid 441 through 444 Processing helix chain '4' and resid 445 through 462 Processing helix chain '4' and resid 472 through 485 Processing helix chain '4' and resid 496 through 504 Processing helix chain '5' and resid 124 through 128 Processing helix chain '5' and resid 159 through 163 Processing helix chain '5' and resid 174 through 179 Processing helix chain '5' and resid 198 through 209 Processing helix chain '5' and resid 213 through 217 Processing helix chain '5' and resid 219 through 224 removed outlier: 3.529A pdb=" N GLU 5 224 " --> pdb=" O ASP 5 221 " (cutoff:3.500A) Processing helix chain '5' and resid 237 through 252 Processing helix chain '5' and resid 253 through 255 No H-bonds generated for 'chain '5' and resid 253 through 255' Processing helix chain '5' and resid 267 through 272 Processing helix chain '5' and resid 273 through 288 Processing helix chain '5' and resid 299 through 315 removed outlier: 3.816A pdb=" N TYR 5 303 " --> pdb=" O ASP 5 299 " (cutoff:3.500A) Processing helix chain '5' and resid 319 through 323 Processing helix chain '5' and resid 324 through 325 No H-bonds generated for 'chain '5' and resid 324 through 325' Processing helix chain '5' and resid 326 through 336 Processing helix chain '5' and resid 357 through 360 Processing helix chain '5' and resid 363 through 371 Processing helix chain '5' and resid 380 through 386 Processing helix chain '5' and resid 401 through 406 removed outlier: 3.968A pdb=" N ILE 5 406 " --> pdb=" O MET 5 402 " (cutoff:3.500A) Processing helix chain '5' and resid 415 through 439 Processing helix chain '5' and resid 440 through 444 Processing helix chain '5' and resid 445 through 462 Processing helix chain '5' and resid 472 through 485 Processing helix chain '5' and resid 496 through 504 removed outlier: 4.431A pdb=" N GLU 5 502 " --> pdb=" O SER 5 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '7' and resid 92 through 94 Processing sheet with id=AA2, first strand: chain '7' and resid 97 through 99 Processing sheet with id=AA3, first strand: chain '8' and resid 164 through 167 removed outlier: 3.762A pdb=" N ILE 8 183 " --> pdb=" O VAL 8 192 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '9' and resid 131 through 135 removed outlier: 6.795A pdb=" N MET 9 132 " --> pdb=" O GLN 9 166 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '9' and resid 164 through 167 current: chain '9' and resid 190 through 195 WARNING: can't find start of bonding for strands! previous: chain '9' and resid 190 through 195 current: chain '0' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 28 through 32 current: chain '0' and resid 50 through 58 removed outlier: 5.748A pdb=" N ILE 0 54 " --> pdb=" O GLN 0 65 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLN 0 65 " --> pdb=" O ILE 0 54 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG 0 56 " --> pdb=" O THR 0 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '0' and resid 61 through 66 current: chain '4' and resid 81 through 90 removed outlier: 5.889A pdb=" N VAL 4 86 " --> pdb=" O GLN 4 97 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN 4 97 " --> pdb=" O VAL 4 86 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU 4 88 " --> pdb=" O VAL 4 95 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '4' and resid 93 through 98 current: chain '5' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 57 through 60 current: chain '5' and resid 81 through 90 removed outlier: 5.975A pdb=" N VAL 5 86 " --> pdb=" O GLN 5 97 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLN 5 97 " --> pdb=" O VAL 5 86 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU 5 88 " --> pdb=" O VAL 5 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Q' and resid 164 through 165 Processing sheet with id=AA6, first strand: chain '6' and resid 317 through 321 removed outlier: 4.057A pdb=" N LEU 6 6 " --> pdb=" O TYR 6 372 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR 6 372 " --> pdb=" O LEU 6 6 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER 6 8 " --> pdb=" O VAL 6 370 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL 6 370 " --> pdb=" O SER 6 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '6' and resid 182 through 185 Processing sheet with id=AA8, first strand: chain 'a' and resid 10 through 18 Processing sheet with id=AA9, first strand: chain 'a' and resid 205 through 209 removed outlier: 4.115A pdb=" N LYS a 224 " --> pdb=" O ILE a 209 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'X' and resid 36 through 38 removed outlier: 6.891A pdb=" N VAL X 10 " --> pdb=" O LEU X 37 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN X 67 " --> pdb=" O ILE X 11 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE X 64 " --> pdb=" O LEU X 89 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE X 91 " --> pdb=" O ILE X 64 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE X 66 " --> pdb=" O ILE X 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 262 through 264 removed outlier: 3.862A pdb=" N GLN c 396 " --> pdb=" O LEU c 262 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE c 363 " --> pdb=" O ILE c 395 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'c' and resid 276 through 277 removed outlier: 3.602A pdb=" N VAL c 270 " --> pdb=" O LYS c 277 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN c 267 " --> pdb=" O HIS c 391 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS c 391 " --> pdb=" O ASN c 267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 300 through 302 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 300 through 302 current: chain 'c' and resid 314 through 326 removed outlier: 3.607A pdb=" N ARG c 331 " --> pdb=" O TYR c 326 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 331 through 334 current: chain 'c' and resid 346 through 350 Processing sheet with id=AB5, first strand: chain '1' and resid 19 through 25 removed outlier: 3.748A pdb=" N TYR 1 20 " --> pdb=" O CYS 1 32 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR 1 30 " --> pdb=" O HIS 1 22 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL 1 24 " --> pdb=" O VAL 1 28 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL 1 28 " --> pdb=" O VAL 1 24 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 28 through 32 current: chain '1' and resid 50 through 58 removed outlier: 6.735A pdb=" N THR 1 63 " --> pdb=" O ILE 1 55 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU 1 57 " --> pdb=" O MET 1 61 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N MET 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 61 through 66 current: chain '2' and resid 50 through 58 removed outlier: 5.966A pdb=" N ILE 2 54 " --> pdb=" O GLN 2 65 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N GLN 2 65 " --> pdb=" O ILE 2 54 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ARG 2 56 " --> pdb=" O THR 2 63 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '2' and resid 61 through 66 current: chain '3' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 57 through 60 current: chain '3' and resid 81 through 90 removed outlier: 6.923A pdb=" N VAL 3 95 " --> pdb=" O LEU 3 87 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N VAL 3 89 " --> pdb=" O LYS 3 93 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LYS 3 93 " --> pdb=" O VAL 3 89 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '1' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 98 through 99 current: chain '1' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 309 through 312 current: chain '1' and resid 401 through 408 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 401 through 408 current: chain '1' and resid 454 through 455 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '1' and resid 164 through 167 removed outlier: 3.785A pdb=" N GLY 1 154 " --> pdb=" O ILE 1 166 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY 1 183 " --> pdb=" O PHE 1 135 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '1' and resid 146 through 147 removed outlier: 3.586A pdb=" N GLY 1 174 " --> pdb=" O ILE 1 147 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU 1 195 " --> pdb=" O SER 1 175 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR 1 177 " --> pdb=" O GLU 1 193 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLU 1 193 " --> pdb=" O THR 1 177 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU 1 192 " --> pdb=" O PHE 1 203 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU 1 194 " --> pdb=" O GLU 1 201 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '1' and resid 295 through 296 Processing sheet with id=AC1, first strand: chain '0' and resid 87 through 90 removed outlier: 3.814A pdb=" N TRP 0 209 " --> pdb=" O VAL 0 88 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '0' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 98 through 99 current: chain '0' and resid 309 through 312 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 309 through 312 current: chain '0' and resid 401 through 408 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 401 through 408 current: chain '0' and resid 454 through 455 No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain '0' and resid 164 through 167 removed outlier: 3.751A pdb=" N ILE 0 166 " --> pdb=" O GLY 0 154 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY 0 154 " --> pdb=" O ILE 0 166 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY 0 183 " --> pdb=" O PHE 0 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '0' and resid 146 through 147 removed outlier: 6.547A pdb=" N GLU 0 193 " --> pdb=" O THR 0 177 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU 0 192 " --> pdb=" O PHE 0 203 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '0' and resid 295 through 297 Processing