Starting phenix.real_space_refine on Mon May 13 11:03:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v83_43017/05_2024/8v83_43017.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v83_43017/05_2024/8v83_43017.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v83_43017/05_2024/8v83_43017.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v83_43017/05_2024/8v83_43017.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v83_43017/05_2024/8v83_43017.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v83_43017/05_2024/8v83_43017.pdb" } resolution = 2.53 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2223 5.49 5 S 204 5.16 5 C 66849 2.51 5 N 21565 2.21 5 O 28381 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "8 PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 119224 Number of models: 1 Model: "" Number of chains: 50 Chain: "1" Number of atoms: 43147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2015, 43147 Classifications: {'RNA': 2015} Modifications used: {'rna2p_pur': 201, 'rna2p_pyr': 119, 'rna3p_pur': 930, 'rna3p_pyr': 764} Link IDs: {'rna2p': 320, 'rna3p': 1694} Chain breaks: 21 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3189 Classifications: {'RNA': 150} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 13, 'rna3p_pur': 61, 'rna3p_pyr': 61} Link IDs: {'rna2p': 27, 'rna3p': 122} Chain breaks: 2 Chain: "6" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1227 Classifications: {'RNA': 58} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 13, 'rna3p_pur': 19, 'rna3p_pyr': 17} Link IDs: {'rna2p': 21, 'rna3p': 36} Chain breaks: 3 Chain: "7" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 87 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "8" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1203 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 1, 'TRANS': 141} Chain breaks: 1 Chain: "A" Number of atoms: 2080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2080 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 240} Chain breaks: 1 Chain: "B" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2626 Classifications: {'peptide': 331} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 319} Chain breaks: 1 Chain: "C" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2611 Classifications: {'peptide': 343} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 326} Chain: "D" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3377 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 21, 'TRANS': 401} Chain breaks: 2 Chain: "E" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1205 Classifications: {'peptide': 151} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 143} Chain breaks: 1 Chain: "F" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1936 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 11, 'TRANS': 229} Chain: "G" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1272 Classifications: {'peptide': 164} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 155} Chain: "H" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1502 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "I" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3126 Classifications: {'peptide': 394} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 381} Chain breaks: 1 Chain: "J" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1271 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 3, 'TRANS': 147} Chain: "K" Number of atoms: 2155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2155 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 11, 'TRANS': 256} Chain breaks: 2 Chain: "L" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 884 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 104} Chain: "M" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1041 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "N" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1513 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 4, 'TRANS': 172} Chain breaks: 1 Chain: "O" Number of atoms: 1486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1486 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "P" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1062 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain breaks: 1 Chain: "Q" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1110 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 7, 'TRANS': 136} Chain: "R" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1578 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 6, 'TRANS': 183} Chain: "S" Number of atoms: 1432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1432 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 7, 'TRANS': 162} Chain: "T" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'TRANS': 78} Chain: "V" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 845 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 7, 'TRANS': 106} Chain breaks: 1 Chain: "W" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1870 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "Y" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "Z" Number of atoms: 2020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2020 Classifications: {'peptide': 253} Link IDs: {'PCIS': 4, 'PTRANS': 9, 'TRANS': 239} Chain breaks: 2 Chain: "a" Number of atoms: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1668 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 200} Chain: "b" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3429 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 21, 'TRANS': 401} Chain breaks: 2 Chain: "e" Number of atoms: 1018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1018 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "f" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "i" Number of atoms: 665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 665 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain: "j" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PCIS': 1, 'TRANS': 70} Chain: "l" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1394 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "m" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1759 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 23, 'TRANS': 187} Chain breaks: 2 Chain: "n" Number of atoms: 2760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2760 Classifications: {'peptide': 337} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 317} Chain breaks: 3 Chain: "o" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1107 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Chain: "q" Number of atoms: 2799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2799 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 341} Chain: "r" Number of atoms: 1489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1489 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 6, 'TRANS': 177} Chain breaks: 4 Chain: "t" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1973 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 9, 'TRANS': 239} Chain breaks: 1 Chain: "u" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 944 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "v" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1242 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain breaks: 1 Chain: "w" Number of atoms: 2058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2058 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 7, 'TRANS': 235} Chain breaks: 1 Chain: "x" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2362 Classifications: {'peptide': 279} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 266} Chain breaks: 1 Chain: "y" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1701 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "u" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 97100 SG CYS j 19 109.085 179.019 168.484 1.00 21.34 S ATOM 97125 SG CYS j 22 112.211 179.482 166.259 1.00 21.12 S ATOM 97225 SG CYS j 34 110.190 176.290 166.291 1.00 20.95 S ATOM 97243 SG CYS j 37 112.256 177.301 169.431 1.00 16.07 S ATOM A08GP SG CYS u 6 56.125 175.596 72.643 1.00 25.53 S ATOM A08ML SG CYS u 32 59.231 177.950 72.757 1.00 32.58 S ATOM A08NH SG CYS u 36 57.182 177.620 75.622 1.00 29.60 S Time building chain proxies: 43.84, per 1000 atoms: 0.37 Number of scatterers: 119224 At special positions: 0 Unit cell: (252.042, 275.34, 322.995, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 204 16.00 P 2223 15.00 O 28381 8.00 N 21565 7.00 C 66849 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 - 3.50 Amino acid : False - 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: 43.00 Conformation dependent library (CDL) restraints added in 9.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 100 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 100 " - pdb=" SG CYS j 37 " pdb=" ZN u 201 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 36 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 32 " pdb="ZN ZN u 201 " - pdb=" SG CYS u 6 " Number of angles added : 6 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16902 Finding SS restraints... Secondary structure from input PDB file: 345 helices and 87 sheets defined 45.8% alpha, 17.0% beta 672 base pairs and 1084 stacking pairs defined. Time for finding SS restraints: 34.40 Creating SS restraints... Processing helix chain '7' and resid 105 through 115 Processing helix chain '8' and resid 296 through 314 removed outlier: 3.621A pdb=" N HIS 8 300 " --> pdb=" O ASP 8 296 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS 8 314 " --> pdb=" O LYS 8 310 " (cutoff:3.500A) Processing helix chain '8' and resid 315 through 337 Processing helix chain '8' and resid 343 through 394 Processing helix chain '8' and resid 397 through 401 Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.840A pdb=" N GLU A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 145 Processing helix chain 'A' and resid 146 through 161 Processing helix chain 'A' and resid 244 through 277 removed outlier: 3.568A pdb=" N ARG A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 141 through 155 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 114 through 130 removed outlier: 3.689A pdb=" N ALA C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 161 through 172 Processing helix chain 'C' and resid 174 through 184 Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 214 through 220 Processing helix chain 'C' and resid 234 through 239 Processing helix chain 'C' and resid 240 through 243 Processing helix chain 'C' and resid 252 through 263 removed outlier: 4.529A pdb=" N ASP C 259 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLN C 260 " --> pdb=" O THR C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 292 through 297 Processing helix chain 'C' and resid 320 through 328 Processing helix chain 'C' and resid 329 through 338 removed outlier: 4.410A pdb=" N VAL C 333 " --> pdb=" O PRO C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 342 removed outlier: 3.897A pdb=" N LYS C 342 " --> pdb=" O LEU C 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 339 through 342' Processing helix chain 'D' and resid 50 through 61 Processing helix chain 'D' and resid 66 through 79 Proline residue: D 74 - end of helix Processing helix chain 'D' and resid 91 through 108 Proline residue: D 99 - end of helix Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 123 through 138 Processing helix chain 'D' and resid 139 through 141 No H-bonds generated for 'chain 'D' and resid 139 through 141' Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 232 through 243 Processing helix chain 'D' and resid 272 through 287 removed outlier: 4.594A pdb=" N PHE D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU D 278 " --> pdb=" O ASP D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 312 Processing helix chain 'D' and resid 324 through 338 Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 369 through 374 Processing helix chain 'D' and resid 395 through 399 removed outlier: 3.942A pdb=" N LEU D 399 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 408 removed outlier: 3.722A pdb=" N TYR D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 436 Processing helix chain 'D' and resid 436 through 457 Processing helix chain 'D' and resid 469 through 478 Processing helix chain 'E' and resid 68 through 73 Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 131 through 150 removed outlier: 3.731A pdb=" N ALA E 147 " --> pdb=" O LYS E 143 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU E 148 " --> pdb=" O ALA E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'F' and resid 9 through 73 Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 120 through 130 removed outlier: 3.764A pdb=" N GLU F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU F 126 " --> pdb=" O ALA F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.770A pdb=" N ILE F 169 " --> pdb=" O ASP F 165 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 177 No H-bonds generated for 'chain 'F' and resid 175 through 177' Processing helix chain 'F' and resid 180 through 190 Processing helix chain 'F' and resid 194 through 202 Processing helix chain 'F' and resid 235 through 244 Processing helix chain 'G' and resid 72 through 77 Processing helix chain 'G' and resid 78 through 80 No H-bonds generated for 'chain 'G' and resid 78 through 80' Processing helix chain 'G' and resid 83 through 96 removed outlier: 3.743A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 119 Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 160 through 165 removed outlier: 4.749A pdb=" N PHE G 165 " --> pdb=" O GLU G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 189 removed outlier: 3.586A pdb=" N LEU G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 223 removed outlier: 4.352A pdb=" N ALA G 209 " --> pdb=" O ALA G 205 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ALA G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 84 removed outlier: 3.653A pdb=" N ALA H 67 " --> pdb=" O LYS H 63 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU H 68 " --> pdb=" O HIS H 64 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ARG H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 109 Processing helix chain 'H' and resid 116 through 120 Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.730A pdb=" N CYS H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 45 Processing helix chain 'I' and resid 119 through 128 removed outlier: 4.207A pdb=" N LEU I 123 " --> pdb=" O ASP I 119 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N SER I 128 " --> pdb=" O GLU I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 301 removed outlier: 3.923A pdb=" N ARG I 300 " --> pdb=" O LEU I 297 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU I 301 " --> pdb=" O PRO I 298 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 297 through 301' Processing helix chain 'I' and resid 327 through 330 removed outlier: 3.575A pdb=" N GLU I 330 " --> pdb=" O THR I 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 327 through 330' Processing helix chain 'J' and resid 197 through 209 Processing helix chain 'J' and resid 216 through 221 removed outlier: 4.037A pdb=" N HIS J 220 " --> pdb=" O SER J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 233 removed outlier: 3.600A pdb=" N HIS J 232 " --> pdb=" O ASN J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 265 Processing helix chain 'J' and resid 281 through 314 removed outlier: 4.119A pdb=" N LYS J 287 " --> pdb=" O GLU J 283 " (cutoff:3.500A) Processing helix chain 'J' and resid 314 through 346 Processing helix chain 'K' and resid 33 through 49 Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 106 through 115 removed outlier: 3.786A pdb=" N TRP K 110 " --> pdb=" O PHE K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 135 removed outlier: 3.862A pdb=" N VAL K 135 " --> pdb=" O ILE K 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 145 removed outlier: 3.640A pdb=" N GLN K 143 " --> pdb=" O ASP K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 163 Processing helix chain 'K' and resid 166 through 176 removed outlier: 3.949A pdb=" N GLN K 176 " --> pdb=" O ALA K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 188 removed outlier: 3.942A pdb=" N THR K 188 " --> pdb=" O SER K 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 185 through 188' Processing helix chain 'K' and resid 189 through 195 removed outlier: 3.536A pdb=" N LEU K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY K 195 " --> pdb=" O PRO K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 201 removed outlier: 3.823A pdb=" N TYR K 199 " --> pdb=" O GLY K 195 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS K 201 " --> pdb=" O LYS K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 218 through 233 removed outlier: 3.807A pdb=" N GLN K 233 " --> pdb=" O VAL K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 255 through 274 Processing helix chain 'K' and resid 297 through 301 removed outlier: 3.752A pdb=" N LEU K 301 " --> pdb=" O LEU K 298 " (cutoff:3.500A) Processing helix chain 'K' and resid 328 through 337 Processing helix chain 'L' and resid 27 through 47 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 94 Processing helix chain 'L' and resid 105 through 122 Processing helix chain 'M' and resid 77 through 89 Processing helix chain 'M' and resid 89 through 97 Processing helix chain 'M' and resid 97 through 112 Processing helix chain 'M' and resid 113 through 136 Processing helix chain 'N' and resid 3 through 12 Processing helix chain 'N' and resid 16 through 32 removed outlier: 3.704A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 145 Processing helix chain 'N' and resid 148 through 157 Proline residue: N 154 - end of helix removed outlier: 3.531A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 173 Processing helix chain 'N' and resid 180 through 185 removed outlier: 4.596A pdb=" N ALA N 185 " --> pdb=" O ASN N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 195 Processing helix chain 'O' and resid 15 through 29 Processing helix chain 'O' and resid 37 through 40 Processing helix chain 'O' and resid 46 through 60 removed outlier: 3.819A pdb=" N PHE O 57 " --> pdb=" O LYS O 53 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'O' and resid 92 through 101 Processing helix chain 'O' and resid 111 through 115 Processing helix chain 'O' and resid 120 through 123 Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 138 through 146 Processing helix chain 'O' and resid 149 through 185 Processing helix chain 'O' and resid 188 through 197 Processing helix chain 'P' and resid 10 through 12 No H-bonds generated for 'chain 'P' and resid 10 through 12' Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 76 removed outlier: 3.526A pdb=" N GLY P 73 " --> pdb=" O THR P 70 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU P 75 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'P' and resid 108 through 110 No H-bonds generated for 'chain 'P' and resid 108 through 110' Processing helix chain 'Q' and resid 23 through 40 Processing helix chain 'Q' and resid 42 through 53 removed outlier: 3.888A pdb=" N LYS Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 71 Processing helix chain 'Q' and resid 75 through 78 removed outlier: 3.593A pdb=" N ASN Q 78 " --> pdb=" O GLY Q 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 75 through 78' Processing helix chain 'Q' and resid 107 through 117 Processing helix chain 'Q' and resid 123 through 131 Processing helix chain 'R' and resid 3 through 13 Processing helix chain 'R' and resid 66 through 70 Processing helix chain 'R' and resid 72 through 76 Processing helix chain 'R' and resid 85 through 97 Processing helix chain 'R' and resid 101 through 128 Processing helix chain 'R' and resid 138 through 156 Processing helix chain 'R' and resid 157 through 173 Processing helix chain 'R' and resid 183 through 191 Processing helix chain 'S' and resid 33 through 50 Processing helix chain 'S' and resid 98 through 114 Processing helix chain 'S' and resid 117 through 119 No H-bonds generated for 'chain 'S' and resid 117 through 119' Processing helix chain 'S' and resid 131 through 135 Processing helix chain 'S' and resid 137 through 142 Processing helix chain 'S' and resid 143 through 145 No H-bonds generated for 'chain 'S' and resid 143 through 145' Processing helix chain 'T' and resid 173 through 215 removed outlier: 4.163A pdb=" N ALA T 185 " --> pdb=" O GLU T 181 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU T 186 " --> pdb=" O LYS T 182 " (cutoff:3.500A) Processing helix chain 'T' and resid 216 through 219 removed outlier: 3.612A pdb=" N ILE T 219 " --> pdb=" O LEU T 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 216 through 219' Processing helix chain 'T' and resid 221 through 250 Processing helix chain 'V' and resid 67 through 70 Processing helix chain 'V' and resid 119 through 126 Processing helix chain 'V' and resid 126 through 132 Processing helix chain 'W' and resid 19 through 37 removed outlier: 3.852A pdb=" N LYS W 23 " --> pdb=" O GLY W 19 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 60 Processing helix chain 'W' and resid 69 through 78 Processing helix chain 'W' and resid 88 through 96 removed outlier: 4.477A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) Processing helix chain 'W' and resid 108 through 119 Processing helix chain 'W' and resid 158 through 160 No H-bonds generated for 'chain 'W' and resid 158 through 160' Processing helix chain 'W' and resid 161 through 168 Processing helix chain 'W' and resid 196 through 207 Processing helix chain 'Y' and resid 11 through 21 Processing helix chain 'Y' and resid 23 through 31 removed outlier: 3.641A pdb=" N VAL Y 29 " --> pdb=" O SER Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 44 Processing helix chain 'Y' and resid 75 through 78 Processing helix chain 'Y' and resid 100 through 102 No H-bonds generated for 'chain 'Y' and resid 100 through 102' Processing helix chain 'Y' and resid 112 through 123 Processing helix chain 'Z' and resid 17 through 22 Processing helix chain 'Z' and resid 31 through 37 Processing helix chain 'Z' and resid 37 through 51 removed outlier: 3.948A pdb=" N ASN Z 41 " --> pdb=" O ASN Z 37 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN Z 42 " --> pdb=" O HIS Z 38 " (cutoff:3.500A) Processing helix chain 'Z' and resid 66 through 78 Proline residue: Z 76 - end of helix Processing helix chain 'Z' and resid 116 through 124 Processing helix chain 'Z' and resid 131 through 137 removed outlier: 3.729A pdb=" N ASN Z 137 " --> pdb=" O ASP Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 155 through 173 removed outlier: 4.117A pdb=" N PHE Z 173 " --> pdb=" O PHE Z 169 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 23 Processing helix chain 'a' and resid 70 through 81 Processing helix chain 'a' and resid 87 through 92 removed outlier: 4.417A pdb=" N LYS a 92 " --> pdb=" O ASP a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 107 Processing helix chain 'a' and resid 119 through 125 Processing helix chain 'a' and resid 126 through 132 Processing helix chain 'a' and resid 143 through 153 Processing helix chain 'a' and resid 175 through 194 Processing helix chain 'b' and resid 13 through 29 Processing helix chain 'b' and resid 38 through 67 Processing helix chain 'b' and resid 70 through 74 removed outlier: 3.758A pdb=" N VAL b 74 " --> pdb=" O ILE b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 75 through 86 Processing helix chain 'b' and resid 87 through 118 removed outlier: 3.938A pdb=" N PHE b 118 " --> pdb=" O ARG b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 143 Processing helix chain 'b' and resid 143 through 158 removed outlier: 3.618A pdb=" N TYR b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 179 through 188 Processing helix chain 'b' and resid 233 through 246 removed outlier: 3.763A pdb=" N SER b 239 " --> pdb=" O ILE b 235 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 275 Processing helix chain 'b' and resid 276 through 279 removed outlier: 3.946A pdb=" N ALA b 279 " --> pdb=" O PRO b 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 276 through 279' Processing helix chain 'b' and resid 306 through 312 removed outlier: 3.945A pdb=" N VAL b 312 " --> pdb=" O SER b 308 " (cutoff:3.500A) Processing helix chain 'b' and resid 324 through 341 Processing helix chain 'b' and resid 379 through 384 Processing helix chain 'b' and resid 398 through 407 Processing helix chain 'b' and resid 415 through 420 removed outlier: 3.939A pdb=" N LYS b 419 " --> pdb=" O LEU b 416 " (cutoff:3.500A) Processing helix chain 'b' and resid 441 through 445 Processing helix chain 'b' and resid 448 through 467 removed outlier: 4.053A pdb=" N LYS b 452 " --> pdb=" O GLU b 448 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 58 Processing helix chain 'e' and resid 78 through 83 Processing helix chain 'e' and resid 84 through 86 No H-bonds generated for 'chain 'e' and resid 84 through 86' Processing helix chain 'e' and resid 101 through 116 removed outlier: 3.774A pdb=" N VAL e 107 " --> pdb=" O LYS e 103 " (cutoff:3.500A) Processing helix chain 'f' and resid 37 through 42 Processing helix chain 'f' and resid 43 through 45 No H-bonds generated for 'chain 'f' and resid 43 through 45' Processing helix chain 'f' and resid 90 through 94 Processing helix chain 'h' and resid 5 through 10 Processing helix chain 'h' and resid 13 through 36 removed outlier: 4.045A pdb=" N LEU h 36 " --> pdb=" O LYS h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 70 removed outlier: 3.889A pdb=" N THR h 46 " --> pdb=" O PRO h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 91 Processing helix chain 'h' and resid 93 through 99 Processing helix chain 'h' and resid 101 through 111 Processing helix chain 'i' and resid 27 through 31 Processing helix chain 'i' and resid 34 through 49 Processing helix chain 'i' and resid 51 through 63 Processing helix chain 'i' and resid 65 through 78 Processing helix chain 'i' and resid 79 through 100 removed outlier: 3.725A pdb=" N HIS i 100 " --> pdb=" O ALA i 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 66 through 68 No H-bonds generated for 'chain 'j' and resid 66 through 68' Processing helix chain 'j' and resid 69 through 76 Processing helix chain 'l' and resid 5 through 18 Processing helix chain 'l' and resid 22 through 30 removed outlier: 3.879A pdb=" N PHE l 26 " --> pdb=" O ARG l 22 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 57 removed outlier: 3.805A pdb=" N SER l 57 " --> pdb=" O LYS l 53 " (cutoff:3.500A) Processing helix chain 'l' and resid 85 through 93 removed outlier: 4.300A pdb=" N LYS l 91 " --> pdb=" O THR l 87 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N HIS l 92 " --> pdb=" O VAL l 88 " (cutoff:3.500A) Processing helix chain 'l' and resid 100 through 110 removed outlier: 3.551A pdb=" N MET l 105 " --> pdb=" O PRO l 101 " (cutoff:3.500A) Proline residue: l 106 - end of helix Processing helix chain 'l' and resid 149 through 156 Processing helix chain 'l' and resid 170 through 176 Processing helix chain 'm' and resid 162 through 167 removed