Starting phenix.real_space_refine on Tue Sep 15 03:57:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dy6_30914/09_2026/7dy6_30914.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dy6_30914/09_2026/7dy6_30914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7dy6_30914/09_2026/7dy6_30914.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dy6_30914/09_2026/7dy6_30914.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dy6_30914/09_2026/7dy6_30914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dy6_30914/09_2026/7dy6_30914.map" model { file = "/net/cci-nas-00/data/ceres_data/7dy6_30914/09_2026/7dy6_30914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dy6_30914/09_2026/7dy6_30914.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 111 5.49 5 Mg 1 5.21 5 S 147 5.16 5 C 21787 2.51 5 N 6208 2.21 5 O 6974 1.98 5 H 532 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.19s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35762 Number of models: 1 Model: "" Number of chains: 12 Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1312 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "I" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1663 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 190} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 1629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1629 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 185} Chain: "K" Number of atoms: 1050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 1050 Classifications: {'peptide': 67} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 62} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 9, 'TRANS': 220} Chain: "B" Number of atoms: 1755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1755 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 216} Chain breaks: 1 Chain: "C" Number of atoms: 10569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10569 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1283} Chain: "D" Number of atoms: 10468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1355, 10468 Classifications: {'peptide': 1355} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1299} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 3845 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 14, 'TRANS': 457} Chain breaks: 2 Chain: "G" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 973 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 2 Chain: "E" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 708 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20330 SG CYS D 70 111.015 85.482 62.736 1.00 42.19 S ATOM 20344 SG CYS D 72 111.755 85.016 59.253 1.00 51.13 S ATOM 20452 SG CYS D 85 114.432 86.041 62.263 1.00 47.40 S ATOM 20476 SG CYS D 88 111.583 88.677 61.110 1.00 49.85 S ATOM 26686 SG CYS D 888 84.637 100.532 121.024 1.00 47.87 S ATOM 26737 SG CYS D 895 83.279 97.123 122.096 1.00 37.53 S ATOM 26758 SG CYS D 898 81.687 100.044 122.885 1.00 37.96 S Time building chain proxies: 7.24, per 1000 atoms: 0.20 Number of scatterers: 35762 At special positions: 0 Unit cell: (172.524, 194.743, 159.454, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 147 16.00 P 111 15.00 Mg 1 11.99 O 6974 8.00 N 6208 7.00 C 21787 6.00 H 532 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 70 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 72 " pdb=" ZN D2003 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 898 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 888 " pdb="ZN ZN D2003 " - pdb=" SG CYS D 895 " Number of angles added : 6 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7798 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 49 sheets defined 36.8% alpha, 7.5% beta 22 base pairs and 52 stacking pairs defined. Time for finding SS restraints: 4.20 Creating SS restraints... Processing helix chain 'I' and resid 19 through 32 removed outlier: 3.590A pdb=" N HIS I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE I 27 " --> pdb=" O HIS I 23 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS I 32 " --> pdb=" O VAL I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 53 removed outlier: 3.591A pdb=" N LEU I 53 " --> pdb=" O ASP I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 83 removed outlier: 3.859A pdb=" N MET I 76 " --> pdb=" O SER I 72 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP I 80 " --> pdb=" O MET I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 98 removed outlier: 3.596A pdb=" N GLY I 97 " --> pdb=" O PRO I 93 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU I 98 " --> pdb=" O VAL I 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 93 through 98' Processing helix chain 'I' and resid 99 through 101 No H-bonds generated for 'chain 'I' and resid 99 through 101' Processing helix chain 'I' and resid 103 through 108 removed outlier: 3.579A pdb=" N LYS I 108 " --> pdb=" O HIS I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 120 removed outlier: 3.901A pdb=" N ILE I 117 " --> pdb=" O LEU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 134 through 139 Processing helix chain 'I' and resid 141 through 146 removed outlier: 4.190A pdb=" N GLN I 145 " --> pdb=" O PRO I 141 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS I 146 " --> pdb=" O VAL I 142 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 141 through 146' Processing helix chain 'I' and resid 155 through 160 removed outlier: 3.513A pdb=" N CYS I 159 " --> pdb=" O SER I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 165 Processing helix chain 'I' and resid 168 through 172 removed outlier: 3.892A pdb=" N LEU I 171 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 188 removed outlier: 3.811A pdb=" N LEU I 183 " --> pdb=" O GLY I 179 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR I 188 " --> pdb=" O LYS I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 198 Processing helix chain 'I' and resid 201 through 209 removed outlier: 3.998A pdb=" N GLU I 206 " --> pdb=" O ALA I 203 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N MET I 207 " --> pdb=" O GLU I 204 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU I 209 " --> pdb=" O GLU I 206 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 33 removed outlier: 3.527A pdb=" N ILE J 27 " --> pdb=" O HIS J 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 83 removed outlier: 3.936A pdb=" N LEU J 79 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP J 80 " --> pdb=" O MET J 76 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE J 83 " --> pdb=" O LEU J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 107 removed outlier: 3.899A pdb=" N ARG J 96 " --> pdb=" O TYR J 92 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY J 97 " --> pdb=" O PRO J 93 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU J 98 " --> pdb=" O VAL J 94 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N HIS J 104 " --> pdb=" O ARG J 100 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE J 106 " --> pdb=" O TYR J 102 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU J 107 " --> pdb=" O MET J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 120 removed outlier: 3.800A pdb=" N ASN J 115 " --> pdb=" O TYR J 111 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N THR J 116 " --> pdb=" O THR J 112 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE J 117 " --> pdb=" O LEU J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 137 removed outlier: 3.938A pdb=" N ASP J 126 " --> pdb=" O ALA J 122 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA J 127 " --> pdb=" O SER J 123 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS J 130 " --> pdb=" O ASP J 126 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN J 131 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU J 135 " --> pdb=" O GLN J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 145 Processing helix chain 'J' and resid 155 through 160 removed outlier: 3.642A pdb=" N TYR J 160 " --> pdb=" O VAL J 157 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 166 Processing helix chain 'J' and resid 167 through 172 Processing helix chain 'J' and resid 183 through 191 removed outlier: 3.929A pdb=" N MET J 187 " --> pdb=" O LEU J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 198 Processing helix chain 'K' and resid 263 through 273 removed outlier: 3.788A pdb=" N LEU K 270 " --> pdb=" O SER K 266 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU K 273 " --> pdb=" O CYS K 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 284 removed outlier: 3.813A pdb=" N VAL K 282 " --> pdb=" O GLY K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 289 Processing helix chain 'K' and resid 300 through 302 No H-bonds generated for 'chain 'K' and resid 300 through 302' Processing helix chain 'K' and resid 303 through 311 removed outlier: 3.810A pdb=" N LEU K 307 " --> pdb=" O ILE K 303 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER K 309 " --> pdb=" O ASP K 305 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG K 310 " --> pdb=" O VAL K 306 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY K 311 " --> pdb=" O LEU K 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 48 removed outlier: 3.573A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.528A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.765A pdb=" N HIS A 160 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 221 Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.967A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 34 through 39' Processing helix chain 'B' and resid 39 through 48 removed outlier: 3.528A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 removed outlier: 4.406A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.712A pdb=" N ILE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 155 through 160' Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 220 through 228 removed outlier: 3.694A pdb=" N GLN B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.557A pdb=" N ASP C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 54 removed outlier: 3.844A pdb=" N ARG C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 88 Processing helix chain 'C' and resid 163 through 167 removed outlier: 4.339A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 removed outlier: 3.926A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 224 removed outlier: 3.779A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.828A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 279 " --> pdb=" O ARG C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.852A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 removed outlier: 3.915A pdb=" N GLN C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.572A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.820A pdb=" N VAL C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 389 removed outlier: 3.740A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 removed outlier: 3.651A pdb=" N SER C 408 " --> pdb=" O LYS C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 437 removed outlier: 3.553A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 451 removed outlier: 4.098A pdb=" N ARG C 451 " --> pdb=" O LEU C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 481 removed outlier: 3.825A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLY C 467 " --> pdb=" O GLN C 463 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS C 476 " --> pdb=" O GLU C 472 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.152A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS C 503 " --> pdb=" O SER C 499 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 820 through 825 removed outlier: 3.799A pdb=" N GLU C 825 " --> pdb=" O ARG C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 3.873A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 977 removed outlier: 3.535A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET C 951 " --> pdb=" O GLU C 947 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN C 952 " --> pdb=" O ILE C 948 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN C 955 " --> pdb=" O MET C 951 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS C 957 " --> pdb=" O LEU C 953 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 965 " --> pdb=" O SER C 961 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE C 972 " --> pdb=" O GLU C 968 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE C 975 " --> pdb=" O LEU C 971 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1023 removed outlier: 3.997A pdb=" N LEU C1011 " --> pdb=" O LYS C1007 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU C1012 " --> pdb=" O GLN C1008 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLN C1017 " --> pdb=" O GLN C1013 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR C1018 " --> pdb=" O LEU C1014 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1031 removed outlier: 3.555A pdb=" N LEU C1029 " --> pdb=" O PHE C1025 " (cutoff:3.500A) Processing helix chain 'C' and resid 1110 through 1121 removed outlier: 3.986A pdb=" N HIS C1116 " --> pdb=" O ILE C1112 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET C1119 " --> pdb=" O THR C1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 1123 through 1132 removed outlier: 3.654A pdb=" N ALA C1130 " --> pdb=" O ASP C1126 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1148 removed outlier: 3.719A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG C1147 " --> pdb=" O GLU C1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 1168 through 1173 Processing helix chain 'C' and resid 1191 through 