sheet with id=AC6, first strand: chain '2' and resid 87 through 90 removed outlier: 3.532A pdb=" N TRP 2 209 " --> pdb=" O VAL 2 88 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '2' and resid 98 through 99 Processing sheet with id=AC8, first strand: chain '2' and resid 164 through 167 removed outlier: 3.867A pdb=" N GLY 2 154 " --> pdb=" O ILE 2 166 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '2' and resid 146 through 147 removed outlier: 6.558A pdb=" N GLU 2 193 " --> pdb=" O THR 2 177 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE 2 179 " --> pdb=" O VAL 2 191 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL 2 191 " --> pdb=" O ILE 2 179 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '2' and resid 219 through 221 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 219 through 221 current: chain '2' and resid 343 through 348 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 343 through 348 current: chain '2' and resid 401 through 410 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 401 through 410 current: chain '2' and resid 454 through 455 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain '2' and resid 226 through 227 removed outlier: 4.591A pdb=" N CYS 2 240 " --> pdb=" O LEU 2 227 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '3' and resid 120 through 123 Processing sheet with id=AD4, first strand: chain '3' and resid 131 through 132 removed outlier: 3.644A pdb=" N LEU 3 297 " --> pdb=" O ILE 3 351 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '3' and resid 192 through 193 Processing sheet with id=AD6, first strand: chain '3' and resid 375 through 376 Processing sheet with id=AD7, first strand: chain '4' and resid 120 through 123 Processing sheet with id=AD8, first strand: chain '4' and resid 131 through 132 removed outlier: 6.528A pdb=" N ALA 4 228 " --> pdb=" O LEU 4 294 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N ILE 4 296 " --> pdb=" O ALA 4 228 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL 4 230 " --> pdb=" O ILE 4 296 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL 4 293 " --> pdb=" O THR 4 349 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '4' and resid 163 through 164 removed outlier: 4.475A pdb=" N ARG 4 340 " --> pdb=" O ILE 4 164 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '4' and resid 170 through 171 Processing sheet with id=AE2, first strand: chain '4' and resid 191 through 193 Processing sheet with id=AE3, first strand: chain '4' and resid 375 through 376 Processing sheet with id=AE4, first strand: chain '5' and resid 120 through 123 removed outlier: 3.525A pdb=" N LEU 5 151 " --> pdb=" O THR 5 121 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP 5 149 " --> pdb=" O VAL 5 123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '5' and resid 131 through 132 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 131 through 132 current: chain '5' and resid 257 through 260 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 257 through 260 current: chain '5' and resid 347 through 355 No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain '5' and resid 376 through 379 removed outlier: 3.599A pdb=" N GLN 5 376 " --> pdb=" O LEU 5 398 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR 5 378 " --> pdb=" O PRO 5 396 " (cutoff:3.500A) 3841 hydrogen bonds defined for protein. 11238 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 23.98 Time building geometry restraints manager: 15.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16138 1.33 - 1.46: 13354 1.46 - 1.58: 36596 1.58 - 1.70: 0 1.70 - 1.82: 685 Bond restraints: 66773 Sorted by residual: bond pdb=" CA ASN 5 345 " pdb=" CB ASN 5 345 " ideal model delta sigma weight residual 1.526 1.576 -0.050 1.76e-02 3.23e+03 7.96e+00 bond pdb=" N TYR R 114 " pdb=" CA TYR R 114 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.24e-02 6.50e+03 7.77e+00 bond pdb=" N PHE i 13 " pdb=" CA PHE i 13 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.28e-02 6.10e+03 7.72e+00 bond pdb=" CA SER 2 316 " pdb=" CB SER 2 316 " ideal model delta sigma weight residual 1.530 1.484 0.046 1.69e-02 3.50e+03 7.49e+00 bond pdb=" N SER c 369 " pdb=" CA SER c 369 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.26e-02 6.30e+03 7.28e+00 ... (remaining 66768 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 88624 2.44 - 4.88: 1468 4.88 - 7.31: 121 7.31 - 9.75: 27 9.75 - 12.19: 4 Bond angle restraints: 90244 Sorted by residual: angle pdb=" N LYS c 373 " pdb=" CA LYS c 373 " pdb=" C LYS c 373 " ideal model delta sigma weight residual 110.80 98.61 12.19 2.13e+00 2.20e-01 3.27e+01 angle pdb=" N PHE 6 291 " pdb=" CA PHE 6 291 " pdb=" CB PHE 6 291 " ideal model delta sigma weight residual 110.28 118.08 -7.80 1.55e+00 4.16e-01 2.53e+01 angle pdb=" N MET l 17 " pdb=" CA MET l 17 " pdb=" CB MET l 17 " ideal model delta sigma weight residual 110.16 117.18 -7.02 1.48e+00 4.57e-01 2.25e+01 angle pdb=" N ILE 1 102 " pdb=" CA ILE 1 102 " pdb=" C ILE 1 102 " ideal model delta sigma weight residual 111.91 108.03 3.88 8.90e-01 1.26e+00 1.90e+01 angle pdb=" C LYS c 373 " pdb=" CA LYS c 373 " pdb=" CB LYS c 373 " ideal model delta sigma weight residual 110.42 118.88 -8.46 1.99e+00 2.53e-01 1.81e+01 ... (remaining 90239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 37183 17.90 - 35.80: 2589 35.80 - 53.70: 447 53.70 - 71.60: 83 71.60 - 89.50: 47 Dihedral angle restraints: 40349 sinusoidal: 16177 harmonic: 24172 Sorted by residual: dihedral pdb=" CA GLY 0 19 " pdb=" C GLY 0 19 " pdb=" N TYR 0 20 " pdb=" CA TYR 0 20 " ideal model delta harmonic sigma weight residual 180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU a 87 " pdb=" C GLU a 87 " pdb=" N VAL a 88 " pdb=" CA VAL a 88 " ideal model delta harmonic sigma weight residual -180.00 -151.74 -28.26 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA SER i 11 " pdb=" C SER i 11 " pdb=" N SER i 12 " pdb=" CA SER i 12 " ideal model delta harmonic sigma weight residual -180.00 -152.74 -27.26 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 40346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 8950 0.066 - 0.133: 1187 0.133 - 0.199: 83 0.199 - 0.265: 6 0.265 - 0.332: 4 Chirality restraints: 10230 Sorted by residual: chirality pdb=" CB VAL 0 79 " pdb=" CA VAL 0 79 " pdb=" CG1 VAL 0 79 " pdb=" CG2 VAL 0 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.75e+00 chirality pdb=" CA TYR i 10 " pdb=" N TYR i 10 " pdb=" C TYR i 10 " pdb=" CB TYR i 10 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB ILE 4 351 " pdb=" CA ILE 4 351 " pdb=" CG1 ILE 4 351 " pdb=" CG2 ILE 4 351 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 10227 not shown) Planarity restraints: 11573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR i 10 " -0.047 2.00e-02 2.50e+03 2.80e-02 1.57e+01 pdb=" CG TYR i 10 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR i 10 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TYR i 10 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR i 10 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR i 10 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR i 10 " -0.009 2.00e-02 2.50e+03 pdb=" OH TYR i 10 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL a 88 " -0.063 5.00e-02 4.00e+02 9.67e-02 1.49e+01 pdb=" N PRO a 89 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO a 89 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO a 89 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE a 381 " -0.012 2.00e-02 2.50e+03 2.70e-02 1.28e+01 pdb=" CG PHE a 381 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE a 381 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 PHE a 381 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE a 381 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE a 381 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE a 381 " -0.000 2.00e-02 2.50e+03 ... (remaining 11570 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 9514 2.76 - 3.29: 68471 3.29 - 3.83: 107415 3.83 - 4.36: 125296 4.36 - 4.90: 209156 Nonbonded interactions: 519852 Sorted by model distance: nonbonded pdb=" O LEU 2 237 " pdb=" NH2 ARG 2 476 " model vdw 2.222 3.120 nonbonded pdb=" O ASN 1 317 " pdb=" ND2 ASN 1 317 " model vdw 2.285 3.120 nonbonded pdb=" O THR 2 315 " pdb=" C SER 2 316 " model vdw 2.371 3.270 nonbonded pdb=" O ASN 1 123 " pdb=" OD1 ASN 1 123 " model vdw 2.433 3.040 nonbonded pdb=" O ALA T 76 " pdb=" OE1 GLN T 80 " model vdw 2.433 3.040 ... (remaining 519847 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 '0' and resid 17 through 616) selection = chain '1' selection = chain '2' } ncs_group { reference = chain '3' selection = (chain '4' and (resid 39 through 216 or resid 224 through 506)) selection = (chain '5' and (resid 39 through 216 or resid 224 through 506)) } ncs_group { reference = chain '8' selection = chain '9' selection = chain 'Q' } ncs_group { reference = chain 'R' selection = chain 'T' selection = chain 'V' } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.640 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: 0.070 Extract box with map and model: 2.160 Check model and map are aligned: 0.390 Set scattering table: 0.480 Process input model: 112.220 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.450 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:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5414 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 66773 Z= 0.280 Angle : 0.773 12.188 90244 Z= 0.429 Chirality : 0.044 0.332 10230 Planarity : 0.006 0.128 11573 Dihedral : 12.897 89.497 24839 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.17 % Favored : 94.74 % Rotamer: Outliers : 0.04 % Allowed : 0.26 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -0.37 (0.09), residues: 8314 helix: 0.92 (0.07), residues: 4593 sheet: -1.97 (0.19), residues: 632 loop : -1.63 (0.11), residues: 3089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP U 218 HIS 0.016 0.001 HIS U 443 PHE 0.057 0.002 PHE a 381 TYR 0.057 0.002 TYR i 10 ARG 0.018 0.001 ARG g 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1796 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1793 time to evaluate : 5.710 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: 7 30 ARG cc_start: 0.7542 (tmm160) cc_final: 0.6816 (tpt90) REVERT: 7 45 ARG cc_start: 0.6861 (mtt90) cc_final: 0.5173 (ptt-90) REVERT: 7 58 MET cc_start: 0.6075 (mmp) cc_final: 0.5417 (mmt) REVERT: 7 173 GLU cc_start: 0.4633 (mt-10) cc_final: 0.4300 (mt-10) REVERT: 7 203 LYS cc_start: 0.7682 (tptp) cc_final: 0.7467 (tptp) REVERT: 8 57 TYR cc_start: 0.6481 (m-10) cc_final: 0.6077 (m-10) REVERT: 8 58 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7273 (tm-30) REVERT: 8 120 VAL cc_start: 0.9015 (t) cc_final: 0.8701 (m) REVERT: 8 164 ASP cc_start: 0.6901 (t0) cc_final: 0.6643 (p0) REVERT: 8 177 ILE cc_start: 0.7660 (mp) cc_final: 0.7005 (mp) REVERT: 8 187 ASP cc_start: 0.7869 (m-30) cc_final: 0.7603 (m-30) REVERT: 9 155 TYR cc_start: 0.7576 (t80) cc_final: 0.7241 (t80) REVERT: 9 202 LEU cc_start: 0.8523 (tp) cc_final: 0.8243 (mm) REVERT: Q 16 MET cc_start: 0.2314 (mmt) cc_final: 0.1668 (mmt) REVERT: Q 36 GLU cc_start: 0.5729 (tp30) cc_final: 0.5032 (mp0) REVERT: Q 60 LYS cc_start: 0.7261 (ptmt) cc_final: 0.6746 (ptmm) REVERT: Q 70 ILE cc_start: 0.8010 (mm) cc_final: 0.7794 (mm) REVERT: Q 77 ASN cc_start: 0.8298 (m-40) cc_final: 0.8012 (t0) REVERT: Q 96 ASN cc_start: 0.7711 (m110) cc_final: 0.7425 (m110) REVERT: Q 120 VAL cc_start: 0.8824 (m) cc_final: 0.8542 (p) REVERT: Q 131 ARG cc_start: 0.7760 (mmt-90) cc_final: 0.7176 (mmm160) REVERT: Q 135 ARG cc_start: 0.8382 (ttt180) cc_final: 0.7647 (mtp180) REVERT: Q 162 ASP cc_start: 0.6762 (p0) cc_final: 0.6317 (p0) REVERT: Q 200 LEU cc_start: 0.8738 (tp) cc_final: 0.8534 (pp) REVERT: R 63 MET cc_start: 0.4241 (mtt) cc_final: 0.3545 (tpt) REVERT: R 113 ASN cc_start: 0.8503 (m-40) cc_final: 0.8223 (m-40) REVERT: T 24 ASP cc_start: 0.5679 (t0) cc_final: 0.5211 (p0) REVERT: V 47 TYR cc_start: 0.5853 (m-10) cc_final: 0.5290 (m-10) REVERT: V 56 GLN cc_start: 0.5422 (mm-40) cc_final: 0.4805 (pt0) REVERT: 6 172 LYS cc_start: 0.4395 (pttt) cc_final: 0.2633 (ttmt) REVERT: 6 257 GLU cc_start: 0.5886 (tm-30) cc_final: 0.5653 (tm-30) REVERT: 6 366 TYR cc_start: 0.3020 (m-80) cc_final: 0.1848 (m-80) REVERT: 6 370 VAL cc_start: 0.6080 (t) cc_final: 0.5688 (m) REVERT: U 162 ASN cc_start: 0.5963 (m-40) cc_final: 0.4097 (t0) REVERT: U 392 LYS cc_start: 0.4174 (mttt) cc_final: 0.2398 (tptp) REVERT: a 95 ILE cc_start: 0.4732 (mt) cc_final: 0.4524 (mt) REVERT: a 230 PHE cc_start: 0.3199 (t80) cc_final: 0.2844 (t80) REVERT: a 231 PHE cc_start: 0.4231 (m-80) cc_final: 0.2880 (m-80) REVERT: a 237 LYS cc_start: 0.5826 (mttt) cc_final: 0.5373 (mptt) REVERT: a 248 ARG cc_start: 0.3246 (mmp-170) cc_final: 0.2411 (ttm-80) REVERT: a 261 ARG cc_start: 0.4500 (ttt180) cc_final: 0.3829 (ttp80) REVERT: a 277 MET cc_start: 0.7487 (mmp) cc_final: 0.6162 (tpt) REVERT: a 385 VAL cc_start: 0.5989 (t) cc_final: 0.5671 (t) REVERT: a 446 MET cc_start: 0.5549 (mtm) cc_final: 0.5063 (mtm) REVERT: a 491 MET cc_start: 0.4345 (ttm) cc_final: 0.4109 (ttm) REVERT: a 545 MET cc_start: 0.4996 (tmm) cc_final: 0.2567 (tpt) REVERT: a 571 LYS cc_start: 0.7760 (pttt) cc_final: 0.7476 (pptt) REVERT: a 807 LEU cc_start: 0.8278 (tp) cc_final: 0.7854 (tp) REVERT: e 61 ASN cc_start: 0.3122 (m-40) cc_final: 0.2868 (m-40) REVERT: b 107 MET cc_start: 0.4285 (mmp) cc_final: 0.3577 (mmp) REVERT: b 178 ILE cc_start: 0.2890 (tt) cc_final: 0.2667 (tt) REVERT: g 44 MET cc_start: 0.6033 (mmp) cc_final: 0.5725 (mmm) REVERT: g 64 ILE cc_start: 0.6618 (mt) cc_final: 0.6395 (mt) REVERT: h 25 PHE cc_start: 0.7918 (m-10) cc_final: 0.7666 (m-80) REVERT: h 118 VAL cc_start: 0.7451 (t) cc_final: 0.7194 (t) REVERT: h 131 MET cc_start: 0.7334 (ttp) cc_final: 0.6646 (ttp) REVERT: h 137 PHE cc_start: 0.5004 (t80) cc_final: 0.4656 (t80) REVERT: h 139 GLU cc_start: 0.5445 (tp30) cc_final: 0.5174 (tp30) REVERT: h 150 LEU cc_start: 0.8062 (mt) cc_final: 0.7858 (mt) REVERT: i 14 PHE cc_start: 0.7414 (m-80) cc_final: 0.6744 (m-80) REVERT: j 23 MET cc_start: 0.7808 (mmm) cc_final: 0.6699 (tpt) REVERT: j 87 TYR cc_start: 0.4806 (m-80) cc_final: 0.3897 (t80) REVERT: k 28 MET cc_start: 0.5099 (mmt) cc_final: 0.3957 (ptm) REVERT: l 137 PHE cc_start: 0.3188 (t80) cc_final: 0.2912 (t80) REVERT: m 17 MET cc_start: 0.6483 (mtm) cc_final: 0.6268 (mtm) REVERT: m 48 ARG cc_start: 0.4808 (mmt180) cc_final: 0.4176 (mmm-85) REVERT: m 52 ILE cc_start: 0.6577 (mt) cc_final: 0.6175 (mt) REVERT: m 86 LEU cc_start: 0.1251 (tp) cc_final: 0.0731 (tp) REVERT: m 123 GLN cc_start: 0.6398 (tt0) cc_final: 0.6156 (tt0) REVERT: o 76 ILE cc_start: 0.7028 (mt) cc_final: 0.6823 (mt) REVERT: X 25 ILE cc_start: 0.8261 (pt) cc_final: 0.7780 (mp) REVERT: c 255 ASN cc_start: -0.0086 (m-40) cc_final: -0.1120 (t0) REVERT: c 298 ASP cc_start: 0.3647 (t0) cc_final: 0.3023 (t0) REVERT: c 377 LEU cc_start: 0.5290 (tp) cc_final: 0.3605 (mt) REVERT: c 429 MET cc_start: 0.4489 (mmm) cc_final: 0.3653 (mmp) REVERT: p 331 MET cc_start: 0.2663 (mmm) cc_final: 0.1924 (mmm) REVERT: 1 22 HIS cc_start: 0.7973 (t-90) cc_final: 0.7691 (t-90) REVERT: 1 194 LEU cc_start: 0.8197 (pt) cc_final: 0.7766 (pt) REVERT: 1 228 LEU cc_start: 0.8314 (tp) cc_final: 0.7581 (mm) REVERT: 1 324 GLU cc_start: 0.8113 (tt0) cc_final: 0.7579 (tt0) REVERT: 1 340 MET cc_start: 0.7694 (mtp) cc_final: 0.7374 (mtp) REVERT: 1 447 SER cc_start: 0.8104 (p) cc_final: 0.7782 (t) REVERT: 1 550 MET cc_start: 0.7779 (tpt) cc_final: 0.6126 (mtt) REVERT: 1 596 LYS cc_start: 0.7855 (tttt) cc_final: 0.7630 (tmtt) REVERT: 0 55 ILE cc_start: 0.9019 (pt) cc_final: 0.8798 (pt) REVERT: 0 77 ASP cc_start: 0.7983 (m-30) cc_final: 0.7596 (m-30) REVERT: 0 135 PHE cc_start: 0.8008 (t80) cc_final: 0.7456 (t80) REVERT: 0 232 ARG cc_start: 0.6900 (ptp-170) cc_final: 0.4805 (ttp80) REVERT: 0 438 LYS cc_start: 0.5530 (mtmt) cc_final: 0.4970 (pttp) REVERT: 2 77 ASP cc_start: 0.7613 (m-30) cc_final: 0.7343 (m-30) REVERT: 2 95 MET cc_start: 0.7736 (mmm) cc_final: 0.7534 (mmm) REVERT: 2 162 ILE cc_start: 0.8687 (mt) cc_final: 0.8414 (pt) REVERT: 2 220 LYS cc_start: 0.7415 (mtmm) cc_final: 0.6974 (mtmm) REVERT: 2 266 TYR cc_start: 0.6597 (m-80) cc_final: 0.6213 (m-80) REVERT: 2 317 ASN cc_start: 0.8716 (t0) cc_final: 0.8154 (t0) REVERT: 2 381 ARG cc_start: 0.8509 (mmp80) cc_final: 0.7965 (mmt180) REVERT: 2 462 ASP cc_start: 0.7692 (m-30) cc_final: 0.7491 (m-30) REVERT: 2 465 TYR cc_start: 0.6586 (m-80) cc_final: 0.5829 (m-80) REVERT: 2 530 ARG cc_start: 0.6042 (mtt180) cc_final: 0.4725 (mtm110) REVERT: 2 586 PHE cc_start: 0.6127 (m-80) cc_final: 0.5497 (m-10) REVERT: 3 49 THR cc_start: 0.8960 (m) cc_final: 0.8378 (p) REVERT: 3 127 MET cc_start: 0.8605 (mtp) cc_final: 0.8218 (mtp) REVERT: 3 152 ASP cc_start: 0.8463 (t0) cc_final: 0.8227 (t0) REVERT: 3 234 MET cc_start: 0.8270 (mtt) cc_final: 0.7989 (mmp) REVERT: 3 249 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7117 (tm-30) REVERT: 3 270 GLU cc_start: 0.8595 (tt0) cc_final: 0.8338 (tt0) REVERT: 3 294 LEU cc_start: 0.8958 (tp) cc_final: 0.8747 (tt) REVERT: 3 355 THR cc_start: 0.8772 (m) cc_final: 0.8159 (p) REVERT: 3 369 THR cc_start: 0.8210 (m) cc_final: 0.8007 (m) REVERT: 3 376 GLN cc_start: 0.7944 (pt0) cc_final: 0.7543 (pt0) REVERT: 3 413 LYS cc_start: 0.6483 (tptm) cc_final: 0.6279 (tptm) REVERT: 3 471 ARG cc_start: 0.4550 (ttm170) cc_final: 0.4159 (ttm170) REVERT: 3 497 GLN cc_start: 0.7796 (mt0) cc_final: 0.6824 (mm110) REVERT: 4 39 TYR cc_start: 0.7080 (p90) cc_final: 0.6249 (p90) REVERT: 4 118 ILE cc_start: 0.8496 (mm) cc_final: 0.8262 (mm) REVERT: 4 127 MET cc_start: 0.8444 (mmm) cc_final: 0.8074 (mmt) REVERT: 4 161 GLN cc_start: 0.8876 (tp40) cc_final: 0.8469 (tp-100) REVERT: 4 162 CYS cc_start: 0.8897 (m) cc_final: 0.7312 (t) REVERT: 4 170 ILE cc_start: 0.8479 (mt) cc_final: 0.8012 (pt) REVERT: 4 244 PHE cc_start: 0.8121 (m-80) cc_final: 0.7551 (m-80) REVERT: 4 300 MET cc_start: 0.8734 (mmm) cc_final: 0.8280 (mmm) REVERT: 4 308 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7328 (ttm170) REVERT: 4 318 PRO cc_start: 0.8931 (Cg_endo) cc_final: 0.8595 (Cg_exo) REVERT: 4 378 TYR cc_start: 0.6261 (t80) cc_final: 0.5770 (t80) REVERT: 4 390 PRO cc_start: 0.8855 (Cg_endo) cc_final: 0.8607 (Cg_exo) REVERT: 4 421 GLN cc_start: 0.8312 (tp40) cc_final: 0.7636 (tp-100) REVERT: 4 455 LEU cc_start: 0.7375 (mt) cc_final: 0.7078 (tt) REVERT: 5 70 GLU cc_start: 0.8252 (tt0) cc_final: 0.8008 (tt0) REVERT: 5 112 CYS cc_start: 0.8922 (t) cc_final: 0.8645 (t) REVERT: 5 127 MET cc_start: 0.8376 (mmt) cc_final: 0.7672 (mmt) REVERT: 5 162 CYS cc_start: 0.7988 (m) cc_final: 0.7067 (p) REVERT: 5 168 GLU cc_start: 0.7658 (pm20) cc_final: 0.7388 (pm20) REVERT: 5 197 LEU cc_start: 0.8475 (mt) cc_final: 0.8177 (mt) REVERT: 5 200 ASN cc_start: 0.8167 (m-40) cc_final: 0.7824 (m-40) REVERT: 5 234 MET cc_start: 0.7871 (ptp) cc_final: 0.7662 (ptp) REVERT: 5 238 MET cc_start: 0.8760 (tmm) cc_final: 0.8535 (tmm) REVERT: 5 244 PHE cc_start: 0.8697 (m-80) cc_final: 0.7844 (m-80) REVERT: 5 269 ILE cc_start: 0.9200 (mp) cc_final: 0.8888 (mp) REVERT: 5 321 ARG cc_start: 0.7992 (tpp80) cc_final: 0.7498 (tpp80) REVERT: 5 327 MET cc_start: 0.7606 (ttt) cc_final: 0.7234 (tmm) REVERT: 5 465 GLN cc_start: 0.8050 (tt0) cc_final: 0.7849 (tt0) REVERT: 5 475 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8388 (mt-10) outliers start: 3 outliers final: 1 residues processed: 1794 average time/residue: 0.6459 time to fit residues: 1987.9549 Evaluate side-chains 1472 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1471 time to evaluate : 5.