outlier: 4.591A pdb=" N GLU m 167 " --> pdb=" O SER m 163 " (cutoff:3.500A) Processing helix chain 'm' and resid 262 through 266 removed outlier: 3.542A pdb=" N ARG m 265 " --> pdb=" O PRO m 262 " (cutoff:3.500A) Processing helix chain 'm' and resid 269 through 285 Processing helix chain 'm' and resid 290 through 305 Processing helix chain 'm' and resid 347 through 357 Processing helix chain 'm' and resid 373 through 377 Processing helix chain 'm' and resid 382 through 397 Processing helix chain 'n' and resid 17 through 26 Processing helix chain 'n' and resid 28 through 40 Processing helix chain 'n' and resid 64 through 73 removed outlier: 3.543A pdb=" N HIS n 73 " --> pdb=" O GLN n 69 " (cutoff:3.500A) Processing helix chain 'n' and resid 74 through 97 removed outlier: 3.814A pdb=" N ALA n 78 " --> pdb=" O GLU n 74 " (cutoff:3.500A) Processing helix chain 'n' and resid 98 through 108 Processing helix chain 'n' and resid 114 through 122 Processing helix chain 'n' and resid 124 through 145 removed outlier: 4.740A pdb=" N ASP n 133 " --> pdb=" O ILE n 129 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP n 134 " --> pdb=" O ARG n 130 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA n 135 " --> pdb=" O ASP n 131 " (cutoff:3.500A) Processing helix chain 'n' and resid 152 through 174 Processing helix chain 'n' and resid 214 through 241 removed outlier: 4.018A pdb=" N MET n 218 " --> pdb=" O ASP n 214 " (cutoff:3.500A) Processing helix chain 'n' and resid 249 through 256 Processing helix chain 'n' and resid 372 through 383 Processing helix chain 'n' and resid 391 through 394 Processing helix chain 'n' and resid 428 through 439 removed outlier: 4.349A pdb=" N ILE n 432 " --> pdb=" O GLN n 428 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE n 433 " --> pdb=" O PRO n 429 " (cutoff:3.500A) Processing helix chain 'n' and resid 443 through 447 removed outlier: 4.107A pdb=" N LYS n 446 " --> pdb=" O PRO n 443 " (cutoff:3.500A) Processing helix chain 'o' and resid 103 through 112 Processing helix chain 'o' and resid 141 through 153 Processing helix chain 'o' and resid 192 through 215 Processing helix chain 'q' and resid 197 through 213 Processing helix chain 'q' and resid 213 through 218 Processing helix chain 'q' and resid 223 through 240 removed outlier: 3.766A pdb=" N TYR q 227 " --> pdb=" O SER q 223 " (cutoff:3.500A) Processing helix chain 'q' and resid 242 through 253 Processing helix chain 'q' and resid 254 through 267 Processing helix chain 'q' and resid 281 through 293 Processing helix chain 'q' and resid 319 through 324 removed outlier: 3.534A pdb=" N LEU q 323 " --> pdb=" O THR q 319 " (cutoff:3.500A) Processing helix chain 'q' and resid 334 through 342 removed outlier: 4.141A pdb=" N VAL q 338 " --> pdb=" O SER q 334 " (cutoff:3.500A) Processing helix chain 'q' and resid 357 through 368 Processing helix chain 'q' and resid 379 through 394 Processing helix chain 'q' and resid 407 through 412 Processing helix chain 'q' and resid 426 through 430 removed outlier: 3.546A pdb=" N VAL q 429 " --> pdb=" O GLY q 426 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE q 430 " --> pdb=" O THR q 427 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 426 through 430' Processing helix chain 'q' and resid 434 through 440 removed outlier: 4.431A pdb=" N VAL q 438 " --> pdb=" O GLN q 434 " (cutoff:3.500A) Processing helix chain 'q' and resid 441 through 463 Proline residue: q 449 - end of helix Processing helix chain 'q' and resid 481 through 496 removed outlier: 4.927A pdb=" N VAL q 488 " --> pdb=" O GLU q 484 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE q 489 " --> pdb=" O ASP q 485 " (cutoff:3.500A) Processing helix chain 'q' and resid 522 through 527 Processing helix chain 'q' and resid 532 through 537 removed outlier: 3.666A pdb=" N TYR q 536 " --> pdb=" O TYR q 532 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 19 through 42 removed outlier: 4.308A pdb=" N SER r 32 " --> pdb=" O GLU r 28 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER r 36 " --> pdb=" O SER r 32 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 73 Processing helix chain 'r' and resid 99 through 118 Processing helix chain 'r' and resid 174 through 178 Processing helix chain 'r' and resid 206 through 213 Processing helix chain 'r' and resid 225 through 229 Processing helix chain 't' and resid 57 through 88 Processing helix chain 't' and resid 156 through 166 Processing helix chain 't' and resid 183 through 191 Processing helix chain 't' and resid 200 through 211 Processing helix chain 't' and resid 231 through 240 removed outlier: 3.986A pdb=" N VAL t 235 " --> pdb=" O ASP t 231 " (cutoff:3.500A) Processing helix chain 't' and resid 246 through 257 Processing helix chain 't' and resid 260 through 268 Processing helix chain 't' and resid 281 through 299 Processing helix chain 't' and resid 313 through 322 Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 52 through 59 Processing helix chain 'u' and resid 66 through 72 removed outlier: 3.920A pdb=" N PHE u 71 " --> pdb=" O THR u 68 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA u 72 " --> pdb=" O LEU u 69 " (cutoff:3.500A) Processing helix chain 'u' and resid 82 through 112 removed outlier: 3.869A pdb=" N ALA u 94 " --> pdb=" O LEU u 90 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG u 95 " --> pdb=" O LYS u 91 " (cutoff:3.500A) Processing helix chain 'v' and resid 4 through 12 Processing helix chain 'v' and resid 21 through 27 Processing helix chain 'v' and resid 33 through 40 Processing helix chain 'v' and resid 45 through 54 Processing helix chain 'v' and resid 157 through 168 Processing helix chain 'v' and resid 178 through 193 Processing helix chain 'v' and resid 195 through 202 Processing helix chain 'v' and resid 211 through 226 Processing helix chain 'w' and resid 2 through 11 Processing helix chain 'w' and resid 14 through 29 removed outlier: 3.825A pdb=" N LYS w 27 " --> pdb=" O GLU w 23 " (cutoff:3.500A) Processing helix chain 'w' and resid 31 through 36 Processing helix chain 'w' and resid 38 through 56 removed outlier: 3.752A pdb=" N PHE w 42 " --> pdb=" O LYS w 38 " (cutoff:3.500A) Processing helix chain 'w' and resid 58 through 72 Processing helix chain 'w' and resid 73 through 77 Processing helix chain 'w' and resid 78 through 83 Processing helix chain 'w' and resid 89 through 110 Processing helix chain 'w' and resid 111 through 113 No H-bonds generated for 'chain 'w' and resid 111 through 113' Processing helix chain 'w' and resid 114 through 139 removed outlier: 4.349A pdb=" N ASP w 119 " --> pdb=" O ARG w 115 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS w 120 " --> pdb=" O TYR w 116 " (cutoff:3.500A) Processing helix chain 'w' and resid 142 through 153 Processing helix chain 'w' and resid 167 through 186 removed outlier: 5.034A pdb=" N LEU w 178 " --> pdb=" O VAL w 174 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ASP w 179 " --> pdb=" O ASP w 175 " (cutoff:3.500A) Processing helix chain 'w' and resid 198 through 211 removed outlier: 3.693A pdb=" N LYS w 211 " --> pdb=" O GLU w 207 " (cutoff:3.500A) Processing helix chain 'w' and resid 213 through 227 removed outlier: 3.870A pdb=" N ILE w 220 " --> pdb=" O ASP w 216 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N PHE w 221 " --> pdb=" O VAL w 217 " (cutoff:3.500A) Processing helix chain 'w' and resid 231 through 242 Processing helix chain 'w' and resid 245 through 251 removed outlier: 4.204A pdb=" N VAL w 249 " --> pdb=" O ASP w 245 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 44 Processing helix chain 'x' and resid 44 through 55 removed outlier: 4.145A pdb=" N ARG x 48 " --> pdb=" O ASN x 44 " (cutoff:3.500A) Processing helix chain 'x' and resid 76 through 85 Processing helix chain 'x' and resid 104 through 118 Processing helix chain 'x' and resid 131 through 142 Processing helix chain 'x' and resid 204 through 218 Processing helix chain 'x' and resid 223 through 226 Processing helix chain 'x' and resid 283 through 289 Processing helix chain 'y' and resid 12 through 16 Processing helix chain 'y' and resid 32 through 43 Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 107 Processing helix chain 'y' and resid 122 through 134 Processing helix chain 'y' and resid 141 through 145 removed outlier: 3.777A pdb=" N GLY y 144 " --> pdb=" O THR y 141 " (cutoff:3.500A) Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 196 Processing helix chain 'y' and resid 211 through 223 Processing sheet with id=AA1, first strand: chain '8' and resid 263 through 265 removed outlier: 3.866A pdb=" N THR Z 329 " --> pdb=" O PHE Z 207 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP Z 209 " --> pdb=" O LYS Z 327 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS Z 327 " --> pdb=" O ASP Z 209 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL Z 268 " --> pdb=" O ARG Z 322 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL Z 266 " --> pdb=" O LYS Z 324 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE Z 326 " --> pdb=" O ALA Z 264 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA Z 264 " --> pdb=" O ILE Z 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '8' and resid 263 through 265 Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 61 removed outlier: 6.747A pdb=" N THR A 33 " --> pdb=" O ARG A 60 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A 34 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N PHE A 89 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ILE A 36 " --> pdb=" O PHE A 89 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N ALA A 91 " --> pdb=" O ILE A 36 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU A 97 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR A 109 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE A 226 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS A 111 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LEU A 117 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG A 218 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 214 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 218 through 227 current: chain 'A' and resid 134 through 140 removed outlier: 8.042A pdb=" N VAL J 223 " --> pdb=" O PRO A 135 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU A 137 " --> pdb=" O VAL J 223 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N SER J 225 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N PHE A 139 " --> pdb=" O SER J 225 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.168A pdb=" N VAL B 158 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL B 87 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N TRP B 106 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL B 89 " --> pdb=" O THR B 104 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR B 104 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY B 91 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.168A pdb=" N VAL B 158 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.156A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE B 359 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N THR B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N VAL B 220 " --> pdb=" O ILE B 335 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA B 217 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ILE B 278 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ALA B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N THR B 276 " --> pdb=" O ALA B 219 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS B 281 " --> pdb=" O LYS B 325 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE B 321 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG B 70 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY B 52 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ASP B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LYS B 50 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 15 through 21 removed outlier: 5.440A pdb=" N ASN C 18 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL C 151 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU C 150 " --> pdb=" O TRP C 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 62 through 64 Processing sheet with id=AB1, first strand: chain 'C' and resid 186 through 187 Processing sheet with id=AB2, first strand: chain 'D' and resid 145 through 148 removed outlier: 6.294A pdb=" N ILE D 117 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ALA D 170 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL D 119 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE D 118 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP D 196 " --> pdb=" O ILE D 118 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE D 120 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU D 193 " --> pdb=" O MET D 225 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N PHE D 227 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE D 195 " --> pdb=" O PHE D 227 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N VAL D 82 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N SER D 228 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY D 84 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 267 through 270 removed outlier: 6.122A pdb=" N ILE D 361 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE D 393 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLN D 363 " --> pdb=" O PHE D 393 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS D 291 " --> pdb=" O TRP D 360 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ILE D 362 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE D 293 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR D 346 " --> pdb=" O LEU D 319 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 77 through 80 removed outlier: 6.652A pdb=" N SER E 66 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR E 54 " --> pdb=" O SER E 66 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR E 38 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL E 39 " --> pdb=" O THR E 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 205 through 206 removed outlier: 4.127A pdb=" N SER F 113 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL F 134 " --> pdb=" O GLY F 230 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 153 through 156 Processing sheet with id=AB7, first strand: chain 'G' and resid 177 through 180 removed outlier: 6.305A pdb=" N VAL G 151 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL G 180 " --> pdb=" O VAL G 151 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE G 153 " --> pdb=" O VAL G 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 3 through 11 removed outlier: 6.933A pdb=" N ILE H 4 " --> pdb=" O ASN H 59 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU H 52 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 32 through 37 Processing sheet with id=AC1, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.539A pdb=" N LYS H 87 " --> pdb=" O LYS H 184 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS H 184 " --> pdb=" O LYS H 87 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS H 89 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AC3, first strand: chain 'I' and resid 34 through 38 removed outlier: 6.546A pdb=" N ARG I 2 " --> pdb=" O LEU I 410 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N PHE I 406 " --> pdb=" O SER I 6 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 47 through 54 removed outlier: 6.589A pdb=" N ALA I 61 " --> pdb=" O ASP I 48 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N MET I 50 " --> pdb=" O ILE I 59 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE I 59 " --> pdb=" O MET I 50 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N VAL I 52 " --> pdb=" O GLU I 57 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N GLU I 57 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL I 66 " --> pdb=" O ARG I 62 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL I 67 " --> pdb=" O SER I 113 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N SER I 113 " --> pdb=" O VAL I 67 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU I 69 " --> pdb=" O THR I 111 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 140 through 145 removed outlier: 3.683A pdb=" N THR I 142 " --> pdb=" O ALA I 158 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU I 163 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N LEU I 164 " --> pdb=" O SER I 180 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N SER I 180 " --> pdb=" O LEU I 164 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE I 166 " --> pdb=" O LEU I 178 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 189 through 192 removed outlier: 3.563A pdb=" N PHE I 189 " --> pdb=" O GLY I 208 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY I 208 " --> pdb=" O PHE I 189 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR I 203 " --> pdb=" O ILE I 219 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLY I 209 " --> pdb=" O LEU I 213 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU I 213 " --> pdb=" O GLY I 209 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE I 214 " --> pdb=" O GLU I 231 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU I 231 " --> pdb=" O ILE I 214 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU I 216 " --> pdb=" O ILE I 229 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 248 through 253 removed outlier: 6.502A pdb=" N ILE I 273 " --> pdb=" O MET I 249 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU I 251 " --> pdb=" O ALA I 271 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA I 271 " --> pdb=" O LEU I 251 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N PHE I 253 " --> pdb=" O GLN I 269 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N GLN I 269 " --> pdb=" O PHE I 253 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N HIS I 278 " --> pdb=" O THR I 274 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA I 292 " --> pdb=" O LYS I 281 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 307 through 308 removed outlier: 7.108A pdb=" N VAL I 342 " --> pdb=" O LYS I 354 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS I 354 " --> pdb=" O VAL I 342 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS I 344 " --> pdb=" O LEU I 352 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 366 through 370 removed outlier: 6.532A pdb=" N ASP I 388 " --> pdb=" O MET I 394 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N MET I 394 " --> pdb=" O ASP I 388 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 243 through 250 removed outlier: 6.616A pdb=" N THR K 243 " --> pdb=" O ASN K 84 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN K 84 " --> pdb=" O THR K 243 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ASN K 245 " --> pdb=" O VAL K 82 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL K 82 " --> pdb=" O ASN K 245 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N HIS K 247 " --> pdb=" O LEU K 80 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU K 80 " --> pdb=" O HIS K 247 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY K 249 " --> pdb=" O LEU K 78 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ARG K 277 " --> pdb=" O TYR K 293 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N TYR K 293 " --> pdb=" O ARG K 277 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE K 279 " --> pdb=" O LEU K 291 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 97 through 100 Processing sheet with id=AD3, first strand: chain 'K' and resid 153 through 156 removed outlier: 6.576A pdb=" N VAL K 123 " --> pdb=" O GLU K 153 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE K 155 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU K 125 " --> pdb=" O ILE K 155 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU K 124 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASP K 183 " --> pdb=" O LEU K 124 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ILE K 126 " --> pdb=" O ASP K 183 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 212 through 213 Processing sheet with id=AD5, first strand: chain 'L' and resid 21 through 24 removed outlier: 6.398A pdb=" N ARG L 21 " --> pdb=" O LEU N 197 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU N 199 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LYS L 23 " --> pdb=" O LEU N 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'L' and resid 57 through 59 Processing sheet with id=AD7, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AD8, first strand: chain 'M' and resid 14 through 15 Processing sheet with id=AD9, first strand: chain 'M' and resid 53 through 59 removed outlier: 4.809A pdb=" N GLY M 48 " --> pdb=" O PRO M 54 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU M 37 " --> pdb=" O LEU M 45 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ASP M 47 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ILE M 35 " --> pdb=" O ASP M 47 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG M 19 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N VAL M 20 " --> pdb=" O THR M 66 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.380A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'O' and resid 6 through 10 removed outlier: 6.233A pdb=" N VAL O 7 " --> pdb=" O VAL O 34 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N VAL O 36 " --> pdb=" O VAL O 7 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE O 9 " --> pdb=" O VAL O 36 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 42 through 44 Processing sheet with id=AE4, first strand: chain 'P' and resid 14 through 22 removed outlier: 5.610A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR P 151 " --> pdb=" O VAL P 114 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL P 114 " --> pdb=" O THR P 151 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AE6, first strand: chain 'Q' and resid 62 through 63 removed outlier: 6.339A pdb=" N VAL Q 81 " --> pdb=" O ALA Q 102 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N LEU Q 104 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 9.470A pdb=" N VAL Q 83 " --> pdb=" O LEU Q 104 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N PHE Q 106 " --> pdb=" O VAL Q 83 " (cutoff:3.500A) removed outlier: 10.768A pdb=" N GLY Q 85 " --> pdb=" O PHE Q 106 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL Q 101 " --> pdb=" O ILE Q 122 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 62 through 63 removed outlier: 6.509A pdb=" N THR Q 80 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'R' and resid 18 through 20 Processing sheet with id=AE9, first strand: chain 'R' and resid 50 through 56 Processing sheet with id=AF1, first strand: chain 'R' and resid 134 through 135 Processing sheet with id=AF2, first strand: chain 'S' and resid 25 through 31 removed outlier: 4.470A pdb=" N GLU S 6 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG S 12 " --> pdb=" O ILE S 58 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE S 58 " --> pdb=" O ARG S 12 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'S' and resid 86 through 96 removed outlier: 7.197A pdb=" N ASN S 74 " --> pdb=" O GLU S 128 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLU S 128 " --> pdb=" O ASN S 74 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY S 76 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N VAL S 126 " --> pdb=" O GLY S 76 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N TRP S 78 " --> pdb=" O LEU S 124 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'V' and resid 22 through 25 removed outlier: 5.382A pdb=" N ARG V 32 " --> pdb=" O CYS V 25 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ALA V 31 " --> pdb=" O GLY V 65 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N GLY V 65 " --> pdb=" O ALA V 31 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ASN V 33 " --> pdb=" O LYS V 63 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET V 59 " --> pdb=" O ILE V 37 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N VAL V 39 " --> pdb=" O MET V 57 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N MET V 57 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA V 99 " --> pdb=" O VAL V 79 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N GLY V 100 " --> pdb=" O ILE V 22 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ASN V 24 " --> pdb=" O GLY V 100 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE V 102 " --> pdb=" O ASN V 24 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'V' and resid 85 through 86 removed outlier: 6.529A pdb=" N PHE V 92 " --> pdb=" O MET u 20 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL u 22 " --> pdb=" O PHE V 92 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N TYR V 94 " --> pdb=" O VAL u 22 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'V' and resid 114 through 118 removed outlier: 8.390A pdb=" N ILE V 114 " --> pdb=" O GLY V 134 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL V 136 " --> pdb=" O ILE V 114 " (cutoff:3.500A) removed outlier: 10.572A pdb=" N GLY V 116 " --> pdb=" O VAL V 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'W' and resid 64 through 66 removed outlier: 4.070A pdb=" N ALA W 219 " --> pdb=" O VAL W 42 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'W' and resid 120 through 123 removed outlier: 3.571A pdb=" N SER W 211 " --> pdb=" O ASP W 123 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'W' and resid 136 through 137 Processing sheet with id=AG1, first strand: chain 'W' and resid 174 through 176 Processing sheet with id=AG2, first strand: chain 'Y' and resid 32 through 34 Processing sheet with id=AG3, first strand: chain 'Y' and resid 94 through 99 removed outlier: 9.609A pdb=" N VAL Y 95 " --> pdb=" O LYS Y 84 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS Y 84 " --> pdb=" O VAL Y 95 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE Y 97 " --> pdb=" O VAL Y 82 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL Y 82 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA Y 79 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL Y 73 " --> pdb=" O ALA Y 79 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLN Y 81 " --> pdb=" O SER Y 71 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LYS Y 69 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL Y 85 " --> pdb=" O GLU Y 67 " (cutoff:3.500A) removed outlier: 9.527A pdb=" N GLU Y 67 " --> pdb=" O VAL Y 85 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU Y 57 " --> pdb=" O ILE Y 106 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE Y 106 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Z' and resid 24 through 29 removed outlier: 6.194A pdb=" N LYS Z 24 " --> pdb=" O VAL Z 79 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL Z 94 " --> pdb=" O VAL Z 111 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS Z 341 " --> pdb=" O THR Z 108 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN Z 110 " --> pdb=" O LEU Z 339 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU Z 339 " --> pdb=" O GLN Z 110 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 164 through 170 removed outlier: 5.099A pdb=" N ALA a 166 