1200 removed outlier: 3.818A pdb=" N LEU C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) Processing helix chain 'C' and resid 1201 through 1203 No H-bonds generated for 'chain 'C' and resid 1201 through 1203' Processing helix chain 'C' and resid 1238 through 1242 removed outlier: 3.806A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1275 Processing helix chain 'C' and resid 1285 through 1290 Processing helix chain 'C' and resid 1307 through 1311 Processing helix chain 'C' and resid 1323 through 1332 removed outlier: 3.571A pdb=" N LYS C1328 " --> pdb=" O ASN C1324 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE C1330 " --> pdb=" O LEU C1326 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 26 through 33 removed outlier: 4.264A pdb=" N SER D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.624A pdb=" N GLU D 100 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.574A pdb=" N LEU D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 136 Processing helix chain 'D' and resid 161 through 167 removed outlier: 3.603A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.844A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LYS D 190 " --> pdb=" O GLN D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 200 through 208 removed outlier: 5.077A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 225 removed outlier: 4.488A pdb=" N THR D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 removed outlier: 3.935A pdb=" N TRP D 236 " --> pdb=" O LYS D 233 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 233 through 236' Processing helix chain 'D' and resid 268 through 286 removed outlier: 3.704A pdb=" N ARG D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 308 removed outlier: 3.937A pdb=" N ARG D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 304 " --> pdb=" O GLN D 300 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 330 Processing helix chain 'D' and resid 370 through 377 removed outlier: 4.313A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.771A pdb=" N GLY D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 396 Processing helix chain 'D' and resid 397 through 403 removed outlier: 3.551A pdb=" N GLU D 402 " --> pdb=" O LYS D 398 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 416 removed outlier: 4.208A pdb=" N ASP D 413 " --> pdb=" O TRP D 409 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE D 416 " --> pdb=" O LEU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 452 through 456 removed outlier: 3.753A pdb=" N ALA D 455 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.562A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.505A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.611A pdb=" N VAL D 592 " --> pdb=" O TYR D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 605 removed outlier: 3.967A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 613 removed outlier: 3.754A pdb=" N ILE D 611 " --> pdb=" O THR D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 621 removed outlier: 3.833A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 632 removed outlier: 4.091A pdb=" N ALA D 630 " --> pdb=" O TYR D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 661 removed outlier: 4.123A pdb=" N ALA D 657 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 670 Processing helix chain 'D' and resid 675 through 702 removed outlier: 3.620A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS D 681 " --> pdb=" O GLU D 677 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE D 685 " --> pdb=" O LYS D 681 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP D 686 " --> pdb=" O VAL D 682 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA D 688 " --> pdb=" O ASP D 684 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER D 694 " --> pdb=" O ASN D 690 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA D 696 " --> pdb=" O ARG D 692 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ASP D 699 " --> pdb=" O LYS D 695 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASN D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 728 Processing helix chain 'D' and resid 733 through 741 removed outlier: 5.077A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 779 removed outlier: 3.592A pdb=" N ILE D 774 " --> pdb=" O LEU D 770 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 787 removed outlier: 3.613A pdb=" N THR D 786 " --> pdb=" O GLY D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 794 Processing helix chain 'D' and resid 796 through 804 removed outlier: 3.511A pdb=" N LEU D 800 " --> pdb=" O LEU D 796 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 801 " --> pdb=" O THR D 797 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 835 through 840 Processing helix chain 'D' and resid 867 through 872 Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.571A pdb=" N CYS D 888 " --> pdb=" O VAL D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.914A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 919 removed outlier: 3.511A pdb=" N ALA D 919 " --> pdb=" O GLY D 916 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 916 through 919' Processing helix chain 'D' and resid 920 through 925 removed outlier: 3.572A pdb=" N GLY D 924 " --> pdb=" O ALA D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 1137 through 1146 removed outlier: 3.923A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1222 removed outlier: 3.618A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 4.029A pdb=" N ASN D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN D1238 " --> pdb=" O VAL D1234 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG D1242 " --> pdb=" O GLN D1238 " (cutoff:3.500A) Processing helix chain 'D' and resid 1243 through 1245 No H-bonds generated for 'chain 'D' and resid 1243 through 1245' Processing helix chain 'D' and resid 1280 through 1291 removed outlier: 3.874A pdb=" N ALA D1288 " --> pdb=" O ARG D1284 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 removed outlier: 3.850A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1334 removed outlier: 3.691A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1334 through 1339 removed outlier: 3.645A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1362 through 1370 removed outlier: 3.755A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET D1370 " --> pdb=" O HIS D1366 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.631A pdb=" N GLU F 104 " --> pdb=" O MET F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 136 removed outlier: 3.633A pdb=" N ASP F 125 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER F 133 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU F 136 " --> pdb=" O CYS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 140 Processing helix chain 'F' and resid 141 through 149 removed outlier: 4.082A pdb=" N GLU F 146 " --> pdb=" O THR F 142 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLN F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 162 removed outlier: 3.796A pdb=" N LEU F 161 " --> pdb=" O ARG F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 221 removed outlier: 3.865A pdb=" N LYS F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 225 Processing helix chain 'F' and resid 226 through 231 removed outlier: 3.994A pdb=" N VAL F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 255 removed outlier: 3.856A pdb=" N SER F 253 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 259 Processing helix chain 'F' and resid 265 through 277 removed outlier: 3.794A pdb=" N LEU F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL F 270 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET F 273 " --> pdb=" O LEU F 269 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL F 275 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET F 277 " --> pdb=" O MET F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 283 through 293 removed outlier: 3.777A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 307 Processing helix chain 'F' and resid 313 through 318 removed outlier: 3.639A pdb=" N ASN F 317 " --> pdb=" O ASP F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 333 removed outlier: 4.280A pdb=" N HIS F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP F 332 " --> pdb=" O GLU F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 342 through 351 removed outlier: 3.502A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 381 removed outlier: 3.900A pdb=" N ARG F 364 " --> pdb=" O ASP F 360 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N MET F 365 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA F 372 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ARG F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 389 removed outlier: 4.041A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER F 389 " --> pdb=" O ARG F 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 383 through 389' Processing helix chain 'F' and resid 406 through 416 removed outlier: 3.935A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS F 414 " --> pdb=" O ILE F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 443 removed outlier: 5.600A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG F 436 " --> pdb=" O THR F 432 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 438 " --> pdb=" O TRP F 434 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE F 443 " --> pdb=" O ILE F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 467 removed outlier: 3.675A pdb=" N ILE F 457 " --> pdb=" O PRO F 453 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU F 458 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR F 459 " --> pdb=" O HIS F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 487 Processing helix chain 'F' and resid 492 through 497 Processing helix chain 'F' and resid 511 through 515 removed outlier: 4.080A pdb=" N GLU F 515 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.589A pdb=" N ASP F 521 " --> pdb=" O HIS F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 547 removed outlier: 4.085A pdb=" N THR F 537 " --> pdb=" O ASP F 533 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG F 541 " --> pdb=" O THR F 537 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA F 543 " --> pdb=" O SER F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 551 removed outlier: 3.839A pdb=" N LEU F 551 " --> pdb=" O LEU F 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 548 through 551' Processing helix chain 'F' and resid 553 through 562 removed outlier: 4.070A pdb=" N VAL F 558 " --> pdb=" O ARG F 554 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 578 removed outlier: 3.802A pdb=" N LYS F 578 " --> pdb=" O GLU F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 598 removed outlier: 3.919A pdb=" N GLU F 591 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ALA F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG F 596 " --> pdb=" O ALA F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 611 Processing helix chain 'E' and resid 15 through 30 removed outlier: 4.394A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 54 removed outlier: 3.557A pdb=" N ILE E 54 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 62 through 88 removed outlier: 3.574A pdb=" N VAL E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLU E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA E 85 " --> pdb=" O GLN E 81 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE E 86 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 62 through 63 Processing sheet with id=AA2, first strand: chain 'J' and resid 37 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 13 through 16 removed outlier: 4.699A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 26 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU A 198 " --> pdb=" O ALA A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.608A pdb=" N VAL A 146 " --> pdb=" O VAL A 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 59 Processing sheet with id=AA6, first strand: chain 'A' and resid 102 through 105 Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.900A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 23 through 24 removed outlier: 4.097A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.798A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.844A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 102 through 104 Processing sheet with id=AB3, first strand: chain 'B' and resid 108 through 110 Processing sheet with id=AB4, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.576A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 69 through 73 removed outlier: 6.920A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 93 through 95 removed outlier: 3.511A pdb=" N ILE C 127 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB8, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AB9, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AC1, first strand: chain 'C' and resid 226 through 230 removed outlier: 4.508A pdb=" N GLU C 226 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC3, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.566A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'C' and resid 633 through 636 Processing sheet with id=AC6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AC7, first strand: chain 'C' and resid 731 through 732 Processing sheet with id=AC8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 3.694A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N MET C1230 " --> pdb=" O MET C 800 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 837 removed outlier: 