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 700 optimal weight: 1.9990 chunk 629 optimal weight: 9.9990 chunk 349 optimal weight: 4.9990 chunk 214 optimal weight: 8.9990 chunk 424 optimal weight: 5.9990 chunk 336 optimal weight: 20.0000 chunk 650 optimal weight: 0.5980 chunk 251 optimal weight: 0.7980 chunk 395 optimal weight: 10.0000 chunk 484 optimal weight: 8.9990 chunk 753 optimal weight: 0.0980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN 7 85 GLN 8 63 GLN 9 78 GLN 6 336 HIS U 196 GLN U 240 GLN U 440 HIS a 363 GLN a 575 ASN a 721 HIS ** a 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 92 GLN ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 183 ASN 1 164 HIS 1 261 GLN 0 522 GLN 2 317 ASN 2 468 HIS 3 350 GLN ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 433 GLN ** 4 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 363 HIS 4 415 HIS ** 4 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 73 HIS ** 5 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 ASN 5 384 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.211294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.180522 restraints weight = 136925.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.177142 restraints weight = 171670.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.178948 restraints weight = 136306.953| |-----------------------------------------------------------------------------| r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 66773 Z= 0.221 Angle : 0.593 10.802 90244 Z= 0.316 Chirality : 0.042 0.299 10230 Planarity : 0.005 0.082 11573 Dihedral : 4.811 89.603 9103 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.34 % Favored : 95.62 % Rotamer: Outliers : 0.09 % Allowed : 3.23 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.18 (0.09), residues: 8314 helix: 1.36 (0.07), residues: 4648 sheet: -1.49 (0.20), residues: 631 loop : -1.48 (0.11), residues: 3035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP 6 282 HIS 0.014 0.001 HIS X 33 PHE 0.028 0.002 PHE 9 18 TYR 0.054 0.002 TYR m 68 ARG 0.009 0.001 ARG 2 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1641 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1635 time to evaluate : 5.669 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: 7 58 MET cc_start: 0.5923 (mmp) cc_final: 0.5530 (mmt) REVERT: 8 120 VAL cc_start: 0.9306 (t) cc_final: 0.8909 (m) REVERT: 8 184 TYR cc_start: 0.7796 (m-80) cc_final: 0.6991 (m-80) REVERT: 9 104 LYS cc_start: 0.8781 (mttt) cc_final: 0.8271 (mtpt) REVERT: 9 155 TYR cc_start: 0.6753 (t80) cc_final: 0.6518 (t80) REVERT: 9 187 ASP cc_start: 0.7516 (p0) cc_final: 0.7217 (p0) REVERT: Q 54 MET cc_start: 0.7666 (mmm) cc_final: 0.7078 (mmm) REVERT: Q 120 VAL cc_start: 0.8627 (m) cc_final: 0.8403 (p) REVERT: Q 135 ARG cc_start: 0.8352 (ttt180) cc_final: 0.7744 (mtp180) REVERT: Q 155 TYR cc_start: 0.8398 (t80) cc_final: 0.8188 (t80) REVERT: Q 193 SER cc_start: 0.8468 (t) cc_final: 0.8111 (t) REVERT: T 24 ASP cc_start: 0.5023 (t0) cc_final: 0.4577 (p0) REVERT: T 113 ASN cc_start: 0.8280 (m110) cc_final: 0.7749 (m110) REVERT: V 44 VAL cc_start: 0.6475 (t) cc_final: 0.6260 (t) REVERT: V 105 GLU cc_start: 0.7066 (tm-30) cc_final: 0.6661 (tm-30) REVERT: 6 61 LEU cc_start: 0.8143 (pp) cc_final: 0.7714 (mt) REVERT: 6 172 LYS cc_start: 0.4149 (pttt) cc_final: 0.2758 (ttmt) REVERT: 6 366 TYR cc_start: 0.3198 (m-80) cc_final: 0.2109 (m-80) REVERT: U 156 MET cc_start: 0.4330 (ptm) cc_final: 0.4082 (ptm) REVERT: U 162 ASN cc_start: 0.4885 (m-40) cc_final: 0.4016 (t0) REVERT: U 325 LYS cc_start: 0.3706 (mmpt) cc_final: 0.2128 (tptt) REVERT: U 392 LYS cc_start: 0.4244 (mttt) cc_final: 0.2577 (tptp) REVERT: a 10 MET cc_start: 0.5603 (mmp) cc_final: 0.5094 (mmm) REVERT: a 88 VAL cc_start: 0.5126 (t) cc_final: 0.4375 (p) REVERT: a 237 LYS cc_start: 0.5402 (mttt) cc_final: 0.5024 (mmtm) REVERT: a 242 LYS cc_start: 0.1815 (tttt) cc_final: 0.1556 (tttt) REVERT: a 261 ARG cc_start: 0.4777 (ttt180) cc_final: 0.4076 (ttp80) REVERT: a 277 MET cc_start: 0.7445 (mmp) cc_final: 0.6115 (tpt) REVERT: a 374 THR cc_start: 0.6127 (p) cc_final: 0.5877 (p) REVERT: a 382 GLN cc_start: 0.7215 (mp10) cc_final: 0.6974 (mm-40) REVERT: a 430 MET cc_start: 0.4161 (ttt) cc_final: 0.3782 (tpp) REVERT: a 446 MET cc_start: 0.5023 (mtm) cc_final: 0.4531 (mtm) REVERT: e 61 ASN cc_start: 0.3766 (m-40) cc_final: 0.3342 (m-40) REVERT: b 203 MET cc_start: 0.3036 (ppp) cc_final: 0.2693 (ptm) REVERT: g 44 MET cc_start: 0.5857 (mmp) cc_final: 0.5603 (mmm) REVERT: g 148 VAL cc_start: 0.5312 (t) cc_final: 0.5093 (t) REVERT: h 25 PHE cc_start: 0.7655 (m-10) cc_final: 0.7333 (m-80) REVERT: h 55 SER cc_start: 0.8042 (m) cc_final: 0.7746 (t) REVERT: h 72 VAL cc_start: 0.7726 (t) cc_final: 0.7281 (p) REVERT: h 108 PHE cc_start: 0.6093 (m-80) cc_final: 0.5768 (m-80) REVERT: h 118 VAL cc_start: 0.7847 (t) cc_final: 0.7456 (t) REVERT: h 128 PHE cc_start: 0.5705 (t80) cc_final: 0.5308 (m-80) REVERT: h 131 MET cc_start: 0.7460 (ttp) cc_final: 0.6785 (ttp) REVERT: h 137 PHE cc_start: 0.5164 (t80) cc_final: 0.4768 (t80) REVERT: h 146 LEU cc_start: 0.5888 (mm) cc_final: 0.5531 (mm) REVERT: i 36 LYS cc_start: 0.6184 (tppt) cc_final: 0.5973 (tppt) REVERT: j 6 ASN cc_start: 0.6334 (m110) cc_final: 0.6056 (m110) REVERT: j 23 MET cc_start: 0.7790 (mmm) cc_final: 0.7021 (tpt) REVERT: j 24 VAL cc_start: 0.7669 (p) cc_final: 0.7374 (p) REVERT: j 48 ARG cc_start: 0.6269 (tpt-90) cc_final: 0.5455 (tpm170) REVERT: j 87 TYR cc_start: 0.4753 (m-80) cc_final: 0.3873 (t80) REVERT: k 28 MET cc_start: 0.5019 (mmt) cc_final: 0.3892 (ptm) REVERT: k 76 ILE cc_start: 0.7929 (mt) cc_final: 0.7682 (mt) REVERT: l 17 MET cc_start: 0.6253 (mpp) cc_final: 0.5515 (mmm) REVERT: m 17 MET cc_start: 0.5509 (mtm) cc_final: 0.5269 (mtm) REVERT: m 48 ARG cc_start: 0.5045 (mmt180) cc_final: 0.4269 (mmm-85) REVERT: m 86 LEU cc_start: 0.1129 (tp) cc_final: 0.0806 (tp) REVERT: o 76 ILE cc_start: 0.6714 (mt) cc_final: 0.6439 (mt) REVERT: o 151 ILE cc_start: 0.5237 (mm) cc_final: 0.5023 (mm) REVERT: X 25 ILE cc_start: 0.8139 (pt) cc_final: 0.7781 (mp) REVERT: d 191 GLU cc_start: 0.6775 (pt0) cc_final: 0.6409 (mt-10) REVERT: d 208 MET cc_start: 0.4336 (mtt) cc_final: 0.3669 (mpp) REVERT: d 240 LEU cc_start: 0.6940 (mt) cc_final: 0.6592 (mt) REVERT: d 323 GLU cc_start: 0.8311 (pp20) cc_final: 0.6337 (mm-30) REVERT: c 255 ASN cc_start: -0.1157 (m-40) cc_final: -0.2168 (t0) REVERT: c 363 PHE cc_start: 0.3965 (t80) cc_final: 0.3555 (t80) REVERT: c 377 LEU cc_start: 0.4605 (tp) cc_final: 0.3488 (mt) REVERT: c 429 MET cc_start: 0.5831 (mmm) cc_final: 0.5248 (mmp) REVERT: p 331 MET cc_start: 0.2323 (mmm) cc_final: 0.1886 (mmm) REVERT: 1 228 LEU cc_start: 0.8522 (tp) cc_final: 0.7792 (mm) REVERT: 1 315 THR cc_start: 0.8091 (p) cc_final: 0.7864 (p) REVERT: 1 428 ILE cc_start: 0.8466 (mt) cc_final: 0.8263 (mt) REVERT: 0 20 TYR cc_start: 0.7271 (p90) cc_final: 0.6665 (p90) REVERT: 0 55 ILE cc_start: 0.8581 (pt) cc_final: 0.8150 (pt) REVERT: 0 77 ASP cc_start: 0.8357 (m-30) cc_final: 0.8055 (m-30) REVERT: 0 94 ILE cc_start: 0.8755 (tp) cc_final: 0.8519 (tp) REVERT: 0 232 ARG cc_start: 0.7035 (ptp-170) cc_final: 0.5216 (ttt180) REVERT: 0 438 LYS cc_start: 0.5684 (mtmt) cc_final: 0.5044 (pttp) REVERT: 2 141 LEU cc_start: 0.6624 (tt) cc_final: 0.6331 (mp) REVERT: 2 220 LYS cc_start: 0.6664 (mtmm) cc_final: 0.6404 (mtmm) REVERT: 2 266 TYR cc_start: 0.6780 (m-80) cc_final: 0.6327 (m-80) REVERT: 2 317 ASN cc_start: 0.8561 (t0) cc_final: 0.8165 (t0) REVERT: 2 345 SER cc_start: 0.8648 (t) cc_final: 0.8437 (t) REVERT: 2 381 ARG cc_start: 0.8445 (mmp80) cc_final: 0.7812 (mmt180) REVERT: 2 530 ARG cc_start: 0.5553 (mtt180) cc_final: 0.4334 (mtm110) REVERT: 2 586 PHE cc_start: 0.5624 (m-80) cc_final: 0.4608 (m-10) REVERT: 3 45 LEU cc_start: 0.8888 (tp) cc_final: 0.8673 (tp) REVERT: 3 270 GLU cc_start: 0.8671 (tt0) cc_final: 0.8441 (tt0) REVERT: 3 368 LEU cc_start: 0.9319 (mt) cc_final: 0.9021 (mt) REVERT: 3 413 LYS cc_start: 0.6369 (tptm) cc_final: 0.6111 (tptm) REVERT: 3 483 LEU cc_start: 0.6856 (mt) cc_final: 0.6221 (mt) REVERT: 3 497 GLN cc_start: 0.7601 (mt0) cc_final: 0.6750 (mm110) REVERT: 4 162 CYS cc_start: 0.7737 (m) cc_final: 0.7353 (t) REVERT: 4 200 ASN cc_start: 0.7622 (m-40) cc_final: 0.7384 (m-40) REVERT: 4 202 ILE cc_start: 0.8388 (tt) cc_final: 0.8063 (tt) REVERT: 4 308 ARG cc_start: 0.7626 (ttp-170) cc_final: 0.7248 (ttm170) REVERT: 4 318 PRO cc_start: 0.8927 (Cg_endo) cc_final: 0.8651 (Cg_exo) REVERT: 4 455 LEU cc_start: 0.7376 (mt) cc_final: 0.7036 (tt) REVERT: 4 465 GLN cc_start: 0.6555 (tp-100) cc_final: 0.6301 (tp-100) REVERT: 5 100 GLU cc_start: 0.8369 (mp0) cc_final: 0.7725 (tp30) REVERT: 5 127 MET cc_start: 0.8359 (mmt) cc_final: 0.8033 (mmt) REVERT: 5 162 CYS cc_start: 0.7363 (m) cc_final: 0.6896 (p) REVERT: 5 244 PHE cc_start: 0.8067 (m-80) cc_final: 0.7454 (m-80) REVERT: 5 269 ILE cc_start: 0.9058 (mp) cc_final: 0.8771 (mp) REVERT: 5 365 ILE cc_start: 0.9038 (mt) cc_final: 0.8792 (mt) REVERT: 5 475 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8118 (mt-10) outliers start: 6 outliers final: 0 residues processed: 1638 average time/residue: 0.6166 time to fit residues: 1717.6169 Evaluate side-chains 1393 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1393 time to evaluate : 5.