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL a 36 " --> pdb=" O ALA a 166 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ALA a 168 " --> pdb=" O LEU a 34 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU a 34 " --> pdb=" O ALA a 168 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY a 170 " --> pdb=" O VAL a 32 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE a 214 " --> pdb=" O VAL a 206 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 85 through 86 removed outlier: 7.555A pdb=" N MET a 85 " --> pdb=" O ILE a 65 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N ILE a 67 " --> pdb=" O MET a 85 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 205 through 211 removed outlier: 6.614A pdb=" N THR b 169 " --> pdb=" O CYS b 249 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU b 251 " --> pdb=" O THR b 169 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU b 171 " --> pdb=" O LEU b 251 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE b 253 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N CYS b 173 " --> pdb=" O PHE b 253 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N MET b 284 " --> pdb=" O SER b 248 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N VAL b 250 " --> pdb=" O MET b 284 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL b 286 " --> pdb=" O VAL b 250 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR b 252 " --> pdb=" O VAL b 286 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 435 through 436 Processing sheet with id=AG9, first strand: chain 'e' and resid 72 through 76 removed outlier: 5.837A pdb=" N LYS e 72 " --> pdb=" O ALA e 93 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU e 95 " --> pdb=" O LYS e 72 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE e 74 " --> pdb=" O GLU e 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'f' and resid 8 through 18 removed outlier: 9.477A pdb=" N VAL f 9 " --> pdb=" O ILE f 32 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ILE f 32 " --> pdb=" O VAL f 9 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N GLY f 11 " --> pdb=" O ILE f 30 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N ILE f 30 " --> pdb=" O GLY f 11 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N HIS f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N SER f 28 " --> pdb=" O HIS f 13 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N SER f 15 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ASN f 26 " --> pdb=" O SER f 15 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN f 17 " --> pdb=" O ASN f 24 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASN f 26 " --> pdb=" O PHE f 85 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE f 85 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL f 80 " --> pdb=" O HIS f 75 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N THR f 84 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N VAL f 71 " --> pdb=" O THR f 84 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE f 64 " --> pdb=" O LYS f 57 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N LYS f 57 " --> pdb=" O ILE f 64 " (cutoff:3.500A) removed outlier: 10.447A pdb=" N VAL f 66 " --> pdb=" O ALA f 55 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N ALA f 55 " --> pdb=" O VAL f 66 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N TRP f 68 " --> pdb=" O TYR f 53 " (cutoff:3.500A) removed outlier: 12.032A pdb=" N TYR f 53 " --> pdb=" O TRP f 68 " (cutoff:3.500A) removed outlier: 11.067A pdb=" N LYS f 70 " --> pdb=" O TYR f 51 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N TYR f 51 " --> pdb=" O LYS f 70 " (cutoff:3.500A) removed outlier: 10.399A pdb=" N THR f 72 " --> pdb=" O ILE f 49 " (cutoff:3.500A) removed outlier: 11.932A pdb=" N ILE f 49 " --> pdb=" O THR f 72 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARG f 48 " --> pdb=" O PHE f 101 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL f 52 " --> pdb=" O SER f 97 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N SER f 97 " --> pdb=" O VAL f 52 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'j' and resid 16 through 18 removed outlier: 3.556A pdb=" N THR j 33 " --> pdb=" O HIS j 28 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'l' and resid 2 through 3 removed outlier: 3.529A pdb=" N VAL l 47 " --> pdb=" O VAL l 36 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY l 71 " --> pdb=" O VAL l 44 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS l 72 " --> pdb=" O ARG l 80 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG l 80 " --> pdb=" O LYS l 72 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'l' and resid 65 through 66 removed outlier: 3.634A pdb=" N SER l 65 " --> pdb=" O VAL q 400 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL q 400 " --> pdb=" O SER l 65 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL q 373 " --> pdb=" O ILE q 399 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N CYS q 401 " --> pdb=" O VAL q 373 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA q 375 " --> pdb=" O CYS q 401 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG q 348 " --> pdb=" O ARG q 417 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LEU q 419 " --> pdb=" O ARG q 348 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU q 350 " --> pdb=" O LEU q 419 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE q 418 " --> pdb=" O VAL q 474 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N SER q 476 " --> pdb=" O ILE q 418 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU q 420 " --> pdb=" O SER q 476 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY q 471 " --> pdb=" O LYS q 548 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'l' and resid 65 through 66 removed outlier: 3.634A pdb=" N SER l 65 " --> pdb=" O VAL q 400 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL q 400 " --> pdb=" O SER l 65 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL q 373 " --> pdb=" O ILE q 399 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N CYS q 401 " --> pdb=" O VAL q 373 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ALA q 375 " --> pdb=" O CYS q 401 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG q 348 " --> pdb=" O ARG q 417 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LEU q 419 " --> pdb=" O ARG q 348 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU q 350 " --> pdb=" O LEU q 419 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE q 418 " --> pdb=" O VAL q 474 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N SER q 476 " --> pdb=" O ILE q 418 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU q 420 " --> pdb=" O SER q 476 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLY q 471 " --> pdb=" O LYS q 548 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL q 543 " --> pdb=" O ARG q 529 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG q 529 " --> pdb=" O VAL q 543 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS q 510 " --> pdb=" O ARG q 530 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'l' and resid 118 through 121 removed outlier: 3.841A pdb=" N LYS l 120 " --> pdb=" O TRP l 98 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP l 98 " --> pdb=" O LYS l 120 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL l 131 " --> pdb=" O PHE l 143 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE l 143 " --> pdb=" O VAL l 131 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL l 133 " --> pdb=" O LEU l 141 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'm' and resid 126 through 127 Processing sheet with id=AH8, first strand: chain 'n' and resid 176 through 181 removed outlier: 6.674A pdb=" N GLN n 189 " --> pdb=" O ARG n 177 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N VAL n 179 " --> pdb=" O TYR n 187 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N TYR n 187 " --> pdb=" O VAL n 179 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'n' and resid 386 through 389 removed outlier: 6.036A pdb=" N VAL n 364 " --> pdb=" O HIS n 409 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE n 411 " --> pdb=" O VAL n 364 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR n 366 " --> pdb=" O ILE n 411 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'o' and resid 117 through 124 removed outlier: 6.724A pdb=" N GLU o 138 " --> pdb=" O LYS o 118 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N VAL o 120 " --> pdb=" O PHE o 136 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE o 136 " --> pdb=" O VAL o 120 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LEU o 122 " --> pdb=" O TYR o 134 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TYR o 134 " --> pdb=" O LEU o 122 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG o 124 " --> pdb=" O ARG o 132 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ARG o 132 " --> pdb=" O ARG o 124 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR o 155 " --> pdb=" O LEU o 162 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'q' and resid 297 through 298 removed outlier: 3.669A pdb=" N ILE q 271 " --> pdb=" O ILE q 309 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'q' and resid 515 through 516 Processing sheet with id=AI4, first strand: chain 'r' and resid 154 through 155 removed outlier: 4.478A pdb=" N HIS r 154 " --> pdb=" O LEU r 215 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'r' and resid 181 through 186 removed outlier: 3.578A pdb=" N VAL r 191 " --> pdb=" O HIS r 186 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE r 220 " --> pdb=" O LYS r 201 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ALA r 257 " --> pdb=" O LYS r 181 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASN r 183 " --> pdb=" O ALA r 257 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU r 259 " --> pdb=" O ASN r 183 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR r 185 " --> pdb=" O LEU r 259 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 't' and resid 129 through 134 removed outlier: 6.992A pdb=" N PHE t 99 " --> pdb=" O VAL t 309 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLU t 311 " --> pdb=" O PHE t 99 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU t 101 " --> pdb=" O GLU t 311 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N VAL t 194 " --> pdb=" O ILE t 310 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N VAL t 312 " --> pdb=" O VAL t 194 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE t 196 " --> pdb=" O VAL t 312 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA t 140 " --> pdb=" O LEU t 179 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR t 173 " --> pdb=" O ARG t 146 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 't' and resid 213 through 216 Processing sheet with id=AI8, first strand: chain 'u' and resid 4 through 5 Processing sheet with id=AI9, first strand: chain 'x' and resid 121 through 123 removed outlier: 6.166A pdb=" N ILE x 95 " --> pdb=" O THR x 122 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE x 147 " --> pdb=" O PHE x 162 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE x 162 " --> pdb=" O ILE x 147 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE x 149 " --> pdb=" O LEU x 160 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU x 160 " --> pdb=" O ILE x 149 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN x 151 " --> pdb=" O THR x 158 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR x 158 " --> pdb=" O LEU x 175 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS x 174 " --> pdb=" O LEU x 267 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU x 267 " --> pdb=" O LYS x 174 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG x 243 " --> pdb=" O LEU x 259 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N PHE x 241 " --> pdb=" O PRO x 261 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N PHE x 263 " --> pdb=" O ILE x 239 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE x 239 " --> pdb=" O PHE x 263 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU x 196 " --> pdb=" O ILE x 230 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU x 232 " --> pdb=" O GLU x 196 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE x 198 " --> pdb=" O LEU x 232 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASN x 234 " --> pdb=" O ILE x 198 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN x 200 " --> pdb=" O ASN x 234 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'x' and resid 121 through 123 removed outlier: 6.166A pdb=" N ILE x 95 " --> pdb=" O THR x 122 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE x 147 " --> pdb=" O PHE x 162 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE x 162 " --> pdb=" O ILE x 147 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE x 149 " --> pdb=" O LEU x 160 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU x 160 " --> pdb=" O ILE x 149 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN x 151 " --> pdb=" O THR x 158 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR x 158 " --> pdb=" O LEU x 175 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LYS x 174 " --> pdb=" O LEU x 267 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU x 267 " --> pdb=" O LYS x 174 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'y' and resid 2 through 5 removed outlier: 6.333A pdb=" N THR y 3 " --> pdb=" O THR y 206 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'y' and resid 17 through 19 Processing sheet with id=AJ4, first strand: chain 'y' and resid 64 through 65 removed outlier: 6.333A pdb=" N LEU y 70 " --> pdb=" O GLN y 95 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL y 97 " --> pdb=" O LEU y 70 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL y 72 " --> pdb=" O VAL y 97 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'y' and resid 108 through 110 Processing sheet with id=AJ6, first strand: chain 'y' and resid 152 through 154 3358 hydrogen bonds defined for protein. 9594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1671 hydrogen bonds 2726 hydrogen bond angles 0 basepair planarities 672 basepair parallelities 1084 stacking parallelities Total time for adding SS restraints: 96.81 Time building geometry restraints manager: 47.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 17348 1.32 - 1.45: 44640 1.45 - 1.57: 59414 1.57 - 1.70: 4417 1.70 - 1.82: 337 Bond restraints: 126156 Sorted by residual: bond pdb=" CG1 ILE f 49 " pdb=" CD1 ILE f 49 " ideal model delta sigma weight residual 1.513 1.448 0.065 3.90e-02 6.57e+02 2.79e+00 bond pdb=" CG1 ILE Y 70 " pdb=" CD1 ILE Y 70 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.07e+00 bond pdb=" CG1 ILE h 118 " pdb=" CD1 ILE h 118 " ideal model delta sigma weight residual 1.513 1.458 0.055 3.90e-02 6.57e+02 1.96e+00 bond pdb=" CG LEU L 85 " pdb=" CD1 LEU L 85 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.88e+00 bond pdb=" C ILE m 136 " pdb=" N LYS m 137 " ideal model delta sigma weight residual 1.339 1.267 0.073 5.57e-02 3.22e+02 1.69e+00 ... (remaining 126151 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.15: 13792 106.15 - 113.13: 71969 113.13 - 120.11: 44069 120.11 - 127.09: 45475 127.09 - 134.07: 5677 Bond angle restraints: 180982 Sorted by residual: angle pdb=" O4' G 1 406 " pdb=" C1' G 1 406 " pdb=" N9 G 1 406 " ideal model delta sigma weight residual 108.20 116.14 -7.94 1.50e+00 4.44e-01 2.80e+01 angle pdb=" C3' C 12889 " pdb=" O3' C 12889 " pdb=" P A 12890 " ideal model delta sigma weight residual 120.20 125.76 -5.56 1.50e+00 4.44e-01 1.37e+01 angle pdb=" C ALA t 304 " pdb=" N ALA t 305 " pdb=" CA ALA t 305 " ideal model delta sigma weight residual 121.54 128.11 -6.57 1.91e+00 2.74e-01 1.18e+01 angle pdb=" O3' C 12889 " pdb=" C3' C 12889 " pdb=" C2' C 12889 " ideal model delta sigma weight residual 109.50 114.44 -4.94 1.50e+00 4.44e-01 1.08e+01 angle pdb=" C3' A 11886 " pdb=" O3' A 11886 " pdb=" P A 11887 " ideal model delta sigma weight residual 120.20 125.05 -4.85 1.50e+00 4.44e-01 1.04e+01 ... (remaining 180977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 73546 35.96 - 71.91: 5353 71.91 - 107.87: 539 107.87 - 143.83: 8 143.83 - 179.79: 25 Dihedral angle restraints: 79471 sinusoidal: 53443 harmonic: 26028 Sorted by residual: dihedral pdb=" O4' U 13214 " pdb=" C1' U 13214 " pdb=" N1 U 13214 " pdb=" C2 U 13214 " ideal model delta sinusoidal sigma weight residual 200.00 27.39 172.61 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U 2 156 " pdb=" C1' U 2 156 " pdb=" N1 U 2 156 " pdb=" C2 U 2 156 " ideal model delta sinusoidal sigma weight residual 200.00 28.45 171.55 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' U 13306 " pdb=" C1' U 13306 " pdb=" N1 U 13306 " pdb=" C2 U 13306 " ideal model delta sinusoidal sigma weight residual 200.00 29.37 170.63 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 79468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 18748 0.050 - 0.100: 2715 0.100 - 0.150: 555 0.150 - 0.200: 26 0.200 - 0.250: 5 Chirality restraints: 22049 Sorted by residual: chirality pdb=" C1' G 1 406 " pdb=" O4' G 1 406 " pdb=" C2' G 1 406 " pdb=" N9 G 1 406 " both_signs ideal model delta sigma weight residual False 2.44 2.19 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C1' A 2 88 " pdb=" O4' A 2 88 " pdb=" C2' A 2 88 " pdb=" N9 A 2 88 " both_signs ideal model delta sigma weight residual False 2.46 2.23 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C1' C 2 21 " pdb=" O4' C 2 21 " pdb=" C2' C 2 21 " pdb=" N1 C 2 21 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 22046 not shown) Planarity restraints: 14697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 39 " 0.613 9.50e-02 1.11e+02 2.75e-01 4.61e+01 pdb=" NE ARG L 39 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG L 39 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG L 39 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG L 39 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 406 " -0.068 2.00e-02 2.50e+03 2.87e-02 2.46e+01 pdb=" N9 G 1 406 " 0.065 2.00e-02 2.50e+03 pdb=" C8 G 1 406 " 0.009 2.00e-02 2.50e+03 pdb=" N7 G 1 406 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G 1 406 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G 1 406 " -0.017 2.00e-02 2.50e+03 pdb=" O6 G 1 406 " -0.013 2.00e-02 2.50e+03 pdb=" N1 G 1 406 " -0.010 2.00e-02 2.50e+03 pdb=" C2 G 1 406 " 0.005 2.00e-02 2.50e+03 pdb=" N2 G 1 406 " 0.006 2.00e-02 2.50e+03 pdb=" N3 G 1 406 " 0.014 2.00e-02 2.50e+03 pdb=" C4 G 1 406 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 39 " -0.047 2.00e-02 2.50e+03 1.93e-02 1.12e+01 pdb=" N9 G 2 39 " 0.041 2.00e-02 2.50e+03 pdb=" C8 G 2 39 " 0.007 2.00e-02 2.50e+03 pdb=" N7 G 2 39 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G 2 39 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 2 39 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G 2 39 " -0.014 2.00e-02 2.50e+03 pdb=" N1 G 2 39 " -0.006 2.00e-02 2.50e+03 pdb=" C2 G 2 39 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G 2 39 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 2 39 " 0.013 2.00e-02 2.50e+03 pdb=" C4 G 2 39 " 0.007 2.00e-02 2.50e+03 ... (remaining 14694 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 6483 2.70 - 3.25: 110010 3.25 - 3.80: 227734 3.80 - 4.35: 288050 4.35 - 4.90: 414403 Nonbonded interactions: 1046680 Sorted by model distance: nonbonded pdb=" O2' G 1 651 " pdb=" OP1 A 11435 " model vdw 2.155 2.440 nonbonded pdb=" O2' G 1 718 " pdb=" OP2 A 1 720 " model vdw 2.186 2.440 nonbonded pdb=" O2' G 13386 " pdb=" OP1 U 13387 " model vdw 2.199 2.440 nonbonded pdb=" NH2 ARG R 132 " pdb=" O GLU x 152 " model vdw 2.202 2.520 nonbonded pdb=" O VAL q 480 " pdb=" NH2 ARG q 530 " model vdw 2.204 2.520 ... (remaining 1046675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 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: 19.610 Check model and map are aligned: 0.660 Set scattering table: 0.770 Process input model: 323.640 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 361.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 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 0.073 126156 Z= 0.233 Angle : 0.538 9.065 180982 Z= 0.281 Chirality : 0.037 0.250 22049 Planarity : 0.005 0.275 14697 Dihedral : 19.880 179.787 62569 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.91 % Allowed : 4.67 % Favored : 94.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.09), residues: 8763 helix: 2.02 (0.09), residues: 3673 sheet: 0.14 (0.14), residues: 1341 loop : 0.13 (0.10), residues: 3749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP e 32 HIS 0.005 0.001 HIS R 106 PHE 0.030 0.002 PHE F 229 TYR 0.019 0.002 TYR Q 33 ARG 0.007 0.001 ARG j 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2029 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1958 time to evaluate : 7.065 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: A 117 LEU cc_start: 0.6720 (tp) cc_final: 0.6441 (tp) REVERT: A 141 GLN cc_start: 0.5352 (tp40) cc_final: 0.5002 (tm-30) REVERT: A 151 LEU cc_start: 0.6938 (tp) cc_final: 0.6653 (tp) REVERT: A 174 ASP cc_start: 0.5596 (t0) cc_final: 0.5378 (t0) REVERT: B 36 ASP cc_start: 0.7696 (t0) cc_final: 0.7470 (t70) REVERT: B 53 MET cc_start: 0.8685 (mtp) cc_final: 0.8365 (mtp) REVERT: B 116 ARG cc_start: 0.8090 (ttm-80) cc_final: 0.7797 (mtt-85) REVERT: B 124 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.6844 (mttt) REVERT: B 190 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7675 (mt-10) REVERT: B 369 ARG cc_start: 0.8023 (mtp180) cc_final: 0.7794 (mtm-85) REVERT: B 377 HIS cc_start: 0.6121 (t-90) cc_final: 0.5781 (t-170) REVERT: C 155 ASP cc_start: 0.7930 (p0) cc_final: 0.7592 (m-30) REVERT: C 304 GLN cc_start: 0.8534 (mt0) cc_final: 0.8028 (mt0) REVERT: C 342 LYS cc_start: 0.8197 (tttt) cc_final: 0.7979 (tttt) REVERT: D 60 MET cc_start: 0.5706 (mtp) cc_final: 0.5350 (mtp) REVERT: D 62 PHE cc_start: 0.5593 (m-80) cc_final: 0.5001 (m-10) REVERT: D 129 GLN cc_start: 0.6293 (tt0) cc_final: 0.6020 (pt0) REVERT: D 138 MET cc_start: 0.7371 (mtp) cc_final: 0.6467 (mtm) REVERT: D 155 ARG cc_start: 0.8126 (mtp180) cc_final: 0.7550 (ttt180) REVERT: D 225 MET cc_start: 0.5661 (mtt) cc_final: 0.5194 (mmp) REVERT: D 307 GLU cc_start: 0.7287 (mt-10) cc_final: 0.7057 (mm-30) REVERT: D 351 ARG cc_start: 0.6169 (mtt180) cc_final: 0.5908 (mmp-170) REVERT: D 355 ILE cc_start: 0.5229 (tp) cc_final: 0.4833 (tp) REVERT: D 419 GLU cc_start: 0.6257 (mt-10) cc_final: 0.5773 (tm-30) REVERT: E 59 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7655 (mp0) REVERT: E 99 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6944 (mm-30) REVERT: E 108 LYS cc_start: 0.7778 (ptpt) cc_final: 0.7346 (mtmt) REVERT: F 20 GLN cc_start: 0.8163 (tp40) cc_final: 0.7610 (tm-30) REVERT: F 25 GLN cc_start: 0.8083 (tt0) cc_final: 0.7815 (tp40) REVERT: G 89 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8377 (mm-30) REVERT: G 93 LEU cc_start: 0.8866 (tp) cc_final: 0.8431 (tp) REVERT: G 100 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7694 (pt0) REVERT: G 104 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8256 (mt-10) REVERT: G 111 LYS cc_start: 0.8157 (ttpp) cc_final: 0.7955 (tttp) REVERT: G 173 MET cc_start: 0.8992 (mmm) cc_final: 0.8542 (mmm) REVERT: H 31 ARG cc_start: 0.7956 (mtp-110) cc_final: 0.7719 (mtp85) REVERT: H 42 ASP cc_start: 0.8699 (m-30) cc_final: 0.8497 (m-30) REVERT: H 54 LYS cc_start: 0.8703 (mttt) cc_final: 0.8495 (ttmt) REVERT: H 63 LYS cc_start: 0.8472 (ptmm) cc_final: 0.7983 (mmtp) REVERT: H 94 TYR cc_start: 0.8738 (p90) cc_final: 0.8437 (p90) REVERT: I 33 PHE cc_start: 0.8670 (m-80) cc_final: 0.8313 (m-80) REVERT: I 120 ASP cc_start: 0.6980 (m-30) cc_final: 0.6077 (p0) REVERT: I 147 LYS cc_start: 0.7527 (tttt) cc_final: 0.7078 (tptp) REVERT: I 314 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7135 (mm-30) REVERT: J 205 LEU cc_start: 0.5071 (tp) cc_final: 0.4848 (tp) REVERT: J 228 ASN cc_start: 0.4309 (OUTLIER) cc_final: 0.3971 (m-40) REVERT: J 285 MET cc_start: 0.5522 (mmm) cc_final: 0.5274 (mmt) REVERT: K 135 VAL cc_start: 0.6170 (p) cc_final: 0.5955 (p) REVERT: K 141 PHE cc_start: 0.5031 (t80) cc_final: 0.4804 (t80) REVERT: K 194 MET cc_start: 0.7022 (mtp) cc_final: 0.6659 (mtp) REVERT: K 225 ASN cc_start: 0.5819 (m-40) cc_final: 0.5587 (m110) REVERT: L 23 LYS cc_start: 0.7558 (ptmt) cc_final: 0.7329 (pttm) REVERT: L 103 ASN cc_start: 0.8520 (m110) cc_final: 0.8246 (m-40) REVERT: L 105 ASN cc_start: 0.8731 (t0) cc_final: 0.8511 (t160) REVERT: L 114 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7898 (tm-30) REVERT: L 122 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8584 (mmtm) REVERT: N 4 TYR cc_start: 0.7984 (m-80) cc_final: 0.7746 (m-10) REVERT: N 5 LYS cc_start: 0.8571 (tptm) cc_final: 0.8335 (tppt) REVERT: N 23 GLN cc_start: 0.7860 (tt0) cc_final: 0.7550 (mm110) REVERT: N 29 GLU cc_start: 0.7942 (tt0) cc_final: 0.7615 (mt-10) REVERT: N 31 ARG cc_start: 0.7342 (mtm110) cc_final: 0.7047 (mtm180) REVERT: N 33 LYS cc_start: 0.8264 (mttt) cc_final: 0.8000 (mttp) REVERT: N 117 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8709 (m-40) REVERT: O 4 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7378 (mm-30) REVERT: O 78 ARG cc_start: 0.8588 (mmp-170) cc_final: 0.8227 (mmp-170) REVERT: O 166 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7977 (mt-10) REVERT: P 153 LYS cc_start: 0.7819 (tptt) cc_final: 0.7589 (pttp) REVERT: Q 92 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.7030 (mpp80) REVERT: R 128 ARG cc_start: 0.8227 (mtp180) cc_final: 0.8019 (ttp-170) REVERT: R 163 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7525 (mt-10) REVERT: S 3 HIS cc_start: 0.5972 (t70) cc_final: 0.5720 (t-90) REVERT: S 47 LYS cc_start: 0.7732 (ttpp) cc_final: 0.7337 (tttm) REVERT: S 83 SER cc_start: 0.6125 (p) cc_final: 0.5912 (t) REVERT: S 104 GLU cc_start: 0.8557 (tt0) cc_final: 0.8153 (mt-10) REVERT: S 131 LYS cc_start: 0.8001 (mttt) cc_final: 0.7573 (mmmt) REVERT: V 53 SER cc_start: 0.8692 (m) cc_final: 0.8286 (t) REVERT: V 59 MET cc_start: 0.8314 (mmt) cc_final: 0.7932 (mmm) REVERT: W 25 ARG cc_start: 0.6373 (ttp80) cc_final: 0.6172 (ttp80) REVERT: W 85 TYR cc_start: 0.5342 (t80) cc_final: 0.4963 (t80) REVERT: W 121 ARG cc_start: 0.5849 (mmm-85) cc_final: 0.5590 (mmm160) REVERT: W 143 TYR cc_start: 0.6829 (m-80) cc_final: 0.6562 (m-80) REVERT: W 222 ASP cc_start: 0.4296 (t0) cc_final: 0.3996 (t0) REVERT: W 231 THR cc_start: 0.5453 (p) cc_final: 0.4908 (p) REVERT: Y 11 ASP cc_start: 0.8691 (t0) cc_final: 0.8447 (t70) REVERT: Y 67 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7559 (mm-30) REVERT: Z 141 LEU cc_start: 0.4002 (tp) cc_final: 0.3582 (mt) REVERT: Z 147 SER cc_start: 0.3444 (p) cc_final: 0.3120 (p) REVERT: Z 169 PHE cc_start: 0.4697 (m-10) cc_final: 0.3500 (m-80) REVERT: Z 176 LEU cc_start: 0.4652 (tt) cc_final: 0.4355 (mp) REVERT: Z 192 ILE cc_start: 0.5008 (mt) cc_final: 0.4648 (mp) REVERT: a 113 SER cc_start: 0.1016 (p) cc_final: 0.0611 (t) REVERT: b 3 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6875 (tp) REVERT: b 185 ARG cc_start: 0.6551 (mtp180) cc_final: 0.6269 (tmt-80) REVERT: b 252 TYR cc_start: 0.6401 (t80) cc_final: 0.5949 (t80) REVERT: b 327 ASN cc_start: 0.6026 (m110) cc_final: 0.5809 (m110) REVERT: b 466 GLU cc_start: 0.5282 (tt0) cc_final: 0.4945 (mm-30) REVERT: e 34 LYS cc_start: 0.8643 (tttp) cc_final: 0.8409 (ttpt) REVERT: h 27 GLU cc_start: 0.7039 (tt0) cc_final: 0.6833 (tt0) REVERT: h 59 ASN cc_start: 0.8425 (t0) cc_final: 0.8144 (m-40) REVERT: i 26 ILE cc_start: 0.8420 (mt) cc_final: 0.8148 (tp) REVERT: i 58 ILE cc_start: 0.7925 (pp) cc_final: 0.7569 (mt) REVERT: i 75 LYS cc_start: 0.8061 (ttmm) cc_final: 0.7746 (mtmt) REVERT: i 88 GLU cc_start: 0.7772 (tp30) cc_final: 0.7206 (tt0) REVERT: i 90 MET cc_start: 0.8453 (mmp) cc_final: 0.8121 (mmp) REVERT: m 355 GLU cc_start: 0.2976 (tt0) cc_final: 0.2675 (tp30) REVERT: n 259 LEU cc_start: 0.4187 (pp) cc_final: 0.3911 (pp) REVERT: q 226 GLU cc_start: 0.2476 (mt-10) cc_final: 0.2197 (mm-30) REVERT: r 194 PHE cc_start: 0.7120 (OUTLIER) cc_final: 0.6356 (t80) REVERT: r 214 VAL cc_start: 0.6004 (t) cc_final: 0.5757 (m) REVERT: t 165 LEU cc_start: 0.6545 (mt) cc_final: 0.6325 (mt) REVERT: t 210 LYS cc_start: 0.6121 (mmtp) cc_final: 0.5855 (mtmt) REVERT: t 236 GLU cc_start: 0.4652 (tt0) cc_final: 0.4436 (tt0) REVERT: u 55 PHE cc_start: 0.7040 (t80) cc_final: 0.6816 (t80) REVERT: u 96 ILE cc_start: 0.7850 (mt) cc_final: 0.7550 (mp) REVERT: u 103 ARG cc_start: 0.6701 (mtt180) cc_final: 0.6336 (mtt180) REVERT: u 105 ARG cc_start: 0.6325 (ttt180) cc_final: 0.6123 (tmm-80) REVERT: v 75 LYS cc_start: 0.6736 (mttt) cc_final: 0.6504 (ptpt) REVERT: v 179 GLU cc_start: 0.8069 (pt0) cc_final: 0.7798 (tt0) REVERT: v 186 GLU cc_start: 0.7856 (tt0) cc_final: 0.7574 (tt0) REVERT: v 188 LEU cc_start: 0.8141 (mt) cc_final: 0.7857 (mt) REVERT: v 211 SER cc_start: 0.8762 (p) cc_final: 0.8526 (p) REVERT: v 214 ASP cc_start: 0.8333 (t0) cc_final: 0.8111 (t0) REVERT: v 219 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7606 (tp) REVERT: w 2 GLU cc_start: 0.6337 (mm-30) cc_final: 0.6117 (tp30) REVERT: w 34 PHE cc_start: 0.6855 (t80) cc_final: 0.6469 (t80) REVERT: w 78 ASP cc_start: 0.7783 (t0) cc_final: 0.7066 (t0) REVERT: w 80 LYS cc_start: 0.7436 (mttt) cc_final: 0.6849 (mmmm) REVERT: w 106 MET cc_start: 0.9043 (mmm) cc_final: 0.8824 (mmm) REVERT: w 179 ASP cc_start: 0.8754 (m-30) cc_final: 0.8446 (m-30) REVERT: w 203 ARG cc_start: 0.6765 (ptp-170) cc_final: 0.6488 (ptm-80) REVERT: w 216 ASP cc_start: 0.7747 (m-30) cc_final: 0.7526 (m-30) REVERT: x 18 ILE cc_start: 0.8961 (mt) cc_final: 0.8549 (mt) REVERT: x 53 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7721 (tmtp) REVERT: x 62 ASN cc_start: 0.7642 (m110) cc_final: 0.7341 (m-40) REVERT: x 67 ASP cc_start: 0.8388 (t70) cc_final: 0.8130 (t70) REVERT: x 258 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: y 1 MET cc_start: 0.5422 (tpt) cc_final: 0.4922 (ttp) REVERT: y 4 ARG cc_start: 0.7970 (mtt90) cc_final: 0.7748 (mtm-85) REVERT: y 57 ARG cc_start: 0.8735 (mtm180) cc_final: 0.8490 (mtp-110) REVERT: y 67 ARG cc_start: 0.7700 (ptt90) cc_final: 0.7357 (ptt90) REVERT: y 98 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7537 (mt-10) REVERT: y 164 GLN cc_start: 0.7563 (mm-40) cc_final: 0.7333 (mm110) REVERT: y 176 LEU cc_start: 0.7242 (mp) cc_final: 0.6917 (tp) REVERT: y 197 MET cc_start: 0.8581 (ptm) cc_final: 0.8223 (ptm) outliers start: 71 outliers final: 23 residues processed: 2010 average time/residue: 2.0354 time to fit residues: 5543.3402 Evaluate side-chains 1313 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1282 time to evaluate : 6.