3.524A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C1054 " --> pdb=" O GLN C 834 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 876 through 877 removed outlier: 4.117A pdb=" N VAL C 877 " --> pdb=" O GLY C 926 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.751A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.570A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 422 " --> pdb=" O HIS D 469 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.570A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1268 through 1269 removed outlier: 3.642A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 347 " --> pdb=" O GLN C1268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 1336 through 1337 Processing sheet with id=AD8, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.675A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 9.984A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AE1, first strand: chain 'D' and resid 252 through 254 removed outlier: 4.074A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 367 through 369 removed outlier: 3.511A pdb=" N ILE D 442 " --> pdb=" O LEU D 368 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 547 through 549 Processing sheet with id=AE4, first strand: chain 'D' and resid 553 through 555 removed outlier: 3.526A pdb=" N GLU D 554 " --> pdb=" O LYS D 566 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 706 through 708 removed outlier: 3.653A pdb=" N ILE D 707 " --> pdb=" O GLU D 714 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 820 through 821 Processing sheet with id=AE7, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.733A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS D 832 " --> pdb=" O VAL D 825 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 958 through 959 removed outlier: 3.859A pdb=" N LYS D 983 " --> pdb=" O LYS D 959 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 966 through 967 Processing sheet with id=AF1, first strand: chain 'D' and resid 1001 through 1003 Processing sheet with id=AF2, first strand: chain 'D' and resid 1036 through 1038 removed outlier: 3.587A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 1162 through 1164 removed outlier: 3.678A pdb=" N THR D1178 " --> pdb=" O ILE D1162 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1277 through 1279 removed outlier: 4.446A pdb=" N LYS D1263 " --> pdb=" O ASP D1305 " (cutoff:3.500A) 771 hydrogen bonds defined for protein. 2046 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 49 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 52 stacking parallelities Total time for adding SS restraints: 8.06 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 531 1.03 - 1.23: 248 1.23 - 1.42: 14412 1.42 - 1.61: 21092 1.61 - 1.81: 260 Bond restraints: 36543 Sorted by residual: bond pdb=" C3' DT H 30 " pdb=" O3' DT H 30 " ideal model delta sigma weight residual 1.435 1.390 0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" C3' DT G 60 " pdb=" C2' DT G 60 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.53e+00 bond pdb=" C3' DG G 58 " pdb=" C2' DG G 58 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.13e+00 bond pdb=" C3' DG H 32 " pdb=" O3' DG H 32 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 9.04e+00 bond pdb=" C3' DT H 10 " pdb=" C2' DT H 10 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.03e+00 ... (remaining 36538 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 49725 2.84 - 5.68: 569 5.68 - 8.51: 34 8.51 - 11.35: 6 11.35 - 14.19: 1 Bond angle restraints: 50335 Sorted by residual: angle pdb=" N ASP F 278 " pdb=" CA ASP F 278 " pdb=" C ASP F 278 " ideal model delta sigma weight residual 113.50 99.31 14.19 1.23e+00 6.61e-01 1.33e+02 angle pdb=" N VAL C1159 " pdb=" CA VAL C1159 " pdb=" C VAL C1159 " ideal model delta sigma weight residual 110.62 121.16 -10.54 1.02e+00 9.61e-01 1.07e+02 angle pdb=" N ASP C1160 " pdb=" CA ASP C1160 " pdb=" C ASP C1160 " ideal model delta sigma weight residual 110.36 120.64 -10.28 1.55e+00 4.16e-01 4.40e+01 angle pdb=" N ILE D1256 " pdb=" CA ILE D1256 " pdb=" C ILE D1256 " ideal model delta sigma weight residual 113.20 107.29 5.91 9.60e-01 1.09e+00 3.79e+01 angle pdb=" N VAL C1138 " pdb=" CA VAL C1138 " pdb=" C VAL C1138 " ideal model delta sigma weight residual 111.91 106.55 5.36 8.90e-01 1.26e+00 3.62e+01 ... (remaining 50330 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 20875 35.73 - 71.46: 1126 71.46 - 107.19: 51 107.19 - 142.92: 1 142.92 - 178.65: 3 Dihedral angle restraints: 22056 sinusoidal: 9962 harmonic: 12094 Sorted by residual: dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -152.20 -27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ARG D 860 " pdb=" C ARG D 860 " pdb=" N ASN D 861 " pdb=" CA ASN D 861 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA THR K 263 " pdb=" C THR K 263 " pdb=" N VAL K 264 " pdb=" CA VAL K 264 " ideal model delta harmonic sigma weight residual -180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 22053 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 5145 0.085 - 0.169: 431 0.169 - 0.254: 8 0.254 - 0.339: 0 0.339 - 0.423: 1 Chirality restraints: 5585 Sorted by residual: chirality pdb=" CA ASP C1160 " pdb=" N ASP C1160 " pdb=" C ASP C1160 " pdb=" CB ASP C1160 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" CA ILE F 141 " pdb=" N ILE F 141 " pdb=" C ILE F 141 " pdb=" CB ILE F 141 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" P DG H 43 " pdb=" OP1 DG H 43 " pdb=" OP2 DG H 43 " pdb=" O5' DG H 43 " both_signs ideal model delta sigma weight residual True 2.34 -2.52 -0.18 2.00e-01 2.50e+01 8.34e-01 ... (remaining 5582 not shown) Planarity restraints: 6085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C1257 " -0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO C1258 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO C1258 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C1258 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO C 552 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 615 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.41e+00 pdb=" N PRO D 616 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 616 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 616 " -0.032 5.00e-02 4.00e+02 ... (remaining 6082 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 245 2.26 - 2.85: 15049 2.85 - 3.43: 41025 3.43 - 4.02: 62809 4.02 - 4.60: 95714 Nonbonded interactions: 214842 Sorted by model distance: nonbonded pdb=" O VAL K 282 " pdb=" H MET K 316 " model vdw 1.676 2.450 nonbonded pdb=" O PRO K 256 " pdb=" H ASP K 259 " model vdw 1.735 2.450 nonbonded pdb=" O VAL K 264 " pdb="HD21 ASN K 268 " model vdw 1.739 2.450 nonbonded pdb=" OD2 ASP K 258 " pdb=" HZ3 LYS K 271 " model vdw 1.828 2.450 nonbonded pdb="HH11 ARG K 284 " pdb=" OE1 GLU K 288 " model vdw 1.918 2.450 ... (remaining 214837 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 19 or resid 22 through 233)) selection = (chain 'B' and resid 7 through 233) } ncs_group { reference = (chain 'I' and resid 10 through 209) selection = (chain 'J' and (resid 10 through 132 or (resid 133 and (name N or name CA or nam \ e C or name O or name CB )) or resid 134 through 209)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.390 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 38.380 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.092 36018 Z= 0.436 Angle : 0.851 14.189 49124 Z= 0.523 Chirality : 0.049 0.423 5585 Planarity : 0.005 0.079 6024 Dihedral : 19.020 178.647 14099 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 35.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.42 % Favored : 85.58 % Rotamer: Outliers : 13.76 % Allowed : 14.55 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.99 (0.10), residues: 4153 helix: -4.59 (0.07), residues: 1378 sheet: -4.33 (0.21), residues: 342 loop : -3.67 (0.11), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1301 TYR 0.019 0.002 TYR A 177 PHE 0.018 0.002 PHE D 380 TRP 0.011 0.002 TRP J 70 HIS 0.008 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00914 / 0.43 (36011) covalent geometry : angle 0.84339 / 0.52 (49118) hydrogen bonds : bond 0.33964 / 38.42 ( 815) hydrogen bonds : angle 12.83602 / 16.70 ( 2136) metal coordination : bond 0.05419 / 4.38 ( 7) metal coordination : angle 10.37397 / 18.63 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 492 poor density : 571 time to evaluate : 1.117 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: I 11 MET cc_start: 0.7430 (ppp) cc_final: 0.5735 (ppp) REVERT: I 108 LYS cc_start: 0.9102 (mmtp) cc_final: 0.8820 (mmmt) REVERT: J 14 PHE cc_start: 0.7699 (m-10) cc_final: 0.7312 (m-10) REVERT: J 20 ILE cc_start: 0.8396 (tt) cc_final: 0.8037 (tt) REVERT: J 37 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7719 (tm-30) REVERT: J 71 GLU cc_start: 0.7256 (tt0) cc_final: 0.6836 (tt0) REVERT: J 103 MET cc_start: 0.8127 (ptm) cc_final: 0.7843 (ptp) REVERT: J 131 GLN cc_start: 0.7476 (mt0) cc_final: 0.7103 (mm-40) REVERT: J 159 CYS cc_start: 0.8511 (t) cc_final: 0.8196 (t) REVERT: J 167 ARG cc_start: 0.7007 (OUTLIER) cc_final: 0.6587 (mmt90) REVERT: J 182 GLU cc_start: 0.5908 (mm-30) cc_final: 0.5698 (mp0) REVERT: J 184 LYS cc_start: 0.7544 (mtpt) cc_final: 0.6636 (tptt) REVERT: J 191 PHE cc_start: 0.6186 (m-10) cc_final: 0.5887 (m-80) REVERT: J 192 GLU cc_start: 0.7436 (OUTLIER) cc_final: 0.7205 (mm-30) REVERT: J 208 ARG cc_start: 0.4787 (ttm170) cc_final: 0.4131 (ttp-170) REVERT: K 289 LEU cc_start: -0.1503 (OUTLIER) cc_final: -0.1716 (tp) REVERT: A 12 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7768 (mmt-90) REVERT: A 25 LYS cc_start: 0.9105 (mtpt) cc_final: 0.8783 (mtpp) REVERT: A 54 CYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7952 (p) REVERT: A 98 VAL cc_start: 0.9456 (OUTLIER) cc_final: 0.9242 (m) REVERT: B 83 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8911 (mt) REVERT: B 91 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7270 (ptm160) REVERT: B 104 LYS cc_start: 0.7313 (tptp) cc_final: 0.7068 (tptt) REVERT: B 147 GLN cc_start: 0.8285 (pt0) cc_final: 0.7289 (pm20) REVERT: B 205 MET cc_start: 0.7713 (ttp) cc_final: 0.7475 (ttt) REVERT: C 80 PHE cc_start: 0.8689 (m-80) cc_final: 0.8435 (m-80) REVERT: C 97 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8454 (mmt180) REVERT: C 194 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8262 (mp) REVERT: C 238 GLN cc_start: 0.4582 (mt0) cc_final: 0.3902 (pm20) REVERT: C 281 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6739 (t0) REVERT: C 286 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.6597 (mm-30) REVERT: C 332 ARG cc_start: 0.7570 (mmt-90) cc_final: 0.6666 (mmm-85) REVERT: C 473 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7454 (mpt180) REVERT: C 626 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7293 (mm-30) REVERT: C 779 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8372 (mtp85) REVERT: C 781 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7618 (t70) REVERT: C 848 GLU cc_start: 0.7234 (mt-10) cc_final: 0.7010 (mt-10) REVERT: C 915 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8419 (t70) REVERT: C 1057 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9051 (ttpt) REVERT: C 1069 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.7400 (mtt180) REVERT: C 1155 VAL cc_start: 0.8903 (OUTLIER) cc_final: 0.8659 (m) REVERT: C 1170 MET cc_start: 0.7718 (mmm) cc_final: 0.7515 (mmt) REVERT: C 1194 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7452 (mt-10) REVERT: C 1240 ASP cc_start: 0.8508 (p0) cc_final: 0.8241 (p0) REVERT: D 7 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7498 (t80) REVERT: D 39 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.9020 (ptpt) REVERT: D 56 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9210 (mt) REVERT: D 172 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6447 (m-80) REVERT: D 205 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6930 (tt) REVERT: D 298 MET cc_start: 0.8562 (ttp) cc_final: 0.8160 (ttp) REVERT: D 304 ASP cc_start: 0.7081 (m-30) cc_final: 0.6880 (m-30) REVERT: D 368 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8870 (tp) REVERT: D 558 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.7518 (p0) REVERT: D 585 LYS cc_start: 0.8638 (mmpt) cc_final: 0.8105 (mmpt) REVERT: D 619 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9068 (tp) REVERT: D 652 GLU cc_start: 0.8356 (mp0) cc_final: 0.7925 (mt-10) REVERT: D 678 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.6532 (tmm160) REVERT: D 679 TYR cc_start: 0.7888 (t80) cc_final: 0.7613 (t80) REVERT: D 777 HIS cc_start: 0.7717 (t70) cc_final: 0.7484 (t-90) REVERT: D 832 LYS cc_start: 0.8100 (mmmt) cc_final: 0.7412 (mtpp) REVERT: D 871 LEU cc_start: 0.8308 (tt) cc_final: 0.8020 (mp) REVERT: D 959 LYS cc_start: 0.6470 (mttt) cc_final: 0.6229 (tptt) REVERT: D 999 TYR cc_start: 0.0108 (OUTLIER) cc_final: -0.0491 (m-80) REVERT: D 1020 TRP cc_start: 0.4427 (OUTLIER) cc_final: 0.3555 (t60) REVERT: D 1037 PHE cc_start: -0.2037 (OUTLIER) cc_final: -0.2336 (m-10) REVERT: D 1156 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8687 (mm) REVERT: D 1195 GLN cc_start: 0.8329 (tt0) cc_final: 0.7413 (pp30) REVERT: D 1281 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: D 1325 PHE cc_start: 0.8794 (OUTLIER) cc_final: 0.8189 (p90) REVERT: F 297 MET cc_start: 0.3670 (ttm) cc_final: 0.3325 (ttt) REVERT: F 339 ARG cc_start: 0.4993 (OUTLIER) cc_final: 0.4414 (ttm-80) REVERT: F 395 THR cc_start: 0.9197 (t) cc_final: 0.8882 (m) REVERT: F 417 ASP cc_start: 0.8422 (t0) cc_final: 0.8131 (t0) REVERT: F 474 MET cc_start: 0.6461 (ttm) cc_final: 0.6110 (ttp) REVERT: F 508 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7563 (tm-30) REVERT: F 523 ILE cc_start: 0.9454 (pt) cc_final: 0.8997 (mt) REVERT: F 540 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8587 (tt) REVERT: F 575 GLU cc_start: 0.8253 (tp30) cc_final: 0.7965 (tp30) REVERT: F 589 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: F 593 LYS cc_start: 0.7800 (mttp) cc_final: 0.7439 (tttt) outliers start: 492 outliers final: 306 residues processed: 1006 average time/residue: 0.2281 time to fit residues: 367.0912 Evaluate side-chains 804 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 344 poor density : 460 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 182 GLU Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain I residue 195 SER Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 167 ARG Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 285 THR Chi-restraints excluded: chain K residue 289 LEU Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 12 ARG Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 212 ASP Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 68 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 281 ASP Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 439 LYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 759 SER Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 827 ARG Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1013 GLN Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1057 LYS Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1203 ASP Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1246 ARG Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1268 GLN Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1308 ILE Chi-restraints excluded: chain C residue 1316 GLU Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 193 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 537 TYR Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 722 ILE Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 751 ASP Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 797 THR Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 961 SER Chi-restraints excluded: chain D residue 967 VAL Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1050 THR Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1156 LEU Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1281 GLU Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1342 ASP Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 225 ARG Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 278 ASP Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 387 VAL Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 537 THR Chi-restraints excluded: chain F residue 540 LEU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 603 ARG Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 607 LEU Chi-restraints excluded: chain F residue 612 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 0.5980 chunk 424 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 37 HIS A 147 GLN A 194 GLN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 ASN B 128 HIS B 147 GLN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 GLN C 139 ASN C 219 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C 387 ASN C 463 GLN C 490 GLN C 658 GLN C 673 HIS ** C 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 834 GLN C 955 GLN C1090 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS C1268 GLN C1336 ASN D 186 GLN D 294 ASN D 419 HIS D 477 GLN D 495 ASN D 560 ASN D 594 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS D 867 GLN ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 HIS F 464 ASN E 43 ASN E 72 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.149462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.111892 restraints weight = 59105.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110821 restraints weight = 55153.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111491 restraints weight = 55392.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.111956 restraints weight = 36978.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113297 restraints weight = 31631.993| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36018 Z= 0.146 Angle : 0.619 11.117 49124 Z= 0.336 Chirality : 0.043 0.276 5585 Planarity : 0.005 0.051 6024 Dihedral : 19.419 175.961 6493 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 37.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 9.76 % Allowed : 18.97 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.29 (0.11), residues: 4153 helix: -3.74 (0.09), residues: 1460 sheet: -3.81 (0.23), residues: 361 loop : -3.39 (0.11), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 322 TYR 0.022 0.001 TYR D 795 PHE 0.020 0.001 PHE B 8 TRP 0.010 0.001 TRP D 33 HIS 0.011 0.001 HIS I 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (36011) covalent geometry : angle 0.61562 / 0.34 (49118) hydrogen bonds : bond 0.07169 / 7.81 ( 815) hydrogen bonds : angle 7.40316 / 9.88 ( 2136) metal coordination : bond 0.00852 / 0.65 ( 7) metal coordination : angle 5.96884 / 10.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 349 poor density : 502 time to evaluate : 1.324 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: I 57 GLN cc_start: 0.6820 (mp10) cc_final: 0.4351 (tm-30) REVERT: J 14 PHE cc_start: 0.7722 (m-10) cc_final: 0.7352 (m-10) REVERT: J 31 GLU cc_start: 0.8927 (tp30) cc_final: 0.8436 (tm-30) REVERT: J 37 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7585 (tm-30) REVERT: J 76 MET cc_start: 0.7997 (ttp) cc_final: 0.7697 (ttm) REVERT: J 103 MET cc_start: 0.7946 (ptm) cc_final: 0.7690 (ptp) REVERT: J 169 PRO cc_start: 0.8376 (Cg_exo) cc_final: 0.8169 (Cg_endo) REVERT: J 182 GLU cc_start: 0.5956 (mm-30) cc_final: 0.5745 (mp0) REVERT: J 184 LYS cc_start: 0.7770 (mtpt) cc_final: 0.6898 (tptt) REVERT: J 192 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.6949 (mm-30) REVERT: J 195 SER cc_start: 0.9265 (p) cc_final: 0.8859 (t) REVERT: J 200 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8044 (tp) REVERT: A 25 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8526 (mttp) REVERT: B 54 CYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7111 (m) REVERT: B 83 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8794 (mt) REVERT: B 91 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6914 (ptm160) REVERT: B 147 GLN cc_start: 0.8502 (pt0) cc_final: 0.8177 (pt0) REVERT: B 233 ASP cc_start: 0.7406 (OUTLIER) cc_final: 0.6280 (m-30) REVERT: C 97 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8335 (mmt90) REVERT: C 194 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8322 (mp) REVERT: C 332 ARG cc_start: 0.7399 (mmt-90) cc_final: 0.6884 (mmm-85) REVERT: C 473 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7089 (mpt180) REVERT: C 539 THR cc_start: 0.8827 (m) cc_final: 0.8327 (p) REVERT: C 626 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7113 (mm-30) REVERT: C 781 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7639 (t70) REVERT: C 827 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8340 (ptm160) REVERT: C 844 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6686 (ptmm) REVERT: C 848 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6801 (mt-10) REVERT: C 915 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8436 (t0) REVERT: C 1057 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.9112 (ttpt) REVERT: C 1151 LEU cc_start: 0.8805 (tp) cc_final: 0.8501 (tp) REVERT: C 1232 MET cc_start: 0.8217 (mmt) cc_final: 0.7912 (mmt) REVERT: C 1240 ASP cc_start: 0.8486 (p0) cc_final: 0.8239 (p0) REVERT: D 6 LYS cc_start: 0.6605 (OUTLIER) cc_final: 0.5943 (pptt) REVERT: D 77 ARG cc_start: 0.8391 (mtp-110) cc_final: 0.8120 (ttm110) REVERT: D 172 PHE cc_start: 0.7224 (OUTLIER) cc_final: 0.6542 (m-80) REVERT: D 331 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9084 (mt) REVERT: D 368 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8478 (tp) REVERT: D 558 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7315 (p0) REVERT: D 585 LYS cc_start: 0.8549 (mmpt) cc_final: 0.8089 (mmpt) REVERT: D 619 ILE cc_start: 0.9202 (tt) cc_final: 0.8960 (tp) REVERT: D 652 GLU cc_start: 0.8217 (mp0) cc_final: 0.7977 (mt-10) REVERT: D 666 GLU cc_start: 0.6438 (tm-30) cc_final: 0.6130 (mm-30) REVERT: D 678 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6257 (tmm160) REVERT: D 700 ASN cc_start: 0.8220 (t0) cc_final: 0.7998 (t0) REVERT: D 777 HIS cc_start: 0.7744 (t70) cc_final: 0.7510 (t70) REVERT: D 781 LYS cc_start: 0.8775 (mttt) cc_final: 0.8461 (mttt) REVERT: D 788 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8329 (tp) REVERT: D 822 MET cc_start: 0.8100 (mmm) cc_final: 0.7884 (mmm) REVERT: D 871 LEU cc_start: 0.8390 (tt) cc_final: 0.7755 (mp) REVERT: D 875 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.7537 (m-40) REVERT: D 959 LYS cc_start: 0.6152 (mttt) cc_final: 0.5698 (tmtt) REVERT: D 999 TYR cc_start: 0.0700 (OUTLIER) cc_final: 0.0206 (m-80) REVERT: D 1020 TRP cc_start: 0.3683 (OUTLIER) cc_final: 0.3115 (t60) REVERT: D 1037 PHE cc_start: -0.1408 (OUTLIER) cc_final: -0.1756 (m-10) REVERT: D 1040 MET cc_start: 0.6207 (ttt) cc_final: 0.5970 (ttt) REVERT: D 1195 GLN cc_start: 0.7891 (tt0) cc_final: 0.7517 (pp30) REVERT: D 1325 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8163 (p90) REVERT: F 131 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.5661 (pp30) REVERT: F 133 SER cc_start: 0.8018 (t) cc_final: 0.7702 (p) REVERT: F 136 GLU cc_start: 0.6569 (pt0) cc_final: 0.5984 (mm-30) REVERT: F 268 TYR cc_start: 0.7398 (OUTLIER) cc_final: 0.7006 (t80) REVERT: F 273 MET cc_start: 0.6531 (ptp) cc_final: 0.6130 (mpp) REVERT: F 297 MET cc_start: 0.4323 (ttm) cc_final: 0.4043 (ttt) REVERT: F 339 ARG cc_start: 0.5166 (OUTLIER) cc_final: 0.4470 (ttm170) REVERT: F 395 THR cc_start: 0.9158 (t) cc_final: 0.8776 (m) REVERT: F 417 ASP cc_start: 0.8212 (t0) cc_final: 0.7971 (t0) REVERT: F 432 THR cc_start: 0.8697 (m) cc_final: 0.8407 (p) REVERT: F 433 TRP cc_start: 0.7884 (t-100) cc_final: 0.7622 (t-100) REVERT: F 508 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7509 (tm-30) REVERT: F 575 GLU cc_start: 0.8006 (tp30) cc_final: 0.7779 (tp30) REVERT: F 589 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7284 (mp10) outliers start: 349 outliers final: 253 residues processed: 811 average time/residue: 0.2125 time to fit residues: 281.6508 Evaluate side-chains 734 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 284 poor density : 450 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain I residue 195 SER Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 285 THR Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 91 ARG Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 4 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 317 LEU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 465 ARG Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 473 ARG Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 779 ARG Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 827 ARG Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1013 GLN Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1057 LYS Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1316 GLU Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 528 THR Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1050 THR Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 537 THR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 612 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 26 optimal weight: 7.9990 chunk 217 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 399 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 255 optimal weight: 4.9990 chunk 354 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 227 optimal weight: 5.9990 chunk 1 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 320 ASN B 103 ASN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 ASN ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 72 GLN E 73 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.146573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.109798 restraints weight = 59466.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108703 restraints weight = 58308.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.108750 restraints weight = 65197.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.109552 restraints weight = 39830.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110951 restraints weight = 32634.679| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 36018 Z= 0.267 Angle : 0.663 8.182 49124 Z= 0.349 Chirality : 0.044 0.202 5585 Planarity : 0.005 0.051 6024 Dihedral : 19.162 178.479 6302 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 40.