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 145 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 360 optimal weight: 10.0000 chunk 654 optimal weight: 6.9990 chunk 717 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 686 optimal weight: 0.0970 chunk 305 optimal weight: 5.9990 chunk 385 optimal weight: 7.9990 chunk 617 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN ** 8 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 77 ASN ** 9 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 35 GLN ** 6 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 239 HIS 6 336 HIS U 420 HIS ** a 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 722 GLN ** a 752 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN l 92 GLN ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 124 GLN ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 82 GLN ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 ASN d 130 HIS d 183 ASN c 297 ASN c 387 GLN 1 261 GLN ** 0 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 251 ASN 3 350 GLN ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 345 ASN ** 4 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 171 GLN ** 5 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 ASN 5 384 HIS 5 415 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.205856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.176143 restraints weight = 138978.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.173883 restraints weight = 165224.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.174392 restraints weight = 134031.076| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 66773 Z= 0.332 Angle : 0.703 13.260 90244 Z= 0.371 Chirality : 0.045 0.305 10230 Planarity : 0.006 0.081 11573 Dihedral : 5.097 81.378 9103 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 0.17 % Allowed : 4.37 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -0.15 (0.09), residues: 8314 helix: 1.06 (0.07), residues: 4641 sheet: -1.43 (0.20), residues: 647 loop : -1.62 (0.11), residues: 3026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP 6 282 HIS 0.015 0.002 HIS 3 363 PHE 0.030 0.003 PHE 4 284 TYR 0.041 0.003 TYR m 68 ARG 0.010 0.001 ARG 5 471 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1614 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1602 time to evaluate : 5.571 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: 7 58 MET cc_start: 0.6382 (mmp) cc_final: 0.5891 (mmt) REVERT: 8 184 TYR cc_start: 0.7967 (m-80) cc_final: 0.7378 (m-80) REVERT: 9 104 LYS cc_start: 0.8763 (mttt) cc_final: 0.8251 (mtpt) REVERT: 9 155 TYR cc_start: 0.6971 (t80) cc_final: 0.6685 (t80) REVERT: 9 187 ASP cc_start: 0.7766 (p0) cc_final: 0.7406 (p0) REVERT: Q 54 MET cc_start: 0.7631 (mmm) cc_final: 0.7005 (mmm) REVERT: Q 135 ARG cc_start: 0.8345 (ttt180) cc_final: 0.7897 (mtp180) REVERT: T 24 ASP cc_start: 0.5150 (t0) cc_final: 0.4638 (p0) REVERT: V 42 MET cc_start: 0.5584 (mmp) cc_final: 0.4877 (tmm) REVERT: V 44 VAL cc_start: 0.6789 (t) cc_final: 0.6461 (t) REVERT: 6 61 LEU cc_start: 0.8067 (pp) cc_final: 0.7680 (mt) REVERT: 6 172 LYS cc_start: 0.3950 (pttt) cc_final: 0.2822 (mttt) REVERT: 6 296 HIS cc_start: 0.6313 (t70) cc_final: 0.6005 (t-90) REVERT: 6 366 TYR cc_start: 0.3478 (m-80) cc_final: 0.2292 (m-80) REVERT: U 156 MET cc_start: 0.4482 (ptm) cc_final: 0.3990 (ptm) REVERT: U 162 ASN cc_start: 0.4871 (m-40) cc_final: 0.4279 (t0) REVERT: U 208 MET cc_start: 0.4175 (tpp) cc_final: 0.3354 (tpp) REVERT: U 325 LYS cc_start: 0.3476 (mmpt) cc_final: 0.3031 (mmtt) REVERT: U 392 LYS cc_start: 0.4117 (mttt) cc_final: 0.2441 (mmmm) REVERT: U 460 MET cc_start: 0.0528 (mmm) cc_final: 0.0292 (mmm) REVERT: a 237 LYS cc_start: 0.5700 (mttt) cc_final: 0.5344 (mptt) REVERT: a 242 LYS cc_start: 0.1866 (tttt) cc_final: 0.1587 (tttt) REVERT: a 261 ARG cc_start: 0.5235 (ttt180) cc_final: 0.4347 (ttp80) REVERT: a 277 MET cc_start: 0.7235 (mmp) cc_final: 0.5816 (tpt) REVERT: a 382 GLN cc_start: 0.7338 (mp10) cc_final: 0.7085 (mm-40) REVERT: a 446 MET cc_start: 0.5103 (mtm) cc_final: 0.4540 (mtm) REVERT: a 491 MET cc_start: 0.4545 (ttm) cc_final: 0.3614 (ttm) REVERT: a 545 MET cc_start: 0.5550 (tmm) cc_final: 0.3808 (tpp) REVERT: a 556 MET cc_start: 0.7492 (ptp) cc_final: 0.6649 (mtp) REVERT: a 640 GLN cc_start: 0.6506 (tt0) cc_final: 0.6303 (tm-30) REVERT: a 741 LEU cc_start: 0.7673 (mm) cc_final: 0.7417 (mm) REVERT: a 742 ARG cc_start: 0.7232 (ptm-80) cc_final: 0.6923 (ptm-80) REVERT: e 61 ASN cc_start: 0.3596 (m-40) cc_final: 0.3231 (m-40) REVERT: g 108 PHE cc_start: 0.7290 (t80) cc_final: 0.7029 (t80) REVERT: h 25 PHE cc_start: 0.7815 (m-10) cc_final: 0.7446 (m-80) REVERT: h 72 VAL cc_start: 0.7888 (t) cc_final: 0.7484 (p) REVERT: h 123 GLN cc_start: 0.6547 (mm-40) cc_final: 0.6154 (tp40) REVERT: h 137 PHE cc_start: 0.5343 (t80) cc_final: 0.4938 (t80) REVERT: h 139 GLU cc_start: 0.5946 (tp30) cc_final: 0.5643 (mm-30) REVERT: h 146 LEU cc_start: 0.5997 (mm) cc_final: 0.5536 (mm) REVERT: h 150 LEU cc_start: 0.8192 (mt) cc_final: 0.7986 (mt) REVERT: i 13 PHE cc_start: 0.6569 (p90) cc_final: 0.5606 (p90) REVERT: i 14 PHE cc_start: 0.7086 (m-80) cc_final: 0.6863 (m-80) REVERT: i 151 ILE cc_start: 0.5277 (pt) cc_final: 0.5047 (pt) REVERT: j 28 MET cc_start: 0.8619 (mmm) cc_final: 0.8332 (mmm) REVERT: j 48 ARG cc_start: 0.6303 (tpt-90) cc_final: 0.5488 (tpm170) REVERT: j 53 MET cc_start: 0.3840 (mmt) cc_final: 0.3414 (mmt) REVERT: j 87 TYR cc_start: 0.4768 (m-80) cc_final: 0.3821 (t80) REVERT: k 28 MET cc_start: 0.5386 (mmt) cc_final: 0.4070 (ptm) REVERT: k 44 MET cc_start: 0.5633 (ttp) cc_final: 0.5355 (tmm) REVERT: k 76 ILE cc_start: 0.7975 (mt) cc_final: 0.7765 (mt) REVERT: l 17 MET cc_start: 0.6174 (mpp) cc_final: 0.5560 (mmt) REVERT: l 25 PHE cc_start: 0.6632 (m-10) cc_final: 0.6103 (m-80) REVERT: m 48 ARG cc_start: 0.4024 (mmt180) cc_final: 0.3591 (mmm-85) REVERT: m 84 ILE cc_start: 0.7716 (tp) cc_final: 0.7416 (tt) REVERT: n 53 MET cc_start: 0.6825 (mmp) cc_final: 0.6586 (mmp) REVERT: o 76 ILE cc_start: 0.6964 (mt) cc_final: 0.6755 (mt) REVERT: o 151 ILE cc_start: 0.5369 (mm) cc_final: 0.5104 (mm) REVERT: d 34 LEU cc_start: 0.3558 (mt) cc_final: 0.2832 (mt) REVERT: d 138 MET cc_start: 0.1690 (mmt) cc_final: 0.1450 (mmt) REVERT: d 150 LEU cc_start: 0.5592 (tt) cc_final: 0.5341 (pp) REVERT: d 191 GLU cc_start: 0.6646 (pt0) cc_final: 0.6392 (mt-10) REVERT: d 208 MET cc_start: 0.3941 (mtt) cc_final: 0.3467 (mtm) REVERT: d 240 LEU cc_start: 0.6607 (mt) cc_final: 0.6403 (mt) REVERT: d 323 GLU cc_start: 0.8292 (pp20) cc_final: 0.6229 (mm-30) REVERT: c 268 PHE cc_start: 0.3520 (t80) cc_final: 0.2765 (t80) REVERT: c 429 MET cc_start: 0.5908 (mmm) cc_final: 0.5667 (mmp) REVERT: p 331 MET cc_start: 0.2545 (mmm) cc_final: -0.1370 (ttt) REVERT: 1 228 LEU cc_start: 0.8636 (tp) cc_final: 0.8137 (tp) REVERT: 1 428 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.8104 (mt) REVERT: 1 548 TYR cc_start: 0.5316 (t80) cc_final: 0.4135 (t80) REVERT: 1 550 MET cc_start: 0.6972 (tpt) cc_final: 0.6360 (mtt) REVERT: 0 20 TYR cc_start: 0.7616 (p90) cc_final: 0.7020 (p90) REVERT: 0 39 MET cc_start: 0.8033 (mmm) cc_final: 0.7786 (mtm) REVERT: 0 77 ASP cc_start: 0.8059 (m-30) cc_final: 0.7724 (m-30) REVERT: 0 89 GLU cc_start: 0.7524 (tt0) cc_final: 0.6934 (tt0) REVERT: 0 127 LEU cc_start: 0.8811 (mt) cc_final: 0.8591 (mm) REVERT: 0 298 VAL cc_start: 0.7664 (t) cc_final: 0.7425 (p) REVERT: 0 476 ARG cc_start: 0.7638 (ttp80) cc_final: 0.7119 (ttm-80) REVERT: 0 522 GLN cc_start: 0.4869 (pt0) cc_final: 0.4250 (mp10) REVERT: 2 141 LEU cc_start: 0.6429 (tt) cc_final: 0.6076 (mp) REVERT: 2 317 ASN cc_start: 0.8671 (t0) cc_final: 0.7982 (t0) REVERT: 2 345 SER cc_start: 0.8708 (t) cc_final: 0.8466 (t) REVERT: 2 381 ARG cc_start: 0.8412 (mmp80) cc_final: 0.7852 (mmt180) REVERT: 2 530 ARG cc_start: 0.5397 (mtt180) cc_final: 0.4081 (mtm110) REVERT: 2 586 PHE cc_start: 0.5869 (m-80) cc_final: 0.4888 (m-80) REVERT: 3 106 ASP cc_start: 0.8649 (t0) cc_final: 0.8369 (t0) REVERT: 3 127 MET cc_start: 0.8632 (mtm) cc_final: 0.8252 (mtp) REVERT: 3 368 LEU cc_start: 0.9297 (mt) cc_final: 0.8990 (mt) REVERT: 3 497 GLN cc_start: 0.7420 (mt0) cc_final: 0.6661 (mm110) REVERT: 4 40 LEU cc_start: 0.8430 (tp) cc_final: 0.8070 (mm) REVERT: 4 70 GLU cc_start: 0.7409 (pt0) cc_final: 0.7130 (pt0) REVERT: 4 162 CYS cc_start: 0.8209 (m) cc_final: 0.7702 (t) REVERT: 4 177 ILE cc_start: 0.8722 (mt) cc_final: 0.8503 (mt) REVERT: 4 201 GLU cc_start: 0.6932 (tm-30) cc_final: 0.6729 (tm-30) REVERT: 4 406 ILE cc_start: 0.8220 (pt) cc_final: 0.7766 (mt) REVERT: 4 455 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6964 (tt) REVERT: 4 484 LEU cc_start: 0.7606 (tt) cc_final: 0.7219 (tt) REVERT: 4 492 LEU cc_start: 0.7566 (mt) cc_final: 0.7119 (mt) REVERT: 5 102 THR cc_start: 0.9171 (p) cc_final: 0.8969 (p) REVERT: 5 112 CYS cc_start: 0.8526 (t) cc_final: 0.8289 (t) REVERT: 5 127 MET cc_start: 0.8257 (mmt) cc_final: 0.7962 (mmt) REVERT: 5 151 LEU cc_start: 0.8755 (mt) cc_final: 0.8516 (mt) REVERT: 5 244 PHE cc_start: 0.8235 (m-80) cc_final: 0.7534 (m-80) REVERT: 5 299 ASP cc_start: 0.7286 (t0) cc_final: 0.6936 (t0) REVERT: 5 321 ARG cc_start: 0.7645 (tpp80) cc_final: 0.7249 (tpp80) REVERT: 5 336 GLU cc_start: 0.7937 (pt0) cc_final: 0.7656 (pt0) REVERT: 5 475 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8236 (mt-10) outliers start: 12 outliers final: 3 residues processed: 1608 average time/residue: 0.6137 time to fit residues: 1671.6386 Evaluate side-chains 1355 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1350 time to evaluate : 6.