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain J residue 228 ASN Chi-restraints excluded: chain N residue 117 ASN Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain T residue 232 VAL Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain l residue 56 THR Chi-restraints excluded: chain n residue 179 VAL Chi-restraints excluded: chain n residue 387 VAL Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 194 PHE Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain v residue 175 ARG Chi-restraints excluded: chain v residue 219 LEU Chi-restraints excluded: chain w residue 69 LEU Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 258 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1093 random chunks: chunk 922 optimal weight: 8.9990 chunk 828 optimal weight: 8.9990 chunk 459 optimal weight: 4.9990 chunk 282 optimal weight: 9.9990 chunk 558 optimal weight: 0.9990 chunk 442 optimal weight: 4.9990 chunk 856 optimal weight: 8.9990 chunk 331 optimal weight: 6.9990 chunk 520 optimal weight: 9.9990 chunk 637 optimal weight: 2.9990 chunk 992 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 393 ASN 8 401 GLN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN ** A 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 211 GLN ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN C 18 ASN D 397 ASN F 12 GLN F 19 GLN F 225 GLN G 221 ASN H 59 ASN H 157 ASN ** H 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 295 GLN N 15 GLN N 32 GLN N 122 ASN P 50 GLN P 92 GLN P 121 GLN Q 45 ASN Q 78 ASN R 17 HIS R 146 GLN S 62 ASN S 74 ASN W 91 GLN Y 120 GLN Z 353 HIS b 234 ASN b 267 GLN e 49 ASN f 106 ASN h 76 GLN i 92 ASN m 305 ASN ** n 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 144 ASN n 191 ASN o 130 ASN q 276 ASN q 330 GLN r 4 ASN r 14 HIS r 40 GLN t 53 ASN u 42 GLN x 24 HIS x 120 ASN x 201 ASN x 208 GLN y 6 GLN y 11 ASN y 157 GLN y 170 GLN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 126156 Z= 0.293 Angle : 0.603 9.315 180982 Z= 0.309 Chirality : 0.040 0.274 22049 Planarity : 0.005 0.083 14697 Dihedral : 21.844 179.776 44177 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.54 % Favored : 97.44 % Rotamer: Outliers : 3.95 % Allowed : 13.04 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.09), residues: 8763 helix: 1.79 (0.08), residues: 3654 sheet: 0.25 (0.14), residues: 1312 loop : 0.07 (0.10), residues: 3797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP e 32 HIS 0.007 0.001 HIS R 106 PHE 0.032 0.002 PHE F 229 TYR 0.028 0.002 TYR Y 74 ARG 0.009 0.001 ARG u 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1565 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 1257 time to evaluate : 7.161 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: 8 345 LYS cc_start: 0.4550 (OUTLIER) cc_final: 0.3632 (ptmt) REVERT: A 155 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7753 (mm) REVERT: A 263 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.6707 (ttt180) REVERT: B 53 MET cc_start: 0.8683 (mtp) cc_final: 0.8366 (mtp) REVERT: B 190 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7789 (mt-10) REVERT: B 369 ARG cc_start: 0.8060 (mtp180) cc_final: 0.7818 (mtm-85) REVERT: B 377 HIS cc_start: 0.6131 (t-90) cc_final: 0.5788 (t-170) REVERT: C 265 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7195 (mp0) REVERT: C 304 GLN cc_start: 0.8523 (mt0) cc_final: 0.7986 (mt0) REVERT: C 338 LYS cc_start: 0.7969 (mmpt) cc_final: 0.7380 (mtmt) REVERT: C 342 LYS cc_start: 0.8178 (tttt) cc_final: 0.7926 (tttt) REVERT: D 62 PHE cc_start: 0.5625 (m-80) cc_final: 0.5205 (m-10) REVERT: D 101 ILE cc_start: 0.6461 (tp) cc_final: 0.5649 (pt) REVERT: D 129 GLN cc_start: 0.6182 (tt0) cc_final: 0.5957 (pt0) REVERT: D 167 MET cc_start: 0.6719 (ttm) cc_final: 0.6364 (tpp) REVERT: D 225 MET cc_start: 0.5532 (mtt) cc_final: 0.5221 (mmm) REVERT: D 347 ASP cc_start: 0.6871 (OUTLIER) cc_final: 0.6229 (m-30) REVERT: D 355 ILE cc_start: 0.5341 (tp) cc_final: 0.4841 (tp) REVERT: D 419 GLU cc_start: 0.6184 (mt-10) cc_final: 0.5747 (tm-30) REVERT: E 59 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7649 (mp0) REVERT: E 99 GLU cc_start: 0.7273 (mm-30) cc_final: 0.6993 (mm-30) REVERT: E 108 LYS cc_start: 0.7666 (ptpt) cc_final: 0.7283 (mtmt) REVERT: F 20 GLN cc_start: 0.8146 (tp40) cc_final: 0.7670 (tm-30) REVERT: F 25 GLN cc_start: 0.8102 (tt0) cc_final: 0.7810 (tp40) REVERT: F 54 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8502 (tt0) REVERT: F 59 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: G 89 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8399 (mm-30) REVERT: G 93 LEU cc_start: 0.8809 (tp) cc_final: 0.8501 (tp) REVERT: G 104 GLU cc_start: 0.8509 (mt-10) cc_final: 0.8213 (mt-10) REVERT: G 111 LYS cc_start: 0.8188 (ttpp) cc_final: 0.7938 (tttp) REVERT: G 173 MET cc_start: 0.8989 (mmm) cc_final: 0.8555 (mmm) REVERT: G 225 LYS cc_start: 0.7554 (OUTLIER) cc_final: 0.7006 (tttm) REVERT: H 42 ASP cc_start: 0.8726 (m-30) cc_final: 0.8506 (m-30) REVERT: H 94 TYR cc_start: 0.8674 (p90) cc_final: 0.8419 (p90) REVERT: I 33 PHE cc_start: 0.8704 (m-80) cc_final: 0.8348 (m-80) REVERT: I 120 ASP cc_start: 0.7257 (m-30) cc_final: 0.6275 (p0) REVERT: I 132 LYS cc_start: 0.8278 (ptmt) cc_final: 0.7958 (pttt) REVERT: I 147 LYS cc_start: 0.7548 (tttt) cc_final: 0.7067 (tptp) REVERT: I 239 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7247 (ttp80) REVERT: I 314 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7124 (mm-30) REVERT: J 205 LEU cc_start: 0.5065 (tp) cc_final: 0.4806 (tp) REVERT: J 228 ASN cc_start: 0.4361 (OUTLIER) cc_final: 0.4018 (m-40) REVERT: K 73 GLU cc_start: 0.5541 (mt-10) cc_final: 0.5196 (mm-30) REVERT: K 141 PHE cc_start: 0.5298 (t80) cc_final: 0.5038 (t80) REVERT: K 194 MET cc_start: 0.7026 (mtp) cc_final: 0.6710 (mtp) REVERT: K 211 THR cc_start: 0.6536 (p) cc_final: 0.6166 (m) REVERT: K 289 LEU cc_start: 0.4511 (OUTLIER) cc_final: 0.4137 (mt) REVERT: L 23 LYS cc_start: 0.7560 (ptmt) cc_final: 0.7310 (pttm) REVERT: L 85 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7972 (pp) REVERT: L 103 ASN cc_start: 0.8583 (m110) cc_final: 0.8351 (m-40) REVERT: L 104 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7509 (mtm180) REVERT: L 105 ASN cc_start: 0.8687 (t0) cc_final: 0.8464 (t160) REVERT: L 114 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7903 (tm-30) REVERT: M 25 LYS cc_start: 0.7993 (pttt) cc_final: 0.7788 (mttp) REVERT: N 5 LYS cc_start: 0.8571 (tptm) cc_final: 0.8237 (tppt) REVERT: N 23 GLN cc_start: 0.7784 (tt0) cc_final: 0.7525 (mm110) REVERT: N 29 GLU cc_start: 0.7931 (tt0) cc_final: 0.7611 (mt-10) REVERT: N 31 ARG cc_start: 0.7346 (mtm110) cc_final: 0.7077 (mtm-85) REVERT: N 33 LYS cc_start: 0.8343 (mttt) cc_final: 0.8110 (mttm) REVERT: O 78 ARG cc_start: 0.8582 (mmp-170) cc_final: 0.8248 (mmp-170) REVERT: O 166 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8019 (mt-10) REVERT: R 59 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8343 (mtpt) REVERT: R 128 ARG cc_start: 0.8235 (mtp180) cc_final: 0.7963 (ttp-170) REVERT: R 163 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7594 (mt-10) REVERT: S 3 HIS cc_start: 0.5982 (t70) cc_final: 0.5750 (t-90) REVERT: S 13 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.6249 (mtt90) REVERT: S 47 LYS cc_start: 0.7868 (ttpp) cc_final: 0.7439 (tttm) REVERT: S 58 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8118 (mm) REVERT: S 83 SER cc_start: 0.6146 (p) cc_final: 0.5910 (t) REVERT: S 104 GLU cc_start: 0.8553 (tt0) cc_final: 0.8150 (mt-10) REVERT: S 131 LYS cc_start: 0.7984 (mttt) cc_final: 0.7535 (mmmt) REVERT: S 134 ASP cc_start: 0.7518 (m-30) cc_final: 0.7300 (m-30) REVERT: V 53 SER cc_start: 0.8664 (m) cc_final: 0.8271 (t) REVERT: V 59 MET cc_start: 0.8344 (mmt) cc_final: 0.7997 (mmm) REVERT: V 88 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.8042 (mmm-85) REVERT: W 85 TYR cc_start: 0.5438 (t80) cc_final: 0.5053 (t80) REVERT: W 90 TYR cc_start: 0.3438 (p90) cc_final: 0.3145 (p90) REVERT: W 121 ARG cc_start: 0.5777 (mmm-85) cc_final: 0.5459 (mmm160) REVERT: W 137 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6565 (mt) REVERT: W 231 THR cc_start: 0.5135 (p) cc_final: 0.4933 (t) REVERT: Y 11 ASP cc_start: 0.8734 (t0) cc_final: 0.8469 (t70) REVERT: Y 26 GLN cc_start: 0.8564 (mt0) cc_final: 0.8293 (mt0) REVERT: Y 69 LYS cc_start: 0.8584 (tttt) cc_final: 0.8246 (ttmm) REVERT: Z 169 PHE cc_start: 0.4668 (m-10) cc_final: 0.3607 (m-80) REVERT: Z 176 LEU cc_start: 0.4674 (tt) cc_final: 0.4349 (mp) REVERT: a 161 LYS cc_start: 0.0467 (ttmm) cc_final: 0.0228 (pttm) REVERT: a 201 VAL cc_start: 0.0417 (p) cc_final: -0.0110 (t) REVERT: b 3 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6858 (tp) REVERT: b 15 ASN cc_start: 0.7318 (m-40) cc_final: 0.6589 (p0) REVERT: b 33 ILE cc_start: 0.5926 (OUTLIER) cc_final: 0.5717 (pp) REVERT: b 106 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: b 185 ARG cc_start: 0.6675 (mtp180) cc_final: 0.6300 (tmt-80) REVERT: b 236 GLU cc_start: 0.6155 (mt-10) cc_final: 0.5913 (mt-10) REVERT: b 252 TYR cc_start: 0.6272 (t80) cc_final: 0.5689 (t80) REVERT: b 288 ASN cc_start: 0.3908 (OUTLIER) cc_final: 0.3653 (p0) REVERT: b 387 LYS cc_start: 0.7450 (tttt) cc_final: 0.6998 (tttp) REVERT: b 397 LYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6487 (mmtm) REVERT: b 466 GLU cc_start: 0.5206 (tt0) cc_final: 0.4781 (mm-30) REVERT: e 34 LYS cc_start: 0.8666 (tttp) cc_final: 0.8407 (ttpt) REVERT: h 59 ASN cc_start: 0.8489 (t0) cc_final: 0.8166 (m-40) REVERT: h 60 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7374 (tt0) REVERT: i 56 ARG cc_start: 0.7494 (ttm-80) cc_final: 0.7264 (ttp-110) REVERT: i 58 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7524 (mt) REVERT: i 75 LYS cc_start: 0.8116 (ttmm) cc_final: 0.7770 (mtmt) REVERT: i 88 GLU cc_start: 0.7781 (tp30) cc_final: 0.7188 (tt0) REVERT: i 90 MET cc_start: 0.8396 (mmp) cc_final: 0.8180 (mmp) REVERT: j 71 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8886 (m) REVERT: l 108 LEU cc_start: -0.1369 (OUTLIER) cc_final: -0.1577 (mp) REVERT: m 299 GLU cc_start: 0.3880 (OUTLIER) cc_final: 0.3431 (tm-30) REVERT: m 342 GLU cc_start: 0.5137 (mp0) cc_final: 0.4467 (mt-10) REVERT: m 355 GLU cc_start: 0.3109 (tt0) cc_final: 0.2787 (tp30) REVERT: n 120 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.5621 (tt0) REVERT: q 209 LYS cc_start: 0.4033 (OUTLIER) cc_final: 0.3813 (ptpt) REVERT: q 226 GLU cc_start: 0.2557 (mt-10) cc_final: 0.2275 (mm-30) REVERT: q 352 MET cc_start: 0.1897 (mmm) cc_final: 0.1093 (mpt) REVERT: q 368 LYS cc_start: 0.2065 (mttt) cc_final: 0.1852 (mmtt) REVERT: r 194 PHE cc_start: 0.7073 (OUTLIER) cc_final: 0.6291 (t80) REVERT: t 165 LEU cc_start: 0.6511 (mt) cc_final: 0.6222 (mt) REVERT: t 182 ASN cc_start: 0.4268 (m-40) cc_final: 0.4065 (m-40) REVERT: t 210 LYS cc_start: 0.6161 (mmtp) cc_final: 0.5851 (mtmt) REVERT: t 233 ASN cc_start: 0.4206 (m-40) cc_final: 0.3998 (t0) REVERT: t 236 GLU cc_start: 0.4777 (tt0) cc_final: 0.4506 (tt0) REVERT: u 82 ASN cc_start: 0.6747 (t0) cc_final: 0.6527 (t0) REVERT: u 90 LEU cc_start: 0.7926 (mt) cc_final: 0.7724 (mm) REVERT: u 96 ILE cc_start: 0.7789 (mt) cc_final: 0.7521 (mp) REVERT: u 104 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6228 (tm-30) REVERT: u 105 ARG cc_start: 0.6374 (ttt180) cc_final: 0.6067 (tmm-80) REVERT: v 67 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7764 (mt-10) REVERT: v 75 LYS cc_start: 0.6826 (mttt) cc_final: 0.6430 (ptpt) REVERT: v 157 GLU cc_start: 0.7647 (tp30) cc_final: 0.7418 (tm-30) REVERT: v 165 LEU cc_start: 0.8653 (tt) cc_final: 0.8440 (tp) REVERT: v 179 GLU cc_start: 0.8114 (pt0) cc_final: 0.7871 (tt0) REVERT: v 182 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7042 (mt-10) REVERT: v 186 GLU cc_start: 0.7859 (tt0) cc_final: 0.7612 (tt0) REVERT: v 214 ASP cc_start: 0.8438 (t0) cc_final: 0.8120 (t0) REVERT: w 34 PHE cc_start: 0.6781 (t80) cc_final: 0.6528 (t80) REVERT: w 78 ASP cc_start: 0.7817 (t0) cc_final: 0.7193 (t0) REVERT: w 80 LYS cc_start: 0.7311 (mttt) cc_final: 0.6773 (mmmm) REVERT: w 203 ARG cc_start: 0.6738 (ptp-170) cc_final: 0.6410 (ptm-80) REVERT: x 18 ILE cc_start: 0.8952 (mt) cc_final: 0.8554 (mt) REVERT: x 62 ASN cc_start: 0.7642 (m110) cc_final: 0.7342 (m-40) REVERT: x 152 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8162 (tm-30) REVERT: x 189 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7901 (mmt180) REVERT: x 258 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: y 1 MET cc_start: 0.5634 (tpt) cc_final: 0.4865 (ttp) REVERT: y 98 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7472 (mt-10) REVERT: y 99 GLU cc_start: 0.8122 (tp30) cc_final: 0.7859 (tp30) REVERT: y 164 GLN cc_start: 0.7538 (mm-40) cc_final: 0.7323 (mm110) REVERT: y 176 LEU cc_start: 0.7319 (mp) cc_final: 0.6980 (tp) REVERT: y 197 MET cc_start: 0.8572 (ptm) cc_final: 0.8195 (ptm) outliers start: 308 outliers final: 134 residues processed: 1451 average time/residue: 1.9656 time to fit residues: 3915.5509 Evaluate side-chains 1317 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1150 time to evaluate : 6.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 345 LYS Chi-restraints excluded: chain 8 residue 355 GLU Chi-restraints excluded: chain 8 residue 374 ASP Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 64 LYS Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 354 ASP Chi-restraints excluded: chain D residue 413 ASN Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 225 LYS Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 146 ILE Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 239 ARG Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain J residue 228 ASN Chi-restraints excluded: chain K residue 74 LEU Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 289 LEU Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 104 ARG Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 145 THR Chi-restraints excluded: chain T residue 175 ASN Chi-restraints excluded: chain T residue 232 VAL Chi-restraints excluded: chain V residue 57 MET Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 137 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 182 ILE Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 57 ILE Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 192 SER Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 33 ILE Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 106 GLU Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 229 THR Chi-restraints excluded: chain b residue 288 ASN Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain b residue 397 LYS Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 71 SER Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain l residue 56 THR Chi-restraints excluded: chain l residue 108 LEU Chi-restraints excluded: chain m residue 299 GLU Chi-restraints excluded: chain n residue 111 SER Chi-restraints excluded: chain n residue 120 GLU Chi-restraints excluded: chain n residue 179 VAL Chi-restraints excluded: chain n residue 227 THR Chi-restraints excluded: chain n residue 256 ILE Chi-restraints excluded: chain n residue 387 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain q residue 209 LYS Chi-restraints excluded: chain q residue 274 ARG Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain q residue 418 ILE Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 183 ASN Chi-restraints excluded: chain r residue 194 PHE Chi-restraints excluded: chain t residue 195 VAL Chi-restraints excluded: chain t residue 227 ILE Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 273 LEU Chi-restraints excluded: chain t residue 282 SER Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 302 SER Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 13 CYS Chi-restraints excluded: chain u residue 89 THR Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain v residue 13 SER Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain v residue 219 LEU Chi-restraints excluded: chain w residue 69 LEU Chi-restraints excluded: chain w residue 174 VAL Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 141 LYS Chi-restraints excluded: chain x residue 152 GLU Chi-restraints excluded: chain x residue 187 HIS Chi-restraints excluded: chain x residue 189 ARG Chi-restraints excluded: chain x residue 224 ILE Chi-restraints excluded: chain x residue 258 GLU Chi-restraints excluded: chain y residue 36 SER Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 91 SER Chi-restraints excluded: chain y residue 167 VAL Chi-restraints excluded: chain y residue 174 SER Chi-restraints excluded: chain y residue 185 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1093 random chunks: chunk 551 optimal weight: 0.8980 chunk 308 optimal weight: 2.9990 chunk 826 optimal weight: 2.9990 chunk 675 optimal weight: 0.5980 chunk 273 optimal weight: 0.0980 chunk 994 optimal weight: 20.0000 chunk 1074 optimal weight: 5.9990 chunk 885 optimal weight: 2.9990 chunk 986 optimal weight: 0.0010 chunk 338 optimal weight: 6.9990 chunk 797 optimal weight: 0.8980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 313 HIS C 18 ASN D 288 GLN D 397 ASN F 19 GLN F 225 GLN G 221 ASN H 59 ASN H 116 ASN H 157 ASN K 247 HIS N 34 ASN ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN Q 78 ASN R 146 GLN ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 ASN T 221 ASN W 128 ASN Y 120 GLN b 429 ASN f 106 ASN h 62 GLN h 99 GLN i 92 ASN l 23 ASN ** n 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 144 ASN o 130 ASN q 276 ASN q 376 ASN ** q 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 53 ASN u 42 GLN w 112 ASN w 229 ASN x 24 HIS x 58 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 126156 Z= 0.124 Angle : 0.478 13.679 180982 Z= 0.247 Chirality : 0.034 0.256 22049 Planarity : 0.004 0.054 14697 Dihedral : 21.674 179.990 44162 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.37 % Allowed : 15.55 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.09), residues: 8763 helix: 2.14 (0.09), residues: 3671 sheet: 0.36 (0.14), residues: 1315 loop : 0.22 (0.10), residues: 3777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP e 32 HIS 0.005 0.001 HIS S 49 PHE 0.027 0.001 PHE D 96 TYR 0.017 0.001 TYR y 35 ARG 0.006 0.000 ARG D 351 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1438 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1253 time to evaluate : 6.383 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: 8 345 LYS cc_start: 0.4619 (OUTLIER) cc_final: 0.3675 (ptmt) REVERT: A 153 LYS cc_start: 0.6300 (ttpp) cc_final: 0.5817 (tttt) REVERT: B 49 TYR cc_start: 0.8494 (m-80) cc_final: 0.8228 (m-80) REVERT: B 53 MET cc_start: 0.8566 (mtp) cc_final: 0.8235 (mtp) REVERT: B 116 ARG cc_start: 0.8097 (ttm-80) cc_final: 0.7838 (mtt-85) REVERT: B 196 ARG cc_start: 0.7214 (ttp-110) cc_final: 0.6635 (ttp80) REVERT: B 369 ARG cc_start: 0.8017 (mtp180) cc_final: 0.7769 (mtm-85) REVERT: B 377 HIS cc_start: 0.6165 (t-90) cc_final: 0.5839 (t-170) REVERT: C 265 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7218 (mp0) REVERT: C 304 GLN cc_start: 0.8512 (mt0) cc_final: 0.8025 (mt0) REVERT: D 62 PHE cc_start: 0.5314 (m-80) cc_final: 0.4801 (m-10) REVERT: D 138 MET cc_start: 0.6712 (OUTLIER) cc_final: 0.6396 (mpp) REVERT: D 167 MET cc_start: 0.6473 (ttm) cc_final: 0.6226 (ttm) REVERT: D 225 MET cc_start: 0.5720 (mtt) cc_final: 0.5273 (mmp) REVERT: D 347 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.6232 (m-30) REVERT: D 355 ILE cc_start: 0.5359 (tp) cc_final: 0.4827 (tp) REVERT: D 419 GLU cc_start: 0.6196 (mt-10) cc_final: 0.5729 (tm-30) REVERT: E 59 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7638 (mp0) REVERT: E 90 LYS cc_start: 0.8198 (mttp) cc_final: 0.7794 (mtpp) REVERT: E 99 GLU cc_start: 0.7303 (mm-30) cc_final: 0.6971 (mm-30) REVERT: E 108 LYS cc_start: 0.7712 (ptpt) cc_final: 0.7398 (mtmt) REVERT: F 20 GLN cc_start: 0.8142 (tp40) cc_final: 0.7745 (tm-30) REVERT: F 25 GLN cc_start: 0.8043 (tt0) cc_final: 0.7803 (tp40) REVERT: F 59 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: F 165 ASP cc_start: 0.8453 (t0) cc_final: 0.8217 (t70) REVERT: G 89 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8286 (mm-30) REVERT: G 93 LEU cc_start: 0.8736 (tp) cc_final: 0.8527 (tp) REVERT: G 173 MET cc_start: 0.8977 (mmm) cc_final: 0.8568 (mmm) REVERT: G 180 VAL cc_start: 0.8641 (t) cc_final: 0.8147 (m) REVERT: H 63 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8032 (mmtp) REVERT: H 118 LEU cc_start: 0.9067 (mt) cc_final: 0.8791 (mt) REVERT: I 120 ASP cc_start: 0.7043 (m-30) cc_final: 0.6129 (p0) REVERT: I 132 LYS cc_start: 0.8214 (ptmt) cc_final: 0.7868 (pttt) REVERT: I 147 LYS cc_start: 0.7594 (tttt) cc_final: 0.7153 (tptp) REVERT: I 314 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7101 (mm-30) REVERT: J 205 LEU cc_start: 0.5024 (tp) cc_final: 0.4716 (tp) REVERT: K 73 GLU cc_start: 0.5356 (mt-10) cc_final: 0.5077 (mm-30) REVERT: K 194 MET cc_start: 0.6805 (mtp) cc_final: 0.6531 (mtp) REVERT: K 211 THR cc_start: 0.6484 (p) cc_final: 0.6254 (m) REVERT: K 248 LEU cc_start: 0.6740 (mp) cc_final: 0.6315 (mm) REVERT: L 23 LYS cc_start: 0.7678 (ptmt) cc_final: 0.7387 (pttm) REVERT: L 85 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7864 (pp) REVERT: L 103 ASN cc_start: 0.8548 (m110) cc_final: 0.8325 (m-40) REVERT: L 105 ASN cc_start: 0.8657 (t0) cc_final: 0.8453 (t160) REVERT: L 114 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7847 (tm-30) REVERT: M 25 LYS cc_start: 0.8002 (pttt) cc_final: 0.7791 (mttp) REVERT: N 5 LYS cc_start: 0.8542 (tptm) cc_final: 0.8159 (tppt) REVERT: N 23 GLN cc_start: 0.7813 (tt0) cc_final: 0.7558 (mm110) REVERT: N 29 GLU cc_start: 0.7887 (tt0) cc_final: 0.7556 (mt-10) REVERT: N 31 ARG cc_start: 0.7348 (mtm110) cc_final: 0.7147 (mtm-85) REVERT: N 33 LYS cc_start: 0.8281 (mttt) cc_final: 0.8023 (mttp) REVERT: O 51 LYS cc_start: 0.8746 (tttm) cc_final: 0.8428 (tttp) REVERT: O 166 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7970 (mt-10) REVERT: R 59 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8411 (mtpt) REVERT: R 163 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7640 (mt-10) REVERT: S 13 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.5971 (mtp85) REVERT: S 47 LYS cc_start: 0.7907 (ttpp) cc_final: 0.7496 (tttm) REVERT: S 87 THR cc_start: 0.6930 (OUTLIER) cc_final: 0.6694 (t) REVERT: S 118 PHE cc_start: 0.8472 (t80) cc_final: 0.8115 (t80) REVERT: S 131 LYS cc_start: 0.7955 (mttt) cc_final: 0.7540 (mmtt) REVERT: S 134 ASP cc_start: 0.7575 (m-30) cc_final: 0.7370 (m-30) REVERT: T 175 ASN cc_start: 0.1374 (OUTLIER) cc_final: 0.0759 (p0) REVERT: V 53 SER cc_start: 0.8596 (m) cc_final: 0.8257 (t) REVERT: V 59 MET cc_start: 0.8330 (mmt) cc_final: 0.7964 (mmm) REVERT: V 88 ARG cc_start: 0.8309 (mmm-85) cc_final: 0.8066 (mmm-85) REVERT: W 85 TYR cc_start: 0.5406 (t80) cc_final: 0.4981 (t80) REVERT: W 115 TYR cc_start: 0.5253 (t80) cc_final: 0.5045 (t80) REVERT: W 121 ARG cc_start: 0.5777 (mmm-85) cc_final: 0.5448 (mmm160) REVERT: Y 11 ASP cc_start: 0.8710 (t0) cc_final: 0.8449 (t70) REVERT: Z 169 PHE cc_start: 0.4527 (m-10) cc_final: 0.3665 (m-80) REVERT: Z 176 LEU cc_start: 0.4516 (tt) cc_final: 0.4275 (mp) REVERT: Z 192 ILE cc_start: 0.4641 (mt) cc_final: 0.4411 (mt) REVERT: a 174 MET cc_start: 0.2249 (mpp) cc_final: 0.1734 (ptm) REVERT: a 201 VAL cc_start: 0.0424 (p) cc_final: -0.0106 (t) REVERT: b 3 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6846 (tp) REVERT: b 15 ASN cc_start: 0.7288 (m-40) cc_final: 0.6556 (p0) REVERT: b 106 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: b 185 ARG cc_start: 0.6578 (mtp180) cc_final: 0.6252 (tpt90) REVERT: b 252 TYR cc_start: 0.6172 (t80) cc_final: 0.5724 (t80) REVERT: b 387 LYS cc_start: 0.7560 (tttt) cc_final: 0.7078 (tttp) REVERT: b 466 GLU cc_start: 0.5257 (tt0) cc_final: 0.4808 (mm-30) REVERT: e 34 LYS cc_start: 0.8607 (tttp) cc_final: 0.8356 (ttpt) REVERT: h 59 ASN cc_start: 0.8392 (t0) cc_final: 0.8122 (m-40) REVERT: i 26 ILE cc_start: 0.8368 (mt) cc_final: 0.8144 (tp) REVERT: i 56 ARG cc_start: 0.7407 (ttm-80) cc_final: 0.7174 (ttm110) REVERT: i 58 ILE cc_start: 0.7752 (pp) cc_final: 0.7512 (mt) REVERT: i 75 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7731 (mtmt) REVERT: i 88 GLU cc_start: 0.7735 (tp30) cc_final: 0.7168 (tt0) REVERT: i 90 MET cc_start: 0.8439 (mmp) cc_final: 0.8103 (mmp) REVERT: l 121 MET cc_start: 0.1668 (ptm) cc_final: 0.0898 (pp-130) REVERT: m 299 GLU cc_start: 0.3807 (OUTLIER) cc_final: 0.3401 (tm-30) REVERT: m 342 GLU cc_start: 0.5146 (mp0) cc_final: 0.4463 (mt-10) REVERT: m 355 GLU cc_start: 0.2902 (tt0) cc_final: 0.2648 (tp30) REVERT: q 209 LYS cc_start: 0.3970 (OUTLIER) cc_final: 0.2441 (tppt) REVERT: q 226 GLU cc_start: 0.2550 (mt-10) cc_final: 0.2254 (mm-30) REVERT: q 352 MET cc_start: 0.1368 (mmm) cc_final: 0.0702 (mpt) REVERT: r 150 MET cc_start: 0.5810 (ptp) cc_final: 0.4895 (ptp) REVERT: r 194 PHE cc_start: 0.6765 (OUTLIER) cc_final: 0.5992 (t80) REVERT: r 210 THR cc_start: 0.6324 (OUTLIER) cc_final: 0.6059 (p) REVERT: t 165 LEU cc_start: 0.6652 (mt) cc_final: 0.6398 (mt) REVERT: t 182 ASN cc_start: 0.4204 (m-40) cc_final: 0.3997 (m-40) REVERT: t 210 LYS cc_start: 0.6071 (mmtp) cc_final: 0.5812 (mtmt) REVERT: t 214 ILE cc_start: 0.4665 (OUTLIER) cc_final: 0.4276 (pp) REVERT: t 233 ASN cc_start: 0.4200 (m-40) cc_final: 0.3983 (t0) REVERT: u 90 LEU cc_start: 0.7912 (mt) cc_final: 0.7709 (mm) REVERT: u 96 ILE cc_start: 0.7782 (mt) cc_final: 0.7522 (mp) REVERT: u 112 MET cc_start: 0.3792 (mmm) cc_final: 0.3378 (mmm) REVERT: v 75 LYS cc_start: 0.6760 (mttt) cc_final: 0.6453 (ptpt) REVERT: v 157 GLU cc_start: 0.7641 (tp30) cc_final: 0.7416 (tm-30) REVERT: v 179 GLU cc_start: 0.8107 (pt0) cc_final: 0.7806 (tt0) REVERT: v 182 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7057 (mt-10) REVERT: v 183 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7818 (mt-10) REVERT: v 186 GLU cc_start: 0.7781 (tt0) cc_final: 0.7534 (tt0) REVERT: v 214 ASP cc_start: 0.8285 (t0) cc_final: 0.8019 (t0) REVERT: w 34 PHE cc_start: 0.6690 (t80) cc_final: 0.6417 (t80) REVERT: w 78 ASP cc_start: 0.7826 (t0) cc_final: 0.7219 (t0) REVERT: w 203 ARG cc_start: 0.6701 (ptp-170) cc_final: 0.6389 (ptm-80) REVERT: x 62 ASN cc_start: 0.7572 (m110) cc_final: 0.7303 (m-40) REVERT: x 67 ASP cc_start: 0.8360 (t70) cc_final: 0.8112 (t70) REVERT: x 189 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7776 (mmt180) REVERT: x 258 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: y 1 MET cc_start: 0.5484 (tpt) cc_final: 0.4816 (ttp) REVERT: y 98 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7405 (mt-10) REVERT: y 99 GLU cc_start: 0.8150 (tp30) cc_final: 0.7870 (tp30) REVERT: y 172 GLU cc_start: 0.6182 (pt0) cc_final: 0.5940 (pt0) REVERT: y 176 LEU cc_start: 0.7248 (mp) cc_final: 0.6927 (tp) REVERT: y 197 MET cc_start: 0.8474 (ptm) cc_final: 0.8126 (ptm) REVERT: y 223 ARG cc_start: 0.7848 (mmm-85) cc_final: 0.7604 (mtp180) outliers start: 185 outliers final: 55 residues processed: 1360 average time/residue: 1.9422 time to fit residues: 3644.5006 Evaluate side-chains 1218 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1144 time to evaluate : 6.