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.68 % Favored : 86.32 % Rotamer: Outliers : 10.85 % Allowed : 19.89 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.10 (0.11), residues: 4153 helix: -3.39 (0.10), residues: 1472 sheet: -3.69 (0.23), residues: 370 loop : -3.42 (0.11), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 278 TYR 0.017 0.002 TYR D 795 PHE 0.019 0.002 PHE D 380 TRP 0.013 0.001 TRP J 166 HIS 0.008 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.27 (36011) covalent geometry : angle 0.66027 / 0.35 (49118) hydrogen bonds : bond 0.06469 / 7.06 ( 815) hydrogen bonds : angle 6.84070 / 9.16 ( 2136) metal coordination : bond 0.01210 / 0.94 ( 7) metal coordination : angle 5.40781 / 9.76 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 388 poor density : 452 time to evaluate : 1.119 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: J 14 PHE cc_start: 0.7833 (m-10) cc_final: 0.7562 (m-10) REVERT: J 19 ASP cc_start: 0.5507 (t0) cc_final: 0.3752 (m-30) REVERT: J 37 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7451 (tm-30) REVERT: J 184 LYS cc_start: 0.7734 (mtpt) cc_final: 0.6818 (tptp) REVERT: J 192 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6792 (mm-30) REVERT: J 195 SER cc_start: 0.9274 (p) cc_final: 0.8962 (t) REVERT: J 200 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8184 (tp) REVERT: A 25 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8809 (ttmm) REVERT: B 54 CYS cc_start: 0.7549 (OUTLIER) cc_final: 0.7228 (m) REVERT: B 147 GLN cc_start: 0.8381 (pt0) cc_final: 0.8157 (pt0) REVERT: B 191 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8132 (ttp-110) REVERT: B 233 ASP cc_start: 0.6990 (OUTLIER) cc_final: 0.6451 (m-30) REVERT: C 97 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8302 (mmt180) REVERT: C 121 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.6656 (mm-30) REVERT: C 194 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8340 (mp) REVERT: C 332 ARG cc_start: 0.7314 (mmt-90) cc_final: 0.6824 (mmm-85) REVERT: C 583 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: C 626 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: C 781 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7796 (t70) REVERT: C 848 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6860 (mt-10) REVERT: C 915 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8467 (t0) REVERT: C 1054 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8879 (mt) REVERT: C 1057 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9117 (ttpt) REVERT: C 1069 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8678 (mtp180) REVERT: C 1232 MET cc_start: 0.8335 (mmt) cc_final: 0.7773 (mmt) REVERT: C 1240 ASP cc_start: 0.8425 (p0) cc_final: 0.8191 (p0) REVERT: D 77 ARG cc_start: 0.8522 (mtp-110) cc_final: 0.8209 (ttm110) REVERT: D 132 LEU cc_start: 0.8540 (tp) cc_final: 0.8107 (tt) REVERT: D 165 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.8386 (t80) REVERT: D 172 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.6107 (m-80) REVERT: D 331 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9082 (mt) REVERT: D 352 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.8876 (ptm-80) REVERT: D 368 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8608 (tp) REVERT: D 585 LYS cc_start: 0.8637 (mmpt) cc_final: 0.8168 (mmpt) REVERT: D 619 ILE cc_start: 0.9228 (tt) cc_final: 0.8981 (tp) REVERT: D 652 GLU cc_start: 0.8214 (mp0) cc_final: 0.8004 (mt-10) REVERT: D 678 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.6459 (tmm160) REVERT: D 679 TYR cc_start: 0.7909 (t80) cc_final: 0.7496 (t80) REVERT: D 757 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8800 (p) REVERT: D 788 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8355 (tp) REVERT: D 822 MET cc_start: 0.8219 (mmm) cc_final: 0.7964 (mmm) REVERT: D 827 GLU cc_start: 0.6812 (tp30) cc_final: 0.6564 (tp30) REVERT: D 871 LEU cc_start: 0.8232 (tt) cc_final: 0.7760 (mp) REVERT: D 875 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.7676 (m-40) REVERT: D 1020 TRP cc_start: 0.3300 (OUTLIER) cc_final: 0.2614 (t60) REVERT: D 1037 PHE cc_start: -0.1409 (OUTLIER) cc_final: -0.1752 (m-10) REVERT: D 1195 GLN cc_start: 0.8019 (tt0) cc_final: 0.7581 (pp30) REVERT: D 1325 PHE cc_start: 0.8859 (OUTLIER) cc_final: 0.8329 (p90) REVERT: F 131 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6611 (pp30) REVERT: F 268 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.7134 (t80) REVERT: F 339 ARG cc_start: 0.5210 (OUTLIER) cc_final: 0.4334 (ttm170) REVERT: F 417 ASP cc_start: 0.8229 (t0) cc_final: 0.7967 (t0) REVERT: F 433 TRP cc_start: 0.8131 (t-100) cc_final: 0.7745 (t-100) REVERT: F 507 MET cc_start: 0.8916 (ttp) cc_final: 0.8550 (ttm) REVERT: F 508 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7377 (tm-30) REVERT: F 575 GLU cc_start: 0.7983 (tp30) cc_final: 0.7738 (tp30) REVERT: F 589 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: E 69 ARG cc_start: 0.8666 (tmm-80) cc_final: 0.8423 (tmm-80) outliers start: 388 outliers final: 300 residues processed: 788 average time/residue: 0.2117 time to fit residues: 274.3361 Evaluate side-chains 764 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 331 poor density : 433 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 128 HIS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 191 ARG Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 415 GLU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 609 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 690 VAL Chi-restraints excluded: chain C residue 694 ARG Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1013 GLN Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1028 LYS Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1057 LYS Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1079 ILE Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain C residue 1316 GLU Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 331 ILE Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 757 THR Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 853 THR Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1029 THR Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1050 THR Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1238 GLN Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 339 ARG Chi-restraints excluded: chain F residue 351 THR Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 605 GLU Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 612 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 163 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 357 optimal weight: 5.9990 chunk 125 optimal weight: 0.0060 chunk 44 optimal weight: 0.6980 chunk 398 optimal weight: 5.9990 chunk 195 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 277 optimal weight: 0.8980 chunk 359 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.1200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 GLN ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 665 GLN ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.150433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.112856 restraints weight = 58558.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111605 restraints weight = 55420.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.111830 restraints weight = 58988.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112452 restraints weight = 40444.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114468 restraints weight = 33513.018| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 36018 Z= 0.102 Angle : 0.504 8.127 49124 Z= 0.275 Chirality : 0.040 0.182 5585 Planarity : 0.003 0.040 6024 Dihedral : 18.724 177.525 6251 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 37.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 8.00 % Allowed : 22.27 % Favored : 69.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.56 (0.11), residues: 4153 helix: -2.88 (0.11), residues: 1466 sheet: -3.41 (0.25), residues: 349 loop : -3.15 (0.11), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 764 TYR 0.022 0.001 TYR D 795 PHE 0.022 0.001 PHE J 191 TRP 0.014 0.001 TRP J 166 HIS 0.006 0.001 HIS D 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (36011) covalent geometry : angle 0.50241 / 0.28 (49118) hydrogen bonds : bond 0.04737 / 5.10 ( 815) hydrogen bonds : angle 5.92567 / 7.94 ( 2136) metal coordination : bond 0.00660 / 0.39 ( 7) metal coordination : angle 3.69464 / 6.82 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 286 poor density : 468 time to evaluate : 1.319 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: I 110 TRP cc_start: 0.7948 (m-10) cc_final: 0.7080 (m-10) REVERT: J 184 LYS cc_start: 0.7645 (mtpt) cc_final: 0.6870 (tptp) REVERT: J 192 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6708 (mm-30) REVERT: J 195 SER cc_start: 0.9207 (p) cc_final: 0.8801 (t) REVERT: J 200 LEU cc_start: 0.8494 (mt) cc_final: 0.8062 (tp) REVERT: A 25 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8506 (mttp) REVERT: B 54 CYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7159 (m) REVERT: B 147 GLN cc_start: 0.8284 (pt0) cc_final: 0.8004 (pt0) REVERT: B 233 ASP cc_start: 0.6806 (OUTLIER) cc_final: 0.6308 (m-30) REVERT: C 97 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8281 (mmt90) REVERT: C 332 ARG cc_start: 0.7199 (mmt-90) cc_final: 0.6781 (mmm-85) REVERT: C 626 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7093 (mm-30) REVERT: C 844 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.6776 (ptmm) REVERT: C 848 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6771 (mt-10) REVERT: C 915 ASP cc_start: 0.8755 (OUTLIER) cc_final: 0.8281 (t0) REVERT: C 919 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8359 (mtp85) REVERT: C 962 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: C 994 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7569 (mtm-85) REVERT: C 1141 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8660 (mp) REVERT: C 1151 LEU cc_start: 0.8747 (tp) cc_final: 0.8426 (tp) REVERT: C 1240 ASP cc_start: 0.8439 (p0) cc_final: 0.8155 (p0) REVERT: D 6 LYS cc_start: 0.6797 (OUTLIER) cc_final: 0.6494 (pptt) REVERT: D 132 LEU cc_start: 0.8349 (tp) cc_final: 0.7920 (tt) REVERT: D 172 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6033 (m-80) REVERT: D 335 GLN cc_start: 0.5129 (OUTLIER) cc_final: 0.4153 (tt0) REVERT: D 352 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8824 (ptm-80) REVERT: D 368 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8549 (tp) REVERT: D 619 ILE cc_start: 0.9258 (tt) cc_final: 0.9051 (tp) REVERT: D 626 TYR cc_start: 0.9055 (m-10) cc_final: 0.8771 (m-80) REVERT: D 678 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6078 (tmm160) REVERT: D 822 MET cc_start: 0.8252 (mmm) cc_final: 0.8019 (mmm) REVERT: D 871 LEU cc_start: 0.8181 (tt) cc_final: 0.7698 (mp) REVERT: D 875 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.7574 (m-40) REVERT: D 1020 TRP cc_start: 0.2932 (OUTLIER) cc_final: 0.2474 (t60) REVERT: D 1037 PHE cc_start: -0.1529 (OUTLIER) cc_final: -0.1814 (m-10) REVERT: D 1195 GLN cc_start: 0.7979 (tt0) cc_final: 0.7563 (pp30) REVERT: D 1325 PHE cc_start: 0.8588 (OUTLIER) cc_final: 0.8086 (p90) REVERT: F 268 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.7135 (t80) REVERT: F 281 ARG cc_start: 0.5277 (OUTLIER) cc_final: 0.4525 (tmm-80) REVERT: F 417 ASP cc_start: 0.8113 (t0) cc_final: 0.7878 (t0) REVERT: F 433 TRP cc_start: 0.7901 (t-100) cc_final: 0.7618 (t-100) REVERT: F 470 MET cc_start: 0.7893 (mmt) cc_final: 0.7527 (mmt) REVERT: F 507 MET cc_start: 0.8849 (ttp) cc_final: 0.8478 (ttm) REVERT: F 508 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7467 (tm-30) REVERT: F 589 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: E 69 ARG cc_start: 0.8654 (tmm-80) cc_final: 0.8432 (tmm-80) outliers start: 286 outliers final: 211 residues processed: 728 average time/residue: 0.1994 time to fit residues: 239.9916 Evaluate side-chains 674 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 234 poor density : 440 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 285 THR Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 877 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 964 LEU Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 175 GLU Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 335 GLN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1050 THR Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 432 THR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 612 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 143 optimal weight: 0.8980 chunk 319 optimal weight: 0.3980 chunk 128 optimal weight: 30.0000 chunk 326 optimal weight: 20.0000 chunk 237 optimal weight: 8.9990 chunk 333 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 44 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 397 optimal weight: 5.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 ASN ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.148704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111849 restraints weight = 58764.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109989 restraints weight = 59398.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110631 restraints weight = 58505.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110862 restraints weight = 46525.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112451 restraints weight = 37294.979| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 36018 Z= 0.172 Angle : 0.539 9.411 49124 Z= 0.287 Chirality : 0.041 0.179 5585 Planarity : 0.003 0.044 6024 Dihedral : 18.511 175.665 6163 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 38.