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 687 optimal weight: 2.9990 chunk 588 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 329 optimal weight: 4.9990 chunk 453 optimal weight: 3.9990 chunk 346 optimal weight: 9.9990 chunk 762 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 605 optimal weight: 0.9990 chunk 416 optimal weight: 10.0000 chunk 726 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN 9 63 GLN ** 9 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 GLN ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 134 ASN 6 336 HIS a 341 GLN a 397 ASN a 535 ASN a 668 HIS a 722 GLN f 57 ASN ** g 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 123 GLN ** X 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 10 ASN ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 ASN d 118 HIS d 130 HIS d 297 HIS c 387 GLN 1 282 ASN ** 0 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 522 GLN 3 209 GLN ** 3 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 205 GLN 5 97 GLN 5 171 GLN ** 5 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 ASN 5 358 ASN 5 384 HIS ** 5 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.207191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.177127 restraints weight = 138373.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.174555 restraints weight = 172588.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.175944 restraints weight = 134941.893| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 66773 Z= 0.244 Angle : 0.621 12.840 90244 Z= 0.327 Chirality : 0.043 0.276 10230 Planarity : 0.005 0.070 11573 Dihedral : 4.941 79.470 9103 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.93 % Favored : 95.02 % Rotamer: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: -0.00 (0.09), residues: 8314 helix: 1.20 (0.07), residues: 4649 sheet: -1.26 (0.21), residues: 629 loop : -1.61 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP 6 282 HIS 0.023 0.001 HIS 6 336 PHE 0.048 0.002 PHE l 90 TYR 0.039 0.002 TYR m 68 ARG 0.011 0.001 ARG 2 364 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1601 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1595 time to evaluate : 5.700 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: 7 58 MET cc_start: 0.6382 (mmp) cc_final: 0.5893 (mmt) REVERT: 7 62 MET cc_start: 0.4446 (ptm) cc_final: 0.4194 (ptm) REVERT: 7 180 ILE cc_start: 0.7380 (mt) cc_final: 0.7089 (mt) REVERT: 7 193 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6648 (mm-30) REVERT: 8 184 TYR cc_start: 0.7880 (m-80) cc_final: 0.7357 (m-80) REVERT: 9 104 LYS cc_start: 0.8829 (mttt) cc_final: 0.8377 (mtpt) REVERT: 9 155 TYR cc_start: 0.6864 (t80) cc_final: 0.6566 (t80) REVERT: 9 187 ASP cc_start: 0.7846 (p0) cc_final: 0.7563 (p0) REVERT: Q 135 ARG cc_start: 0.8571 (ttt180) cc_final: 0.7783 (mtp180) REVERT: R 113 ASN cc_start: 0.8086 (m-40) cc_final: 0.7843 (m-40) REVERT: T 24 ASP cc_start: 0.5176 (t0) cc_final: 0.4708 (p0) REVERT: T 113 ASN cc_start: 0.8218 (m110) cc_final: 0.7933 (m110) REVERT: V 42 MET cc_start: 0.5904 (mmp) cc_final: 0.5038 (tmm) REVERT: V 44 VAL cc_start: 0.6941 (t) cc_final: 0.6512 (t) REVERT: V 105 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6751 (tm-30) REVERT: 6 61 LEU cc_start: 0.8048 (pp) cc_final: 0.7705 (mt) REVERT: 6 74 GLN cc_start: 0.7706 (tm-30) cc_final: 0.7284 (tm-30) REVERT: 6 172 LYS cc_start: 0.3923 (pttt) cc_final: 0.2885 (mttt) REVERT: 6 242 ARG cc_start: 0.5140 (ptp-170) cc_final: 0.3725 (mmm-85) REVERT: 6 296 HIS cc_start: 0.6391 (t70) cc_final: 0.6156 (t-90) REVERT: 6 366 TYR cc_start: 0.3527 (m-80) cc_final: 0.2012 (m-80) REVERT: U 155 LEU cc_start: 0.4853 (tp) cc_final: 0.4635 (tp) REVERT: U 156 MET cc_start: 0.4485 (ptm) cc_final: 0.4254 (ptm) REVERT: U 162 ASN cc_start: 0.4664 (m-40) cc_final: 0.4102 (t0) REVERT: U 208 MET cc_start: 0.4201 (tpp) cc_final: 0.3575 (tpp) REVERT: U 325 LYS cc_start: 0.3427 (mmpt) cc_final: 0.3078 (mmtt) REVERT: U 392 LYS cc_start: 0.3650 (mttt) cc_final: 0.2161 (mmmm) REVERT: U 460 MET cc_start: -0.0083 (mmm) cc_final: -0.0499 (mmm) REVERT: a 237 LYS cc_start: 0.5514 (mttt) cc_final: 0.5170 (mptt) REVERT: a 261 ARG cc_start: 0.5286 (ttt180) cc_final: 0.4414 (ttp80) REVERT: a 277 MET cc_start: 0.7099 (mmp) cc_final: 0.5707 (tpt) REVERT: a 372 ASN cc_start: 0.7309 (t0) cc_final: 0.6820 (t0) REVERT: a 446 MET cc_start: 0.5158 (mtm) cc_final: 0.4594 (mtm) REVERT: a 491 MET cc_start: 0.5056 (ttm) cc_final: 0.4200 (ttm) REVERT: a 556 MET cc_start: 0.7356 (ptp) cc_final: 0.6535 (mtp) REVERT: a 742 ARG cc_start: 0.7161 (ptm-80) cc_final: 0.6756 (ptm-80) REVERT: e 61 ASN cc_start: 0.3669 (m-40) cc_final: 0.3320 (m-40) REVERT: g 108 PHE cc_start: 0.7274 (t80) cc_final: 0.6986 (t80) REVERT: g 148 VAL cc_start: 0.4861 (t) cc_final: 0.4657 (t) REVERT: h 25 PHE cc_start: 0.7828 (m-10) cc_final: 0.7486 (m-80) REVERT: h 72 VAL cc_start: 0.7765 (t) cc_final: 0.7350 (p) REVERT: h 123 GLN cc_start: 0.6361 (mm-40) cc_final: 0.6077 (tp40) REVERT: h 137 PHE cc_start: 0.5765 (t80) cc_final: 0.5340 (t80) REVERT: h 139 GLU cc_start: 0.5784 (tp30) cc_final: 0.5311 (mm-30) REVERT: h 146 LEU cc_start: 0.5673 (mm) cc_final: 0.5366 (mm) REVERT: h 150 LEU cc_start: 0.8237 (mt) cc_final: 0.8027 (mt) REVERT: i 13 PHE cc_start: 0.6602 (p90) cc_final: 0.5619 (p90) REVERT: i 14 PHE cc_start: 0.7004 (m-80) cc_final: 0.6784 (m-80) REVERT: i 86 LEU cc_start: 0.5590 (tp) cc_final: 0.5145 (tp) REVERT: i 151 ILE cc_start: 0.5000 (pt) cc_final: 0.4778 (pt) REVERT: j 28 MET cc_start: 0.8683 (mmm) cc_final: 0.8299 (mmm) REVERT: j 48 ARG cc_start: 0.6169 (tpt-90) cc_final: 0.5275 (tpm170) REVERT: j 87 TYR cc_start: 0.4717 (m-80) cc_final: 0.3967 (t80) REVERT: k 28 MET cc_start: 0.5338 (mmt) cc_final: 0.4107 (ptm) REVERT: k 44 MET cc_start: 0.5765 (ttp) cc_final: 0.5399 (tmm) REVERT: l 17 MET cc_start: 0.5950 (mpp) cc_final: 0.5582 (mmt) REVERT: m 17 MET cc_start: 0.5705 (mtm) cc_final: 0.5485 (mtm) REVERT: m 48 ARG cc_start: 0.3897 (mmt180) cc_final: 0.3426 (mmm-85) REVERT: m 84 ILE cc_start: 0.7748 (tp) cc_final: 0.7418 (tt) REVERT: n 53 MET cc_start: 0.6733 (mmp) cc_final: 0.6528 (mmp) REVERT: o 151 ILE cc_start: 0.5413 (mm) cc_final: 0.5144 (mm) REVERT: d 138 MET cc_start: 0.1324 (mmt) cc_final: 0.1102 (mmt) REVERT: d 191 GLU cc_start: 0.6471 (pt0) cc_final: 0.6147 (mt-10) REVERT: d 208 MET cc_start: 0.3905 (mtt) cc_final: 0.3285 (mpp) REVERT: d 240 LEU cc_start: 0.6590 (mt) cc_final: 0.6314 (mt) REVERT: d 323 GLU cc_start: 0.8214 (pp20) cc_final: 0.6228 (mm-30) REVERT: c 268 PHE cc_start: 0.3608 (t80) cc_final: 0.2855 (t80) REVERT: c 363 PHE cc_start: 0.4010 (t80) cc_final: 0.3536 (t80) REVERT: c 377 LEU cc_start: 0.4838 (tp) cc_final: 0.4199 (mt) REVERT: c 387 GLN cc_start: 0.7512 (tt0) cc_final: 0.7198 (tt0) REVERT: p 331 MET cc_start: 0.2581 (mmm) cc_final: -0.1439 (ttt) REVERT: 1 22 HIS cc_start: 0.7907 (t-90) cc_final: 0.7680 (t-90) REVERT: 1 228 LEU cc_start: 0.8685 (tp) cc_final: 0.8174 (tp) REVERT: 1 378 LEU cc_start: 0.8519 (mt) cc_final: 0.8264 (mt) REVERT: 1 548 TYR cc_start: 0.5330 (t80) cc_final: 0.4227 (t80) REVERT: 1 567 TRP cc_start: 0.7157 (t60) cc_final: 0.5923 (t60) REVERT: 1 579 TYR cc_start: 0.6087 (t80) cc_final: 0.5886 (t80) REVERT: 0 298 VAL cc_start: 0.7736 (t) cc_final: 0.7492 (p) REVERT: 2 65 GLN cc_start: 0.6391 (tp40) cc_final: 0.5404 (tp40) REVERT: 2 317 ASN cc_start: 0.8734 (t0) cc_final: 0.8122 (t0) REVERT: 2 381 ARG cc_start: 0.8380 (mmp80) cc_final: 0.7864 (mmt180) REVERT: 2 481 GLU cc_start: 0.6650 (tp30) cc_final: 0.6374 (tp30) REVERT: 2 492 ILE cc_start: 0.5454 (mt) cc_final: 0.5102 (mt) REVERT: 2 530 ARG cc_start: 0.5540 (mtt180) cc_final: 0.4159 (mtm110) REVERT: 2 586 PHE cc_start: 0.5799 (m-80) cc_final: 0.4678 (m-10) REVERT: 3 45 LEU cc_start: 0.9072 (tp) cc_final: 0.8849 (tp) REVERT: 3 106 ASP cc_start: 0.8637 (t0) cc_final: 0.8416 (t70) REVERT: 3 127 MET cc_start: 0.8542 (mtm) cc_final: 0.8290 (mtp) REVERT: 3 185 ARG cc_start: 0.7039 (mtp180) cc_final: 0.6328 (mtm110) REVERT: 3 270 GLU cc_start: 0.8683 (tt0) cc_final: 0.8354 (tt0) REVERT: 3 368 LEU cc_start: 0.9176 (mt) cc_final: 0.8855 (mt) REVERT: 3 403 LYS cc_start: 0.8359 (tttp) cc_final: 0.8148 (tttm) REVERT: 3 435 MET cc_start: 0.5599 (tmm) cc_final: 0.5200 (tmm) REVERT: 3 497 GLN cc_start: 0.7384 (mt0) cc_final: 0.6608 (mm110) REVERT: 4 162 CYS cc_start: 0.8379 (m) cc_final: 0.7862 (t) REVERT: 4 177 ILE cc_start: 0.8597 (mt) cc_final: 0.8370 (mt) REVERT: 4 308 ARG cc_start: 0.7940 (ttp-170) cc_final: 0.7279 (ttm170) REVERT: 4 335 TYR cc_start: 0.8054 (m-10) cc_final: 0.7221 (m-10) REVERT: 4 433 GLN cc_start: 0.5488 (mm110) cc_final: 0.5158 (mm110) REVERT: 4 455 LEU cc_start: 0.7495 (mt) cc_final: 0.6991 (tt) REVERT: 4 484 LEU cc_start: 0.7694 (tt) cc_final: 0.7314 (tt) REVERT: 4 492 LEU cc_start: 0.7520 (mt) cc_final: 0.7152 (mt) REVERT: 5 118 ILE cc_start: 0.9515 (pt) cc_final: 0.9282 (pt) REVERT: 5 127 MET cc_start: 0.8320 (mmt) cc_final: 0.8077 (mmt) REVERT: 5 244 PHE cc_start: 0.8078 (m-80) cc_final: 0.7699 (m-80) REVERT: 5 299 ASP cc_start: 0.7226 (t0) cc_final: 0.6904 (t0) REVERT: 5 321 ARG cc_start: 0.7598 (tpp80) cc_final: 0.6924 (tpp80) outliers start: 6 outliers final: 0 residues processed: 1599 average time/residue: 0.6323 time to fit residues: 1726.9361 Evaluate side-chains 1334 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1334 time to evaluate : 5.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 17 optimal weight: 0.9980 chunk 782 optimal weight: 4.9990 chunk 284 optimal weight: 1.9990 chunk 718 optimal weight: 4.9990 chunk 608 optimal weight: 0.0170 chunk 581 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 534 optimal weight: 7.9990 chunk 780 optimal weight: 0.7980 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN 9 96 ASN ** 9 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 13 GLN R 98 GLN T 91 ASN V 109 GLN 6 39 ASN 6 106 GLN 6 286 ASN 6 336 HIS ** U 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 341 GLN a 397 ASN a 722 GLN ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 124 GLN ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 HIS d 48 HIS d 84 HIS c 364 HIS 1 261 GLN ** 0 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 251 ASN ** 3 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 470 ASN ** 4 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 415 HIS ** 5 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 ASN 5 384 HIS ** 5 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.210382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.180663 restraints weight = 136679.