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 345 LYS Chi-restraints excluded: chain 8 residue 355 GLU Chi-restraints excluded: chain 8 residue 374 ASP Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 138 MET Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain T residue 175 ASN Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 106 GLU Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain m residue 299 GLU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 179 VAL Chi-restraints excluded: chain n residue 189 GLN Chi-restraints excluded: chain n residue 387 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 151 SER Chi-restraints excluded: chain q residue 209 LYS Chi-restraints excluded: chain q residue 383 THR Chi-restraints excluded: chain q residue 418 ILE Chi-restraints excluded: chain q residue 502 VAL Chi-restraints excluded: chain r residue 35 ILE Chi-restraints excluded: chain r residue 194 PHE Chi-restraints excluded: chain r residue 210 THR Chi-restraints excluded: chain t residue 195 VAL Chi-restraints excluded: chain t residue 214 ILE Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 302 SER Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 13 CYS Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain v residue 219 LEU Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 60 ILE Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 189 ARG Chi-restraints excluded: chain x residue 258 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1093 random chunks: chunk 982 optimal weight: 6.9990 chunk 747 optimal weight: 0.0000 chunk 516 optimal weight: 20.0000 chunk 110 optimal weight: 7.9990 chunk 474 optimal weight: 0.7980 chunk 667 optimal weight: 9.9990 chunk 997 optimal weight: 6.9990 chunk 1056 optimal weight: 9.9990 chunk 521 optimal weight: 7.9990 chunk 945 optimal weight: 30.0000 chunk 284 optimal weight: 4.9990 overall best weight: 3.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 309 ASN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 121 ASN ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN D 397 ASN F 19 GLN F 225 GLN G 221 ASN H 59 ASN H 157 ASN ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 GLN N 32 GLN O 55 HIS ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN P 121 GLN ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 HIS R 146 GLN S 62 ASN Y 120 GLN a 182 GLN b 429 ASN f 106 ASN h 62 GLN i 92 ASN ** n 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 130 ASN o 149 GLN ** q 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 346 ASN q 376 ASN t 53 ASN u 42 GLN ** w 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 24 HIS x 120 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 126156 Z= 0.278 Angle : 0.574 10.200 180982 Z= 0.294 Chirality : 0.039 0.269 22049 Planarity : 0.005 0.082 14697 Dihedral : 21.713 179.783 44142 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.60 % Allowed : 15.63 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.09), residues: 8763 helix: 1.93 (0.09), residues: 3662 sheet: 0.32 (0.14), residues: 1331 loop : 0.12 (0.10), residues: 3770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 200 HIS 0.007 0.001 HIS m 170 PHE 0.032 0.002 PHE F 229 TYR 0.022 0.002 TYR a 41 ARG 0.008 0.001 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1423 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1142 time to evaluate : 7.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 345 LYS cc_start: 0.4596 (OUTLIER) cc_final: 0.3632 (ptmt) REVERT: A 153 LYS cc_start: 0.6306 (ttpp) cc_final: 0.5809 (tttt) REVERT: B 53 MET cc_start: 0.8703 (mtp) cc_final: 0.8306 (mtp) REVERT: B 146 ARG cc_start: 0.6887 (ttp80) cc_final: 0.6654 (ttp-110) REVERT: B 369 ARG cc_start: 0.8090 (mtp180) cc_final: 0.7841 (mtm-85) REVERT: B 377 HIS cc_start: 0.6148 (t-90) cc_final: 0.5827 (t-170) REVERT: C 73 ARG cc_start: 0.8316 (mtt180) cc_final: 0.7901 (mmt-90) REVERT: C 160 GLN cc_start: 0.8768 (OUTLIER) cc_final: 0.8227 (mm110) REVERT: C 265 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7191 (mp0) REVERT: C 304 GLN cc_start: 0.8506 (mt0) cc_final: 0.7946 (mt0) REVERT: C 338 LYS cc_start: 0.8066 (mmpt) cc_final: 0.7459 (mtmt) REVERT: D 62 PHE cc_start: 0.5476 (m-80) cc_final: 0.4994 (m-10) REVERT: D 167 MET cc_start: 0.6466 (ttm) cc_final: 0.6016 (ttm) REVERT: D 225 MET cc_start: 0.5586 (mtt) cc_final: 0.5178 (mmp) REVERT: D 347 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6449 (m-30) REVERT: D 355 ILE cc_start: 0.5410 (tp) cc_final: 0.4900 (tp) REVERT: D 419 GLU cc_start: 0.6211 (mt-10) cc_final: 0.5754 (tm-30) REVERT: E 13 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7554 (mm-30) REVERT: E 59 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7664 (mp0) REVERT: E 99 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7053 (mm-30) REVERT: E 108 LYS cc_start: 0.7710 (ptpt) cc_final: 0.7308 (mtmt) REVERT: E 133 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6953 (pm20) REVERT: F 20 GLN cc_start: 0.8159 (tp40) cc_final: 0.7752 (tm-30) REVERT: F 25 GLN cc_start: 0.8100 (tt0) cc_final: 0.7816 (tp40) REVERT: F 54 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8506 (tt0) REVERT: F 56 GLU cc_start: 0.8473 (tt0) cc_final: 0.8230 (tt0) REVERT: F 59 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7413 (tm-30) REVERT: G 89 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8337 (mm-30) REVERT: G 93 LEU cc_start: 0.8794 (tp) cc_final: 0.8534 (tp) REVERT: G 173 MET cc_start: 0.8967 (mmm) cc_final: 0.8548 (mmm) REVERT: G 225 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.6947 (tttm) REVERT: H 46 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8509 (p) REVERT: I 33 PHE cc_start: 0.8671 (m-80) cc_final: 0.8275 (m-80) REVERT: I 120 ASP cc_start: 0.7222 (m-30) cc_final: 0.6237 (p0) REVERT: I 132 LYS cc_start: 0.8310 (ptmt) cc_final: 0.7899 (mtmm) REVERT: I 147 LYS cc_start: 0.7609 (tttt) cc_final: 0.7077 (mmmt) REVERT: I 314 GLU cc_start: 0.7395 (mt-10) cc_final: 0.7144 (mm-30) REVERT: J 205 LEU cc_start: 0.5037 (tp) cc_final: 0.4683 (tp) REVERT: K 73 GLU cc_start: 0.5546 (mt-10) cc_final: 0.5259 (mm-30) REVERT: K 194 MET cc_start: 0.6931 (mtp) cc_final: 0.6632 (mtp) REVERT: L 23 LYS cc_start: 0.7648 (ptmt) cc_final: 0.7370 (pttm) REVERT: L 85 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8071 (pp) REVERT: L 103 ASN cc_start: 0.8584 (m110) cc_final: 0.8352 (m-40) REVERT: L 104 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7491 (mtm180) REVERT: L 105 ASN cc_start: 0.8716 (t0) cc_final: 0.8499 (t160) REVERT: L 114 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7860 (tm-30) REVERT: L 115 ARG cc_start: 0.8632 (ttt90) cc_final: 0.8387 (ttt90) REVERT: M 25 LYS cc_start: 0.7970 (pttt) cc_final: 0.7765 (mttp) REVERT: N 5 LYS cc_start: 0.8596 (tptm) cc_final: 0.8350 (tppt) REVERT: N 23 GLN cc_start: 0.7803 (tt0) cc_final: 0.7507 (mm110) REVERT: N 29 GLU cc_start: 0.7921 (tt0) cc_final: 0.7626 (mt-10) REVERT: N 31 ARG cc_start: 0.7319 (mtm110) cc_final: 0.7037 (mtm180) REVERT: N 33 LYS cc_start: 0.8337 (mttt) cc_final: 0.8123 (mttp) REVERT: N 197 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7759 (tp) REVERT: O 53 LYS cc_start: 0.8347 (ttmm) cc_final: 0.7655 (tttt) REVERT: O 55 HIS cc_start: 0.7856 (OUTLIER) cc_final: 0.6654 (m90) REVERT: O 117 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.8270 (ptp-170) REVERT: O 166 GLU cc_start: 0.8215 (mt-10) cc_final: 0.8002 (mt-10) REVERT: R 59 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8341 (mtpt) REVERT: R 109 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8789 (mtmp) REVERT: S 13 ARG cc_start: 0.6439 (OUTLIER) cc_final: 0.6178 (mtt90) REVERT: S 47 LYS cc_start: 0.7885 (ttpp) cc_final: 0.7468 (tttm) REVERT: S 58 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8121 (mm) REVERT: S 83 SER cc_start: 0.6090 (p) cc_final: 0.5868 (t) REVERT: S 87 THR cc_start: 0.6956 (OUTLIER) cc_final: 0.6707 (t) REVERT: S 90 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8359 (ptp) REVERT: S 104 GLU cc_start: 0.8492 (tt0) cc_final: 0.8092 (mt-10) REVERT: S 131 LYS cc_start: 0.7946 (mttt) cc_final: 0.7503 (mmmt) REVERT: S 134 ASP cc_start: 0.7574 (m-30) cc_final: 0.7350 (m-30) REVERT: V 53 SER cc_start: 0.8648 (m) cc_final: 0.8265 (t) REVERT: V 59 MET cc_start: 0.8330 (mmt) cc_final: 0.7954 (mmm) REVERT: V 70 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7448 (mtt180) REVERT: W 85 TYR cc_start: 0.5524 (t80) cc_final: 0.5045 (t80) REVERT: W 121 ARG cc_start: 0.5791 (mmm-85) cc_final: 0.5414 (mmm160) REVERT: W 137 ILE cc_start: 0.6963 (OUTLIER) cc_final: 0.6658 (mt) REVERT: Y 11 ASP cc_start: 0.8741 (t0) cc_final: 0.8462 (t70) REVERT: Y 69 LYS cc_start: 0.8613 (tttt) cc_final: 0.8285 (ttmm) REVERT: Z 169 PHE cc_start: 0.4482 (m-10) cc_final: 0.3633 (m-80) REVERT: Z 176 LEU cc_start: 0.4621 (tt) cc_final: 0.4348 (mp) REVERT: a 174 MET cc_start: 0.2329 (mpp) cc_final: 0.1891 (ptp) REVERT: a 194 LEU cc_start: 0.0427 (OUTLIER) cc_final: 0.0120 (mt) REVERT: a 201 VAL cc_start: 0.0713 (OUTLIER) cc_final: 0.0168 (t) REVERT: b 3 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6959 (tp) REVERT: b 15 ASN cc_start: 0.7323 (m-40) cc_final: 0.6590 (p0) REVERT: b 106 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: b 114 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6522 (ttt-90) REVERT: b 185 ARG cc_start: 0.6679 (mtp180) cc_final: 0.6299 (tmt-80) REVERT: b 252 TYR cc_start: 0.6198 (t80) cc_final: 0.5751 (t80) REVERT: b 288 ASN cc_start: 0.4167 (OUTLIER) cc_final: 0.3679 (p0) REVERT: b 329 MET cc_start: 0.6725 (mmp) cc_final: 0.6505 (mpm) REVERT: b 387 LYS cc_start: 0.7572 (tttt) cc_final: 0.7081 (tttp) REVERT: b 397 LYS cc_start: 0.6888 (OUTLIER) cc_final: 0.6664 (mmtm) REVERT: e 34 LYS cc_start: 0.8682 (tttp) cc_final: 0.8416 (ttpt) REVERT: h 59 ASN cc_start: 0.8479 (t0) cc_final: 0.8170 (m-40) REVERT: h 60 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7304 (tt0) REVERT: i 26 ILE cc_start: 0.8430 (mt) cc_final: 0.8196 (tp) REVERT: i 56 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.7253 (ttm110) REVERT: i 58 ILE cc_start: 0.7811 (OUTLIER) cc_final: 0.7502 (mt) REVERT: i 70 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7871 (mtt90) REVERT: i 75 LYS cc_start: 0.8031 (ttmm) cc_final: 0.7697 (mtmt) REVERT: i 88 GLU cc_start: 0.7769 (tp30) cc_final: 0.7195 (tt0) REVERT: i 90 MET cc_start: 0.8410 (mmp) cc_final: 0.8162 (mmp) REVERT: m 289 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7756 (mp) REVERT: m 299 GLU cc_start: 0.3888 (OUTLIER) cc_final: 0.3451 (tm-30) REVERT: m 355 GLU cc_start: 0.3034 (tt0) cc_final: 0.2710 (tp30) REVERT: n 106 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.6041 (tm-30) REVERT: q 209 LYS cc_start: 0.4324 (OUTLIER) cc_final: 0.2689 (tppt) REVERT: q 226 GLU cc_start: 0.2657 (mt-10) cc_final: 0.2212 (mm-30) REVERT: r 194 PHE cc_start: 0.7054 (OUTLIER) cc_final: 0.6109 (t80) REVERT: t 165 LEU cc_start: 0.6532 (mt) cc_final: 0.6255 (mt) REVERT: t 182 ASN cc_start: 0.4189 (m-40) cc_final: 0.3885 (m-40) REVERT: t 210 LYS cc_start: 0.6152 (mmtp) cc_final: 0.5847 (mtmt) REVERT: t 214 ILE cc_start: 0.4749 (OUTLIER) cc_final: 0.4323 (pp) REVERT: t 233 ASN cc_start: 0.4262 (m-40) cc_final: 0.4008 (t0) REVERT: u 90 LEU cc_start: 0.7940 (mt) cc_final: 0.7728 (mm) REVERT: u 96 ILE cc_start: 0.7744 (mt) cc_final: 0.7490 (mp) REVERT: u 104 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.6288 (tm-30) REVERT: v 75 LYS cc_start: 0.6776 (mttt) cc_final: 0.6380 (ptpt) REVERT: v 157 GLU cc_start: 0.7660 (tp30) cc_final: 0.7437 (tm-30) REVERT: v 179 GLU cc_start: 0.8141 (pt0) cc_final: 0.7910 (tt0) REVERT: v 182 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7073 (mt-10) REVERT: v 186 GLU cc_start: 0.7840 (tt0) cc_final: 0.7583 (tt0) REVERT: v 214 ASP cc_start: 0.8418 (t0) cc_final: 0.8129 (t0) REVERT: w 32 LYS cc_start: 0.6648 (pttm) cc_final: 0.6242 (mppt) REVERT: w 34 PHE cc_start: 0.6705 (t80) cc_final: 0.6451 (t80) REVERT: w 78 ASP cc_start: 0.7892 (t0) cc_final: 0.7268 (t0) REVERT: w 80 LYS cc_start: 0.7293 (mttt) cc_final: 0.6760 (mmmm) REVERT: w 203 ARG cc_start: 0.6731 (ptp-170) cc_final: 0.6394 (ptm-80) REVERT: x 62 ASN cc_start: 0.7626 (m110) cc_final: 0.7329 (m-40) REVERT: x 67 ASP cc_start: 0.8360 (t70) cc_final: 0.8083 (t70) REVERT: x 141 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8193 (mtpt) REVERT: x 152 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8134 (tm-30) REVERT: x 189 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7884 (mmt180) REVERT: x 258 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8168 (tt0) REVERT: y 1 MET cc_start: 0.5591 (tpt) cc_final: 0.4823 (ttp) REVERT: y 98 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7424 (mt-10) REVERT: y 99 GLU cc_start: 0.8143 (tp30) cc_final: 0.7858 (tp30) REVERT: y 136 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6631 (tt0) REVERT: y 172 GLU cc_start: 0.6369 (pt0) cc_final: 0.6160 (pt0) REVERT: y 176 LEU cc_start: 0.7267 (mp) cc_final: 0.6949 (tp) REVERT: y 197 MET cc_start: 0.8586 (ptm) cc_final: 0.8136 (ptm) outliers start: 281 outliers final: 138 residues processed: 1319 average time/residue: 1.9507 time to fit residues: 3559.0888 Evaluate side-chains 1291 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1111 time to evaluate : 7.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 297 VAL Chi-restraints excluded: chain 8 residue 345 LYS Chi-restraints excluded: chain 8 residue 355 GLU Chi-restraints excluded: chain 8 residue 374 ASP Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 224 ASP Chi-restraints excluded: chain G residue 225 LYS Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain J residue 334 LEU Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 185 SER Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 104 ARG Chi-restraints excluded: chain L residue 106 GLN Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain T residue 175 ASN Chi-restraints excluded: chain T residue 202 LEU Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 70 ARG Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 137 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain W residue 191 GLU Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 111 VAL Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 192 SER Chi-restraints excluded: chain a residue 194 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 64 ILE Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 106 GLU Chi-restraints excluded: chain b residue 114 ARG Chi-restraints excluded: chain b residue 115 LEU Chi-restraints excluded: chain b residue 288 ASN Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain b residue 397 LYS Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 70 ARG Chi-restraints excluded: chain i residue 97 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain l residue 9 THR Chi-restraints excluded: chain l residue 123 ASP Chi-restraints excluded: chain m residue 254 MET Chi-restraints excluded: chain m residue 289 ILE Chi-restraints excluded: chain m residue 299 GLU Chi-restraints excluded: chain n residue 106 GLU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 179 VAL Chi-restraints excluded: chain n residue 189 GLN Chi-restraints excluded: chain n residue 227 THR Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain n residue 387 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 151 SER Chi-restraints excluded: chain q residue 209 LYS Chi-restraints excluded: chain q residue 211 LEU Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain q residue 345 GLU Chi-restraints excluded: chain q residue 383 THR Chi-restraints excluded: chain q residue 418 ILE Chi-restraints excluded: chain q residue 502 VAL Chi-restraints excluded: chain r residue 183 ASN Chi-restraints excluded: chain r residue 194 PHE Chi-restraints excluded: chain t residue 53 ASN Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain t residue 195 VAL Chi-restraints excluded: chain t residue 214 ILE Chi-restraints excluded: chain t residue 227 ILE Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 273 LEU Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 302 SER Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 13 CYS Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 89 THR Chi-restraints excluded: chain u residue 104 GLU Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain v residue 165 LEU Chi-restraints excluded: chain v residue 219 LEU Chi-restraints excluded: chain w residue 69 LEU Chi-restraints excluded: chain w residue 174 VAL Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 60 ILE Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 152 GLU Chi-restraints excluded: chain x residue 189 ARG Chi-restraints excluded: chain x residue 258 GLU Chi-restraints excluded: chain y residue 36 SER Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 91 SER Chi-restraints excluded: chain y residue 143 SER Chi-restraints excluded: chain y residue 167 VAL Chi-restraints excluded: chain y residue 174 SER Chi-restraints excluded: chain y residue 185 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1093 random chunks: chunk 879 optimal weight: 8.9990 chunk 599 optimal weight: 0.1980 chunk 15 optimal weight: 10.0000 chunk 786 optimal weight: 6.9990 chunk 435 optimal weight: 5.9990 chunk 901 optimal weight: 0.0470 chunk 730 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 539 optimal weight: 0.2980 chunk 948 optimal weight: 0.0470 chunk 266 optimal weight: 7.9990 overall best weight: 1.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 121 ASN ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN F 19 GLN F 225 GLN H 59 ASN H 157 ASN J 203 HIS L 120 GLN O 55 HIS ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN P 121 GLN Q 78 ASN R 146 GLN ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 ASN Y 120 GLN a 182 GLN b 429 ASN f 106 ASN i 92 ASN ** n 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 144 ASN n 395 GLN o 130 ASN ** q 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 389 ASN ** q 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 53 ASN u 42 GLN w 229 ASN x 24 HIS x 120 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 126156 Z= 0.140 Angle : 0.485 10.224 180982 Z= 0.251 Chirality : 0.034 0.233 22049 Planarity : 0.004 0.056 14697 Dihedral : 21.650 179.647 44140 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.90 % Allowed : 16.68 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.09), residues: 8763 helix: 2.07 (0.09), residues: 3671 sheet: 0.36 (0.14), residues: 1325 loop : 0.17 (0.10), residues: 3767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP e 32 HIS 0.025 0.001 HIS O 55 PHE 0.028 0.001 PHE D 96 TYR 0.017 0.001 TYR y 35 ARG 0.008 0.000 ARG u 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1389 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1163 time to evaluate : 7.287 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: 8 345 LYS cc_start: 0.4587 (OUTLIER) cc_final: 0.3642 (ptmt) REVERT: 8 401 GLN cc_start: 0.7638 (mt0) cc_final: 0.7356 (mt0) REVERT: A 117 LEU cc_start: 0.7091 (tp) cc_final: 0.6736 (mt) REVERT: A 153 LYS cc_start: 0.6293 (ttpp) cc_final: 0.5843 (tttt) REVERT: B 53 MET cc_start: 0.8633 (mtp) cc_final: 0.8325 (mtp) REVERT: B 190 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7512 (mt-10) REVERT: B 377 HIS cc_start: 0.6152 (t-90) cc_final: 0.5816 (t-170) REVERT: C 73 ARG cc_start: 0.8276 (mtt180) cc_final: 0.7511 (mtm180) REVERT: C 160 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8229 (mm110) REVERT: C 265 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7211 (mp0) REVERT: C 304 GLN cc_start: 0.8499 (mt0) cc_final: 0.8005 (mt0) REVERT: D 62 PHE cc_start: 0.5357 (m-80) cc_final: 0.4834 (m-10) REVERT: D 167 MET cc_start: 0.6410 (ttm) cc_final: 0.5928 (ttm) REVERT: D 225 MET cc_start: 0.5707 (mtt) cc_final: 0.5229 (mmp) REVERT: D 326 GLN cc_start: 0.7062 (tp40) cc_final: 0.6755 (tm-30) REVERT: D 347 ASP cc_start: 0.6676 (OUTLIER) cc_final: 0.6276 (m-30) REVERT: D 355 ILE cc_start: 0.5345 (tp) cc_final: 0.4824 (tp) REVERT: D 419 GLU cc_start: 0.6221 (mt-10) cc_final: 0.5755 (tm-30) REVERT: E 59 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7639 (mp0) REVERT: E 99 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7061 (mm-30) REVERT: E 108 LYS cc_start: 0.7668 (ptpt) cc_final: 0.7302 (mtmt) REVERT: E 133 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6996 (pm20) REVERT: F 20 GLN cc_start: 0.8142 (tp40) cc_final: 0.7748 (tm-30) REVERT: F 25 GLN cc_start: 0.7946 (tt0) cc_final: 0.7734 (tp40) REVERT: F 59 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: F 233 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.6756 (mm-30) REVERT: G 89 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8264 (mm-30) REVERT: G 93 LEU cc_start: 0.8730 (tp) cc_final: 0.8525 (tp) REVERT: G 173 MET cc_start: 0.8972 (mmm) cc_final: 0.8558 (mmm) REVERT: G 180 VAL cc_start: 0.8631 (t) cc_final: 0.8135 (m) REVERT: H 63 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.8042 (mmtp) REVERT: H 118 LEU cc_start: 0.9072 (mt) cc_final: 0.8823 (mt) REVERT: H 134 ILE cc_start: 0.8576 (mt) cc_final: 0.8305 (mt) REVERT: I 33 PHE cc_start: 0.8665 (m-80) cc_final: 0.8299 (m-80) REVERT: I 50 MET cc_start: 0.8519 (mtm) cc_final: 0.8265 (mtm) REVERT: I 120 ASP cc_start: 0.7183 (m-30) cc_final: 0.6181 (p0) REVERT: I 132 LYS cc_start: 0.8241 (ptmt) cc_final: 0.7874 (pttt) REVERT: I 314 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7113 (mm-30) REVERT: J 205 LEU cc_start: 0.5077 (tp) cc_final: 0.4711 (tp) REVERT: K 194 MET cc_start: 0.6836 (mtp) cc_final: 0.6549 (mtp) REVERT: L 23 LYS cc_start: 0.7663 (ptmt) cc_final: 0.7417 (pttt) REVERT: L 85 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7876 (pp) REVERT: L 103 ASN cc_start: 0.8551 (m110) cc_final: 0.8332 (m-40) REVERT: L 114 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7868 (tm-30) REVERT: N 5 LYS cc_start: 0.8599 (tptm) cc_final: 0.8232 (tppt) REVERT: N 23 GLN cc_start: 0.7754 (tt0) cc_final: 0.7529 (mm110) REVERT: N 29 GLU cc_start: 0.7906 (tt0) cc_final: 0.7606 (mt-10) REVERT: N 31 ARG cc_start: 0.7342 (mtm110) cc_final: 0.7121 (mtm-85) REVERT: N 33 LYS cc_start: 0.8321 (mttt) cc_final: 0.8055 (mttp) REVERT: N 197 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7811 (tp) REVERT: O 166 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7976 (mt-10) REVERT: R 59 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8411 (mtpt) REVERT: R 102 LYS cc_start: 0.8589 (mttp) cc_final: 0.8107 (pttt) REVERT: S 13 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.6021 (mtp85) REVERT: S 47 LYS cc_start: 0.7910 (ttpp) cc_final: 0.7486 (tttm) REVERT: S 58 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8079 (mm) REVERT: S 60 SER cc_start: 0.8667 (OUTLIER) cc_final: 0.8441 (t) REVERT: S 63 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8616 (tt0) REVERT: S 87 THR cc_start: 0.6944 (OUTLIER) cc_final: 0.6712 (t) REVERT: S 90 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8319 (ptp) REVERT: S 131 LYS cc_start: 0.7929 (mttt) cc_final: 0.7509 (mmmt) REVERT: S 134 ASP cc_start: 0.7599 (m-30) cc_final: 0.7384 (m-30) REVERT: T 175 ASN cc_start: 0.1405 (OUTLIER) cc_final: 0.0779 (p0) REVERT: V 53 SER cc_start: 0.8610 (m) cc_final: 0.8272 (t) REVERT: V 59 MET cc_start: 0.8341 (mmt) cc_final: 0.7974 (mmm) REVERT: W 85 TYR cc_start: 0.5456 (t80) cc_final: 0.5025 (t80) REVERT: W 121 ARG cc_start: 0.5747 (mmm-85) cc_final: 0.5353 (mmm160) REVERT: Y 11 ASP cc_start: 0.8749 (t0) cc_final: 0.8471 (t70) REVERT: Z 28 ILE cc_start: 0.5270 (pt) cc_final: 0.5045 (pp) REVERT: Z 169 PHE cc_start: 0.4645 (m-10) cc_final: 0.3868 (m-80) REVERT: a 174 MET cc_start: 0.2371 (tpp) cc_final: 0.1861 (ptm) REVERT: a 194 LEU cc_start: 0.0380 (OUTLIER) cc_final: 