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.08 % Favored : 88.92 % Rotamer: Outliers : 8.36 % Allowed : 22.35 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.36 (0.11), residues: 4153 helix: -2.62 (0.12), residues: 1460 sheet: -3.29 (0.24), residues: 375 loop : -3.10 (0.12), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 77 TYR 0.017 0.001 TYR D 795 PHE 0.012 0.001 PHE C 405 TRP 0.008 0.001 TRP J 166 HIS 0.008 0.001 HIS I 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (36011) covalent geometry : angle 0.53727 / 0.29 (49118) hydrogen bonds : bond 0.04699 / 5.04 ( 815) hydrogen bonds : angle 5.80455 / 7.80 ( 2136) metal coordination : bond 0.00877 / 0.68 ( 7) metal coordination : angle 3.48925 / 6.36 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 299 poor density : 443 time to evaluate : 1.343 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: I 170 GLN cc_start: 0.7459 (tm-30) cc_final: 0.7048 (tt0) REVERT: J 184 LYS cc_start: 0.7798 (mtpt) cc_final: 0.7022 (tptp) REVERT: J 192 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.6627 (mm-30) REVERT: J 195 SER cc_start: 0.9248 (p) cc_final: 0.8895 (t) REVERT: J 200 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8175 (tp) REVERT: A 25 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8731 (ttmm) REVERT: B 54 CYS cc_start: 0.7522 (OUTLIER) cc_final: 0.7237 (m) REVERT: B 147 GLN cc_start: 0.8305 (pt0) cc_final: 0.8022 (pt0) REVERT: B 219 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.8182 (ttm170) REVERT: B 233 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6365 (m-30) REVERT: C 9 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8398 (mtpp) REVERT: C 30 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9024 (tt) REVERT: C 97 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8311 (mmt90) REVERT: C 332 ARG cc_start: 0.7189 (mmt-90) cc_final: 0.6659 (mmm-85) REVERT: C 626 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: C 761 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8857 (mp10) REVERT: C 848 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6896 (mt-10) REVERT: C 915 ASP cc_start: 0.8773 (OUTLIER) cc_final: 0.8390 (t0) REVERT: C 919 ARG cc_start: 0.9145 (OUTLIER) cc_final: 0.8660 (mtp85) REVERT: C 962 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7807 (tm-30) REVERT: C 1033 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7629 (ttp-170) REVERT: C 1069 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8796 (mtp180) REVERT: C 1141 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8664 (mp) REVERT: C 1151 LEU cc_start: 0.8821 (tp) cc_final: 0.8568 (tp) REVERT: C 1240 ASP cc_start: 0.8420 (p0) cc_final: 0.8164 (p0) REVERT: D 6 LYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6651 (pptt) REVERT: D 132 LEU cc_start: 0.8489 (tp) cc_final: 0.8042 (tt) REVERT: D 172 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.6092 (m-80) REVERT: D 368 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8501 (tp) REVERT: D 678 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6208 (tmm160) REVERT: D 788 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8347 (tp) REVERT: D 871 LEU cc_start: 0.8201 (tt) cc_final: 0.7715 (mp) REVERT: D 875 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.7624 (m-40) REVERT: D 1020 TRP cc_start: 0.2996 (OUTLIER) cc_final: 0.2489 (t60) REVERT: D 1037 PHE cc_start: -0.1523 (OUTLIER) cc_final: -0.1776 (m-10) REVERT: D 1195 GLN cc_start: 0.7970 (tt0) cc_final: 0.7575 (pp30) REVERT: D 1325 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8323 (p90) REVERT: F 268 TYR cc_start: 0.7431 (OUTLIER) cc_final: 0.7146 (t80) REVERT: F 281 ARG cc_start: 0.5264 (OUTLIER) cc_final: 0.3664 (tmm-80) REVERT: F 417 ASP cc_start: 0.8140 (t0) cc_final: 0.7892 (t0) REVERT: F 433 TRP cc_start: 0.8010 (t-100) cc_final: 0.7671 (t-100) REVERT: F 470 MET cc_start: 0.7940 (mmt) cc_final: 0.7228 (mmt) REVERT: F 507 MET cc_start: 0.8875 (ttp) cc_final: 0.8523 (ttm) REVERT: F 508 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7333 (tm-30) REVERT: F 589 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7164 (mp10) REVERT: E 69 ARG cc_start: 0.8626 (tmm-80) cc_final: 0.8351 (tmm-80) outliers start: 299 outliers final: 241 residues processed: 703 average time/residue: 0.2077 time to fit residues: 241.1148 Evaluate side-chains 694 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 425 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 116 THR Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain I residue 195 SER Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 285 THR Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 709 ARG Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 974 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1101 LEU Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1238 GLN Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 432 THR Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 612 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 134 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 6 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 425 optimal weight: 0.3980 chunk 157 optimal weight: 2.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.112305 restraints weight = 58584.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.110516 restraints weight = 55477.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.111357 restraints weight = 55905.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111603 restraints weight = 40965.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112973 restraints weight = 34245.594| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 36018 Z= 0.131 Angle : 0.494 8.666 49124 Z= 0.266 Chirality : 0.040 0.179 5585 Planarity : 0.003 0.039 6024 Dihedral : 18.364 173.917 6145 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 37.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 8.03 % Allowed : 22.85 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.09 (0.12), residues: 4153 helix: -2.36 (0.12), residues: 1468 sheet: -3.25 (0.25), residues: 352 loop : -2.95 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 77 TYR 0.016 0.001 TYR D 795 PHE 0.011 0.001 PHE C 405 TRP 0.007 0.001 TRP J 166 HIS 0.012 0.001 HIS I 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (36011) covalent geometry : angle 0.49266 / 0.27 (49118) hydrogen bonds : bond 0.04259 / 4.57 ( 815) hydrogen bonds : angle 5.51059 / 7.40 ( 2136) metal coordination : bond 0.00763 / 0.54 ( 7) metal coordination : angle 3.04760 / 5.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 287 poor density : 448 time to evaluate : 1.416 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: I 57 GLN cc_start: 0.7489 (mp10) cc_final: 0.7034 (mp10) REVERT: J 103 MET cc_start: 0.8218 (mtp) cc_final: 0.8009 (mtm) REVERT: J 184 LYS cc_start: 0.7787 (mtpt) cc_final: 0.7060 (tptp) REVERT: J 192 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6778 (mm-30) REVERT: J 195 SER cc_start: 0.9245 (p) cc_final: 0.8854 (t) REVERT: J 200 LEU cc_start: 0.8573 (mt) cc_final: 0.8090 (tp) REVERT: A 25 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8547 (mttp) REVERT: B 54 CYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7202 (m) REVERT: B 147 GLN cc_start: 0.8347 (pt0) cc_final: 0.8096 (pt0) REVERT: B 233 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6395 (m-30) REVERT: C 9 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8382 (mtpp) REVERT: C 30 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.9101 (tt) REVERT: C 97 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8280 (mmt90) REVERT: C 332 ARG cc_start: 0.7212 (mmt-90) cc_final: 0.6678 (mmm-85) REVERT: C 626 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7154 (mm-30) REVERT: C 754 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8837 (p) REVERT: C 761 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8814 (mp10) REVERT: C 848 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6836 (mt-10) REVERT: C 915 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8376 (t0) REVERT: C 919 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8579 (mtp85) REVERT: C 1033 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7746 (ttp-170) REVERT: C 1141 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8662 (mp) REVERT: C 1151 LEU cc_start: 0.8811 (tp) cc_final: 0.8510 (tp) REVERT: C 1240 ASP cc_start: 0.8435 (p0) cc_final: 0.8129 (p0) REVERT: D 6 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6648 (pptt) REVERT: D 132 LEU cc_start: 0.8438 (tp) cc_final: 0.7993 (tt) REVERT: D 172 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.5897 (m-80) REVERT: D 573 THR cc_start: 0.9320 (OUTLIER) cc_final: 0.9091 (p) REVERT: D 626 TYR cc_start: 0.8998 (m-10) cc_final: 0.8651 (m-80) REVERT: D 678 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.5982 (tmm160) REVERT: D 712 GLN cc_start: 0.7936 (mt0) cc_final: 0.7567 (pp30) REVERT: D 788 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8317 (tp) REVERT: D 871 LEU cc_start: 0.8168 (tt) cc_final: 0.7602 (mp) REVERT: D 875 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.7652 (m-40) REVERT: D 1020 TRP cc_start: 0.2963 (OUTLIER) cc_final: 0.2447 (t60) REVERT: D 1037 PHE cc_start: -0.1683 (OUTLIER) cc_final: -0.1915 (m-10) REVERT: D 1195 GLN cc_start: 0.7941 (tt0) cc_final: 0.7564 (pp30) REVERT: D 1203 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7564 (ttm110) REVERT: D 1281 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6725 (mt-10) REVERT: D 1325 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8198 (p90) REVERT: F 268 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.7086 (t80) REVERT: F 281 ARG cc_start: 0.5184 (OUTLIER) cc_final: 0.4435 (tmm-80) REVERT: F 417 ASP cc_start: 0.8102 (t0) cc_final: 0.7871 (t0) REVERT: F 433 TRP cc_start: 0.8019 (t-100) cc_final: 0.7683 (t-100) REVERT: F 445 ASP cc_start: 0.8229 (t0) cc_final: 0.7844 (t0) REVERT: F 446 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.8794 (pm20) REVERT: F 472 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7363 (mp10) REVERT: F 507 MET cc_start: 0.8864 (ttp) cc_final: 0.8515 (ttm) REVERT: F 508 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7412 (tm-30) REVERT: F 589 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7150 (mp10) REVERT: E 61 ASN cc_start: 0.8745 (t0) cc_final: 0.8383 (t0) REVERT: E 69 ARG cc_start: 0.8572 (tmm-80) cc_final: 0.8362 (tmm-80) outliers start: 287 outliers final: 229 residues processed: 697 average time/residue: 0.2099 time to fit residues: 241.2177 Evaluate side-chains 688 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 256 poor density : 432 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 285 THR Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 540 ARG Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 466 MET Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 432 THR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 472 GLN Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 363 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 226 optimal weight: 7.9990 chunk 335 optimal weight: 30.0000 chunk 18 optimal weight: 40.0000 chunk 416 optimal weight: 50.0000 chunk 85 optimal weight: 7.9990 chunk 273 optimal weight: 7.9990 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.146039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.109549 restraints weight = 59276.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.107930 restraints weight = 56633.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.108696 restraints weight = 58716.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.109037 restraints weight = 39882.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109699 restraints weight = 34056.576| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 36018 Z= 0.288 Angle : 0.649 10.287 49124 Z= 0.337 Chirality : 0.044 0.180 5585 Planarity : 0.005 0.048 6024 Dihedral : 18.490 171.883 6116 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 41.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 14.18 % Favored : 85.79 % Rotamer: Outliers : 9.48 % Allowed : 22.15 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.28 (0.12), residues: 4153 helix: -2.47 (0.12), residues: 1469 sheet: -3.32 (0.24), residues: 370 loop : -3.10 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 709 TYR 0.020 0.002 TYR D 555 PHE 0.023 0.002 PHE C 545 TRP 0.007 0.001 TRP J 166 HIS 0.008 0.001 HIS I 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00675 / 0.29 (36011) covalent geometry : angle 0.64755 / 0.34 (49118) hydrogen bonds : bond 0.04922 / 5.34 ( 815) hydrogen bonds : angle 5.89662 / 7.89 ( 2136) metal coordination : bond 0.01276 / 1.09 ( 7) metal coordination : angle 3.79066 / 6.88 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 339 poor density : 425 time to evaluate : 1.363 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: J 103 MET cc_start: 0.8074 (mtp) cc_final: 0.7831 (mtt) REVERT: J 184 LYS cc_start: 0.7773 (mtpt) cc_final: 0.6939 (tptp) REVERT: J 192 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.6812 (mm-30) REVERT: J 195 SER cc_start: 0.9276 (p) cc_final: 0.8945 (t) REVERT: J 200 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8197 (tp) REVERT: A 25 LYS cc_start: 0.9076 (mtpt) cc_final: 0.8837 (ttmm) REVERT: B 54 CYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7252 (m) REVERT: B 147 GLN cc_start: 0.8346 (pt0) cc_final: 0.8049 (pt0) REVERT: B 233 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6546 (m-30) REVERT: C 9 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8436 (mtpp) REVERT: C 97 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8336 (mmt180) REVERT: C 332 ARG cc_start: 0.7269 (mmt-90) cc_final: 0.6690 (mmm-85) REVERT: C 583 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7189 (mt-10) REVERT: C 626 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: C 848 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6957 (mt-10) REVERT: C 915 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8446 (t0) REVERT: C 1069 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8722 (mtp180) REVERT: C 1240 ASP cc_start: 0.8410 (p0) cc_final: 0.8163 (p0) REVERT: D 6 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6725 (pptt) REVERT: D 86 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7929 (pt0) REVERT: D 132 LEU cc_start: 0.8607 (tp) cc_final: 0.8125 (tt) REVERT: D 165 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.8289 (t80) REVERT: D 172 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.5537 (m-80) REVERT: D 368 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8522 (tp) REVERT: D 678 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6488 (tmm160) REVERT: D 788 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8328 (tp) REVERT: D 871 LEU cc_start: 0.8098 (tt) cc_final: 0.7713 (mp) REVERT: D 875 ASN cc_start: 0.8506 (OUTLIER) cc_final: 0.7685 (m-40) REVERT: D 1020 TRP cc_start: 0.3327 (OUTLIER) cc_final: 0.2506 (t60) REVERT: D 1037 PHE cc_start: -0.1366 (OUTLIER) cc_final: -0.1680 (m-10) REVERT: D 1195 GLN cc_start: 0.7914 (tt0) cc_final: 0.7554 (pp30) REVERT: D 1203 ARG cc_start: 0.7868 (ttm170) cc_final: 0.7619 (ttm110) REVERT: D 1325 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8421 (p90) REVERT: F 268 TYR cc_start: 0.7401 (OUTLIER) cc_final: 0.7075 (t80) REVERT: F 281 ARG cc_start: 0.5261 (OUTLIER) cc_final: 0.4332 (tmm-80) REVERT: F 417 ASP cc_start: 0.8150 (t0) cc_final: 0.7917 (t0) REVERT: F 433 TRP cc_start: 0.8073 (t-100) cc_final: 0.7723 (t-100) REVERT: F 445 ASP cc_start: 0.8130 (t0) cc_final: 0.7841 (t0) REVERT: F 446 GLN cc_start: 0.9386 (OUTLIER) cc_final: 0.8831 (pm20) REVERT: F 507 MET cc_start: 0.8957 (ttp) cc_final: 0.8620 (ttm) REVERT: F 508 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7285 (tm-30) REVERT: F 561 MET cc_start: 0.8186 (ttm) cc_final: 0.7452 (tpp) REVERT: F 589 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7109 (mp10) REVERT: E 69 ARG cc_start: 0.8608 (tmm-80) cc_final: 0.8401 (tmm-80) outliers start: 339 outliers final: 275 residues processed: 716 average time/residue: 0.2109 time to fit residues: 251.1730 Evaluate side-chains 719 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 300 poor density : 419 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain I residue 195 SER Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain I residue 201 THR Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 126 ASP Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 137 LEU Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 285 THR Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 393 ASP Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 540 ARG Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1308 ILE Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 357 VAL Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 525 MET Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 673 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1042 ASP Chi-restraints excluded: chain D residue 1050 THR Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1088 VAL Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1180 VAL Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 268 TYR Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 432 THR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 537 THR Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 84 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 50 optimal weight: 0.7980 chunk 415 optimal weight: 50.0000 chunk 8 optimal weight: 7.9990 chunk 328 optimal weight: 0.8980 chunk 420 optimal weight: 9.9990 chunk 389 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 231 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.149029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.110888 restraints weight = 58556.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.109794 restraints weight = 41563.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.109720 restraints weight = 52021.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.110685 restraints weight = 31882.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112343 restraints weight = 25853.530| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 36018 Z= 0.131 Angle : 0.506 8.780 49124 Z= 0.271 Chirality : 0.040 0.176 5585 Planarity : 0.003 0.041 6024 Dihedral : 18.344 170.917 6115 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 38.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 7.80 % Allowed : 23.75 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.98 (0.12), residues: 4153 helix: -2.21 (0.13), residues: 1469 sheet: -3.18 (0.25), residues: 351 loop : -2.93 (0.12), residues: 2333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 77 TYR 0.021 0.001 TYR D 795 PHE 0.022 0.001 PHE C 545 TRP 0.006 0.001 TRP K 321 HIS 0.007 0.001 HIS I 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (36011) covalent geometry : angle 0.50518 / 0.27 (49118) hydrogen bonds : bond 0.04235 / 4.55 ( 815) hydrogen bonds : angle 5.43986 / 7.29 ( 2136) metal coordination : bond 0.00796 / 0.60 ( 7) metal coordination : angle 3.13912 / 5.73 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 279 poor density : 437 time to evaluate : 1.619 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: I 57 GLN cc_start: 0.7186 (mp10) cc_final: 0.6832 (mp10) REVERT: J 103 MET cc_start: 0.8041 (mtp) cc_final: 0.7722 (mtt) REVERT: J 184 LYS cc_start: 0.7562 (mtpt) cc_final: 0.6752 (tptp) REVERT: J 192 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6783 (mm-30) REVERT: J 195 SER cc_start: 0.9205 (p) cc_final: 0.8836 (t) REVERT: J 200 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8099 (tp) REVERT: A 25 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8542 (mttp) REVERT: B 54 CYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7168 (m) REVERT: B 147 GLN cc_start: 0.8307 (pt0) cc_final: 0.8050 (pt0) REVERT: B 233 ASP cc_start: 0.7049 (OUTLIER) cc_final: 0.6419 (m-30) REVERT: C 9 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8366 (mtpp) REVERT: C 30 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9105 (tt) REVERT: C 46 GLN cc_start: 0.7232 (tm-30) cc_final: 0.6979 (tm-30) REVERT: C 97 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8282 (mmt90) REVERT: C 332 ARG cc_start: 0.7362 (mmt-90) cc_final: 0.6744 (mmm-85) REVERT: C 626 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7256 (mm-30) REVERT: C 754 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8887 (p) REVERT: C 848 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6913 (mt-10) REVERT: C 915 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8352 (t0) REVERT: C 919 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8507 (mtp85) REVERT: C 1151 LEU cc_start: 0.8867 (tp) cc_final: 0.8582 (tp) REVERT: C 1240 ASP cc_start: 0.8343 (p0) cc_final: 0.8041 (p0) REVERT: D 6 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6810 (pptt) REVERT: D 86 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7894 (pt0) REVERT: D 132 LEU cc_start: 0.8358 (tp) cc_final: 0.7920 (tt) REVERT: D 172 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.5681 (m-80) REVERT: D 264 ASP cc_start: 0.8276 (m-30) cc_final: 0.8076 (m-30) REVERT: D 626 TYR cc_start: 0.9057 (m-10) cc_final: 0.8784 (m-80) REVERT: D 678 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6193 (tmm160) REVERT: D 788 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8277 (tp) REVERT: D 871 LEU cc_start: 0.8058 (tt) cc_final: 0.7654 (mp) REVERT: D 875 ASN cc_start: 0.8491 (OUTLIER) cc_final: 0.7687 (m-40) REVERT: D 1020 TRP cc_start: 0.2999 (OUTLIER) cc_final: 0.2451 (t60) REVERT: D 1037 PHE cc_start: -0.1690 (OUTLIER) cc_final: -0.1952 (m-10) REVERT: D 1195 GLN cc_start: 0.7973 (tt0) cc_final: 0.7520 (pp30) REVERT: D 1203 ARG cc_start: 0.7843 (ttm170) cc_final: 0.7595 (ttm110) REVERT: D 1325 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8191 (p90) REVERT: F 281 ARG cc_start: 0.5250 (OUTLIER) cc_final: 0.4657 (tmm-80) REVERT: F 417 ASP cc_start: 0.8136 (t0) cc_final: 0.7901 (t0) REVERT: F 433 TRP cc_start: 0.7903 (t-100) cc_final: 0.7679 (t-100) REVERT: F 445 ASP cc_start: 0.8216 (t0) cc_final: 0.7947 (t0) REVERT: F 446 GLN cc_start: 0.9359 (OUTLIER) cc_final: 0.8911 (pm20) REVERT: F 507 MET cc_start: 0.8879 (ttp) cc_final: 0.8531 (ttm) REVERT: F 508 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7233 (tm-30) REVERT: F 561 MET cc_start: 0.8191 (ttm) cc_final: 0.7604 (tpp) REVERT: F 589 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7092 (mp10) REVERT: E 69 ARG cc_start: 0.8573 (tmm-80) cc_final: 0.8301 (tmm-80) outliers start: 279 outliers final: 235 residues processed: 680 average time/residue: 0.2252 time to fit residues: 254.5157 Evaluate side-chains 689 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 258 poor density : 431 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain I residue 195 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 285 THR Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 286 GLU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 540 ARG Chi-restraints excluded: chain C residue 588 GLU Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 573 THR Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 618 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1037 PHE Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 432 THR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 612 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 48 optimal weight: 20.0000 chunk 5 optimal weight: 50.0000 chunk 311 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 128 optimal weight: 8.9990 chunk 83 optimal weight: 0.0870 chunk 121 optimal weight: 10.0000 chunk 295 optimal weight: 0.0000 chunk 57 optimal weight: 9.9990 chunk 240 optimal weight: 0.6980 overall best weight: 3.5566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.148246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.111331 restraints weight = 58805.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.109873 restraints weight = 55958.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.110291 restraints weight = 59786.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110875 restraints weight = 39318.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111772 restraints weight = 32663.903| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 36018 Z= 0.179 Angle : 0.539 9.712 49124 Z= 0.284 Chirality : 0.041 0.177 5585 Planarity : 0.004 0.044 6024 Dihedral : 18.302 171.472 6105 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 39.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 7.75 % Allowed : 24.03 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.93 (0.12), residues: 4153 helix: -2.12 (0.13), residues: 1473 sheet: -3.05 (0.25), residues: 365 loop : -2.96 (0.12), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 88 TYR 0.024 0.001 TYR F 268 PHE 0.013 0.001 PHE C 405 TRP 0.005 0.001 TRP K 321 HIS 0.007 0.001 HIS I 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (36011) covalent geometry : angle 0.53816 / 0.28 (49118) hydrogen bonds : bond 0.04246 / 4.60 ( 815) hydrogen bonds : angle 5.44631 / 7.31 ( 2136) metal coordination : bond 0.00869 / 0.67 ( 7) metal coordination : angle 3.06627 / 5.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 277 poor density : 433 time to evaluate : 1.298 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: I 57 GLN cc_start: 0.7188 (mp10) cc_final: 0.6980 (mp10) REVERT: I 85 HIS cc_start: 0.7012 (m170) cc_final: 0.5129 (m90) REVERT: I 170 GLN cc_start: 0.7595 (tm-30) cc_final: 0.7168 (tt0) REVERT: J 103 MET cc_start: 0.8078 (mtp) cc_final: 0.7801 (mtt) REVERT: J 184 LYS cc_start: 0.7694 (mtpt) cc_final: 0.6934 (tptp) REVERT: J 192 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6741 (mm-30) REVERT: J 195 SER cc_start: 0.9262 (p) cc_final: 0.8939 (t) REVERT: J 200 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8170 (tp) REVERT: A 25 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8752 (ttmm) REVERT: B 54 CYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7239 (m) REVERT: B 147 GLN cc_start: 0.8333 (pt0) cc_final: 0.8010 (pt0) REVERT: B 233 ASP cc_start: 0.7143 (OUTLIER) cc_final: 0.6492 (m-30) REVERT: C 8 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8283 (mtmt) REVERT: C 9 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8400 (mtpp) REVERT: C 46 GLN cc_start: 0.7285 (tm-30) cc_final: 0.7018 (tm-30) REVERT: C 97 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8281 (mmt90) REVERT: C 332 ARG cc_start: 0.7244 (mmt-90) cc_final: 0.6684 (mmm-85) REVERT: C 484 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7365 (mt) REVERT: C 626 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7249 (mm-30) REVERT: C 754 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8905 (p) REVERT: C 848 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6926 (mt-10) REVERT: C 915 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8393 (t0) REVERT: C 919 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8478 (mtp85) REVERT: C 1018 TYR cc_start: 0.5125 (OUTLIER) cc_final: 0.4885 (p90) REVERT: C 1151 LEU cc_start: 0.8909 (tp) cc_final: 0.8635 (tp) REVERT: C 1240 ASP cc_start: 0.8409 (p0) cc_final: 0.8105 (p0) REVERT: D 6 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.6826 (pptt) REVERT: D 86 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7897 (pt0) REVERT: D 132 LEU cc_start: 0.8504 (tp) cc_final: 0.8033 (tt) REVERT: D 172 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.5682 (m-80) REVERT: D 368 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8481 (tp) REVERT: D 626 TYR cc_start: 0.9069 (m-10) cc_final: 0.8777 (m-80) REVERT: D 678 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6258 (tmm160) REVERT: D 788 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8312 (tp) REVERT: D 871 LEU cc_start: 0.8052 (tt) cc_final: 0.7652 (mp) REVERT: D 875 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.7695 (m-40) REVERT: D 1020 TRP cc_start: 0.3045 (OUTLIER) cc_final: 0.2446 (t60) REVERT: D 1195 GLN cc_start: 0.7911 (tt0) cc_final: 0.7536 (pp30) REVERT: D 1203 ARG cc_start: 0.7842 (ttm170) cc_final: 0.7593 (ttm110) REVERT: D 1325 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8332 (p90) REVERT: F 281 ARG cc_start: 0.5268 (OUTLIER) cc_final: 0.4625 (tmm-80) REVERT: F 417 ASP cc_start: 0.8136 (t0) cc_final: 0.7910 (t0) REVERT: F 433 TRP cc_start: 0.7876 (t-100) cc_final: 0.7649 (t-100) REVERT: F 445 ASP cc_start: 0.8144 (t0) cc_final: 0.7902 (t0) REVERT: F 446 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.8966 (pm20) REVERT: F 507 MET cc_start: 0.8920 (ttp) cc_final: 0.8575 (ttm) REVERT: F 508 GLU cc_start: 0.7869 (tm-30) cc_final: 0.7313 (tm-30) REVERT: F 561 MET cc_start: 0.8224 (ttm) cc_final: 0.7708 (tpp) REVERT: F 589 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7143 (mp10) REVERT: E 69 ARG cc_start: 0.8569 (tmm-80) cc_final: 0.8298 (tmm-80) outliers start: 277 outliers final: 244 residues processed: 682 average time/residue: 0.2165 time to fit residues: 245.2262 Evaluate side-chains 697 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 269 poor density : 428 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain I residue 195 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 285 THR Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 829 THR Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1308 ILE Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1050 THR Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 432 THR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 612 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 38 optimal weight: 20.0000 chunk 60 optimal weight: 10.0000 chunk 222 optimal weight: 0.1980 chunk 9 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 413 optimal weight: 50.0000 chunk 251 optimal weight: 10.0000 chunk 317 optimal weight: 10.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C 832 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.149059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112414 restraints weight = 59010.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.111192 restraints weight = 57244.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111357 restraints weight = 61866.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112272 restraints weight = 41328.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.113412 restraints weight = 33286.810| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36018 Z= 0.151 Angle : 0.513 9.359 49124 Z= 0.272 Chirality : 0.040 0.175 5585 Planarity : 0.003 0.041 6024 Dihedral : 18.229 171.216 6100 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 38.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 7.61 % Allowed : 24.25 % Favored : 68.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.12), residues: 4153 helix: -1.97 (0.13), residues: 1478 sheet: -2.97 (0.25), residues: 361 loop : -2.89 (0.12), residues: 2314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 77 TYR 0.021 0.001 TYR D 795 PHE 0.017 0.001 PHE C 545 TRP 0.006 0.001 TRP K 321 HIS 0.006 0.001 HIS I 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (36011) covalent geometry : angle 0.51172 / 0.27 (49118) hydrogen bonds : bond 0.04056 / 4.38 ( 815) hydrogen bonds : angle 5.28311 / 7.08 ( 2136) metal coordination : bond 0.00809 / 0.62 ( 7) metal coordination : angle 2.92058 / 5.32 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8306 Ramachandran restraints generated. 4153 Oldfield, 0 Emsley, 4153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 272 poor density : 449 time to evaluate : 1.229 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: I 85 HIS cc_start: 0.6966 (m170) cc_final: 0.5148 (m90) REVERT: J 103 MET cc_start: 0.8129 (mtp) cc_final: 0.7873 (mtt) REVERT: J 184 LYS cc_start: 0.7687 (mtpt) cc_final: 0.6916 (tptp) REVERT: J 192 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.6733 (mm-30) REVERT: J 195 SER cc_start: 0.9209 (p) cc_final: 0.8852 (t) REVERT: J 200 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8179 (tp) REVERT: A 25 LYS cc_start: 0.9015 (mtpt) cc_final: 0.8722 (mtpp) REVERT: B 54 CYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7222 (m) REVERT: B 147 GLN cc_start: 0.8311 (pt0) cc_final: 0.8059 (pt0) REVERT: B 233 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6468 (m-30) REVERT: C 8 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8253 (mtmt) REVERT: C 9 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8580 (mtpp) REVERT: C 46 GLN cc_start: 0.7252 (tm-30) cc_final: 0.6996 (tm-30) REVERT: C 97 ARG cc_start: 0.8562 (OUTLIER) cc_final: 0.8237 (mmt90) REVERT: C 159 SER cc_start: 0.8738 (p) cc_final: 0.8456 (t) REVERT: C 332 ARG cc_start: 0.7349 (mmt-90) cc_final: 0.6747 (mmm-85) REVERT: C 484 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7332 (mt) REVERT: C 626 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7201 (mm-30) REVERT: C 754 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8876 (p) REVERT: C 848 GLU cc_start: 0.7135 (mt-10) cc_final: 0.6903 (mt-10) REVERT: C 915 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8355 (t0) REVERT: C 919 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8512 (mtp85) REVERT: C 1018 TYR cc_start: 0.5224 (OUTLIER) cc_final: 0.4917 (p90) REVERT: C 1151 LEU cc_start: 0.8874 (tp) cc_final: 0.8596 (tp) REVERT: C 1240 ASP cc_start: 0.8363 (p0) cc_final: 0.8073 (p0) REVERT: D 6 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6837 (pptt) REVERT: D 86 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: D 132 LEU cc_start: 0.8357 (tp) cc_final: 0.7892 (tt) REVERT: D 172 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.5590 (m-80) REVERT: D 264 ASP cc_start: 0.8356 (m-30) cc_final: 0.8145 (m-30) REVERT: D 352 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8456 (ptm160) REVERT: D 626 TYR cc_start: 0.9046 (m-10) cc_final: 0.8718 (m-80) REVERT: D 678 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.6236 (tmm160) REVERT: D 788 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8301 (tp) REVERT: D 871 LEU cc_start: 0.8137 (tt) cc_final: 0.7714 (mp) REVERT: D 875 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.7701 (m-40) REVERT: D 1020 TRP cc_start: 0.3056 (OUTLIER) cc_final: 0.2467 (t60) REVERT: D 1195 GLN cc_start: 0.7905 (tt0) cc_final: 0.7536 (pp30) REVERT: D 1203 ARG cc_start: 0.7833 (ttm170) cc_final: 0.7578 (ttm110) REVERT: D 1325 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8227 (p90) REVERT: F 154 GLU cc_start: 0.2338 (OUTLIER) cc_final: 0.1960 (tp30) REVERT: F 281 ARG cc_start: 0.5235 (OUTLIER) cc_final: 0.4659 (tmm-80) REVERT: F 417 ASP cc_start: 0.8112 (t0) cc_final: 0.7887 (t0) REVERT: F 445 ASP cc_start: 0.8169 (t0) cc_final: 0.7949 (t0) REVERT: F 446 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8970 (pm20) REVERT: F 507 MET cc_start: 0.8883 (ttp) cc_final: 0.8544 (ttm) REVERT: F 508 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7239 (tm-30) REVERT: F 561 MET cc_start: 0.8206 (ttm) cc_final: 0.7728 (tpp) REVERT: F 589 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7168 (mp10) REVERT: E 69 ARG cc_start: 0.8552 (tmm-80) cc_final: 0.8292 (tmm-80) outliers start: 272 outliers final: 242 residues processed: 687 average time/residue: 0.2235 time to fit residues: 254.5498 Evaluate side-chains 711 residues out of total 3596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 268 poor density : 443 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 27 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 137 LEU Chi-restraints excluded: chain I residue 152 ASP Chi-restraints excluded: chain I residue 171 LEU Chi-restraints excluded: chain I residue 175 PHE Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain I residue 195 SER Chi-restraints excluded: chain J residue 15 SER Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 74 ILE Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 139 ILE Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain K residue 277 TYR Chi-restraints excluded: chain K residue 285 THR Chi-restraints excluded: chain K residue 303 ILE Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 204 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 214 GLU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 8 LYS Chi-restraints excluded: chain C residue 9 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 74 ARG Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 97 ARG Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 351 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 426 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 443 ASP Chi-restraints excluded: chain C residue 466 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 749 ASP Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 754 THR Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 844 LYS Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 959 ASP Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1033 ARG Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1046 VAL Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1186 VAL Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 6 LYS Chi-restraints excluded: chain D residue 9 LYS Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 67 ASP Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 105 ILE Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 126 LEU Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 237 MET Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 352 ARG Chi-restraints excluded: chain D residue 381 ILE Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 431 ARG Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 531 LYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 578 ILE Chi-restraints excluded: chain D residue 594 GLN Chi-restraints excluded: chain D residue 617 THR Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 713 GLU Chi-restraints excluded: chain D residue 724 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 769 VAL Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 847 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 872 LEU Chi-restraints excluded: chain D residue 875 ASN Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 922 SER Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 952 VAL Chi-restraints excluded: chain D residue 1002 VAL Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1024 THR Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1093 THR Chi-restraints excluded: chain D residue 1115 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1187 GLU Chi-restraints excluded: chain D residue 1220 ILE Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1240 VAL Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1267 VAL Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 281 ARG Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 390 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 432 THR Chi-restraints excluded: chain F residue 442 SER Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 479 THR Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 612 ASP Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 50.0000 chunk 303 optimal weight: 9.9990 chunk 267 optimal weight: 0.6980 chunk 158 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 422 optimal weight: 4.9990 chunk 45 optimal weight: 30.0000 chunk 233 optimal weight: 0.0010 chunk 271 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 overall best weight: 1.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 HIS ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN ** D 954 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 968 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.150234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.112103 restraints weight = 58251.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.110526 restraints weight = 45989.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.111589 restraints weight = 44918.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.111769 restraints weight = 33512.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112515 restraints weight = 28583.627| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36018 Z= 0.106 Angle : 0.478 9.305 49124 Z= 0.255 Chirality : 0.039 0.174 5585 Planarity : 0.003 0.041 6024 Dihedral : 18.103 171.241 6100 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 38.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 6.80 % Allowed : 25.23 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.57 (0.12), residues: 4153 helix: -1.75 (0.13), residues: 1491 sheet: -2.84 (0.25), residues: 365 loop : -2.80 (0.12), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 77 TYR 0.021 0.001 TYR D 795 PHE 0.011 0.001 PHE B 8 TRP 0.010 0.001 TRP F 433 HIS 0.005 0.001 HIS I 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (36011) covalent geometry : angle 0.47704 / 0.26 (49118) hydrogen bonds : bond 0.03775 / 4.08 ( 815) hydrogen bonds : angle 5.06405 / 6.77 ( 2136) metal coordination : bond 0.00585 / 0.40 ( 7) metal coordination : angle 2.39968 / 4.37 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6410.72 seconds wall clock time: 111 minutes 32.49 seconds (6692.49 seconds total)