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.178513 restraints weight = 159268.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.178480 restraints weight = 143793.125| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 66773 Z= 0.175 Angle : 0.579 12.906 90244 Z= 0.303 Chirality : 0.042 0.363 10230 Planarity : 0.004 0.061 11573 Dihedral : 4.667 76.414 9103 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.28 % Favored : 95.68 % Rotamer: Outliers : 0.10 % Allowed : 2.32 % Favored : 97.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.34 (0.09), residues: 8314 helix: 1.48 (0.08), residues: 4641 sheet: -1.08 (0.22), residues: 586 loop : -1.47 (0.11), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.001 TRP 6 282 HIS 0.013 0.001 HIS U 370 PHE 0.037 0.002 PHE U 245 TYR 0.044 0.002 TYR m 68 ARG 0.007 0.000 ARG 1 571 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1601 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 1594 time to evaluate : 5.711 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: 7 58 MET cc_start: 0.6415 (mmp) cc_final: 0.6036 (mmt) REVERT: 7 62 MET cc_start: 0.4504 (ptm) cc_final: 0.4111 (ptm) REVERT: 7 114 GLU cc_start: 0.3115 (mp0) cc_final: 0.2341 (tt0) REVERT: 8 78 GLN cc_start: 0.8891 (mp10) cc_final: 0.8619 (mp10) REVERT: 8 184 TYR cc_start: 0.7951 (m-80) cc_final: 0.7409 (m-80) REVERT: 9 104 LYS cc_start: 0.8714 (mttt) cc_final: 0.8256 (mtpt) REVERT: 9 155 TYR cc_start: 0.6741 (t80) cc_final: 0.6492 (t80) REVERT: 9 187 ASP cc_start: 0.7863 (p0) cc_final: 0.7493 (p0) REVERT: Q 135 ARG cc_start: 0.8610 (ttt180) cc_final: 0.7893 (mtp180) REVERT: Q 163 VAL cc_start: 0.5794 (m) cc_final: 0.5591 (m) REVERT: R 88 GLN cc_start: 0.8338 (pp30) cc_final: 0.7892 (pp30) REVERT: R 113 ASN cc_start: 0.8116 (m-40) cc_final: 0.7642 (m-40) REVERT: T 24 ASP cc_start: 0.5305 (t0) cc_final: 0.4818 (p0) REVERT: T 113 ASN cc_start: 0.8171 (m110) cc_final: 0.7779 (m-40) REVERT: V 42 MET cc_start: 0.5764 (mmp) cc_final: 0.5115 (tmm) REVERT: V 44 VAL cc_start: 0.6703 (t) cc_final: 0.6451 (t) REVERT: V 105 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6864 (tm-30) REVERT: 6 61 LEU cc_start: 0.8094 (pp) cc_final: 0.7792 (mt) REVERT: 6 76 MET cc_start: 0.3842 (ttm) cc_final: 0.3598 (tpp) REVERT: 6 172 LYS cc_start: 0.3817 (pttt) cc_final: 0.2859 (mttt) REVERT: 6 242 ARG cc_start: 0.5298 (ptp-170) cc_final: 0.3841 (mmm-85) REVERT: 6 296 HIS cc_start: 0.6505 (t70) cc_final: 0.6291 (t-90) REVERT: U 100 MET cc_start: 0.3442 (mmp) cc_final: 0.2083 (ptt) REVERT: U 208 MET cc_start: 0.4369 (tpp) cc_final: 0.3782 (tpp) REVERT: U 256 MET cc_start: 0.2513 (tmm) cc_final: 0.1992 (tmm) REVERT: U 325 LYS cc_start: 0.3601 (mmpt) cc_final: 0.3251 (mmtt) REVERT: U 392 LYS cc_start: 0.4119 (mttt) cc_final: 0.2547 (mmmm) REVERT: U 428 ILE cc_start: 0.6054 (tt) cc_final: 0.5766 (tp) REVERT: U 434 LYS cc_start: 0.2748 (mtmt) cc_final: 0.1754 (tmtt) REVERT: U 460 MET cc_start: 0.0794 (mmt) cc_final: 0.0192 (mmt) REVERT: a 98 GLU cc_start: 0.4881 (tp30) cc_final: 0.4541 (tm-30) REVERT: a 237 LYS cc_start: 0.5415 (mttt) cc_final: 0.5100 (mptt) REVERT: a 261 ARG cc_start: 0.5144 (ttt180) cc_final: 0.4366 (ttp80) REVERT: a 277 MET cc_start: 0.7149 (mmp) cc_final: 0.5779 (tpt) REVERT: a 372 ASN cc_start: 0.7493 (t0) cc_final: 0.7181 (t0) REVERT: a 382 GLN cc_start: 0.7182 (mp10) cc_final: 0.6920 (mm-40) REVERT: a 446 MET cc_start: 0.5045 (mtm) cc_final: 0.4577 (mtm) REVERT: a 491 MET cc_start: 0.4826 (ttm) cc_final: 0.4225 (ttm) REVERT: a 640 GLN cc_start: 0.6431 (tt0) cc_final: 0.6203 (tm-30) REVERT: a 719 MET cc_start: 0.5165 (mmp) cc_final: 0.4535 (tmm) REVERT: a 742 ARG cc_start: 0.7211 (ptm-80) cc_final: 0.6895 (ptm-80) REVERT: a 822 PHE cc_start: 0.5511 (t80) cc_final: 0.5012 (t80) REVERT: e 61 ASN cc_start: 0.3899 (m-40) cc_final: 0.3486 (m-40) REVERT: f 11 LEU cc_start: 0.3482 (mp) cc_final: 0.3132 (mt) REVERT: b 107 MET cc_start: 0.3590 (mmp) cc_final: 0.3148 (mmp) REVERT: b 180 GLU cc_start: 0.5380 (pm20) cc_final: 0.5073 (pm20) REVERT: g 44 MET cc_start: 0.3947 (mmm) cc_final: 0.3574 (tpp) REVERT: g 148 VAL cc_start: 0.4955 (t) cc_final: 0.4717 (t) REVERT: g 152 LEU cc_start: 0.6470 (mm) cc_final: 0.5966 (tp) REVERT: h 25 PHE cc_start: 0.7858 (m-10) cc_final: 0.7509 (m-80) REVERT: h 72 VAL cc_start: 0.7721 (t) cc_final: 0.7301 (p) REVERT: h 123 GLN cc_start: 0.6506 (mm-40) cc_final: 0.6151 (tp40) REVERT: h 137 PHE cc_start: 0.5703 (t80) cc_final: 0.5198 (t80) REVERT: h 139 GLU cc_start: 0.5724 (tp30) cc_final: 0.5355 (mm-30) REVERT: h 146 LEU cc_start: 0.5720 (mm) cc_final: 0.5385 (mm) REVERT: h 150 LEU cc_start: 0.8235 (mt) cc_final: 0.8030 (mt) REVERT: i 13 PHE cc_start: 0.6504 (p90) cc_final: 0.5642 (p90) REVERT: j 48 ARG cc_start: 0.5978 (tpt-90) cc_final: 0.5402 (tpm170) REVERT: j 87 TYR cc_start: 0.4620 (m-80) cc_final: 0.3920 (t80) REVERT: k 28 MET cc_start: 0.5121 (mmt) cc_final: 0.3919 (ptm) REVERT: k 44 MET cc_start: 0.5625 (ttp) cc_final: 0.4879 (tmm) REVERT: k 71 VAL cc_start: 0.7533 (t) cc_final: 0.7311 (t) REVERT: l 17 MET cc_start: 0.5974 (mpp) cc_final: 0.5624 (mmt) REVERT: m 23 MET cc_start: 0.3151 (mmm) cc_final: 0.2822 (mmm) REVERT: m 48 ARG cc_start: 0.3954 (mmt180) cc_final: 0.3516 (mmm-85) REVERT: m 86 LEU cc_start: 0.1085 (tp) cc_final: 0.0883 (tp) REVERT: n 53 MET cc_start: 0.6643 (mmp) cc_final: 0.6270 (mmp) REVERT: o 23 MET cc_start: 0.7709 (mmt) cc_final: 0.7483 (mmt) REVERT: o 44 MET cc_start: 0.5820 (mmm) cc_final: 0.5442 (mmm) REVERT: o 151 ILE cc_start: 0.5340 (mm) cc_final: 0.5072 (mm) REVERT: X 25 ILE cc_start: 0.7688 (pt) cc_final: 0.7450 (mp) REVERT: X 82 GLN cc_start: 0.4843 (tm-30) cc_final: 0.4468 (mm-40) REVERT: d 191 GLU cc_start: 0.6224 (pt0) cc_final: 0.5930 (mt-10) REVERT: d 208 MET cc_start: 0.3754 (mtt) cc_final: 0.3165 (mpp) REVERT: d 323 GLU cc_start: 0.7942 (pp20) cc_final: 0.6068 (mm-30) REVERT: c 363 PHE cc_start: 0.3928 (t80) cc_final: 0.3487 (t80) REVERT: c 376 ASN cc_start: 0.6464 (t0) cc_final: 0.6236 (t0) REVERT: c 377 LEU cc_start: 0.5123 (tp) cc_final: 0.4004 (mt) REVERT: p 331 MET cc_start: 0.2523 (mmm) cc_final: 0.2319 (mmm) REVERT: 1 42 LEU cc_start: 0.8591 (tt) cc_final: 0.8318 (tt) REVERT: 1 228 LEU cc_start: 0.8676 (tp) cc_final: 0.8211 (tp) REVERT: 1 340 MET cc_start: 0.7247 (ttp) cc_final: 0.6297 (ttt) REVERT: 1 550 MET cc_start: 0.7042 (tpt) cc_final: 0.6208 (mtt) REVERT: 1 567 TRP cc_start: 0.6792 (t60) cc_final: 0.6047 (t60) REVERT: 0 153 TYR cc_start: 0.7451 (p90) cc_final: 0.7234 (p90) REVERT: 0 475 LEU cc_start: 0.6875 (mp) cc_final: 0.6629 (mp) REVERT: 0 574 MET cc_start: 0.5080 (tmm) cc_final: 0.4623 (tmm) REVERT: 2 65 GLN cc_start: 0.5792 (tp40) cc_final: 0.5065 (tp40) REVERT: 2 213 GLN cc_start: 0.7439 (pm20) cc_final: 0.6785 (pm20) REVERT: 2 317 ASN cc_start: 0.8495 (t0) cc_final: 0.7982 (t0) REVERT: 2 381 ARG cc_start: 0.8180 (mmp80) cc_final: 0.7868 (mmt180) REVERT: 2 492 ILE cc_start: 0.5496 (mt) cc_final: 0.4973 (mt) REVERT: 2 530 ARG cc_start: 0.5521 (mtt180) cc_final: 0.4131 (mtm110) REVERT: 2 608 MET cc_start: 0.0933 (mtt) cc_final: 0.0719 (ttm) REVERT: 3 126 ASP cc_start: 0.8055 (p0) cc_final: 0.7845 (p0) REVERT: 3 169 MET cc_start: 0.7212 (mtt) cc_final: 0.6963 (mtt) REVERT: 3 270 GLU cc_start: 0.8713 (tt0) cc_final: 0.8301 (tt0) REVERT: 3 326 TYR cc_start: 0.7803 (p90) cc_final: 0.6512 (p90) REVERT: 3 368 LEU cc_start: 0.9197 (mt) cc_final: 0.8944 (mm) REVERT: 3 403 LYS cc_start: 0.8180 (tttp) cc_final: 0.7970 (tttm) REVERT: 3 497 GLN cc_start: 0.7313 (mt0) cc_final: 0.6542 (mm110) REVERT: 4 47 TYR cc_start: 0.9077 (m-80) cc_final: 0.8844 (m-10) REVERT: 4 162 CYS cc_start: 0.8184 (m) cc_final: 0.7866 (t) REVERT: 4 308 ARG cc_start: 0.7908 (ttp-170) cc_final: 0.7285 (ttm170) REVERT: 4 433 GLN cc_start: 0.5453 (mm110) cc_final: 0.5006 (mm110) REVERT: 4 435 MET cc_start: 0.6857 (tmm) cc_final: 0.6096 (ppp) REVERT: 4 455 LEU cc_start: 0.7337 (mt) cc_final: 0.6906 (tt) REVERT: 4 484 LEU cc_start: 0.7612 (tt) cc_final: 0.7209 (tt) REVERT: 5 127 MET cc_start: 0.8280 (mmt) cc_final: 0.7849 (mmt) REVERT: 5 231 PHE cc_start: 0.7774 (t80) cc_final: 0.7419 (t80) REVERT: 5 244 PHE cc_start: 0.7928 (m-80) cc_final: 0.7641 (m-80) REVERT: 5 321 ARG cc_start: 0.7542 (tpp80) cc_final: 0.6952 (tpp80) REVERT: 5 365 ILE cc_start: 0.9036 (mt) cc_final: 0.8742 (mt) outliers start: 7 outliers final: 2 residues processed: 1597 average time/residue: 0.6134 time to fit residues: 1674.1611 Evaluate side-chains 1343 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 1341 time to evaluate : 5.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 805 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 671 optimal weight: 0.4980 chunk 452 optimal weight: 0.4980 chunk 59 optimal weight: 10.0000 chunk 164 optimal weight: 0.0270 chunk 169 optimal weight: 6.9990 chunk 524 optimal weight: 0.0970 chunk 347 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 231 optimal weight: 9.9990 overall best weight: 0.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 7 46 GLN 8 206 GLN ** 9 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 149 GLN ** 9 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 GLN ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 46 GLN 6 144 ASN 6 336 HIS U 162 ASN ** U 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 363 GLN a 397 ASN a 644 GLN a 722 GLN ** l 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 HIS X 35 ASN ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 108 ASN ** d 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 609 GLN ** 0 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 350 GLN ** 3 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 ASN ** 5 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 461 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.211578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.180616 restraints weight = 135700.