0.0079 (mt) REVERT: a 201 VAL cc_start: 0.0713 (OUTLIER) cc_final: 0.0150 (t) REVERT: b 3 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7047 (tp) REVERT: b 15 ASN cc_start: 0.7376 (m-40) cc_final: 0.6637 (p0) REVERT: b 106 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7352 (mt-10) REVERT: b 114 ARG cc_start: 0.7384 (OUTLIER) cc_final: 0.6489 (ttt-90) REVERT: b 145 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6653 (m-30) REVERT: b 185 ARG cc_start: 0.6618 (mtp180) cc_final: 0.6242 (tpt90) REVERT: b 252 TYR cc_start: 0.6253 (t80) cc_final: 0.5885 (t80) REVERT: b 288 ASN cc_start: 0.4170 (OUTLIER) cc_final: 0.3611 (p0) REVERT: b 387 LYS cc_start: 0.7572 (tttt) cc_final: 0.7076 (tttp) REVERT: e 34 LYS cc_start: 0.8650 (tttp) cc_final: 0.8391 (ttpt) REVERT: h 59 ASN cc_start: 0.8460 (t0) cc_final: 0.8168 (m-40) REVERT: h 60 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7313 (tt0) REVERT: i 26 ILE cc_start: 0.8400 (mt) cc_final: 0.8161 (tp) REVERT: i 56 ARG cc_start: 0.7387 (ttm-80) cc_final: 0.7185 (ttm110) REVERT: i 58 ILE cc_start: 0.7737 (pp) cc_final: 0.7498 (mt) REVERT: i 75 LYS cc_start: 0.7904 (ttmm) cc_final: 0.7567 (mtmt) REVERT: i 88 GLU cc_start: 0.7764 (tp30) cc_final: 0.7193 (tt0) REVERT: i 90 MET cc_start: 0.8432 (mmp) cc_final: 0.8179 (mmp) REVERT: l 121 MET cc_start: 0.1504 (ptm) cc_final: 0.0733 (pp-130) REVERT: m 299 GLU cc_start: 0.3848 (OUTLIER) cc_final: 0.3404 (tm-30) REVERT: m 342 GLU cc_start: 0.5417 (mp0) cc_final: 0.4791 (mt-10) REVERT: m 346 LEU cc_start: 0.4249 (tt) cc_final: 0.3978 (mt) REVERT: m 355 GLU cc_start: 0.2944 (tt0) cc_final: 0.2616 (tp30) REVERT: o 134 TYR cc_start: 0.8008 (p90) cc_final: 0.6669 (p90) REVERT: o 200 MET cc_start: 0.3704 (pp-130) cc_final: 0.3279 (ttp) REVERT: q 209 LYS cc_start: 0.4311 (OUTLIER) cc_final: 0.2707 (tppt) REVERT: q 226 GLU cc_start: 0.2607 (mt-10) cc_final: 0.2393 (mm-30) REVERT: q 352 MET cc_start: 0.1838 (mmm) cc_final: 0.1090 (mpt) REVERT: q 442 GLU cc_start: 0.1835 (OUTLIER) cc_final: 0.1348 (pt0) REVERT: r 150 MET cc_start: 0.5910 (ptp) cc_final: 0.4908 (ptp) REVERT: r 194 PHE cc_start: 0.6947 (OUTLIER) cc_final: 0.5979 (t80) REVERT: r 210 THR cc_start: 0.6340 (OUTLIER) cc_final: 0.6123 (p) REVERT: t 165 LEU cc_start: 0.6596 (mt) cc_final: 0.6328 (mt) REVERT: t 182 ASN cc_start: 0.4085 (m-40) cc_final: 0.3778 (m-40) REVERT: t 210 LYS cc_start: 0.6038 (mmtp) cc_final: 0.5784 (mtmt) REVERT: t 214 ILE cc_start: 0.4793 (OUTLIER) cc_final: 0.4424 (pp) REVERT: t 233 ASN cc_start: 0.4177 (m-40) cc_final: 0.3944 (t0) REVERT: u 96 ILE cc_start: 0.7698 (mt) cc_final: 0.7443 (mp) REVERT: v 75 LYS cc_start: 0.6737 (mttt) cc_final: 0.6359 (ptpt) REVERT: v 157 GLU cc_start: 0.7659 (tp30) cc_final: 0.7430 (tm-30) REVERT: v 179 GLU cc_start: 0.8123 (pt0) cc_final: 0.7907 (tt0) REVERT: v 182 GLU cc_start: 0.7431 (mt-10) cc_final: 0.7060 (mt-10) REVERT: v 183 GLU cc_start: 0.7939 (mt-10) cc_final: 0.7716 (mt-10) REVERT: v 186 GLU cc_start: 0.7813 (tt0) cc_final: 0.7545 (tt0) REVERT: v 214 ASP cc_start: 0.8349 (t0) cc_final: 0.8056 (t0) REVERT: w 32 LYS cc_start: 0.6586 (pttm) cc_final: 0.6243 (mppt) REVERT: w 34 PHE cc_start: 0.6655 (t80) cc_final: 0.6402 (t80) REVERT: w 78 ASP cc_start: 0.7808 (t0) cc_final: 0.7209 (t0) REVERT: w 80 LYS cc_start: 0.7260 (mttt) cc_final: 0.6769 (mmmm) REVERT: w 203 ARG cc_start: 0.6709 (ptp-170) cc_final: 0.6374 (ptm-80) REVERT: w 216 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7623 (t0) REVERT: x 62 ASN cc_start: 0.7645 (m110) cc_final: 0.7363 (m-40) REVERT: x 67 ASP cc_start: 0.8382 (t70) cc_final: 0.8125 (t70) REVERT: x 141 LYS cc_start: 0.8359 (mtpt) cc_final: 0.8076 (mtmm) REVERT: x 152 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8130 (tm-30) REVERT: x 189 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7829 (mmt180) REVERT: x 258 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: y 1 MET cc_start: 0.5490 (tpt) cc_final: 0.4746 (ttp) REVERT: y 99 GLU cc_start: 0.8153 (tp30) cc_final: 0.7912 (tp30) REVERT: y 129 ILE cc_start: 0.7442 (mt) cc_final: 0.7127 (mt) REVERT: y 172 GLU cc_start: 0.6259 (pt0) cc_final: 0.6042 (pt0) REVERT: y 176 LEU cc_start: 0.7249 (mp) cc_final: 0.6933 (tp) REVERT: y 197 MET cc_start: 0.8535 (ptm) cc_final: 0.8178 (ptm) outliers start: 226 outliers final: 106 residues processed: 1302 average time/residue: 1.9694 time to fit residues: 3538.5720 Evaluate side-chains 1255 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1113 time to evaluate : 7.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 345 LYS Chi-restraints excluded: chain 8 residue 355 GLU Chi-restraints excluded: chain 8 residue 374 ASP Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain J residue 287 LYS Chi-restraints excluded: chain J residue 334 LEU Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain K residue 291 LEU Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain M residue 41 GLN Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 63 GLN Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain T residue 175 ASN Chi-restraints excluded: chain T residue 202 LEU Chi-restraints excluded: chain T residue 232 VAL Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 111 VAL Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 79 SER Chi-restraints excluded: chain a residue 194 LEU Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 106 GLU Chi-restraints excluded: chain b residue 114 ARG Chi-restraints excluded: chain b residue 115 LEU Chi-restraints excluded: chain b residue 145 ASP Chi-restraints excluded: chain b residue 288 ASN Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 74 LYS Chi-restraints excluded: chain l residue 76 THR Chi-restraints excluded: chain m residue 179 ARG Chi-restraints excluded: chain m residue 254 MET Chi-restraints excluded: chain m residue 299 GLU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 179 VAL Chi-restraints excluded: chain n residue 231 PHE Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain n residue 387 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 151 SER Chi-restraints excluded: chain o residue 190 THR Chi-restraints excluded: chain q residue 209 LYS Chi-restraints excluded: chain q residue 211 LEU Chi-restraints excluded: chain q residue 383 THR Chi-restraints excluded: chain q residue 418 ILE Chi-restraints excluded: chain q residue 442 GLU Chi-restraints excluded: chain q residue 502 VAL Chi-restraints excluded: chain q residue 514 THR Chi-restraints excluded: chain r residue 183 ASN Chi-restraints excluded: chain r residue 194 PHE Chi-restraints excluded: chain r residue 210 THR Chi-restraints excluded: chain r residue 214 VAL Chi-restraints excluded: chain t residue 53 ASN Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain t residue 195 VAL Chi-restraints excluded: chain t residue 214 ILE Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 302 SER Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 13 CYS Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain v residue 219 LEU Chi-restraints excluded: chain w residue 69 LEU Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain w residue 216 ASP Chi-restraints excluded: chain x residue 60 ILE Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 152 GLU Chi-restraints excluded: chain x residue 189 ARG Chi-restraints excluded: chain x residue 258 GLU Chi-restraints excluded: chain x residue 272 ARG Chi-restraints excluded: chain y residue 91 SER Chi-restraints excluded: chain y residue 174 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1093 random chunks: chunk 355 optimal weight: 2.9990 chunk 951 optimal weight: 20.0000 chunk 208 optimal weight: 10.0000 chunk 620 optimal weight: 0.7980 chunk 260 optimal weight: 9.9990 chunk 1057 optimal weight: 10.0000 chunk 877 optimal weight: 0.9990 chunk 489 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 349 optimal weight: 20.0000 chunk 555 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 121 ASN ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN F 19 GLN F 225 GLN H 59 ASN H 157 ASN J 203 HIS ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 GLN N 32 GLN O 55 HIS ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 45 GLN P 92 GLN P 121 GLN ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 HIS R 146 GLN S 62 ASN Y 120 GLN Z 131 ASN a 140 HIS a 182 GLN b 429 ASN f 106 ASN i 92 ASN l 82 HIS ** n 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 144 ASN o 130 ASN q 389 ASN t 53 ASN u 42 GLN ** w 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 24 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 126156 Z= 0.254 Angle : 0.563 10.852 180982 Z= 0.290 Chirality : 0.038 0.262 22049 Planarity : 0.005 0.075 14697 Dihedral : 21.704 179.929 44140 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.71 % Allowed : 16.55 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.09), residues: 8763 helix: 1.86 (0.08), residues: 3673 sheet: 0.28 (0.14), residues: 1328 loop : 0.09 (0.10), residues: 3762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP 8 365 HIS 0.006 0.001 HIS m 170 PHE 0.030 0.002 PHE F 229 TYR 0.021 0.002 TYR Q 33 ARG 0.009 0.001 ARG u 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1145 time to evaluate : 7.101 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: 8 345 LYS cc_start: 0.4589 (OUTLIER) cc_final: 0.3634 (ptmt) REVERT: 8 401 GLN cc_start: 0.7673 (mt0) cc_final: 0.7422 (mt0) REVERT: A 117 LEU cc_start: 0.7069 (tp) cc_final: 0.6716 (mt) REVERT: A 153 LYS cc_start: 0.6382 (ttpp) cc_final: 0.5930 (tttt) REVERT: B 53 MET cc_start: 0.8733 (mtp) cc_final: 0.8373 (mtp) REVERT: B 190 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7525 (mt-10) REVERT: B 196 ARG cc_start: 0.7277 (ttp-110) cc_final: 0.6736 (ttp80) REVERT: B 377 HIS cc_start: 0.6121 (t-90) cc_final: 0.5797 (t-170) REVERT: C 73 ARG cc_start: 0.8305 (mtt180) cc_final: 0.7886 (mmt-90) REVERT: C 160 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8316 (mm110) REVERT: C 265 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7188 (mp0) REVERT: C 304 GLN cc_start: 0.8497 (mt0) cc_final: 0.7942 (mt0) REVERT: C 338 LYS cc_start: 0.8091 (mmpt) cc_final: 0.7458 (mtmt) REVERT: D 62 PHE cc_start: 0.5512 (m-80) cc_final: 0.5126 (m-10) REVERT: D 167 MET cc_start: 0.6522 (ttm) cc_final: 0.5988 (ttm) REVERT: D 225 MET cc_start: 0.5579 (mtt) cc_final: 0.5163 (mmp) REVERT: D 326 GLN cc_start: 0.7081 (tp40) cc_final: 0.6774 (tm-30) REVERT: D 347 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6311 (m-30) REVERT: D 355 ILE cc_start: 0.5348 (tp) cc_final: 0.4836 (tp) REVERT: D 419 GLU cc_start: 0.6223 (mt-10) cc_final: 0.5746 (tm-30) REVERT: E 13 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7556 (mm-30) REVERT: E 59 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7682 (mp0) REVERT: E 99 GLU cc_start: 0.7295 (mm-30) cc_final: 0.7029 (mm-30) REVERT: E 108 LYS cc_start: 0.7690 (ptpt) cc_final: 0.7299 (mtmt) REVERT: E 133 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6960 (pm20) REVERT: F 20 GLN cc_start: 0.8105 (tp40) cc_final: 0.7708 (tm-30) REVERT: F 25 GLN cc_start: 0.8101 (tt0) cc_final: 0.7825 (tp40) REVERT: F 47 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7317 (mtp180) REVERT: F 59 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7379 (tm-30) REVERT: F 233 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6982 (mm-30) REVERT: G 93 LEU cc_start: 0.8801 (tp) cc_final: 0.8555 (tp) REVERT: G 173 MET cc_start: 0.8975 (mmm) cc_final: 0.8562 (mmm) REVERT: G 225 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7112 (ttpp) REVERT: I 33 PHE cc_start: 0.8672 (m-80) cc_final: 0.8262 (m-80) REVERT: I 120 ASP cc_start: 0.7297 (m-30) cc_final: 0.6253 (p0) REVERT: I 314 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7131 (mm-30) REVERT: J 205 LEU cc_start: 0.5110 (tp) cc_final: 0.4759 (tp) REVERT: K 194 MET cc_start: 0.6936 (mtp) cc_final: 0.6536 (mtp) REVERT: L 23 LYS cc_start: 0.7617 (ptmt) cc_final: 0.7386 (pttt) REVERT: L 85 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7948 (pp) REVERT: L 103 ASN cc_start: 0.8577 (m110) cc_final: 0.8353 (m-40) REVERT: L 114 GLN cc_start: 0.8086 (mm-40) cc_final: 0.7855 (tm-30) REVERT: N 5 LYS cc_start: 0.8597 (tptm) cc_final: 0.8249 (tppt) REVERT: N 23 GLN cc_start: 0.7790 (tt0) cc_final: 0.7520 (mm110) REVERT: N 29 GLU cc_start: 0.7906 (tt0) cc_final: 0.7590 (mt-10) REVERT: N 31 ARG cc_start: 0.7326 (mtm110) cc_final: 0.7035 (mtm180) REVERT: N 33 LYS cc_start: 0.8340 (mttt) cc_final: 0.8075 (mttp) REVERT: N 197 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7693 (tp) REVERT: O 55 HIS cc_start: 0.7783 (OUTLIER) cc_final: 0.6557 (m90) REVERT: O 117 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8333 (ptp-170) REVERT: O 166 GLU cc_start: 0.8216 (mt-10) cc_final: 0.8002 (mt-10) REVERT: R 59 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8341 (mtpt) REVERT: R 102 LYS cc_start: 0.8667 (mttp) cc_final: 0.8176 (pttt) REVERT: R 109 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8821 (mtmp) REVERT: S 13 ARG cc_start: 0.6467 (OUTLIER) cc_final: 0.6163 (mtt90) REVERT: S 47 LYS cc_start: 0.7877 (ttpp) cc_final: 0.7472 (tttm) REVERT: S 58 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8142 (mm) REVERT: S 83 SER cc_start: 0.6065 (p) cc_final: 0.5856 (t) REVERT: S 90 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8358 (ptp) REVERT: S 104 GLU cc_start: 0.8491 (tt0) cc_final: 0.8084 (mt-10) REVERT: S 131 LYS cc_start: 0.7919 (mttt) cc_final: 0.7495 (mmmt) REVERT: S 134 ASP cc_start: 0.7556 (m-30) cc_final: 0.7333 (m-30) REVERT: V 53 SER cc_start: 0.8639 (m) cc_final: 0.8237 (t) REVERT: V 59 MET cc_start: 0.8343 (mmt) cc_final: 0.7967 (mmm) REVERT: W 85 TYR cc_start: 0.5594 (t80) cc_final: 0.5059 (t80) REVERT: W 121 ARG cc_start: 0.5784 (mmm-85) cc_final: 0.5356 (mmm160) REVERT: W 157 MET cc_start: 0.6683 (ttm) cc_final: 0.6388 (ttp) REVERT: Y 11 ASP cc_start: 0.8746 (t0) cc_final: 0.8466 (t70) REVERT: Y 69 LYS cc_start: 0.8663 (tttt) cc_final: 0.8316 (ttmm) REVERT: Z 141 LEU cc_start: 0.3502 (OUTLIER) cc_final: 0.3048 (tp) REVERT: Z 169 PHE cc_start: 0.4505 (m-10) cc_final: 0.3671 (m-80) REVERT: a 174 MET cc_start: 0.2315 (tpp) cc_final: 0.1857 (ptm) REVERT: a 201 VAL cc_start: 0.0780 (OUTLIER) cc_final: 0.0247 (t) REVERT: b 3 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7101 (tp) REVERT: b 15 ASN cc_start: 0.7395 (m-40) cc_final: 0.6661 (p0) REVERT: b 106 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7336 (mt-10) REVERT: b 114 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6461 (ttt-90) REVERT: b 145 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6666 (m-30) REVERT: b 185 ARG cc_start: 0.6741 (mtp180) cc_final: 0.6347 (tmt-80) REVERT: b 227 ARG cc_start: 0.4679 (mtp180) cc_final: 0.4461 (mtt90) REVERT: b 252 TYR cc_start: 0.6209 (t80) cc_final: 0.5902 (t80) REVERT: b 288 ASN cc_start: 0.4188 (OUTLIER) cc_final: 0.3639 (p0) REVERT: b 387 LYS cc_start: 0.7565 (tttt) cc_final: 0.7065 (tttp) REVERT: e 34 LYS cc_start: 0.8678 (tttp) cc_final: 0.8413 (ttpt) REVERT: h 59 ASN cc_start: 0.8468 (t0) cc_final: 0.8137 (m-40) REVERT: h 60 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: i 58 ILE cc_start: 0.7794 (OUTLIER) cc_final: 0.7501 (mt) REVERT: i 75 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7650 (mtmt) REVERT: i 88 GLU cc_start: 0.7738 (tp30) cc_final: 0.7159 (tt0) REVERT: i 90 MET cc_start: 0.8415 (mmp) cc_final: 0.8166 (mmp) REVERT: l 121 MET cc_start: 0.1684 (ptm) cc_final: 0.0936 (pp-130) REVERT: m 181 MET cc_start: 0.3888 (mmm) cc_final: 0.3551 (mmm) REVERT: m 289 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7759 (mp) REVERT: m 299 GLU cc_start: 0.3888 (OUTLIER) cc_final: 0.3451 (tm-30) REVERT: m 342 GLU cc_start: 0.5199 (mp0) cc_final: 0.4473 (mt-10) REVERT: m 346 LEU cc_start: 0.4381 (tt) cc_final: 0.4121 (mt) REVERT: m 355 GLU cc_start: 0.2998 (tt0) cc_final: 0.2649 (tp30) REVERT: n 366 TYR cc_start: 0.2412 (t80) cc_final: 0.2201 (t80) REVERT: o 134 TYR cc_start: 0.8052 (p90) cc_final: 0.6680 (p90) REVERT: q 209 LYS cc_start: 0.4235 (OUTLIER) cc_final: 0.2627 (tppt) REVERT: q 226 GLU cc_start: 0.2650 (mt-10) cc_final: 0.2211 (mm-30) REVERT: q 250 PHE cc_start: 0.0425 (t80) cc_final: 0.0206 (t80) REVERT: q 352 MET cc_start: 0.1923 (mmm) cc_final: 0.1075 (mpt) REVERT: q 442 GLU cc_start: 0.1921 (OUTLIER) cc_final: 0.1510 (pt0) REVERT: r 194 PHE cc_start: 0.7078 (OUTLIER) cc_final: 0.6064 (t80) REVERT: t 93 ILE cc_start: 0.5251 (OUTLIER) cc_final: 0.4897 (pt) REVERT: t 165 LEU cc_start: 0.6490 (mt) cc_final: 0.6227 (mt) REVERT: t 181 LYS cc_start: 0.5577 (mppt) cc_final: 0.5238 (mmtm) REVERT: t 182 ASN cc_start: 0.4202 (m-40) cc_final: 0.3894 (m-40) REVERT: t 210 LYS cc_start: 0.5867 (mmtp) cc_final: 0.5618 (mtmt) REVERT: t 214 ILE cc_start: 0.4723 (OUTLIER) cc_final: 0.4271 (pp) REVERT: t 233 ASN cc_start: 0.4351 (m-40) cc_final: 0.4016 (t0) REVERT: t 316 SER cc_start: 0.5861 (p) cc_final: 0.5622 (p) REVERT: u 96 ILE cc_start: 0.7664 (mt) cc_final: 0.7423 (mp) REVERT: v 75 LYS cc_start: 0.6789 (mttt) cc_final: 0.6343 (ptpt) REVERT: v 157 GLU cc_start: 0.7680 (tp30) cc_final: 0.7426 (tm-30) REVERT: v 179 GLU cc_start: 0.8131 (pt0) cc_final: 0.7907 (tt0) REVERT: v 182 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7106 (mt-10) REVERT: v 186 GLU cc_start: 0.7836 (tt0) cc_final: 0.7578 (tt0) REVERT: v 214 ASP cc_start: 0.8428 (t0) cc_final: 0.8083 (t0) REVERT: w 32 LYS cc_start: 0.6605 (pttm) cc_final: 0.6242 (mppt) REVERT: w 78 ASP cc_start: 0.7740 (t0) cc_final: 0.7203 (t0) REVERT: w 80 LYS cc_start: 0.7301 (mttt) cc_final: 0.6779 (mmmm) REVERT: w 203 ARG cc_start: 0.6793 (ptp-170) cc_final: 0.6467 (ptm-80) REVERT: w 216 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7624 (t0) REVERT: x 62 ASN cc_start: 0.7688 (m110) cc_final: 0.7403 (m-40) REVERT: x 67 ASP cc_start: 0.8342 (t70) cc_final: 0.8059 (t70) REVERT: x 141 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8165 (mtpt) REVERT: x 152 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: x 174 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8572 (mmmt) REVERT: x 189 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7886 (mmt180) REVERT: x 258 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: y 1 MET cc_start: 0.5634 (tpt) cc_final: 0.4853 (ttp) REVERT: y 129 ILE cc_start: 0.7433 (mt) cc_final: 0.7131 (mt) REVERT: y 176 LEU cc_start: 0.7277 (mp) cc_final: 0.6944 (tp) REVERT: y 197 MET cc_start: 0.8594 (ptm) cc_final: 0.8231 (ptm) outliers start: 289 outliers final: 157 residues processed: 1330 average time/residue: 1.9662 time to fit residues: 3616.7710 Evaluate side-chains 1298 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1102 time to evaluate : 7.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 297 VAL Chi-restraints excluded: chain 8 residue 345 LYS Chi-restraints excluded: chain 8 residue 355 GLU Chi-restraints excluded: chain 8 residue 374 ASP Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 225 LYS Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 350 ARG Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain J residue 287 LYS Chi-restraints excluded: chain J residue 334 LEU Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 106 GLN Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 90 MET Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain T residue 175 ASN Chi-restraints excluded: chain T residue 202 LEU Chi-restraints excluded: chain T residue 232 VAL Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain Y residue 72 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 57 ILE Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 111 VAL Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 141 LEU Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 192 SER Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain b residue 3 LEU Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 106 GLU Chi-restraints excluded: chain b residue 114 ARG Chi-restraints excluded: chain b residue 115 LEU Chi-restraints excluded: chain b residue 145 ASP Chi-restraints excluded: chain b residue 288 ASN Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 97 SER Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain l residue 9 THR Chi-restraints excluded: chain l residue 56 THR Chi-restraints excluded: chain l residue 76 THR Chi-restraints excluded: chain l residue 162 VAL Chi-restraints excluded: chain m residue 179 ARG Chi-restraints excluded: chain m residue 254 MET Chi-restraints excluded: chain m residue 289 ILE Chi-restraints excluded: chain m residue 299 GLU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 179 VAL Chi-restraints excluded: chain n residue 250 LEU Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain n residue 387 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 151 SER Chi-restraints excluded: chain o residue 190 THR Chi-restraints excluded: chain q residue 209 LYS Chi-restraints excluded: chain q residue 211 LEU Chi-restraints excluded: chain q residue 242 THR Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain q residue 383 THR Chi-restraints excluded: chain q residue 418 ILE Chi-restraints excluded: chain q residue 442 GLU Chi-restraints excluded: chain q residue 502 VAL Chi-restraints excluded: chain q residue 514 THR Chi-restraints excluded: chain r residue 183 ASN Chi-restraints excluded: chain r residue 194 PHE Chi-restraints excluded: chain r residue 214 VAL Chi-restraints excluded: chain t residue 53 ASN Chi-restraints excluded: chain t residue 93 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain t residue 195 VAL Chi-restraints excluded: chain t residue 214 ILE Chi-restraints excluded: chain t residue 227 ILE Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 278 SER Chi-restraints excluded: chain t residue 282 SER Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 302 SER Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 13 CYS Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 89 THR Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain v residue 165 LEU Chi-restraints excluded: chain v residue 219 LEU Chi-restraints excluded: chain w residue 38 LYS Chi-restraints excluded: chain w residue 69 LEU Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain w residue 216 ASP Chi-restraints excluded: chain x residue 26 LYS Chi-restraints excluded: chain x residue 60 ILE Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 117 ILE Chi-restraints excluded: chain x residue 152 GLU Chi-restraints excluded: chain x residue 189 ARG Chi-restraints excluded: chain x residue 258 GLU Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 91 SER Chi-restraints excluded: chain y residue 174 SER Chi-restraints excluded: chain y residue 185 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1093 random chunks: chunk 1019 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 602 optimal weight: 9.9990 chunk 772 optimal weight: 7.9990 chunk 598 optimal weight: 3.9990 chunk 890 optimal weight: 7.9990 chunk 590 optimal weight: 9.9990 chunk 1053 optimal weight: 2.9990 chunk 659 optimal weight: 2.9990 chunk 642 optimal weight: 7.9990 chunk 486 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 121 ASN ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS D 251 ASN D 288 GLN D 397 ASN F 12 GLN F 19 GLN F 225 GLN ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN H 157 ASN J 203 HIS ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN P 121 GLN ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 HIS R 146 GLN S 62 ASN T 221 ASN T 249 ASN W 205 GLN Y 120 GLN a 200 ASN b 429 ASN f 106 ASN i 92 ASN m 155 ASN n 144 ASN n 191 ASN o 130 ASN q 369 ASN q 389 ASN t 53 ASN u 42 GLN ** w 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 24 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 126156 Z= 0.323 Angle : 0.621 10.614 180982 Z= 0.318 Chirality : 0.041 0.282 22049 Planarity : 0.005 0.083 14697 Dihedral : 21.795 179.958 44140 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.91 % Allowed : 16.88 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.52 % 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: 0.99 (0.09), residues: 8763 helix: 1.61 (0.08), residues: 3670 sheet: 0.19 (0.14), residues: 1334 loop : -0.02 (0.10), residues: 3759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP N 200 HIS 0.045 0.002 HIS O 55 PHE 0.033 0.002 PHE F 229 TYR 0.022 0.002 TYR Q 33 ARG 0.009 0.001 ARG u 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1420 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 305 poor density : 1115 time to evaluate : 7.249 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: 8 345 LYS cc_start: 0.4574 (OUTLIER) cc_final: 0.3650 (ptmt) REVERT: 8 401 GLN cc_start: 0.7750 (mt0) cc_final: 0.7461 (mt0) REVERT: A 117 LEU cc_start: 0.7096 (tp) cc_final: 0.6799 (mt) REVERT: A 153 LYS cc_start: 0.6382 (ttpp) cc_final: 0.5903 (tttt) REVERT: B 53 MET cc_start: 0.8759 (mtp) cc_final: 0.8356 (mtp) REVERT: B 190 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7587 (mt-10) REVERT: B 377 HIS cc_start: 0.6145 (t-90) cc_final: 0.5812 (t-170) REVERT: C 160 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8319 (mm110) REVERT: C 265 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7185 (mp0) REVERT: C 304 GLN cc_start: 0.8507 (mt0) cc_final: 0.7951 (mt0) REVERT: C 338 LYS cc_start: 0.8138 (mmpt) cc_final: 0.7473 (mtmt) REVERT: D 167 MET cc_start: 0.6575 (ttm) cc_final: 0.6034 (ttm) REVERT: D 225 MET cc_start: 0.5590 (mtt) cc_final: 0.5165 (mmp) REVERT: D 347 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6429 (m-30) REVERT: D 355 ILE cc_start: 0.5458 (tp) cc_final: 0.4938 (tp) REVERT: D 419 GLU cc_start: 0.6223 (mt-10) cc_final: 0.5740 (tm-30) REVERT: E 13 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7581 (mm-30) REVERT: E 59 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7655 (mp0) REVERT: E 99 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6968 (mm-30) REVERT: E 108 LYS cc_start: 0.7758 (ptpt) cc_final: 0.7356 (mtmt) REVERT: E 133 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7041 (pm20) REVERT: F 20 GLN cc_start: 0.8087 (tp40) cc_final: 0.7670 (tm-30) REVERT: F 25 GLN cc_start: 0.8116 (tt0) cc_final: 0.7846 (tp40) REVERT: F 47 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7295 (mtp180) REVERT: F 59 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: F 233 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7077 (mm-30) REVERT: G 93 LEU cc_start: 0.8805 (tp) cc_final: 0.8560 (tp) REVERT: G 173 MET cc_start: 0.8992 (mmm) cc_final: 0.8578 (mmm) REVERT: G 225 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7099 (ttpp) REVERT: I 33 PHE cc_start: 0.8676 (m-80) cc_final: 0.8231 (m-80) REVERT: I 120 ASP cc_start: 0.7347 (m-30) cc_final: 0.6275 (p0) REVERT: I 314 GLU cc_start: 0.7328 (mt-10) cc_final: 0.7098 (mm-30) REVERT: K 194 MET cc_start: 0.6996 (mtp) cc_final: 0.6658 (mtp) REVERT: L 23 LYS cc_start: 0.7649 (ptmt) cc_final: 0.7439 (pttt) REVERT: L 85 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8050 (pp) REVERT: L 103 ASN cc_start: 0.8654 (m110) cc_final: 0.8421 (m-40) REVERT: L 104 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7472 (mtm180) REVERT: L 114 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7874 (tm-30) REVERT: N 5 LYS cc_start: 0.8597 (tptm) cc_final: 0.8260 (tppt) REVERT: N 23 GLN cc_start: 0.7829 (tt0) cc_final: 0.7536 (mm110) REVERT: N 29 GLU cc_start: 0.7905 (tt0) cc_final: 0.7588 (mt-10) REVERT: N 31 ARG cc_start: 0.7359 (mtm110) cc_final: 0.7073 (mtm180) REVERT: N 33 LYS cc_start: 0.8367 (mttt) cc_final: 0.8125 (mttp) REVERT: N 197 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7767 (tp) REVERT: O 117 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8302 (ptp-170) REVERT: O 166 GLU cc_start: 0.8220 (mt-10) cc_final: 0.8006 (mt-10) REVERT: R 59 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8299 (mtpt) REVERT: R 92 GLN cc_start: 0.8993 (mt0) cc_final: 0.8792 (mt0) REVERT: R 102 LYS cc_start: 0.8650 (mttp) cc_final: 0.8183 (pttt) REVERT: R 109 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8794 (mtmp) REVERT: S 13 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.6236 (mtt90) REVERT: S 47 LYS cc_start: 0.7873 (ttpp) cc_final: 0.7458 (tttm) REVERT: S 58 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8150 (mm) REVERT: S 83 SER cc_start: 0.6074 (p) cc_final: 0.5849 (t) REVERT: S 104 GLU cc_start: 0.8488 (tt0) cc_final: 0.8094 (mt-10) REVERT: S 131 LYS cc_start: 0.7904 (mttt) cc_final: 0.7484 (mmmt) REVERT: S 134 ASP cc_start: 0.7501 (m-30) cc_final: 0.7278 (m-30) REVERT: V 59 MET cc_start: 0.8336 (mmt) cc_final: 0.7960 (mmm) REVERT: W 5 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8153 (pttm) REVERT: W 85 TYR cc_start: 0.5596 (t80) cc_final: 0.5125 (t80) REVERT: W 121 ARG cc_start: 0.5773 (mmm-85) cc_final: 0.5439 (mmm160) REVERT: W 157 MET cc_start: 0.6710 (ttm) cc_final: 0.6362 (ttp) REVERT: Y 11 ASP cc_start: 0.8736 (t0) cc_final: 0.8463 (t70) REVERT: Y 26 GLN cc_start: 0.8564 (mt0) cc_final: 0.8303 (mt0) REVERT: Y 69 LYS cc_start: 0.8678 (tttt) cc_final: 0.8346 (ttmm) REVERT: Z 141 LEU cc_start: 0.3552 (OUTLIER) cc_final: 0.3115 (tp) REVERT: Z 169 PHE cc_start: 0.4511 (m-10) cc_final: 0.3707 (m-80) REVERT: a 201 VAL cc_start: 0.0722 (OUTLIER) cc_final: 0.0163 (t) REVERT: b 106 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7348 (mt-10) REVERT: b 114 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.6454 (ttt-90) REVERT: b 185 ARG cc_start: 0.6766 (mtp180) cc_final: 0.6368 (tmt-80) REVERT: b 227 ARG cc_start: 0.4603 (mtp180) cc_final: 0.4392 (mtt90) REVERT: b 387 LYS cc_start: 0.7567 (tttt) cc_final: 0.7069 (tttp) REVERT: e 34 LYS cc_start: 0.8680 (tttp) cc_final: 0.8413 (ttpt) REVERT: h 59 ASN cc_start: 0.8493 (t0) cc_final: 0.8142 (m-40) REVERT: h 60 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: i 58 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7556 (mt) REVERT: i 75 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7702 (mtmt) REVERT: i 88 GLU cc_start: 0.7705 (tp30) cc_final: 0.7219 (tt0) REVERT: m 289 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7781 (mp) REVERT: m 299 GLU cc_start: 0.3916 (OUTLIER) cc_final: 0.3467 (tm-30) REVERT: m 342 GLU cc_start: 0.5285 (mp0) cc_final: 0.4278 (mt-10) REVERT: m 346 LEU cc_start: 0.4228 (tt) cc_final: 0.3951 (mt) REVERT: m 355 GLU cc_start: 0.3066 (tt0) cc_final: 0.2682 (tp30) REVERT: n 130 ARG cc_start: 0.4482 (OUTLIER) cc_final: 0.4176 (ptp90) REVERT: q 209 LYS cc_start: 0.4274 (OUTLIER) cc_final: 0.4042 (ptpt) REVERT: q 226 GLU cc_start: 0.2662 (mt-10) cc_final: 0.2196 (mm-30) REVERT: q 442 GLU cc_start: 0.2059 (OUTLIER) cc_final: 0.1729 (pt0) REVERT: r 38 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7726 (mtp180) REVERT: r 194 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6196 (t80) REVERT: r 210 THR cc_start: 0.6148 (OUTLIER) cc_final: 0.5929 (p) REVERT: t 181 LYS cc_start: 0.5615 (mppt) cc_final: 0.5266 (mmtm) REVERT: t 214 ILE cc_start: 0.4578 (OUTLIER) cc_final: 0.4159 (pp) REVERT: t 233 ASN cc_start: 0.4124 (m-40) cc_final: 0.3883 (t0) REVERT: u 90 LEU cc_start: 0.7918 (mt) cc_final: 0.7709 (mm) REVERT: u 96 ILE cc_start: 0.7673 (mt) cc_final: 0.7428 (mp) REVERT: v 75 LYS cc_start: 0.6813 (mttt) cc_final: 0.6382 (ptpt) REVERT: v 182 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7089 (mt-10) REVERT: v 186 GLU cc_start: 0.7865 (tt0) cc_final: 0.7609 (tt0) REVERT: v 214 ASP cc_start: 0.8462 (t0) cc_final: 0.8147 (t0) REVERT: w 78 ASP cc_start: 0.7773 (t0) cc_final: 0.7243 (t0) REVERT: w 80 LYS cc_start: 0.7306 (mttt) cc_final: 0.6770 (mmmm) REVERT: w 203 ARG cc_start: 0.6803 (ptp-170) cc_final: 0.6477 (ptm-80) REVERT: x 62 ASN cc_start: 0.7736 (m110) cc_final: 0.7471 (m-40) REVERT: x 67 ASP cc_start: 0.8354 (t70) cc_final: 0.8089 (t70) REVERT: x 141 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8182 (mtpt) REVERT: x 152 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: x 189 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7915 (mmt180) REVERT: x 258 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8152 (tt0) REVERT: y 1 MET cc_start: 0.5537 (tpt) cc_final: 0.4904 (ttp) REVERT: y 176 LEU cc_start: 0.7190 (mp) cc_final: 0.6830 (tp) REVERT: y 197 MET cc_start: 0.8598 (ptm) cc_final: 0.8239 (ptm) outliers start: 305 outliers final: 184 residues processed: 1327 average time/residue: 1.9565 time to fit residues: 3616.8801 Evaluate side-chains 1291 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1070 time to evaluate : 7.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 297 VAL Chi-restraints excluded: chain 8 residue 340 ILE Chi-restraints excluded: chain 8 residue 345 LYS Chi-restraints excluded: chain 8 residue 355 GLU Chi-restraints excluded: chain 8 residue 374 ASP Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 275 LYS Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 434 LYS Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 142 SER Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 132 VAL Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain G residue 225 LYS Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 350 ARG Chi-restraints excluded: chain I residue 413 VAL Chi-restraints excluded: chain J residue 287 LYS Chi-restraints excluded: chain J residue 334 LEU Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 104 ARG Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain O residue 117 ARG Chi-restraints excluded: chain O residue 138 LEU Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain R residue 109 LYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain S residue 3 HIS Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain T residue 175 ASN Chi-restraints excluded: chain T residue 202 LEU Chi-restraints excluded: chain T residue 232 VAL Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain Y residue 72 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 57 ILE Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 111 VAL Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 141 LEU Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 167 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 192 SER Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain b residue 64 ILE Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 106 GLU Chi-restraints excluded: chain b residue 114 ARG Chi-restraints excluded: chain b residue 115 LEU Chi-restraints excluded: chain b residue 171 LEU Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 249 CYS Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain i residue 17 VAL Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain i residue 97 SER Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain l residue 9 THR Chi-restraints excluded: chain l residue 56 THR Chi-restraints excluded: chain l residue 76 THR Chi-restraints excluded: chain l residue 162 VAL Chi-restraints excluded: chain m residue 254 MET Chi-restraints excluded: chain m residue 289 ILE Chi-restraints excluded: chain m residue 299 GLU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain n residue 179 VAL Chi-restraints excluded: chain n residue 227 THR Chi-restraints excluded: chain n residue 250 LEU Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain n residue 387 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 151 SER Chi-restraints excluded: chain o residue 190 THR Chi-restraints excluded: chain o residue 201 LYS Chi-restraints excluded: chain q residue 209 LYS Chi-restraints excluded: chain q residue 211 LEU Chi-restraints excluded: chain q residue 242 THR Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain q residue 383 THR Chi-restraints excluded: chain q residue 418 ILE Chi-restraints excluded: chain q residue 424 CYS Chi-restraints excluded: chain q residue 442 GLU Chi-restraints excluded: chain q residue 502 VAL Chi-restraints excluded: chain q residue 514 THR Chi-restraints excluded: chain r residue 38 ARG Chi-restraints excluded: chain r residue 183 ASN Chi-restraints excluded: chain r residue 194 PHE Chi-restraints excluded: chain r residue 210 THR Chi-restraints excluded: chain r residue 214 VAL Chi-restraints excluded: chain r residue 225 VAL Chi-restraints excluded: chain t residue 93 ILE Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain t residue 195 VAL Chi-restraints excluded: chain t residue 214 ILE Chi-restraints excluded: chain t residue 227 ILE Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 273 LEU Chi-restraints excluded: chain t residue 278 SER Chi-restraints excluded: chain t residue 282 SER Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 302 SER Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 13 CYS Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 89 THR Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain v residue 165 LEU Chi-restraints excluded: chain v residue 219 LEU Chi-restraints excluded: chain w residue 38 LYS Chi-restraints excluded: chain w residue 69 LEU Chi-restraints excluded: chain w residue 174 VAL Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 26 LYS Chi-restraints excluded: chain x residue 60 ILE Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 152 GLU Chi-restraints excluded: chain x residue 189 ARG Chi-restraints excluded: chain x residue 258 GLU Chi-restraints excluded: chain y residue 36 SER Chi-restraints excluded: chain y residue 74 THR Chi-restraints excluded: chain y residue 91 SER Chi-restraints excluded: chain y residue 143 SER Chi-restraints excluded: chain y residue 167 VAL Chi-restraints excluded: chain y residue 174 SER Chi-restraints excluded: chain y residue 185 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1093 random chunks: chunk 651 optimal weight: 6.9990 chunk 420 optimal weight: 5.9990 chunk 629 optimal weight: 6.9990 chunk 317 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 chunk 669 optimal weight: 3.9990 chunk 717 optimal weight: 0.2980 chunk 520 optimal weight: 30.0000 chunk 98 optimal weight: 10.0000 chunk 828 optimal weight: 2.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN F 19 GLN F 225 GLN H 59 ASN H 157 ASN ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 HIS R 146 GLN ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 ASN Y 120 GLN a 197 ASN b 429 ASN f 106 ASN i 92 ASN n 144 ASN ** n 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 130 ASN q 389 ASN t 291 GLN u 42 GLN v 29 ASN ** w 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 126156 Z= 0.218 Angle : 0.549 11.575 180982 Z= 0.284 Chirality : 0.037 0.306 22049 Planarity : 0.004 0.069 14697 Dihedral : 21.733 179.851 44138 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.35 % Allowed : 17.92 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.09), residues: 8763 helix: 1.73 (0.08), residues: 3661 sheet: 0.23 (0.14), residues: 1309 loop : 0.00 (0.10), residues: 3793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP e 32 HIS 0.011 0.001 HIS l 82 PHE 0.027 0.002 PHE F 229 TYR 0.019 0.002 TYR Q 33 ARG 0.009 0.001 ARG u 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1099 time to evaluate : 7.045 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: 8 345 LYS cc_start: 0.4480 (OUTLIER) cc_final: 0.3553 (ptmt) REVERT: 8 401 GLN cc_start: 0.7700 (mt0) cc_final: 0.7463 (mt0) REVERT: A 117 LEU cc_start: 0.7090 (tp) cc_final: 0.6787 (mt) REVERT: A 153 LYS cc_start: 0.6330 (ttpp) cc_final: 0.5878 (tttt) REVERT: B 53 MET cc_start: 0.8710 (mtp) cc_final: 0.8345 (mtp) REVERT: B 190 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7484 (mt-10) REVERT: B 377 HIS cc_start: 0.6126 (t-90) cc_final: 0.5793 (t-170) REVERT: B 384 LYS cc_start: 0.7042 (ptmm) cc_final: 0.6756 (ptmm) REVERT: C 73 ARG cc_start: 0.8284 (mtt180) cc_final: 0.7897 (mmt-90) REVERT: C 160 GLN cc_start: 0.8763 (OUTLIER) cc_final: 0.8184 (mm110) REVERT: C 265 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7212 (mp0) REVERT: C 304 GLN cc_start: 0.8503 (mt0) cc_final: 0.8021 (mt0) REVERT: C 338 LYS cc_start: 0.7984 (mmpt) cc_final: 0.7398 (mtmt) REVERT: D 167 MET cc_start: 0.6526 (ttm) cc_final: 0.5960 (ttm) REVERT: D 196 ASP cc_start: 0.5762 (OUTLIER) cc_final: 0.5210 (m-30) REVERT: D 197 GLU cc_start: 0.5982 (mt-10) cc_final: 0.5683 (mt-10) REVERT: D 225 MET cc_start: 0.5537 (mtt) cc_final: 0.5132 (mmp) REVERT: D 347 ASP cc_start: 0.6723 (OUTLIER) cc_final: 0.6272 (m-30) REVERT: D 355 ILE cc_start: 0.5386 (tp) cc_final: 0.4874 (tp) REVERT: D 392 MET cc_start: 0.7290 (ttp) cc_final: 0.7024 (tmm) REVERT: D 419 GLU cc_start: 0.6198 (mt-10) cc_final: 0.5716 (tm-30) REVERT: E 13 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7521 (mm-30) REVERT: E 59 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7659 (mp0) REVERT: E 99 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6995 (mm-30) REVERT: E 108 LYS cc_start: 0.7770 (ptpt) cc_final: 0.7369 (mtmt) REVERT: E 133 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6977 (pm20) REVERT: F 20 GLN cc_start: 0.8091 (tp40) cc_final: 0.7681 (tm-30) REVERT: F 25 GLN cc_start: 0.7988 (tt0) cc_final: 0.7770 (tp40) REVERT: F 47 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.7316 (mtp180) REVERT: F 59 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: F 233 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6879 (mm-30) REVERT: G 173 MET cc_start: 0.8983 (mmm) cc_final: 0.8567 (mmm) REVERT: I 33 PHE cc_start: 0.8674 (m-80) cc_final: 0.8297 (m-80) REVERT: I 120 ASP cc_start: 0.7342 (m-30) cc_final: 0.6281 (p0) REVERT: I 314 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7107 (mm-30) REVERT: J 205 LEU cc_start: 0.5082 (tp) cc_final: 0.4814 (tp) REVERT: K 194 MET cc_start: 0.6958 (mtp) cc_final: 0.6623 (mtp) REVERT: L 23 LYS cc_start: 0.7645 (ptmt) cc_final: 0.7425 (pttt) REVERT: L 85 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7959 (pp) REVERT: L 103 ASN cc_start: 0.8606 (m110) cc_final: 0.8373 (m-40) REVERT: L 104 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7551 (mtm180) REVERT: L 114 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7831 (tm-30) REVERT: N 5 LYS cc_start: 0.8591 (tptm) cc_final: 0.8245 (tppt) REVERT: N 23 GLN cc_start: 0.7810 (tt0) cc_final: 0.7518 (mm110) REVERT: N 29 GLU cc_start: 0.7897 (tt0) cc_final: 0.7645 (mt-10) REVERT: N 31 ARG cc_start: 0.7366 (mtm110) cc_final: 0.7015 (mtm-85) REVERT: N 32 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7088 (mp10) REVERT: N 33 LYS cc_start: 0.8457 (mttt) cc_final: 0.8222 (mttp) REVERT: N 197 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7749 (tp) REVERT: O 166 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8007 (mt-10) REVERT: R 59 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8290 (mtpt) REVERT: R 102 LYS cc_start: 0.8643 (mttp) cc_final: 0.8193 (pttt) REVERT: S 13 ARG cc_start: 0.6464 (OUTLIER) cc_final: 0.6174 (mtt90) REVERT: S 47 LYS cc_start: 0.7868 (ttpp) cc_final: 0.7470 (tttm) REVERT: S 58 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8145 (mm) REVERT: S 104 GLU cc_start: 0.8487 (tt0) cc_final: 0.8080 (mt-10) REVERT: S 131 LYS cc_start: 0.7905 (mttt) cc_final: 0.7483 (mmmt) REVERT: S 134 ASP cc_start: 0.7509 (m-30) cc_final: 0.7289 (m-30) REVERT: T 175 ASN cc_start: 0.1432 (OUTLIER) cc_final: 0.0894 (p0) REVERT: V 59 MET cc_start: 0.8330 (mmt) cc_final: 0.7961 (mmm) REVERT: W 5 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.8081 (pttm) REVERT: W 46 ASP cc_start: 0.6182 (OUTLIER) cc_final: 0.5856 (t0) REVERT: W 85 TYR cc_start: 0.5568 (t80) cc_final: 0.5047 (t80) REVERT: W 121 ARG cc_start: 0.5736 (mmm-85) cc_final: 0.5404 (mmm160) REVERT: W 157 MET cc_start: 0.6596 (ttm) cc_final: 0.6305 (ttp) REVERT: Y 11 ASP cc_start: 0.8746 (t0) cc_final: 0.8467 (t70) REVERT: Z 141 LEU cc_start: 0.3473 (OUTLIER) cc_final: 0.3208 (tp) REVERT: Z 169 PHE cc_start: 0.4480 (m-10) cc_final: 0.3715 (m-80) REVERT: a 192 SER cc_start: 0.2990 (OUTLIER) cc_final: 0.2650 (m) REVERT: a 201 VAL cc_start: 0.0667 (OUTLIER) cc_final: 0.0125 (t) REVERT: b 106 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: b 114 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6458 (ttt-90) REVERT: b 185 ARG cc_start: 0.6702 (mtp180) cc_final: 0.6352 (tmt-80) REVERT: b 227 ARG cc_start: 0.4614 (mtp180) cc_final: 0.4393 (mtt90) REVERT: b 387 LYS cc_start: 0.7563 (tttt) cc_final: 0.7049 (tttp) REVERT: b 432 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7710 (tpp) REVERT: e 34 LYS cc_start: 0.8657 (tttp) cc_final: 0.8403 (ttpt) REVERT: f 33 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7979 (tt0) REVERT: h 59 ASN cc_start: 0.8479 (t0) cc_final: 0.8137 (m-40) REVERT: h 60 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: i 58 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7500 (mt) REVERT: i 75 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7670 (mtmt) REVERT: i 88 GLU cc_start: 0.7721 (tp30) cc_final: 0.7227 (tt0) REVERT: m 289 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7773 (mp) REVERT: m 342 GLU cc_start: 0.5317 (mp0) cc_final: 0.4289 (mt-10) REVERT: m 355 GLU cc_start: 0.2986 (tt0) cc_final: 0.2556 (tp30) REVERT: o 200 MET cc_start: 0.3623 (pp-130) cc_final: 0.3106 (ttp) REVERT: q 226 GLU cc_start: 0.2639 (mt-10) cc_final: 0.2200 (mm-30) REVERT: q 366 MET cc_start: 0.2106 (OUTLIER) cc_final: 0.1804 (pmt) REVERT: q 442 GLU cc_start: 0.1982 (OUTLIER) cc_final: 0.1556 (pt0) REVERT: r 194 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6098 (t80) REVERT: r 209 TYR cc_start: 0.6268 (OUTLIER) cc_final: 0.6051 (m-10) REVERT: r 210 THR cc_start: 0.6340 (OUTLIER) cc_final: 0.6090 (p) REVERT: t 181 LYS cc_start: 0.5604 (mppt) cc_final: 0.5233 (mmtm) REVERT: t 214 ILE cc_start: 0.4785 (OUTLIER) cc_final: 0.4388 (pp) REVERT: t 233 ASN cc_start: 0.4128 (m-40) cc_final: 0.3878 (t0) REVERT: u 90 LEU cc_start: 0.7920 (mt) cc_final: 0.7719 (mm) REVERT: u 96 ILE cc_start: 0.7722 (mt) cc_final: 0.7493 (mp) REVERT: v 75 LYS cc_start: 0.6810 (mttt) cc_final: 0.6391 (ptpt) REVERT: v 182 GLU cc_start: 0.7450 (mt-10) cc_final: 0.7087 (mt-10) REVERT: v 186 GLU cc_start: 0.7835 (tt0) cc_final: 0.7579 (tt0) REVERT: v 214 ASP cc_start: 0.8420 (t0) cc_final: 0.8075 (t0) REVERT: w 32 LYS cc_start: 0.6881 (pttm) cc_final: 0.6423 (mppt) REVERT: w 78 ASP cc_start: 0.7729 (t0) cc_final: 0.7164 (t0) REVERT: w 80 LYS cc_start: 0.7293 (mttt) cc_final: 0.6779 (mmmm) REVERT: w 203 ARG cc_start: 0.6792 (ptp-170) cc_final: 0.6469 (ptm-80) REVERT: x 62 ASN cc_start: 0.7668 (m110) cc_final: 0.7390 (m-40) REVERT: x 67 ASP cc_start: 0.8365 (t70) cc_final: 0.8041 (t70) REVERT: x 141 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8171 (mtpt) REVERT: x 152 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: x 174 LYS cc_start: 0.8902 (mtmt) cc_final: 0.8672 (mmmt) REVERT: x 189 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7881 (mmt180) REVERT: x 258 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: y 1 MET cc_start: 0.5360 (tpt) cc_final: 0.4751 (ttp) REVERT: y 99 GLU cc_start: 0.8144 (tp30) cc_final: 0.7880 (tp30) REVERT: y 129 ILE cc_start: 0.7595 (mt) cc_final: 0.7262 (mt) REVERT: y 176 LEU cc_start: 0.7267 (mp) cc_final: 0.6930 (tp) REVERT: y 197 MET cc_start: 0.8574 (ptm) cc_final: 0.8215 (ptm) REVERT: y 223 ARG cc_start: 0.7890 (mmm-85) cc_final: 0.7495 (mtp85) outliers start: 261 outliers final: 157 residues processed: 1276 average time/residue: 2.0691 time to fit residues: 3668.1618 Evaluate side-chains 1277 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1081 time to evaluate : 7.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 297 VAL Chi-restraints excluded: chain 8 residue 345 LYS Chi-restraints excluded: chain 8 residue 355 GLU Chi-restraints excluded: chain 8 residue 374 ASP Chi-restraints excluded: chain A residue 28 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 14 GLU Chi-restraints excluded: chain C residue 58 HIS Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 160 GLN Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 274 ASP Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 47 ARG Chi-restraints excluded: chain F residue 59 GLU Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 233 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 215 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 142 THR Chi-restraints excluded: chain I residue 350 ARG Chi-restraints excluded: chain J residue 287 LYS Chi-restraints excluded: chain J residue 334 LEU Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain K residue 281 ILE Chi-restraints excluded: chain K residue 283 THR Chi-restraints excluded: chain K residue 288 VAL Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain L residue 104 ARG Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 16 GLU Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 32 GLN Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 190 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain Q residue 129 VAL Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 141 LYS Chi-restraints excluded: chain T residue 175 ASN Chi-restraints excluded: chain T residue 202 LEU Chi-restraints excluded: chain T residue 232 VAL Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain W residue 5 LYS Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 118 SER Chi-restraints excluded: chain W residue 158 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 88 SER Chi-restraints excluded: chain Z residue 111 VAL Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 141 LEU Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 167 VAL Chi-restraints excluded: chain a residue 178 VAL Chi-restraints excluded: chain a residue 192 SER Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 104 LEU Chi-restraints excluded: chain b residue 106 GLU Chi-restraints excluded: chain b residue 114 ARG Chi-restraints excluded: chain b residue 115 LEU Chi-restraints excluded: chain b residue 192 VAL Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain f residue 33 GLU Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain h residue 60 GLU Chi-restraints excluded: chain h residue 101 THR Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 58 ILE Chi-restraints excluded: chain j residue 15 SER Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain l residue 56 THR Chi-restraints excluded: chain l residue 76 THR Chi-restraints excluded: chain l residue 123 ASP Chi-restraints excluded: chain m residue 254 MET Chi-restraints excluded: chain m residue 289 ILE Chi-restraints excluded: chain m residue 352 GLU Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 179 VAL Chi-restraints excluded: chain n residue 250 LEU Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain n residue 387 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 151 SER Chi-restraints excluded: chain o residue 190 THR Chi-restraints excluded: chain q residue 211 LEU Chi-restraints excluded: chain q residue 334 SER Chi-restraints excluded: chain q residue 366 MET Chi-restraints excluded: chain q residue 383 THR Chi-restraints excluded: chain q residue 424 CYS Chi-restraints excluded: chain q residue 442 GLU Chi-restraints excluded: chain q residue 502 VAL Chi-restraints excluded: chain q residue 514 THR Chi-restraints excluded: chain r residue 183 ASN Chi-restraints excluded: chain r residue 194 PHE Chi-restraints excluded: chain r residue 209 TYR Chi-restraints excluded: chain r residue 210 THR Chi-restraints excluded: chain r residue 214 VAL Chi-restraints excluded: chain r residue 225 VAL Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 166 LEU Chi-restraints excluded: chain t residue 195 VAL Chi-restraints excluded: chain t residue 214 ILE Chi-restraints excluded: chain t residue 227 ILE Chi-restraints excluded: chain t residue 235 VAL Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 273 LEU Chi-restraints excluded: chain t residue 278 SER Chi-restraints excluded: chain t residue 282 SER Chi-restraints excluded: chain t residue 283 LEU Chi-restraints excluded: chain t residue 302 SER Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 13 CYS Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain u residue 89 THR Chi-restraints excluded: chain v residue 29 ASN Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 61 THR Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain v residue 165 LEU Chi-restraints excluded: chain v residue 219 LEU Chi-restraints excluded: chain w residue 30 THR Chi-restraints excluded: chain w residue 38 LYS Chi-restraints excluded: chain w residue 69 LEU Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 60 ILE Chi-restraints excluded: chain x residue 65 VAL Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 117 ILE Chi-restraints excluded: chain x residue 152 GLU Chi-restraints excluded: chain x residue 189 ARG Chi-restraints excluded: chain x residue 258 GLU Chi-restraints excluded: chain y residue 91 SER Chi-restraints excluded: chain y residue 174 SER Chi-restraints excluded: chain y residue 185 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1093 random chunks: chunk 958 optimal weight: 2.9990 chunk 1009 optimal weight: 0.9990 chunk 920 optimal weight: 0.3980 chunk 981 optimal weight: 0.9990 chunk 1008 optimal weight: 1.9990 chunk 590 optimal weight: 10.0000 chunk 427 optimal weight: 0.9990 chunk 770 optimal weight: 0.4980 chunk 301 optimal weight: 4.9990 chunk 887 optimal weight: 20.0000 chunk 928 optimal weight: 30.0000 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 GLN B 313 HIS D 397 ASN F 19 GLN F 225 GLN H 157 ASN ** K 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 105 ASN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN O 55 HIS ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 121 GLN ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 ASN T 221 ASN Y 120 GLN b 429 ASN f 106 ASN ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 92 ASN ** n 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 144 ASN ** n 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 130 ASN q 369 ASN q 389 ASN t 291 GLN u 42 GLN ** w 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 126156 Z= 0.128 Angle : 0.484 12.307 180982 Z= 0.250 Chirality : 0.034 0.282 22049 Planarity : 0.004 0.056 14697 Dihedral : 21.598 179.959 44138 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.99 % Allowed : 19.42 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.09), residues: 8763 helix: 1.98 (0.09), residues: 3680 sheet: 0.32 (0.14), residues: 1298 loop : 0.12 (0.10), residues: 3785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 106 HIS 0.010 0.001 HIS l 82 PHE 0.024 0.001 PHE t 99 TYR 0.024 0.001 TYR q 531 ARG 0.009 0.000 ARG u 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1300 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1145 time to evaluate : 7.084 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: 8 308 LYS cc_start: 0.4642 (tptp) cc_final: 0.4199 (mmmm) REVERT: 8 340 ILE cc_start: 0.4681 (OUTLIER) cc_final: 0.3957 (tp) REVERT: A 153 LYS cc_start: 0.6246 (ttpp) cc_final: 0.5817 (tttt) REVERT: B 53 MET cc_start: 0.8585 (mtp) cc_final: 0.8237 (mtp) REVERT: B 190 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7451 (mt-10) REVERT: B 196 ARG cc_start: 0.7211 (ttp-110) cc_final: 0.6563 (ttp80) REVERT: B 371 GLN cc_start: 0.8298 (mm-40) cc_final: 0.8052 (mm110) REVERT: B 377 HIS cc_start: 0.6058 (t-90) cc_final: 0.5728 (t-170) REVERT: C 73 ARG cc_start: 0.8281 (mtt180) cc_final: 0.7516 (mtm180) REVERT: C 265 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7162 (mp0) REVERT: C 304 GLN cc_start: 0.8492 (mt0) cc_final: 0.7999 (mt0) REVERT: C 338 LYS cc_start: 0.7856 (mmpt) cc_final: 0.7317 (mtmt) REVERT: D 167 MET cc_start: 0.6456 (ttm) cc_final: 0.5879 (ttm) REVERT: D 196 ASP cc_start: 0.5505 (OUTLIER) cc_final: 0.4977 (m-30) REVERT: D 197 GLU cc_start: 0.6038 (mt-10) cc_final: 0.5776 (mt-10) REVERT: D 225 MET cc_start: 0.5508 (mtt) cc_final: 0.5123 (mmp) REVERT: D 326 GLN cc_start: 0.7146 (tp40) cc_final: 0.6837 (tm-30) REVERT: D 347 ASP cc_start: 0.6645 (OUTLIER) cc_final: 0.6322 (m-30) REVERT: D 355 ILE cc_start: 0.5235 (tp) cc_final: 0.4731 (tp) REVERT: D 392 MET cc_start: 0.7309 (ttp) cc_final: 0.7064 (tmm) REVERT: D 419 GLU cc_start: 0.6191 (mt-10) cc_final: 0.5739 (tm-30) REVERT: E 59 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7646 (mp0) REVERT: E 99 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7142 (mm-30) REVERT: E 108 LYS cc_start: 0.7668 (ptpt) cc_final: 0.7340 (mtmt) REVERT: E 133 GLU cc_start: 0.7495 (pp20) cc_final: 0.6973 (pm20) REVERT: F 20 GLN cc_start: 0.8144 (tp40) cc_final: 0.7750 (tm-30) REVERT: F 25 GLN cc_start: 0.7971 (tt0) cc_final: 0.7746 (tp40) REVERT: G 89 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8236 (mm-30) REVERT: G 173 MET cc_start: 0.8963 (mmm) cc_final: 0.8543 (mmm) REVERT: G 180 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8061 (m) REVERT: H 63 LYS cc_start: 0.8624 (ptmm) cc_final: 0.8047 (mmtp) REVERT: H 110 LYS cc_start: 0.7775 (ttmt) cc_final: 0.7418 (tttm) REVERT: H 118 LEU cc_start: 0.9086 (mt) cc_final: 0.8793 (mt) REVERT: H 134 ILE cc_start: 0.8595 (mt) cc_final: 0.8321 (mt) REVERT: I 33 PHE cc_start: 0.8656 (m-80) cc_final: 0.8286 (m-80) REVERT: I 120 ASP cc_start: 0.7308 (m-30) cc_final: 0.6265 (p0) REVERT: I 132 LYS cc_start: 0.8220 (ptmt) cc_final: 0.7830 (pttt) REVERT: I 314 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7098 (mm-30) REVERT: J 205 LEU cc_start: 0.5033 (tp) cc_final: 0.4756 (tp) REVERT: K 194 MET cc_start: 0.6814 (mtp) cc_final: 0.6444 (mtp) REVERT: L 23 LYS cc_start: 0.7640 (ptmt) cc_final: 0.7398 (pttt) REVERT: L 85 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.7831 (pp) REVERT: L 103 ASN cc_start: 0.8584 (m110) cc_final: 0.8373 (m-40) REVERT: N 5 LYS cc_start: 0.8573 (tptm) cc_final: 0.8213 (tppt) REVERT: N 23 GLN cc_start: 0.7800 (tt0) cc_final: 0.7551 (mm110) REVERT: N 29 GLU cc_start: 0.7876 (tt0) cc_final: 0.7569 (mt-10) REVERT: N 31 ARG cc_start: 0.7292 (mtm110) cc_final: 0.7071 (mtm-85) REVERT: N 33 LYS cc_start: 0.8421 (mttt) cc_final: 0.8198 (mttp) REVERT: N 197 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7802 (tp) REVERT: O 166 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7987 (mt-10) REVERT: R 59 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8396 (mtpt) REVERT: R 102 LYS cc_start: 0.8600 (mttp) cc_final: 0.8187 (pttt) REVERT: S 13 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5924 (mtp85) REVERT: S 47 LYS cc_start: 0.7872 (ttpp) cc_final: 0.7478 (tttm) REVERT: S 58 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8066 (mm) REVERT: S 131 LYS cc_start: 0.7896 (mttt) cc_final: 0.7502 (mmtt) REVERT: S 134 ASP cc_start: 0.7549 (m-30) cc_final: 0.7347 (m-30) REVERT: T 175 ASN cc_start: 0.1531 (OUTLIER) cc_final: 0.1013 (p0) REVERT: V 53 SER cc_start: 0.8588 (m) cc_final: 0.8269 (t) REVERT: V 59 MET cc_start: 0.8336 (mmt) cc_final: 0.7973 (mmm) REVERT: W 85 TYR cc_start: 0.5537 (t80) cc_final: 0.4979 (t80) REVERT: W 121 ARG cc_start: 0.5741 (mmm-85) cc_final: 0.5326 (mmm160) REVERT: Y 11 ASP cc_start: 0.8716 (t0) cc_final: 0.8434 (t70) REVERT: Y 91 ASN cc_start: 0.8404 (p0) cc_final: 0.8176 (p0) REVERT: Z 26 MET cc_start: 0.2361 (ptm) cc_final: 0.1855 (mtt) REVERT: Z 141 LEU cc_start: 0.3463 (OUTLIER) cc_final: 0.3218 (tp) REVERT: Z 169 PHE cc_start: 0.4539 (m-10) cc_final: 0.3559 (m-80) REVERT: a 201 VAL cc_start: 0.0989 (OUTLIER) cc_final: 0.0432 (t) REVERT: b 59 GLU cc_start: 0.7173 (tm-30) cc_final: 0.6927 (tm-30) REVERT: b 106 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: b 114 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6477 (ttt-90) REVERT: b 185 ARG cc_start: 0.6646 (mtp180) cc_final: 0.6262 (tpt90) REVERT: b 387 LYS cc_start: 0.7540 (tttt) cc_final: 0.7046 (tttp) REVERT: e 34 LYS cc_start: 0.8577 (tttp) cc_final: 0.8352 (ttpt) REVERT: h 59 ASN cc_start: 0.8394 (t0) cc_final: 0.8090 (m-40) REVERT: i 26 ILE cc_start: 0.8399 (mt) cc_final: 0.8180 (tp) REVERT: i 58 ILE cc_start: 0.7664 (pp) cc_final: 0.7411 (mt) REVERT: i 75 LYS cc_start: 0.7861 (ttmm) cc_final: 0.7521 (mtmt) REVERT: i 88 GLU cc_start: 0.7744 (tp30) cc_final: 0.7183 (tt0) REVERT: m 181 MET cc_start: 0.4028 (mmm) cc_final: 0.3668 (mmm) REVERT: m 342 GLU cc_start: 0.5262 (mp0) cc_final: 0.4244 (mt-10) REVERT: m 355 GLU cc_start: 0.2935 (tt0) cc_final: 0.2542 (tp30) REVERT: n 239 ASP cc_start: 0.4122 (OUTLIER) cc_final: 0.3554 (m-30) REVERT: n 427 ILE cc_start: 0.2884 (OUTLIER) cc_final: 0.2368 (mt) REVERT: o 134 TYR cc_start: 0.8015 (p90) cc_final: 0.6672 (p90) REVERT: o 165 ARG cc_start: 0.6814 (ttm-80) cc_final: 0.6517 (ttm-80) REVERT: q 209 LYS cc_start: 0.4726 (pttm) cc_final: 0.3023 (tppt) REVERT: q 352 MET cc_start: 0.2138 (mmm) cc_final: 0.1823 (mmt) REVERT: q 366 MET cc_start: 0.1695 (OUTLIER) cc_final: 0.1442 (pmt) REVERT: r 194 PHE cc_start: 0.6839 (OUTLIER) cc_final: 0.5960 (t80) REVERT: r 210 THR cc_start: 0.6245 (OUTLIER) cc_final: 0.5989 (p) REVERT: r 230 MET cc_start: 0.1818 (tmm) cc_final: 0.0347 (ttm) REVERT: t 165 LEU cc_start: 0.6646 (mt) cc_final: 0.6442 (mt) REVERT: t 181 LYS cc_start: 0.5630 (mppt) cc_final: 0.5337 (mmtm) REVERT: t 233 ASN cc_start: 0.4407 (m-40) cc_final: 0.4118 (t0) REVERT: t 291 GLN cc_start: 0.5966 (tt0) cc_final: 0.5581 (tp40) REVERT: t 311 GLU cc_start: 0.4976 (tp30) cc_final: 0.4671 (mt-10) REVERT: u 82 ASN cc_start: 0.6695 (t0) cc_final: 0.6424 (t0) REVERT: u 96 ILE cc_start: 0.7769 (mt) cc_final: 0.7556 (mp) REVERT: v 75 LYS cc_start: 0.6760 (mttt) cc_final: 0.6375 (ptpt) REVERT: v 214 ASP cc_start: 0.8285 (t0) cc_final: 0.8025 (t0) REVERT: v 221 ARG cc_start: 0.7966 (ttm170) cc_final: 0.7392 (ttm170) REVERT: w 32 LYS cc_start: 0.6621 (pttm) cc_final: 0.6234 (mppt) REVERT: w 76 TYR cc_start: 0.8787 (m-80) cc_final: 0.8472 (m-80) REVERT: w 78 ASP cc_start: 0.7734 (t0) cc_final: 0.7156 (t0) REVERT: w 80 LYS cc_start: 0.7295 (mttt) cc_final: 0.6778 (mmmm) REVERT: w 203 ARG cc_start: 0.6699 (ptp-170) cc_final: 0.6357 (ptm-80) REVERT: x 62 ASN cc_start: 0.7653 (m110) cc_final: 0.7397 (m-40) REVERT: x 141 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8039 (mtmm) REVERT: x 152 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: x 174 LYS cc_start: 0.8719 (mtmt) cc_final: 0.8515 (mmmt) REVERT: x 189 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7844 (mmt180) REVERT: x 258 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7989 (tt0) REVERT: y 1 MET cc_start: 0.5373 (tpt) cc_final: 0.4762 (ttp) REVERT: y 129 ILE cc_start: 0.7529 (mt) cc_final: 0.7148 (mt) REVERT: y 176 LEU cc_start: 0.7230 (mp) cc_final: 0.6915 (tp) REVERT: y 197 MET cc_start: 0.8489 (ptm) cc_final: 0.8152 (ptm) REVERT: y 223 ARG cc_start: 0.7883 (mmm-85) cc_final: 0.7577 (mtp180) outliers start: 155 outliers final: 83 residues processed: 1245 average time/residue: 2.0070 time to fit residues: 3432.2281 Evaluate side-chains 1198 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1092 time to evaluate : 6.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 340 ILE Chi-restraints excluded: chain 8 residue 355 GLU Chi-restraints excluded: chain 8 residue 374 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain C residue 259 ASP Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain T residue 175 ASN Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 158 ILE Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain Y residue 72 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 141 LEU Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 106 GLU Chi-restraints excluded: chain b residue 114 ARG Chi-restraints excluded: chain b residue 115 LEU Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain l residue 76 THR Chi-restraints excluded: chain m residue 143 VAL Chi-restraints excluded: chain m residue 254 MET Chi-restraints excluded: chain n residue 15 PHE Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 179 VAL Chi-restraints excluded: chain n residue 239 ASP Chi-restraints excluded: chain n residue 371 VAL Chi-restraints excluded: chain n residue 387 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 151 SER Chi-restraints excluded: chain q residue 366 MET Chi-restraints excluded: chain q residue 383 THR Chi-restraints excluded: chain q residue 424 CYS Chi-restraints excluded: chain q residue 502 VAL Chi-restraints excluded: chain r residue 194 PHE Chi-restraints excluded: chain r residue 210 THR Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 195 VAL Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 302 SER Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 13 CYS Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain v residue 165 LEU Chi-restraints excluded: chain v residue 194 ASP Chi-restraints excluded: chain v residue 197 LYS Chi-restraints excluded: chain v residue 219 LEU Chi-restraints excluded: chain w residue 69 LEU Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 60 ILE Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 152 GLU Chi-restraints excluded: chain x residue 189 ARG Chi-restraints excluded: chain x residue 258 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1093 random chunks: chunk 978 optimal weight: 5.9990 chunk 644 optimal weight: 0.6980 chunk 1038 optimal weight: 9.9990 chunk 633 optimal weight: 0.9980 chunk 492 optimal weight: 9.9990 chunk 721 optimal weight: 20.0000 chunk 1088 optimal weight: 4.9990 chunk 1002 optimal weight: 0.0770 chunk 867 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 669 optimal weight: 7.9990 overall best weight: 1.5340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 HIS A 95 GLN B 121 ASN B 313 HIS D 397 ASN F 19 GLN F 225 GLN H 59 ASN H 157 ASN J 196 ASN M 41 GLN ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN P 121 GLN ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 ASN Y 120 GLN b 429 ASN f 106 ASN ** i 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 130 ASN o 149 GLN q 389 ASN ** t 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 42 GLN v 29 ASN ** w 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 24 HIS Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 126156 Z= 0.152 Angle : 0.493 11.617 180982 Z= 0.255 Chirality : 0.035 0.272 22049 Planarity : 0.004 0.058 14697 Dihedral : 21.554 179.889 44137 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.68 % Allowed : 20.01 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.09), residues: 8763 helix: 1.99 (0.09), residues: 3673 sheet: 0.33 (0.14), residues: 1325 loop : 0.14 (0.10), residues: 3765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP e 32 HIS 0.008 0.001 HIS l 82 PHE 0.047 0.001 PHE q 262 TYR 0.021 0.001 TYR y 202 ARG 0.009 0.000 ARG u 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17526 Ramachandran restraints generated. 8763 Oldfield, 0 Emsley, 8763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1240 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1109 time to evaluate : 7.171 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: 8 308 LYS cc_start: 0.4644 (tptp) cc_final: 0.4193 (mmmm) REVERT: 8 340 ILE cc_start: 0.4707 (OUTLIER) cc_final: 0.4158 (tt) REVERT: 8 345 LYS cc_start: 0.4404 (OUTLIER) cc_final: 0.3520 (ptmt) REVERT: A 117 LEU cc_start: 0.6893 (tp) cc_final: 0.6446 (tp) REVERT: A 153 LYS cc_start: 0.6346 (ttpp) cc_final: 0.5913 (tttt) REVERT: A 218 ARG cc_start: 0.5910 (ttm170) cc_final: 0.5607 (mtm-85) REVERT: B 53 MET cc_start: 0.8620 (mtp) cc_final: 0.8261 (mtp) REVERT: B 190 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7475 (mt-10) REVERT: B 196 ARG cc_start: 0.7230 (ttp-110) cc_final: 0.6588 (ttp80) REVERT: B 377 HIS cc_start: 0.6038 (t-90) cc_final: 0.5697 (t-170) REVERT: C 265 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7183 (mp0) REVERT: C 304 GLN cc_start: 0.8491 (mt0) cc_final: 0.7994 (mt0) REVERT: C 338 LYS cc_start: 0.7874 (mmpt) cc_final: 0.7322 (mtmt) REVERT: D 65 MET cc_start: 0.5731 (ttm) cc_final: 0.5423 (mtp) REVERT: D 167 MET cc_start: 0.6459 (ttm) cc_final: 0.5881 (ttm) REVERT: D 180 GLN cc_start: 0.7434 (mm110) cc_final: 0.7228 (mm110) REVERT: D 196 ASP cc_start: 0.5586 (m-30) cc_final: 0.4981 (m-30) REVERT: D 197 GLU cc_start: 0.6012 (mt-10) cc_final: 0.5619 (mt-10) REVERT: D 225 MET cc_start: 0.5538 (mtt) cc_final: 0.5119 (mmp) REVERT: D 347 ASP cc_start: 0.6650 (OUTLIER) cc_final: 0.6285 (m-30) REVERT: D 355 ILE cc_start: 0.5290 (tp) cc_final: 0.4771 (tp) REVERT: D 392 MET cc_start: 0.7271 (ttp) cc_final: 0.7009 (tmm) REVERT: D 419 GLU cc_start: 0.6139 (mt-10) cc_final: 0.5664 (tm-30) REVERT: E 59 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7643 (mp0) REVERT: E 99 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7129 (mm-30) REVERT: E 108 LYS cc_start: 0.7728 (ptpt) cc_final: 0.7361 (mtmt) REVERT: E 133 GLU cc_start: 0.7470 (pp20) cc_final: 0.6973 (pm20) REVERT: F 20 GLN cc_start: 0.8076 (tp40) cc_final: 0.7701 (tm-30) REVERT: F 25 GLN cc_start: 0.7940 (tt0) cc_final: 0.7738 (tp40) REVERT: G 173 MET cc_start: 0.8959 (mmm) cc_final: 0.8540 (mmm) REVERT: H 31 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7647 (mtp85) REVERT: H 63 LYS cc_start: 0.8631 (ptmm) cc_final: 0.8051 (mmtp) REVERT: H 118 LEU cc_start: 0.9083 (mt) cc_final: 0.8792 (mt) REVERT: I 120 ASP cc_start: 0.7256 (m-30) cc_final: 0.6238 (p0) REVERT: I 314 GLU cc_start: 0.7342 (mt-10) cc_final: 0.7106 (mm-30) REVERT: J 205 LEU cc_start: 0.5035 (tp) cc_final: 0.4755 (tp) REVERT: K 194 MET cc_start: 0.6862 (mtp) cc_final: 0.6523 (mtp) REVERT: L 23 LYS cc_start: 0.7579 (ptmt) cc_final: 0.7353 (pttt) REVERT: L 85 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.7803 (pp) REVERT: L 103 ASN cc_start: 0.8563 (m110) cc_final: 0.8358 (m-40) REVERT: N 5 LYS cc_start: 0.8583 (tptm) cc_final: 0.8220 (tppt) REVERT: N 23 GLN cc_start: 0.7792 (tt0) cc_final: 0.7533 (mm110) REVERT: N 29 GLU cc_start: 0.7863 (tt0) cc_final: 0.7578 (mt-10) REVERT: N 31 ARG cc_start: 0.7313 (mtm110) cc_final: 0.7094 (mtm-85) REVERT: N 33 LYS cc_start: 0.8405 (mttt) cc_final: 0.8177 (mttp) REVERT: N 197 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7765 (tp) REVERT: O 55 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.6504 (m90) REVERT: O 166 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7989 (mt-10) REVERT: P 46 LYS cc_start: 0.7852 (tttp) cc_final: 0.7652 (mttp) REVERT: R 59 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8321 (mtpt) REVERT: R 102 LYS cc_start: 0.8657 (mttp) cc_final: 0.8236 (pttt) REVERT: S 13 ARG cc_start: 0.6385 (OUTLIER) cc_final: 0.5945 (mtp85) REVERT: S 47 LYS cc_start: 0.7865 (ttpp) cc_final: 0.7468 (tttm) REVERT: S 58 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8119 (mm) REVERT: S 131 LYS cc_start: 0.7915 (mttt) cc_final: 0.7505 (mmmt) REVERT: S 134 ASP cc_start: 0.7615 (m-30) cc_final: 0.7413 (m-30) REVERT: T 175 ASN cc_start: 0.1550 (OUTLIER) cc_final: 0.1020 (p0) REVERT: V 53 SER cc_start: 0.8589 (m) cc_final: 0.8222 (t) REVERT: V 59 MET cc_start: 0.8345 (mmt) cc_final: 0.7980 (mmm) REVERT: W 85 TYR cc_start: 0.5549 (t80) cc_final: 0.4997 (t80) REVERT: W 121 ARG cc_start: 0.5674 (mmm-85) cc_final: 0.5353 (mmm160) REVERT: W 157 MET cc_start: 0.6541 (ttm) cc_final: 0.6189 (ttp) REVERT: Y 11 ASP cc_start: 0.8742 (t0) cc_final: 0.8448 (t70) REVERT: Y 91 ASN cc_start: 0.8348 (p0) cc_final: 0.8126 (p0) REVERT: Z 141 LEU cc_start: 0.3249 (OUTLIER) cc_final: 0.3018 (tp) REVERT: Z 169 PHE cc_start: 0.4414 (m-10) cc_final: 0.3652 (m-80) REVERT: a 201 VAL cc_start: 0.1012 (OUTLIER) cc_final: 0.0472 (t) REVERT: b 106 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: b 114 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6470 (ttt-90) REVERT: b 185 ARG cc_start: 0.6655 (mtp180) cc_final: 0.6318 (tmt-80) REVERT: b 229 THR cc_start: 0.3220 (m) cc_final: 0.2778 (t) REVERT: b 387 LYS cc_start: 0.7544 (tttt) cc_final: 0.7040 (tttp) REVERT: b 432 MET cc_start: 0.7916 (OUTLIER) cc_final: 0.7683 (tpp) REVERT: e 34 LYS cc_start: 0.8635 (tttp) cc_final: 0.8391 (ttpt) REVERT: h 59 ASN cc_start: 0.8442 (t0) cc_final: 0.8139 (m-40) REVERT: i 26 ILE cc_start: 0.8405 (mt) cc_final: 0.8182 (tp) REVERT: i 58 ILE cc_start: 0.7686 (pp) cc_final: 0.7393 (mt) REVERT: i 75 LYS cc_start: 0.7853 (ttmm) cc_final: 0.7509 (mtmt) REVERT: i 88 GLU cc_start: 0.7764 (tp30) cc_final: 0.7199 (tt0) REVERT: m 181 MET cc_start: 0.4076 (mmm) cc_final: 0.3743 (mmm) REVERT: m 342 GLU cc_start: 0.5265 (mp0) cc_final: 0.4232 (mt-10) REVERT: m 355 GLU cc_start: 0.2932 (tt0) cc_final: 0.2534 (tp30) REVERT: n 427 ILE cc_start: 0.2880 (OUTLIER) cc_final: 0.2367 (mt) REVERT: o 134 TYR cc_start: 0.8006 (p90) cc_final: 0.6664 (p90) REVERT: o 165 ARG cc_start: 0.6807 (ttm-80) cc_final: 0.6522 (ttm-80) REVERT: o 200 MET cc_start: 0.3797 (ppp) cc_final: 0.3308 (pp-130) REVERT: q 259 MET cc_start: 0.1160 (mmm) cc_final: 0.0661 (mmt) REVERT: q 366 MET cc_start: 0.1577 (OUTLIER) cc_final: 0.1295 (pmt) REVERT: q 418 ILE cc_start: 0.0734 (mp) cc_final: 0.0412 (mp) REVERT: r 194 PHE cc_start: 0.6825 (OUTLIER) cc_final: 0.5955 (t80) REVERT: r 210 THR cc_start: 0.6205 (OUTLIER) cc_final: 0.5973 (p) REVERT: r 230 MET cc_start: 0.1836 (tmm) cc_final: 0.0301 (ttm) REVERT: t 53 ASN cc_start: 0.4012 (p0) cc_final: 0.2918 (t0) REVERT: t 165 LEU cc_start: 0.6534 (mt) cc_final: 0.6327 (mt) REVERT: t 181 LYS cc_start: 0.5621 (mppt) cc_final: 0.5300 (mmtm) REVERT: t 311 GLU cc_start: 0.5174 (tp30) cc_final: 0.4117 (tm-30) REVERT: u 82 ASN cc_start: 0.6779 (t0) cc_final: 0.6528 (t0) REVERT: u 96 ILE cc_start: 0.7770 (mt) cc_final: 0.7558 (mp) REVERT: v 75 LYS cc_start: 0.6782 (mttt) cc_final: 0.6383 (ptpt) REVERT: v 182 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6962 (mt-10) REVERT: v 214 ASP cc_start: 0.8312 (t0) cc_final: 0.8074 (t0) REVERT: w 32 LYS cc_start: 0.6607 (pttm) cc_final: 0.6232 (mppt) REVERT: w 76 TYR cc_start: 0.8807 (m-80) cc_final: 0.8532 (m-80) REVERT: w 78 ASP cc_start: 0.7743 (t0) cc_final: 0.7192 (t0) REVERT: w 80 LYS cc_start: 0.7303 (mttt) cc_final: 0.6793 (mmmm) REVERT: w 203 ARG cc_start: 0.6764 (ptp-170) cc_final: 0.6452 (ptm-80) REVERT: x 62 ASN cc_start: 0.7692 (m110) cc_final: 0.7426 (m-40) REVERT: x 67 ASP cc_start: 0.8347 (t70) cc_final: 0.8087 (t70) REVERT: x 141 LYS cc_start: 0.8313 (mtpt) cc_final: 0.8014 (mtmm) REVERT: x 152 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8140 (tm-30) REVERT: x 174 LYS cc_start: 0.8796 (mtmt) cc_final: 0.8581 (mmmt) REVERT: x 189 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7806 (mmt180) REVERT: x 258 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: y 1 MET cc_start: 0.5385 (tpt) cc_final: 0.4770 (ttp) REVERT: y 129 ILE cc_start: 0.7520 (mt) cc_final: 0.7131 (mt) REVERT: y 176 LEU cc_start: 0.7278 (mp) cc_final: 0.6960 (tp) REVERT: y 197 MET cc_start: 0.8508 (ptm) cc_final: 0.8166 (ptm) outliers start: 131 outliers final: 89 residues processed: 1196 average time/residue: 2.0248 time to fit residues: 3337.8404 Evaluate side-chains 1193 residues out of total 7800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1081 time to evaluate : 6.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 8 residue 340 ILE Chi-restraints excluded: chain 8 residue 345 LYS Chi-restraints excluded: chain 8 residue 355 GLU Chi-restraints excluded: chain 8 residue 374 ASP Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain C residue 5 GLN Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 427 SER Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 5 LYS Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain H residue 22 SER Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 187 VAL Chi-restraints excluded: chain L residue 81 LYS Chi-restraints excluded: chain L residue 85 LEU Chi-restraints excluded: chain M residue 12 TRP Chi-restraints excluded: chain N residue 13 LYS Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain O residue 55 HIS Chi-restraints excluded: chain P residue 66 SER Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain Q residue 9 GLN Chi-restraints excluded: chain Q residue 17 THR Chi-restraints excluded: chain Q residue 64 VAL Chi-restraints excluded: chain R residue 59 LYS Chi-restraints excluded: chain R residue 172 SER Chi-restraints excluded: chain S residue 13 ARG Chi-restraints excluded: chain S residue 58 ILE Chi-restraints excluded: chain T residue 175 ASN Chi-restraints excluded: chain V residue 120 LYS Chi-restraints excluded: chain W residue 45 LEU Chi-restraints excluded: chain W residue 164 THR Chi-restraints excluded: chain W residue 173 THR Chi-restraints excluded: chain Y residue 72 SER Chi-restraints excluded: chain Y residue 95 VAL Chi-restraints excluded: chain Y residue 105 VAL Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 43 LEU Chi-restraints excluded: chain Z residue 64 SER Chi-restraints excluded: chain Z residue 129 SER Chi-restraints excluded: chain Z residue 135 VAL Chi-restraints excluded: chain Z residue 141 LEU Chi-restraints excluded: chain Z residue 164 VAL Chi-restraints excluded: chain a residue 36 VAL Chi-restraints excluded: chain a residue 201 VAL Chi-restraints excluded: chain a residue 216 LEU Chi-restraints excluded: chain b residue 86 TYR Chi-restraints excluded: chain b residue 106 GLU Chi-restraints excluded: chain b residue 114 ARG Chi-restraints excluded: chain b residue 115 LEU Chi-restraints excluded: chain b residue 194 VAL Chi-restraints excluded: chain b residue 328 VAL Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 435 ILE Chi-restraints excluded: chain e residue 21 HIS Chi-restraints excluded: chain e residue 31 ASN Chi-restraints excluded: chain f residue 49 ILE Chi-restraints excluded: chain l residue 9 THR Chi-restraints excluded: chain l residue 76 THR Chi-restraints excluded: chain m residue 143 VAL Chi-restraints excluded: chain m residue 254 MET Chi-restraints excluded: chain n residue 115 ASP Chi-restraints excluded: chain n residue 179 VAL Chi-restraints excluded: chain n residue 387 VAL Chi-restraints excluded: chain n residue 427 ILE Chi-restraints excluded: chain o residue 96 SER Chi-restraints excluded: chain o residue 102 PHE Chi-restraints excluded: chain o residue 151 SER Chi-restraints excluded: chain q residue 366 MET Chi-restraints excluded: chain q residue 383 THR Chi-restraints excluded: chain q residue 424 CYS Chi-restraints excluded: chain q residue 489 ILE Chi-restraints excluded: chain q residue 502 VAL Chi-restraints excluded: chain r residue 194 PHE Chi-restraints excluded: chain r residue 210 THR Chi-restraints excluded: chain t residue 133 THR Chi-restraints excluded: chain t residue 195 VAL Chi-restraints excluded: chain t residue 250 ILE Chi-restraints excluded: chain t residue 302 SER Chi-restraints excluded: chain t residue 318 LEU Chi-restraints excluded: chain u residue 13 CYS Chi-restraints excluded: chain v residue 46 MET Chi-restraints excluded: chain v residue 157 GLU Chi-restraints excluded: chain v residue 165 LEU Chi-restraints excluded: chain v residue 194 ASP Chi-restraints excluded: chain v residue 197 LYS Chi-restraints excluded: chain v residue 219 LEU Chi-restraints excluded: chain w residue 29 LEU Chi-restraints excluded: chain w residue 69 LEU Chi-restraints excluded: chain w residue 205 ILE Chi-restraints excluded: chain x residue 106 SER Chi-restraints excluded: chain x residue 152 GLU Chi-restraints excluded: chain x residue 189 ARG Chi-restraints excluded: chain x residue 258 GLU Chi-restraints excluded: chain y residue 185 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1093 random chunks: chunk 531 optimal weight: 4.9990 chunk 688 optimal weight: 10.0000 chunk 923 optimal weight: 8.9990 chunk 265 optimal weight: 10.0000 chunk 799 optimal weight: 9.9990 chunk 128 optimal weight: 40.0000 chunk 240 optimal weight: 0.0370 chunk 868 optimal weight: 7.9990 chunk 363 optimal weight: 0.0040 chunk 891 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 overall best weight: 4.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 121 ASN ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN F 19 GLN F 225 GLN ** G 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 9 GLN ** H 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 ASN ** J 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN N 32 GLN ** O 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 92 GLN P 121 GLN ** Q 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 HIS ** S 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 62 ASN T 221 ASN W 44 HIS Y 120 GLN b 429 ASN f 106 ASN ** n 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 191 ASN o 130 ASN ** q 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 369 ASN q 389 ASN ** t 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 291 GLN u 24 ASN u 42 GLN v 29 ASN ** w 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 24 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.220691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.182488 restraints weight = 106562.709| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 1.81 r_work: 0.3644 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 126156 Z= 0.308 Angle : 0.613 11.163 180982 Z= 0.313 Chirality : 0.040 0.285 22049 Planarity : 0.005 0.082 14697 Dihedral : 21.704 179.737 44137 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.14 % Allowed : 19.76 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.09), residues: 8763 helix: 1.69 (0.08), residues: 3667 sheet: 0.21 (0.14), residues: 1325 loop : 0.01 (0.10), residues: 3771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 28 HIS 0.010 0.001 HIS K 104 PHE 0.045 0.002 PHE q 262 TYR 0.023 0.002 TYR y 202 ARG 0.010 0.001 ARG u 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49206.67 seconds wall clock time: 847 minutes 9.71 seconds (50829.71 seconds total)