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.179255 restraints weight = 140853.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.179890 restraints weight = 108597.307| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 66773 Z= 0.169 Angle : 0.561 11.425 90244 Z= 0.293 Chirality : 0.041 0.377 10230 Planarity : 0.004 0.064 11573 Dihedral : 4.480 74.929 9103 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.11 % Favored : 95.85 % Rotamer: Outliers : 0.04 % Allowed : 1.49 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.88 % 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: 0.54 (0.09), residues: 8314 helix: 1.62 (0.08), residues: 4644 sheet: -1.05 (0.21), residues: 610 loop : -1.33 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.001 TRP 6 282 HIS 0.011 0.001 HIS 3 363 PHE 0.030 0.002 PHE a 301 TYR 0.042 0.001 TYR i 144 ARG 0.007 0.000 ARG 0 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16628 Ramachandran restraints generated. 8314 Oldfield, 0 Emsley, 8314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1606 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 1603 time to evaluate : 5.685 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: 7 58 MET cc_start: 0.6476 (mmp) cc_final: 0.6041 (mmt) REVERT: 7 62 MET cc_start: 0.4729 (ptm) cc_final: 0.4304 (ptm) REVERT: 7 114 GLU cc_start: 0.2796 (mp0) cc_final: 0.2208 (tt0) REVERT: 7 193 GLU cc_start: 0.7628 (mm-30) cc_final: 0.6990 (mm-30) REVERT: 7 207 GLU cc_start: 0.5557 (tt0) cc_final: 0.5136 (tt0) REVERT: 9 187 ASP cc_start: 0.7884 (p0) cc_final: 0.7500 (p0) REVERT: Q 20 GLU cc_start: 0.2655 (tp30) cc_final: 0.1395 (mp0) REVERT: Q 92 THR cc_start: 0.7947 (p) cc_final: 0.7214 (t) REVERT: Q 135 ARG cc_start: 0.8649 (ttt180) cc_final: 0.8174 (mtp180) REVERT: R 88 GLN cc_start: 0.8322 (pp30) cc_final: 0.7854 (pp30) REVERT: R 113 ASN cc_start: 0.8189 (m-40) cc_final: 0.7721 (m-40) REVERT: T 24 ASP cc_start: 0.5113 (t0) cc_final: 0.4482 (p0) REVERT: T 84 MET cc_start: 0.6584 (mtp) cc_final: 0.5910 (mtp) REVERT: T 105 GLU cc_start: 0.7238 (tp30) cc_final: 0.6571 (mm-30) REVERT: T 113 ASN cc_start: 0.8058 (m110) cc_final: 0.7782 (t0) REVERT: V 42 MET cc_start: 0.5536 (mmp) cc_final: 0.5134 (tmm) REVERT: V 98 GLN cc_start: 0.6046 (mt0) cc_final: 0.5787 (tt0) REVERT: V 105 GLU cc_start: 0.7103 (tm-30) cc_final: 0.6764 (tm-30) REVERT: 6 58 LEU cc_start: 0.7427 (tp) cc_final: 0.7185 (tp) REVERT: 6 61 LEU cc_start: 0.8092 (pp) cc_final: 0.7830 (mt) REVERT: 6 172 LYS cc_start: 0.4047 (pttt) cc_final: 0.3101 (mttt) REVERT: 6 242 ARG cc_start: 0.5290 (ptp-170) cc_final: 0.3821 (mmm-85) REVERT: 6 296 HIS cc_start: 0.6543 (t70) cc_final: 0.6288 (t-90) REVERT: U 100 MET cc_start: 0.3636 (mmp) cc_final: 0.2427 (ptt) REVERT: U 156 MET cc_start: 0.4221 (ptm) cc_final: 0.3808 (ptm) REVERT: U 162 ASN cc_start: 0.4634 (m-40) cc_final: 0.4381 (t0) REVERT: U 208 MET cc_start: 0.4273 (tpp) cc_final: 0.3683 (tpp) REVERT: U 299 ARG cc_start: 0.3806 (tpt90) cc_final: 0.3271 (ttt180) REVERT: U 325 LYS cc_start: 0.3464 (mmpt) cc_final: 0.3114 (mmtt) REVERT: U 392 LYS cc_start: 0.4229 (mttt) cc_final: 0.2768 (mmmm) REVERT: U 428 ILE cc_start: 0.6213 (tt) cc_final: 0.6011 (tp) REVERT: U 434 LYS cc_start: 0.3763 (mtmm) cc_final: 0.2904 (tmtt) REVERT: U 448 VAL cc_start: 0.2117 (t) cc_final: 0.1700 (m) REVERT: U 460 MET cc_start: 0.0613 (mmt) cc_final: 0.0226 (mmm) REVERT: a 59 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7597 (tm-30) REVERT: a 237 LYS cc_start: 0.5349 (mttt) cc_final: 0.4977 (mptt) REVERT: a 261 ARG cc_start: 0.5148 (ttt180) cc_final: 0.4361 (ttp80) REVERT: a 277 MET cc_start: 0.7140 (mmp) cc_final: 0.5768 (tpt) REVERT: a 372 ASN cc_start: 0.7233 (t0) cc_final: 0.6696 (t0) REVERT: a 446 MET cc_start: 0.5127 (mtm) cc_final: 0.4631 (mtm) REVERT: a 491 MET cc_start: 0.4955 (ttm) cc_final: 0.4674 (ttm) REVERT: a 822 PHE cc_start: 0.5452 (t80) cc_final: 0.4989 (t80) REVERT: e 61 ASN cc_start: 0.3930 (m-40) cc_final: 0.3471 (m-40) REVERT: f 11 LEU cc_start: 0.3592 (mp) cc_final: 0.3248 (mt) REVERT: b 107 MET cc_start: 0.3906 (mmp) cc_final: 0.3583 (mmm) REVERT: g 108 PHE cc_start: 0.7583 (t80) cc_final: 0.7368 (t80) REVERT: g 148 VAL cc_start: 0.5292 (t) cc_final: 0.5033 (t) REVERT: g 152 LEU cc_start: 0.6371 (mm) cc_final: 0.5854 (tp) REVERT: h 25 PHE cc_start: 0.7967 (m-10) cc_final: 0.7546 (m-80) REVERT: h 72 VAL cc_start: 0.7599 (t) cc_final: 0.7160 (p) REVERT: h 93 LEU cc_start: 0.8024 (tp) cc_final: 0.7797 (tp) REVERT: h 97 LEU cc_start: 0.8604 (mt) cc_final: 0.8388 (mt) REVERT: h 123 GLN cc_start: 0.6486 (mm-40) cc_final: 0.6148 (tp40) REVERT: h 137 PHE cc_start: 0.5705 (t80) cc_final: 0.5233 (t80) REVERT: h 139 GLU cc_start: 0.5654 (tp30) cc_final: 0.5301 (mm-30) REVERT: h 146 LEU cc_start: 0.5654 (mm) cc_final: 0.5374 (mm) REVERT: i 13 PHE cc_start: 0.6491 (p90) cc_final: 0.5816 (p90) REVERT: j 6 ASN cc_start: 0.6229 (m110) cc_final: 0.5891 (m110) REVERT: j 48 ARG cc_start: 0.5989 (tpt-90) cc_final: 0.5473 (tpm170) REVERT: j 87 TYR cc_start: 0.4901 (m-80) cc_final: 0.4155 (t80) REVERT: k 28 MET cc_start: 0.5296 (mmt) cc_final: 0.4057 (ptm) REVERT: k 44 MET cc_start: 0.5759 (ttp) cc_final: 0.5031 (tmm) REVERT: k 71 VAL cc_start: 0.7469 (t) cc_final: 0.7209 (t) REVERT: k 104 LEU cc_start: 0.7361 (tp) cc_final: 0.6912 (tp) REVERT: l 17 MET cc_start: 0.5419 (mpp) cc_final: 0.5148 (mmt) REVERT: m 17 MET cc_start: 0.5690 (mtm) cc_final: 0.5384 (mtm) REVERT: m 23 MET cc_start: 0.2919 (mmm) cc_final: 0.2609 (mmm) REVERT: m 48 ARG cc_start: 0.3728 (mmt180) cc_final: 0.3326 (mmm-85) REVERT: m 70 LEU cc_start: 0.6856 (tp) cc_final: 0.6622 (tp) REVERT: m 84 ILE cc_start: 0.7594 (tp) cc_final: 0.7333 (tt) REVERT: m 86 LEU cc_start: 0.0788 (tp) cc_final: 0.0540 (tp) REVERT: n 54 LYS cc_start: 0.4867 (tppt) cc_final: 0.4428 (tppt) REVERT: n 112 ILE cc_start: 0.7017 (tt) cc_final: 0.6667 (mm) REVERT: o 151 ILE cc_start: 0.5214 (mm) cc_final: 0.4922 (mm) REVERT: X 25 ILE cc_start: 0.7708 (pt) cc_final: 0.7369 (mp) REVERT: X 82 GLN cc_start: 0.4689 (tm-30) cc_final: 0.4416 (mm-40) REVERT: d 191 GLU cc_start: 0.6341 (pt0) cc_final: 0.5950 (mt-10) REVERT: d 323 GLU cc_start: 0.7925 (pp20) cc_final: 0.6044 (mm-30) REVERT: c 363 PHE cc_start: 0.3966 (t80) cc_final: 0.3558 (t80) REVERT: c 377 LEU cc_start: 0.5155 (tp) cc_final: 0.3828 (mt) REVERT: 1 228 LEU cc_start: 0.8646 (tp) cc_final: 0.8078 (tp) REVERT: 1 340 MET cc_start: 0.7019 (ttp) cc_final: 0.6357 (ttt) REVERT: 1 548 TYR cc_start: 0.5175 (t80) cc_final: 0.4203 (t80) REVERT: 1 550 MET cc_start: 0.7261 (tpt) cc_final: 0.6159 (mtt) REVERT: 0 475 LEU cc_start: 0.6949 (mp) cc_final: 0.6735 (mp) REVERT: 0 544 MET cc_start: 0.4305 (mmm) cc_final: 0.3376 (tmm) REVERT: 0 574 MET cc_start: 0.5557 (tmm) cc_final: 0.3467 (tmm) REVERT: 2 65 GLN cc_start: 0.5751 (tp40) cc_final: 0.5244 (tp40) REVERT: 2 106 LEU cc_start: 0.8183 (mm) cc_final: 0.7978 (mm) REVERT: 2 213 GLN cc_start: 0.7235 (pm20) cc_final: 0.6843 (pm20) REVERT: 2 360 GLU cc_start: 0.6811 (mp0) cc_final: 0.6561 (mp0) REVERT: 2 381 ARG cc_start: 0.8282 (mmp80) cc_final: 0.7593 (mmm160) REVERT: 2 492 ILE cc_start: 0.5547 (mt) cc_final: 0.5224 (mt) REVERT: 2 530 ARG cc_start: 0.5503 (mtt180) cc_final: 0.4199 (mtm110) REVERT: 2 584 MET cc_start: 0.5563 (mtp) cc_final: 0.5222 (mtp) REVERT: 3 118 ILE cc_start: 0.8916 (pt) cc_final: 0.8710 (pt) REVERT: 3 169 MET cc_start: 0.7215 (mtt) cc_final: 0.6952 (mtt) REVERT: 3 227 PHE cc_start: 0.7460 (m-80) cc_final: 0.7196 (m-10) REVERT: 3 270 GLU cc_start: 0.8743 (tt0) cc_final: 0.8324 (tt0) REVERT: 3 326 TYR cc_start: 0.7782 (p90) cc_final: 0.6525 (p90) REVERT: 3 368 LEU cc_start: 0.9019 (mt) cc_final: 0.8591 (mp) REVERT: 3 369 THR cc_start: 0.8533 (m) cc_final: 0.8218 (m) REVERT: 3 402 MET cc_start: 0.7088 (tpp) cc_final: 0.6580 (tpp) REVERT: 3 435 MET cc_start: 0.5571 (tmm) cc_final: 0.4729 (tmm) REVERT: 3 497 GLN cc_start: 0.7262 (mt0) cc_final: 0.6512 (mm110) REVERT: 4 40 LEU cc_start: 0.8286 (tp) cc_final: 0.7959 (mm) REVERT: 4 47 TYR cc_start: 0.9109 (m-80) cc_final: 0.8905 (m-10) REVERT: 4 162 CYS cc_start: 0.7968 (m) cc_final: 0.7648 (t) REVERT: 4 308 ARG cc_start: 0.8145 (ttp-170) cc_final: 0.7517 (ttm170) REVERT: 4 433 GLN cc_start: 0.5327 (mm110) cc_final: 0.4853 (mm110) REVERT: 4 435 MET cc_start: 0.6945 (tmm) cc_final: 0.6090 (ppp) REVERT: 4 455 LEU cc_start: 0.7329 (mt) cc_final: 0.6776 (tt) REVERT: 4 484 LEU cc_start: 0.7552 (tt) cc_final: 0.7257 (tt) REVERT: 5 127 MET cc_start: 0.8375 (mmt) cc_final: 0.7824 (mmt) REVERT: 5 231 PHE cc_start: 0.7814 (t80) cc_final: 0.7437 (t80) REVERT: 5 244 PHE cc_start: 0.7907 (m-80) cc_final: 0.7648 (m-80) REVERT: 5 365 ILE cc_start: 0.9028 (mt) cc_final: 0.8780 (mt) REVERT: 5 470 ASN cc_start: 0.7426 (m-40) cc_final: 0.7030 (t0) outliers start: 3 outliers final: 0 residues processed: 1605 average time/residue: 0.6173 time to fit residues: 1693.4632 Evaluate side-chains 1334 residues out of total 7054 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1334 time to evaluate : 5.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 830 random chunks: chunk 388 optimal weight: 6.9990 chunk 267 optimal weight: 20.0000 chunk 365 optimal weight: 0.9990 chunk 425 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 554 optimal weight: 0.4980 chunk 285 optimal weight: 5.9990 chunk 343 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 749 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: