Starting phenix.real_space_refine on Fri Oct 30 04:39:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c97_30307/10_2026/7c97_30307.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c97_30307/10_2026/7c97_30307.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7c97_30307/10_2026/7c97_30307.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c97_30307/10_2026/7c97_30307.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7c97_30307/10_2026/7c97_30307.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c97_30307/10_2026/7c97_30307.cif" model { file = "/net/cci-nas-00/data/ceres_data/7c97_30307/10_2026/7c97_30307.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c97_30307/10_2026/7c97_30307.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 21672 2.51 5 N 6173 2.21 5 O 6943 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 99 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35581 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: 10368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1343, 10368 Classifications: {'peptide': 1343} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 55, 'TRANS': 1287} 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: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} 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: "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 20230 SG CYS D 70 111.100 84.467 62.617 1.00 14.03 S ATOM 20244 SG CYS D 72 111.997 83.736 59.315 1.00 18.97 S ATOM 20352 SG CYS D 85 114.539 84.803 62.251 1.00 19.52 S ATOM 20376 SG CYS D 88 111.467 87.575 61.109 1.00 24.48 S ATOM 26586 SG CYS D 888 84.673 99.016 120.932 1.00 18.36 S ATOM 26637 SG CYS D 895 83.190 95.803 122.142 1.00 12.88 S ATOM 26658 SG CYS D 898 81.593 98.760 122.911 1.00 10.20 S Time building chain proxies: 6.77, per 1000 atoms: 0.19 Number of scatterers: 35581 At special positions: 0 Unit cell: (172.524, 193.436, 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 6943 8.00 N 6173 7.00 C 21672 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: 3.00 Conformation dependent library (CDL) restraints added in 1.3 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 88 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 85 " 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 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7754 Finding SS restraints... Secondary structure from input PDB file: 162 helices and 50 sheets defined 39.3% alpha, 8.6% beta 21 base pairs and 49 stacking pairs defined. Time for finding SS restraints: 3.46 Creating SS restraints... Processing helix chain 'I' and resid 19 through 32 removed outlier: 3.520A pdb=" N HIS I 23 " --> pdb=" O ASP I 19 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE I 27 " --> pdb=" O HIS I 23 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS I 32 " --> pdb=" O VAL I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 53 removed outlier: 3.528A pdb=" N ILE I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 83 removed outlier: 3.850A pdb=" N ASP I 80 " --> pdb=" O MET I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 108 removed outlier: 3.653A pdb=" N GLU I 98 " --> pdb=" O VAL I 94 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N MET I 103 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N HIS I 104 " --> pdb=" O ARG I 100 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 120 Processing helix chain 'I' and resid 121 through 139 removed outlier: 3.547A pdb=" N ASP I 126 " --> pdb=" O ALA I 122 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU I 135 " --> pdb=" O GLN I 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 146 removed outlier: 4.432A pdb=" N GLN I 145 " --> pdb=" O PRO I 141 " (cutoff:3.500A) removed outlier: 3.715A 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: 3.523A pdb=" N CYS I 159 " --> pdb=" O SER I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 167 removed outlier: 3.587A pdb=" N ARG I 167 " --> pdb=" O PRO I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 172 removed outlier: 3.802A pdb=" N LEU I 171 " --> pdb=" O LEU I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 179 through 191 removed outlier: 3.971A pdb=" N LEU I 183 " --> pdb=" O GLY I 179 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG I 189 " --> pdb=" O GLY I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 193 through 198 Processing helix chain 'I' and resid 201 through 206 removed outlier: 3.519A pdb=" N GLU I 206 " --> pdb=" O GLU I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 209 No H-bonds generated for 'chain 'I' and resid 207 through 209' Processing helix chain 'J' and resid 19 through 33 Processing helix chain 'J' and resid 47 through 52 removed outlier: 3.858A pdb=" N LEU J 50 " --> pdb=" O PRO J 47 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE J 51 " --> pdb=" O GLN J 48 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP J 52 " --> pdb=" O ASP J 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 47 through 52' Processing helix chain 'J' and resid 72 through 83 removed outlier: 3.747A pdb=" N GLU J 77 " --> pdb=" O ARG J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 107 removed outlier: 3.721A pdb=" N ARG J 96 " --> pdb=" O TYR J 92 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY J 97 " --> pdb=" O PRO J 93 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU J 98 " --> pdb=" O VAL J 94 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS J 104 " --> pdb=" O ARG J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 114 Processing helix chain 'J' and resid 114 through 119 Processing helix chain 'J' and resid 121 through 139 removed outlier: 3.706A pdb=" N ASP J 126 " --> pdb=" O ALA J 122 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA J 127 " --> pdb=" O SER J 123 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS J 130 " --> pdb=" O ASP J 126 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN J 131 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU J 135 " --> pdb=" O GLN J 131 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 145 Processing helix chain 'J' and resid 155 through 160 removed outlier: 3.715A 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 180 through 191 removed outlier: 3.943A pdb=" N GLY J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N TYR J 186 " --> pdb=" O GLU J 182 " (cutoff:3.500A) removed outlier: 3.780A 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 'J' and resid 201 through 206 removed outlier: 4.016A pdb=" N GLU J 206 " --> pdb=" O GLU J 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 256 through 261 removed outlier: 4.055A pdb=" N LEU K 260 " --> pdb=" O VAL K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 263 through 273 removed outlier: 4.039A pdb=" N LEU K 270 " --> pdb=" O SER K 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 277 through 281 removed outlier: 3.521A pdb=" N ASP K 280 " --> pdb=" O TYR K 277 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 289 removed outlier: 3.512A pdb=" N LEU K 289 " --> pdb=" O GLU K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 311 removed outlier: 3.802A pdb=" N ILE K 303 " --> pdb=" O SER K 299 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS K 304 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL K 306 " --> pdb=" O GLU K 302 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU K 307 " --> pdb=" O ILE K 303 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG K 310 " --> pdb=" O VAL K 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.565A pdb=" N ASN A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 48 " --> pdb=" O ARG A 44 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N MET A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.831A 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: 3.624A pdb=" N HIS A 160 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 removed outlier: 4.119A pdb=" N THR A 222 " --> pdb=" O ARG A 218 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 Processing helix chain 'B' and resid 34 through 48 removed outlier: 4.028A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA B 42 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 86 removed outlier: 3.855A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 removed outlier: 3.734A pdb=" N ILE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.674A 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 228 removed outlier: 4.009A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.539A pdb=" N LYS C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.542A pdb=" N ASP C 33 " --> pdb=" O SER C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 54 removed outlier: 3.676A pdb=" N ARG C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 88 Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.973A pdb=" N SER C 167 " --> pdb=" O THR C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 removed outlier: 3.930A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.994A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.500A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.825A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 removed outlier: 3.657A pdb=" N GLN C 327 " --> pdb=" O ALA C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.501A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR C 350 " --> pdb=" O TYR C 346 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 371 removed outlier: 3.549A pdb=" N VAL C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.989A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.689A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.678A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.166A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 4.371A 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: 3.717A pdb=" N GLU C 825 " --> pdb=" O ARG C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 3.833A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 977 removed outlier: 3.505A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET C 951 " --> pdb=" O GLU C 947 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 952 " --> pdb=" O ILE C 948 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS C 957 " --> pdb=" O LEU C 953 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY C 970 " --> pdb=" O ILE C 966 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1010 Processing helix chain 'C' and resid 1010 through 1038 removed outlier: 3.926A pdb=" N GLN C1017 " --> pdb=" O GLN C1013 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1132 removed outlier: 3.573A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N HIS C1116 " --> pdb=" O ILE C1112 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N MET C1119 " --> pdb=" O THR C1115 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS C1122 " --> pdb=" O GLY C1118 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP C1126 " --> pdb=" O LYS C1122 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C1130 " --> pdb=" O ASP C1126 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET C1131 " --> pdb=" O LYS C1127 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1151 removed outlier: 3.572A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR C1149 " --> pdb=" O ILE C1145 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP C1150 " --> pdb=" O GLN C1146 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU C1151 " --> pdb=" O ARG C1147 " (cutoff:3.500A) Processing helix chain 'C' and resid 1168 through 1173 Processing helix chain 'C' and resid 1175 through 1179 removed outlier: 4.170A pdb=" N LYS C1178 " --> pdb=" O ASN C1175 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1200 removed outlier: 3.540A 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: 3.739A pdb=" N ASP C1241 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1274 Processing helix chain 'C' and resid 1275 through 1280 Processing helix chain 'C' and resid 1285 through 1290 Processing helix chain 'C' and resid 1303 through 1309 removed outlier: 3.700A pdb=" N ILE C1308 " --> pdb=" O MET C1304 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C1309 " --> pdb=" O TYR C1305 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.780A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL C1325 " --> pdb=" O GLU C1321 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU C1326 " --> pdb=" O SER C1322 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C1330 " --> pdb=" O LEU C1326 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.517A pdb=" N ARG D 31 " --> pdb=" O PRO D 27 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER D 32 " --> pdb=" O ASP D 28 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.693A 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: 3.619A 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 170 removed outlier: 3.523A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.749A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 187 " --> pdb=" O GLU D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 208 removed outlier: 3.537A pdb=" N GLU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 225 removed outlier: 4.411A pdb=" N THR D 218 " --> pdb=" O ARG D 214 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS D 219 " --> pdb=" O LYS D 215 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS D 222 " --> pdb=" O THR D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 230 removed outlier: 4.450A pdb=" N GLN D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 removed outlier: 4.024A 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: 3.703A pdb=" N ARG D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU D 283 " --> pdb=" O LEU D 279 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 308 removed outlier: 3.828A pdb=" N ARG D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU D 301 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA D 302 " --> pdb=" O MET D 298 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ASP D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 removed outlier: 3.848A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 327 through 332' Processing helix chain 'D' and resid 370 through 377 removed outlier: 4.284A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.633A pdb=" N GLY D 383 " --> pdb=" O PRO D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 removed outlier: 3.666A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG D 403 " --> pdb=" O LYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 416 removed outlier: 4.086A pdb=" N ASP D 413 " --> pdb=" O TRP D 409 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLU D 414 " --> pdb=" O ASP D 410 " (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 450 through 456 removed outlier: 3.852A 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: 3.560A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.520A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.589A pdb=" N VAL D 592 " --> pdb=" O TYR D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 600 through 613 removed outlier: 3.556A pdb=" N ASN D 606 " --> pdb=" O SER D 602 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS D 608 " --> pdb=" O MET D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 616 through 634 removed outlier: 3.904A pdb=" N ASP D 622 " --> pdb=" O VAL D 618 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN D 623 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE D 624 " --> pdb=" O PHE D 620 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA D 630 " --> pdb=" O TYR D 626 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 663 removed outlier: 4.010A pdb=" N ALA D 657 " --> pdb=" O ILE D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 670 Processing helix chain 'D' and resid 675 through 702 removed outlier: 4.200A pdb=" N LYS D 681 " --> pdb=" O GLU D 677 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA D 688 " --> pdb=" O ASP D 684 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER D 694 " --> pdb=" O ASN D 690 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 696 " --> pdb=" O ARG D 692 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP D 699 " --> pdb=" O LYS D 695 " (cutoff:3.500A) removed outlier: 4.520A 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: 5.086A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 782 removed outlier: 3.577A 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: 4.478A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG D 780 " --> pdb=" O THR D 776 " (cutoff:3.500A) Processing helix chain 'D' and resid 782 through 804 removed outlier: 3.506A pdb=" N THR D 786 " --> pdb=" O GLY D 782 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR D 795 " --> pdb=" O ALA D 791 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR D 797 " --> pdb=" O SER D 793 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG D 799 " --> pdb=" O TYR D 795 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL D 801 " --> pdb=" O THR D 797 " (cutoff:3.500A) removed outlier: 3.909A 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 875 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.780A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 1137 through 1146 removed outlier: 3.970A pdb=" N VAL D1141 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.619A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1242 removed outlier: 3.737A pdb=" N ASN D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN D1238 " --> pdb=" O VAL D1234 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.595A 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 1287 Processing helix chain 'D' and resid 1308 through 1313 removed outlier: 3.644A pdb=" N SER D1313 " --> pdb=" O ILE D1309 " (cutoff:3.500A) Processing helix chain 'D' and resid 1328 through 1339 removed outlier: 3.710A pdb=" N THR D1333 " --> pdb=" O THR D1329 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D1335 " --> pdb=" O VAL D1331 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1362 through 1370 removed outlier: 3.809A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 11 removed outlier: 3.703A pdb=" N VAL E 10 " --> pdb=" O GLN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 30 removed outlier: 3.834A pdb=" N ARG E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.645A pdb=" N ILE E 49 " --> pdb=" O LYS E 45 " (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 80 removed outlier: 3.515A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN E 70 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 Processing helix chain 'F' and resid 112 through 136 removed outlier: 3.827A pdb=" N ASN F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 3.891A 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 152 removed outlier: 3.637A pdb=" N GLU F 146 " --> pdb=" O THR F 142 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLU F 152 " --> pdb=" O TYR F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 214 through 221 removed outlier: 3.617A pdb=" N ARG F 218 " --> pdb=" O PRO F 214 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLU F 219 " --> pdb=" O GLU F 215 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE F 221 " --> pdb=" O ALA F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 231 removed outlier: 4.737A pdb=" N VAL F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 234 No H-bonds generated for 'chain 'F' and resid 232 through 234' Processing helix chain 'F' and resid 244 through 255 removed outlier: 4.170A pdb=" N ILE F 249 " --> pdb=" O ALA F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 259 Processing helix chain 'F' and resid 262 through 292 removed outlier: 3.669A pdb=" N PHE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP F 267 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL F 275 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP F 278 " --> pdb=" O ARG F 274 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR F 282 " --> pdb=" O ASP F 278 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N GLN F 283 " --> pdb=" O ARG F 279 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET F 288 " --> pdb=" O GLU F 284 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 307 removed outlier: 4.576A pdb=" N PHE F 302 " --> pdb=" O PRO F 298 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE F 306 " --> pdb=" O PHE F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 318 Processing helix chain 'F' and resid 319 through 323 removed outlier: 3.619A pdb=" N ASN F 323 " --> pdb=" O ILE F 320 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 331 removed outlier: 3.877A pdb=" N HIS F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 Processing helix chain 'F' and resid 342 through 351 removed outlier: 3.543A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 381 removed outlier: 3.757A pdb=" N MET F 365 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER F 366 " --> pdb=" O ASN F 362 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.991A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER F 389 " --> pdb=" O ARG F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 416 removed outlier: 3.655A pdb=" N GLN F 406 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU F 407 " --> pdb=" O ASP F 403 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN F 409 " --> pdb=" O ILE F 405 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS F 414 " --> pdb=" O ILE F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 443 removed outlier: 5.229A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA F 438 " --> pdb=" O TRP F 434 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 removed outlier: 3.681A pdb=" N ILE F 457 " --> pdb=" O PRO F 453 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU F 458 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR F 459 " --> pdb=" O HIS F 455 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN F 469 " --> pdb=" O ARG F 465 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU F 471 " --> pdb=" O SER F 467 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 472 " --> pdb=" O ARG F 468 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU F 473 " --> pdb=" O GLN F 469 " (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: 4.085A pdb=" N GLU F 515 " --> pdb=" O GLY F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.552A pdb=" N ASP F 521 " --> pdb=" O HIS F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 547 removed outlier: 3.526A pdb=" N THR F 536 " --> pdb=" O LEU F 532 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR F 537 " --> pdb=" O ASP F 533 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG F 541 " --> pdb=" O THR F 537 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ALA F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA F 543 " --> pdb=" O SER F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 551 removed outlier: 3.679A 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: 4.029A pdb=" N VAL F 558 " --> pdb=" O ARG F 554 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU F 559 " --> pdb=" O GLU F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 581 removed outlier: 3.601A pdb=" N LYS F 578 " --> pdb=" O GLU F 574 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE F 580 " --> pdb=" O VAL F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 600 removed outlier: 3.817A pdb=" N GLU F 591 " --> pdb=" O ILE F 587 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG F 596 " --> pdb=" O ALA F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 611 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 17 removed outlier: 4.680A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 198 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 202 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.532A 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 90 through 91 Processing sheet with id=AA7, first strand: chain 'A' and resid 102 through 105 Processing sheet with id=AA8, first strand: chain 'A' and resid 110 through 111 removed outlier: 6.925A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 23 through 24 removed outlier: 4.101A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AB2, first strand: chain 'B' and resid 97 through 99 removed outlier: 6.799A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.872A pdb=" N ARG B 91 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 102 through 104 Processing sheet with id=AB5, first strand: chain 'B' and resid 108 through 110 Processing sheet with id=AB6, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.547A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.298A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA C 94 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N GLY C 125 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU C 96 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N TYR C 123 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N VAL C 98 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU C 121 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU C 100 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 115 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB9, first strand: chain 'C' and resid 451 through 453 removed outlier: 3.761A pdb=" N SER C 531 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AC2, first strand: chain 'C' and resid 195 through 196 Processing sheet with id=AC3, first strand: chain 'C' and resid 226 through 230 removed outlier: 4.422A pdb=" N GLU C 226 " --> pdb=" O PHE C 337 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 239 through 240 Processing sheet with id=AC5, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.854A pdb=" N ARG C 267 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 301 through 302 Processing sheet with id=AC7, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.502A pdb=" N THR C 589 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC9, first strand: chain 'C' and resid 633 through 637 Processing sheet with id=AD1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'C' and resid 731 through 732 Processing sheet with id=AD3, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AD4, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 3.715A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL C1097 " --> pdb=" O LEU C 817 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET C1230 " --> pdb=" O MET C 800 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 832 through 837 removed outlier: 3.836A pdb=" N LEU C1054 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.733A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AD8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.553A pdb=" N HIS C1244 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU D 422 " --> pdb=" O HIS D 469 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1268 through 1269 Processing sheet with id=AE1, first strand: chain 'C' and resid 1336 through 1339 Processing sheet with id=AE2, first strand: chain 'D' and resid 105 through 112 removed outlier: 6.948A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 9.987A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.013A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 145 through 147 Processing sheet with id=AE4, first strand: chain 'D' and resid 252 through 254 removed outlier: 4.055A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N PHE D 260 " --> pdb=" O ILE F 505 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 547 through 549 Processing sheet with id=AE6, first strand: chain 'D' and resid 553 through 554 removed outlier: 3.602A pdb=" N GLU D 554 " --> pdb=" O LYS D 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AE8, first strand: chain 'D' and resid 820 through 821 Processing sheet with id=AE9, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AF1, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.589A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1001 through 1003 Processing sheet with id=AF3, first strand: chain 'D' and resid 1035 through 1038 removed outlier: 4.453A pdb=" N LEU D1078 " --> pdb=" O TYR D1099 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 1162 through 1164 removed outlier: 3.681A pdb=" N THR D1178 " --> pdb=" O ILE D1162 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER D1164 " --> pdb=" O VAL D1176 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU D1188 " --> pdb=" O LEU D1175 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 1277 through 1279 903 hydrogen bonds defined for protein. 2466 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 49 stacking parallelities Total time for adding SS restraints: 8.80 Time building geometry restraints manager: 4.00 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: 176 1.23 - 1.42: 14413 1.42 - 1.61: 20981 1.61 - 1.81: 260 Bond restraints: 36361 Sorted by residual: bond pdb=" C LYS C 697 " pdb=" N PRO C 698 " ideal model delta sigma weight residual 1.335 1.295 0.040 8.70e-03 1.32e+04 2.14e+01 bond pdb=" C3' DA G 40 " pdb=" C2' DA G 40 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG G 58 " pdb=" C2' DG G 58 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.86e+00 bond pdb=" C3' DT G 34 " pdb=" C2' DT G 34 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.67e+00 bond pdb=" C3' DT H 30 " pdb=" O3' DT H 30 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.32e+00 ... (remaining 36356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 48502 2.07 - 4.15: 1460 4.15 - 6.22: 118 6.22 - 8.30: 10 8.30 - 10.37: 3 Bond angle restraints: 50093 Sorted by residual: angle pdb=" N VAL C1159 " pdb=" CA VAL C1159 " pdb=" C VAL C1159 " ideal model delta sigma weight residual 110.62 120.58 -9.96 1.02e+00 9.61e-01 9.53e+01 angle pdb=" N ASP C1160 " pdb=" CA ASP C1160 " pdb=" C ASP C1160 " ideal model delta sigma weight residual 109.41 119.78 -10.37 1.52e+00 4.33e-01 4.65e+01 angle pdb=" N LYS D 334 " pdb=" CA LYS D 334 " pdb=" C LYS D 334 " ideal model delta sigma weight residual 112.72 106.60 6.12 1.14e+00 7.69e-01 2.88e+01 angle pdb=" CA LEU C 27 " pdb=" C LEU C 27 " pdb=" N LEU C 28 " ideal model delta sigma weight residual 116.84 125.13 -8.29 1.71e+00 3.42e-01 2.35e+01 angle pdb=" O4' DA H 40 " pdb=" C4' DA H 40 " pdb=" C3' DA H 40 " ideal model delta sigma weight residual 106.00 103.15 2.85 6.00e-01 2.78e+00 2.25e+01 ... (remaining 50088 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 20825 35.82 - 71.64: 1058 71.64 - 107.47: 52 107.47 - 143.29: 0 143.29 - 179.11: 4 Dihedral angle restraints: 21939 sinusoidal: 9912 harmonic: 12027 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 -152.71 -27.29 0 5.00e+00 4.00e-02 2.98e+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 -154.45 -25.55 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA SER D 503 " pdb=" C SER D 503 " pdb=" N GLN D 504 " pdb=" CA GLN D 504 " ideal model delta harmonic sigma weight residual 180.00 -155.42 -24.58 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 21936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4715 0.063 - 0.125: 803 0.125 - 0.188: 36 0.188 - 0.251: 1 0.251 - 0.313: 1 Chirality restraints: 5556 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 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA VAL C1159 " pdb=" N VAL C1159 " pdb=" C VAL C1159 " pdb=" CB VAL C1159 " both_signs ideal model delta sigma weight residual False 2.44 2.24 0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CA LEU C1161 " pdb=" N LEU C1161 " pdb=" C LEU C1161 " pdb=" CB LEU C1161 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 5553 not shown) Planarity restraints: 6055 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C1257 " -0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO C1258 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO C1258 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C1258 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " 0.041 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO C 552 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 615 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO D 616 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 616 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 616 " -0.032 5.00e-02 4.00e+02 ... (remaining 6052 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 245 2.26 - 2.85: 14684 2.85 - 3.43: 41308 3.43 - 4.02: 62895 4.02 - 4.60: 95232 Nonbonded interactions: 214364 Sorted by model distance: nonbonded pdb=" O VAL K 282 " pdb=" H MET K 316 " model vdw 1.681 2.450 nonbonded pdb=" O VAL K 264 " pdb="HD21 ASN K 268 " model vdw 1.748 2.450 nonbonded pdb=" O LEU K 307 " pdb=" H LEU K 312 " model vdw 1.769 2.450 nonbonded pdb=" OD1 ASP K 280 " pdb=" HE1 TRP K 321 " model vdw 1.941 2.450 nonbonded pdb=" O ASN K 320 " pdb="HD21 ASN K 320 " model vdw 1.968 2.450 ... (remaining 214359 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.110 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 38.710 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.007 0.120 35836 Z= 0.372 Angle : 0.847 16.095 48882 Z= 0.542 Chirality : 0.045 0.313 5556 Planarity : 0.005 0.081 5994 Dihedral : 18.520 179.108 14026 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 33.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.28 % Favored : 87.58 % Rotamer: Outliers : 11.86 % Allowed : 13.41 % Favored : 74.73 % 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: -5.70 (0.10), residues: 4130 helix: -4.29 (0.07), residues: 1437 sheet: -3.87 (0.21), residues: 389 loop : -3.51 (0.11), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 195 TYR 0.017 0.002 TYR C 578 PHE 0.013 0.002 PHE D 380 TRP 0.007 0.001 TRP F 326 HIS 0.005 0.001 HIS C 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.37 (35829) covalent geometry : angle 0.83270 / 0.54 (48876) hydrogen bonds : bond 0.32756 / 35.86 ( 948) hydrogen bonds : angle 11.79859 / 15.25 ( 2552) metal coordination : bond 0.07805 / 6.28 ( 7) metal coordination : angle 14.02232 / 25.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1052 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 422 poor density : 630 time to evaluate : 1.279 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 11 MET cc_start: 0.7442 (ppp) cc_final: 0.5742 (ppp) REVERT: I 57 GLN cc_start: 0.5676 (mt0) cc_final: 0.4821 (tp40) REVERT: I 101 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8790 (tm) REVERT: I 189 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5437 (ttm-80) REVERT: I 192 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6859 (pm20) REVERT: J 14 PHE cc_start: 0.7286 (m-10) cc_final: 0.6839 (m-10) REVERT: J 184 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7514 (tptt) REVERT: K 289 LEU cc_start: -0.1890 (OUTLIER) cc_final: -0.2158 (tt) REVERT: A 25 LYS cc_start: 0.8867 (mtpt) cc_final: 0.8605 (mtpp) REVERT: B 7 GLU cc_start: 0.4675 (OUTLIER) cc_final: 0.4365 (pm20) REVERT: B 18 GLN cc_start: 0.8022 (mm-40) cc_final: 0.7714 (mm-40) REVERT: B 49 SER cc_start: 0.8092 (p) cc_final: 0.7771 (p) REVERT: B 77 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7321 (m-30) REVERT: B 83 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8672 (mt) REVERT: B 205 MET cc_start: 0.7348 (ttp) cc_final: 0.7148 (ttt) REVERT: C 8 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8032 (mttm) REVERT: C 9 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8538 (mtpp) REVERT: C 32 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8755 (tp) REVERT: C 81 ASP cc_start: 0.7971 (m-30) cc_final: 0.7611 (m-30) REVERT: C 197 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7833 (ttt180) REVERT: C 299 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6634 (ptmt) REVERT: C 332 ARG cc_start: 0.7028 (mmt-90) cc_final: 0.6672 (mmm-85) REVERT: C 370 MET cc_start: 0.7427 (tpt) cc_final: 0.6989 (tpt) REVERT: C 403 MET cc_start: 0.7199 (tmm) cc_final: 0.6905 (tmt) REVERT: C 473 ARG cc_start: 0.7772 (ttm110) cc_final: 0.7389 (mmt180) REVERT: C 626 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7097 (mm-30) REVERT: C 704 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8873 (tmm) REVERT: C 827 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.8145 (ptm160) REVERT: C 915 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8485 (t70) REVERT: C 1057 LYS cc_start: 0.9440 (OUTLIER) cc_final: 0.9128 (ttpt) REVERT: C 1134 GLN cc_start: 0.7530 (OUTLIER) cc_final: 0.6971 (mm-40) REVERT: C 1155 VAL cc_start: 0.8758 (OUTLIER) cc_final: 0.8510 (m) REVERT: C 1194 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7225 (mt-10) REVERT: D 172 PHE cc_start: 0.7045 (OUTLIER) cc_final: 0.5225 (m-80) REVERT: D 255 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7859 (mt) REVERT: D 290 ILE cc_start: 0.9261 (tp) cc_final: 0.8938 (tt) REVERT: D 298 MET cc_start: 0.8165 (ttp) cc_final: 0.7848 (ttp) REVERT: D 368 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8840 (tp) REVERT: D 558 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7068 (p0) REVERT: D 619 ILE cc_start: 0.9237 (OUTLIER) cc_final: 0.8997 (tp) REVERT: D 634 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7509 (mtp85) REVERT: D 652 GLU cc_start: 0.8047 (mp0) cc_final: 0.7827 (mt-10) REVERT: D 679 TYR cc_start: 0.8258 (t80) cc_final: 0.8000 (t80) REVERT: D 700 ASN cc_start: 0.7745 (t0) cc_final: 0.7463 (t0) REVERT: D 821 MET cc_start: 0.6325 (tpp) cc_final: 0.6072 (mtm) REVERT: D 929 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.6751 (pm20) REVERT: D 930 LEU cc_start: 0.7403 (mt) cc_final: 0.7088 (mt) REVERT: D 999 TYR cc_start: 0.1032 (OUTLIER) cc_final: 0.0128 (m-80) REVERT: D 1023 HIS cc_start: 0.3567 (OUTLIER) cc_final: 0.2059 (p-80) REVERT: D 1052 GLU cc_start: 0.5207 (OUTLIER) cc_final: 0.4700 (mt-10) REVERT: D 1156 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8349 (mm) REVERT: D 1197 ASN cc_start: 0.8001 (m110) cc_final: 0.7262 (m-40) REVERT: D 1282 TYR cc_start: 0.7428 (m-10) cc_final: 0.7217 (m-10) REVERT: D 1325 PHE cc_start: 0.8513 (OUTLIER) cc_final: 0.8201 (p90) REVERT: E 18 ASP cc_start: 0.8349 (p0) cc_final: 0.7964 (p0) REVERT: E 56 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: F 131 GLN cc_start: 0.7182 (OUTLIER) cc_final: 0.5402 (pp30) REVERT: F 152 GLU cc_start: 0.2605 (OUTLIER) cc_final: 0.1891 (tp30) REVERT: F 232 ARG cc_start: 0.3572 (OUTLIER) cc_final: 0.2695 (tpt-90) REVERT: F 252 LEU cc_start: 0.5089 (OUTLIER) cc_final: 0.4563 (tp) REVERT: F 316 PHE cc_start: 0.3054 (OUTLIER) cc_final: 0.2755 (m-80) REVERT: F 446 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8858 (pm20) REVERT: F 472 GLN cc_start: 0.8675 (OUTLIER) cc_final: 0.7110 (mp10) REVERT: F 500 ILE cc_start: 0.7746 (mm) cc_final: 0.7517 (mt) REVERT: F 507 MET cc_start: 0.8829 (ttp) cc_final: 0.8554 (ttm) REVERT: F 540 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8839 (tt) REVERT: F 573 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7739 (mt) REVERT: F 579 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7548 (tt0) REVERT: F 589 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7284 (mp10) outliers start: 422 outliers final: 239 residues processed: 991 average time/residue: 0.2253 time to fit residues: 355.7608 Evaluate side-chains 753 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 282 poor density : 471 time to evaluate : 1.285 ------------------------------------------------------------------------------- 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 49 ASP Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 101 LEU Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 118 ILE 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 183 LEU Chi-restraints excluded: chain K residue 254 LEU 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 13 LEU Chi-restraints excluded: chain A residue 22 THR 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 129 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 211 ILE 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 77 ASP Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL 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 162 GLU 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 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 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 197 ARG Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 320 ASP Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 384 LEU 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 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 492 MET Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU 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 699 LEU Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 704 MET 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 759 SER Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 790 ASP Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 827 ARG Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 877 VAL 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 966 ILE Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 991 LYS 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 1047 LEU Chi-restraints excluded: chain C residue 1057 LYS 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 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 1174 GLU Chi-restraints excluded: chain C residue 1198 LEU Chi-restraints excluded: chain C residue 1203 ASP 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 1259 LEU 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 1337 ILE 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 109 SER Chi-restraints excluded: chain D residue 114 ILE 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 193 ASP Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 300 GLN Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 368 LEU Chi-restraints excluded: chain D residue 401 VAL 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 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 563 LEU 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 634 ARG Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 666 GLU 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 710 ASP Chi-restraints excluded: chain D residue 713 GLU 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 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 925 GLU Chi-restraints excluded: chain D residue 929 GLN 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 1023 HIS Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1038 THR Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1052 GLU Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1156 LEU 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 1246 VAL 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 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 E residue 4 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 160 ASP Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 316 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 342 GLN 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 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 472 GLN Chi-restraints excluded: chain F residue 525 ASP Chi-restraints excluded: chain F residue 533 ASP 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 573 LEU Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 591 GLU Chi-restraints excluded: chain F residue 604 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 401, 155, 244] chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 10.0000 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.0870 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 23 HIS I 24 GLN I 57 GLN J 115 ASN K 283 GLN A 147 GLN A 194 GLN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN B 103 ASN B 147 GLN C 120 GLN C 219 GLN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 GLN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN C 673 HIS C 808 ASN C 834 GLN C 955 GLN C1111 GLN C1264 GLN C1268 GLN D 186 GLN D 294 ASN D 419 HIS D 477 GLN D 495 ASN D 594 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS D 867 GLN ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 954 ASN ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN E 43 ASN E 73 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 HIS F 464 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.152588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.123906 restraints weight = 57987.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123695 restraints weight = 141941.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124865 restraints weight = 106101.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124931 restraints weight = 64147.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127483 restraints weight = 52172.371| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35836 Z= 0.134 Angle : 0.606 12.656 48882 Z= 0.330 Chirality : 0.042 0.227 5556 Planarity : 0.004 0.045 5994 Dihedral : 18.869 176.763 6362 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 36.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 8.29 % Allowed : 18.11 % Favored : 73.60 % 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: -4.80 (0.11), residues: 4130 helix: -3.17 (0.10), residues: 1516 sheet: -3.30 (0.23), residues: 383 loop : -3.23 (0.12), residues: 2231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 363 TYR 0.016 0.001 TYR D 555 PHE 0.020 0.001 PHE B 8 TRP 0.012 0.001 TRP D 33 HIS 0.010 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (35829) covalent geometry : angle 0.59982 / 0.33 (48876) hydrogen bonds : bond 0.07323 / 8.34 ( 948) hydrogen bonds : angle 6.70879 / 8.71 ( 2552) metal coordination : bond 0.01009 / 0.58 ( 7) metal coordination : angle 7.66497 / 14.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 295 poor density : 515 time to evaluate : 1.241 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 57 GLN cc_start: 0.5917 (mt0) cc_final: 0.5132 (tp40) REVERT: I 160 TYR cc_start: 0.8883 (m-80) cc_final: 0.8144 (m-80) REVERT: I 189 ARG cc_start: 0.5532 (OUTLIER) cc_final: 0.4990 (ttm-80) REVERT: J 14 PHE cc_start: 0.7388 (m-10) cc_final: 0.7041 (m-10) REVERT: J 19 ASP cc_start: 0.5357 (t0) cc_final: 0.4243 (m-30) REVERT: J 20 ILE cc_start: 0.7746 (tt) cc_final: 0.7385 (tt) REVERT: J 57 GLN cc_start: 0.7391 (mm-40) cc_final: 0.7141 (mm-40) REVERT: J 115 ASN cc_start: 0.6818 (OUTLIER) cc_final: 0.6536 (t0) REVERT: J 184 LYS cc_start: 0.7957 (mtpt) cc_final: 0.6917 (tptp) REVERT: J 192 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6663 (mm-30) REVERT: A 25 LYS cc_start: 0.9027 (mtpt) cc_final: 0.8744 (ttmm) REVERT: B 18 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7546 (mm-40) REVERT: B 77 ASP cc_start: 0.7705 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: B 83 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8657 (mt) REVERT: B 162 GLU cc_start: 0.2105 (OUTLIER) cc_final: 0.1243 (tm-30) REVERT: C 8 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7568 (mttm) REVERT: C 9 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8544 (mtpp) REVERT: C 299 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6639 (ptmt) REVERT: C 315 MET cc_start: 0.8156 (tpp) cc_final: 0.7888 (tmm) REVERT: C 332 ARG cc_start: 0.6964 (mmt-90) cc_final: 0.6669 (mmm-85) REVERT: C 626 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7171 (mm-30) REVERT: C 903 ARG cc_start: 0.7613 (mmt-90) cc_final: 0.6952 (mmt-90) REVERT: C 1057 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9078 (ttpt) REVERT: C 1134 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7063 (mm-40) REVERT: C 1321 GLU cc_start: 0.7988 (tp30) cc_final: 0.7541 (tp30) REVERT: D 172 PHE cc_start: 0.7212 (OUTLIER) cc_final: 0.5329 (m-80) REVERT: D 255 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7794 (mt) REVERT: D 368 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8648 (tp) REVERT: D 531 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8982 (mttm) REVERT: D 558 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7115 (p0) REVERT: D 614 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8753 (tt) REVERT: D 619 ILE cc_start: 0.9274 (tt) cc_final: 0.8974 (tp) REVERT: D 654 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.8818 (mp) REVERT: D 677 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7068 (mm-30) REVERT: D 678 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.6138 (tmm160) REVERT: D 679 TYR cc_start: 0.8138 (t80) cc_final: 0.7789 (t80) REVERT: D 777 HIS cc_start: 0.7631 (t-90) cc_final: 0.7186 (t-90) REVERT: D 788 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8394 (tp) REVERT: D 821 MET cc_start: 0.6580 (tpp) cc_final: 0.6331 (mtm) REVERT: D 827 GLU cc_start: 0.5852 (tp30) cc_final: 0.5590 (tp30) REVERT: D 929 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.6642 (pm20) REVERT: D 930 LEU cc_start: 0.7258 (mt) cc_final: 0.6822 (mt) REVERT: D 999 TYR cc_start: 0.0344 (OUTLIER) cc_final: -0.0258 (m-80) REVERT: D 1023 HIS cc_start: 0.3468 (OUTLIER) cc_final: 0.2013 (p-80) REVERT: D 1195 GLN cc_start: 0.8292 (pp30) cc_final: 0.7677 (pp30) REVERT: D 1325 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8177 (p90) REVERT: E 56 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: E 61 ASN cc_start: 0.8385 (t0) cc_final: 0.8123 (t0) REVERT: F 131 GLN cc_start: 0.6730 (OUTLIER) cc_final: 0.5487 (pp30) REVERT: F 218 ARG cc_start: 0.6921 (mtm110) cc_final: 0.6388 (tpp80) REVERT: F 232 ARG cc_start: 0.3387 (OUTLIER) cc_final: 0.1071 (tpt-90) REVERT: F 252 LEU cc_start: 0.5252 (OUTLIER) cc_final: 0.4864 (tp) REVERT: F 316 PHE cc_start: 0.2962 (OUTLIER) cc_final: 0.1949 (m-80) REVERT: F 445 ASP cc_start: 0.8038 (t0) cc_final: 0.7738 (t0) REVERT: F 446 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.8884 (pm20) REVERT: F 507 MET cc_start: 0.8851 (ttp) cc_final: 0.8553 (ttm) REVERT: F 579 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.7209 (tp40) REVERT: F 589 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.6942 (mp10) outliers start: 295 outliers final: 183 residues processed: 766 average time/residue: 0.2036 time to fit residues: 253.6352 Evaluate side-chains 662 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 446 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain I residue 200 LEU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU 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 26 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL 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 162 GLU 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 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 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 216 THR Chi-restraints excluded: chain C residue 279 LYS Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 384 LEU Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 422 LYS Chi-restraints excluded: chain C residue 443 ASP 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 524 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 702 THR 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 802 VAL 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 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 991 LYS 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 1057 LYS Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1077 SER 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 1151 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 1295 SER Chi-restraints excluded: chain C residue 1337 ILE 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 114 ILE Chi-restraints excluded: chain D residue 134 ASP Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 192 MET Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 255 LEU 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 368 LEU 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 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 563 LEU Chi-restraints excluded: chain D residue 564 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 614 LEU 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 661 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 678 ARG 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 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU 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 925 GLU Chi-restraints excluded: chain D residue 929 GLN 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 1023 HIS Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1234 VAL 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 1351 VAL Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 GLU 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 229 VAL Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 252 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 316 PHE Chi-restraints excluded: chain F residue 333 VAL 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 429 THR Chi-restraints excluded: chain F residue 446 GLN Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 525 ASP Chi-restraints excluded: chain F residue 533 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 604 SER Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: [224, 186, 362, 41, 348, 72, 46, 149, 15, 177, 414] chunk 224 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 362 optimal weight: 8.9990 chunk 41 optimal weight: 20.0000 chunk 348 optimal weight: 9.9990 chunk 72 optimal weight: 10.0000 chunk 46 optimal weight: 0.4980 chunk 149 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 414 optimal weight: 9.9990 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 24 GLN ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 37 HIS B 93 GLN C 139 ASN ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 HIS C 490 GLN C 677 ASN C 832 HIS C1336 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 560 ASN D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1279 GLN E 43 ASN E 70 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.148656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114003 restraints weight = 58733.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.113388 restraints weight = 75905.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113604 restraints weight = 81269.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.114593 restraints weight = 46073.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.116817 restraints weight = 36554.861| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 35836 Z= 0.240 Angle : 0.624 10.444 48882 Z= 0.333 Chirality : 0.042 0.156 5556 Planarity : 0.004 0.046 5994 Dihedral : 18.523 176.934 6155 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 38.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.77 % Favored : 89.23 % Rotamer: Outliers : 8.60 % Allowed : 18.92 % Favored : 72.48 % 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: -4.44 (0.11), residues: 4130 helix: -2.69 (0.11), residues: 1524 sheet: -3.17 (0.24), residues: 390 loop : -3.15 (0.12), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 903 TYR 0.021 0.002 TYR F 148 PHE 0.018 0.002 PHE C 337 TRP 0.011 0.001 TRP I 70 HIS 0.009 0.001 HIS J 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.24 (35829) covalent geometry : angle 0.61898 / 0.33 (48876) hydrogen bonds : bond 0.06501 / 7.27 ( 948) hydrogen bonds : angle 6.30102 / 8.19 ( 2552) metal coordination : bond 0.01366 / 0.94 ( 7) metal coordination : angle 6.86899 / 13.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 306 poor density : 445 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 57 GLN cc_start: 0.6318 (mt0) cc_final: 0.5488 (tm-30) REVERT: I 85 HIS cc_start: 0.7301 (m170) cc_final: 0.6575 (m170) REVERT: I 89 MET cc_start: 0.8276 (mmm) cc_final: 0.7808 (mmm) REVERT: I 192 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: J 19 ASP cc_start: 0.6042 (t0) cc_final: 0.4343 (m-30) REVERT: J 23 HIS cc_start: 0.7799 (t-170) cc_final: 0.7559 (t-170) REVERT: J 57 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.7134 (mm-40) REVERT: J 184 LYS cc_start: 0.7941 (mtpt) cc_final: 0.6863 (tptp) REVERT: J 192 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.6779 (mm-30) REVERT: J 195 SER cc_start: 0.9051 (p) cc_final: 0.8740 (t) REVERT: A 25 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8482 (mtpp) REVERT: B 7 GLU cc_start: 0.4528 (OUTLIER) cc_final: 0.4122 (mp0) REVERT: B 51 MET cc_start: 0.7442 (ttt) cc_final: 0.7130 (ttt) REVERT: B 77 ASP cc_start: 0.7714 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: B 83 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8712 (mt) REVERT: B 162 GLU cc_start: 0.1930 (OUTLIER) cc_final: 0.1188 (tt0) REVERT: C 8 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8010 (mttm) REVERT: C 9 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8428 (mtpp) REVERT: C 245 ARG cc_start: 0.8487 (ttm170) cc_final: 0.8033 (ttm170) REVERT: C 270 THR cc_start: 0.1981 (OUTLIER) cc_final: 0.1712 (p) REVERT: C 278 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6433 (mp0) REVERT: C 299 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6673 (ptmt) REVERT: C 315 MET cc_start: 0.8295 (tpp) cc_final: 0.7768 (tmm) REVERT: C 332 ARG cc_start: 0.7041 (mmt-90) cc_final: 0.6623 (mmm-85) REVERT: C 626 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7157 (mm-30) REVERT: C 915 ASP cc_start: 0.8847 (OUTLIER) cc_final: 0.8510 (t70) REVERT: C 919 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8425 (mtp85) REVERT: C 1057 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9088 (ttpt) REVERT: C 1069 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8700 (mtp180) REVERT: C 1134 GLN cc_start: 0.7399 (OUTLIER) cc_final: 0.7062 (mm-40) REVERT: C 1321 GLU cc_start: 0.8047 (tp30) cc_final: 0.7645 (tp30) REVERT: D 44 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8184 (mt) REVERT: D 172 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.5038 (m-80) REVERT: D 255 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7869 (mt) REVERT: D 368 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8691 (tp) REVERT: D 422 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8912 (mp) REVERT: D 531 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.8968 (mtmp) REVERT: D 558 ASP cc_start: 0.7754 (OUTLIER) cc_final: 0.7394 (p0) REVERT: D 619 ILE cc_start: 0.9212 (tt) cc_final: 0.8930 (tp) REVERT: D 654 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.8902 (mp) REVERT: D 678 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6198 (tmm160) REVERT: D 679 TYR cc_start: 0.8243 (t80) cc_final: 0.7973 (t80) REVERT: D 777 HIS cc_start: 0.7580 (t-90) cc_final: 0.7183 (t-90) REVERT: D 788 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8463 (tp) REVERT: D 821 MET cc_start: 0.6469 (tpp) cc_final: 0.6207 (mtm) REVERT: D 827 GLU cc_start: 0.6289 (tp30) cc_final: 0.6041 (tp30) REVERT: D 832 LYS cc_start: 0.7839 (mmmt) cc_final: 0.7172 (mmmt) REVERT: D 929 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7057 (pm20) REVERT: D 999 TYR cc_start: 0.0329 (OUTLIER) cc_final: -0.0441 (m-80) REVERT: D 1023 HIS cc_start: 0.3364 (OUTLIER) cc_final: 0.2038 (p-80) REVERT: D 1140 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8740 (tpp80) REVERT: D 1325 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8309 (p90) REVERT: E 56 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: F 131 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6239 (pp30) REVERT: F 220 LYS cc_start: 0.3705 (OUTLIER) cc_final: 0.2778 (mmtt) REVERT: F 232 ARG cc_start: 0.3968 (OUTLIER) cc_final: 0.2675 (tpt-90) REVERT: F 266 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.6682 (t80) REVERT: F 316 PHE cc_start: 0.2485 (OUTLIER) cc_final: 0.1823 (m-80) REVERT: F 322 MET cc_start: 0.2997 (tpt) cc_final: 0.2105 (mmm) REVERT: F 445 ASP cc_start: 0.8146 (t0) cc_final: 0.7853 (t0) REVERT: F 446 GLN cc_start: 0.9439 (OUTLIER) cc_final: 0.8977 (pm20) REVERT: F 507 MET cc_start: 0.8947 (ttp) cc_final: 0.8691 (ttm) REVERT: F 579 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7547 (tp40) REVERT: F 589 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7075 (mp10) outliers start: 306 outliers final: 224 residues processed: 707 average time/residue: 0.1985 time to fit residues: 230.2553 Evaluate side-chains 696 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 266 poor density : 430 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain I residue 49 ASP Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain I residue 118 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 192 GLU Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 57 GLN Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 22 THR 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 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 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 29 GLU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 58 GLU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 98 VAL 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 162 GLU Chi-restraints excluded: chain B residue 178 SER 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 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 79 VAL Chi-restraints excluded: chain C residue 91 THR 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 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS 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 366 ILE Chi-restraints excluded: chain C residue 384 LEU 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 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 487 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE 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 734 ILE Chi-restraints excluded: chain C residue 748 ILE 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 802 VAL Chi-restraints excluded: chain C residue 829 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 948 ILE Chi-restraints excluded: chain C residue 991 LYS 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 1057 LYS Chi-restraints excluded: chain C residue 1069 ARG 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 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1166 ASP 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 1295 SER Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain C residue 1339 LEU 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 44 ILE Chi-restraints excluded: chain D residue 46 TYR 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 172 PHE Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 255 LEU 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 347 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 354 VAL 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 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 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 474 LEU 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 531 LYS Chi-restraints excluded: chain D residue 558 ASP Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 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 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 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 769 VAL 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 857 LEU 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 925 GLU Chi-restraints excluded: chain D residue 929 GLN 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 1023 HIS Chi-restraints excluded: chain D residue 1027 VAL Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1140 ARG Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1234 VAL 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 1351 VAL Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 109 GLU 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 220 LYS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain F residue 232 ARG Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 316 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 365 MET 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 412 LEU Chi-restraints excluded: chain F residue 429 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 525 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 604 SER Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: [76, 93, 16, 27, 243, 408, 246, 232, 3, 169, 32] chunk 76 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 243 optimal weight: 7.9990 chunk 408 optimal weight: 7.9990 chunk 246 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 3 optimal weight: 50.0000 chunk 169 optimal weight: 7.9990 chunk 32 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 24 GLN ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN K 320 ASN B 84 ASN B 93 GLN ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN C 677 ASN D 45 ASN ** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN E 70 GLN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.147913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.113395 restraints weight = 58549.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.112129 restraints weight = 73439.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.113038 restraints weight = 76725.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.113368 restraints weight = 43185.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.115306 restraints weight = 37074.876| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 35836 Z= 0.246 Angle : 0.625 10.482 48882 Z= 0.331 Chirality : 0.043 0.177 5556 Planarity : 0.004 0.046 5994 Dihedral : 18.479 175.646 6127 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 40.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 9.84 % Allowed : 19.60 % Favored : 70.57 % 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: -4.22 (0.12), residues: 4130 helix: -2.38 (0.12), residues: 1529 sheet: -3.12 (0.23), residues: 406 loop : -3.12 (0.12), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 232 TYR 0.015 0.002 TYR F 148 PHE 0.017 0.002 PHE C 545 TRP 0.010 0.001 TRP F 433 HIS 0.007 0.001 HIS C1244 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.25 (35829) covalent geometry : angle 0.62104 / 0.33 (48876) hydrogen bonds : bond 0.05744 / 6.52 ( 948) hydrogen bonds : angle 6.02288 / 7.83 ( 2552) metal coordination : bond 0.01508 / 1.08 ( 7) metal coordination : angle 6.44333 / 12.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 350 poor density : 450 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 56 ASN cc_start: 0.7492 (p0) cc_final: 0.6742 (p0) REVERT: I 57 GLN cc_start: 0.6361 (mt0) cc_final: 0.5544 (tm-30) REVERT: I 85 HIS cc_start: 0.6966 (m170) cc_final: 0.6250 (m170) REVERT: I 89 MET cc_start: 0.8377 (mmm) cc_final: 0.7867 (mmm) REVERT: J 19 ASP cc_start: 0.6082 (t0) cc_final: 0.4352 (m-30) REVERT: J 103 MET cc_start: 0.7795 (mtp) cc_final: 0.7538 (mtt) REVERT: J 115 ASN cc_start: 0.6828 (OUTLIER) cc_final: 0.6427 (t0) REVERT: J 184 LYS cc_start: 0.7866 (mtpt) cc_final: 0.6727 (tptp) REVERT: J 192 GLU cc_start: 0.7441 (OUTLIER) cc_final: 0.6846 (mm-30) REVERT: J 195 SER cc_start: 0.9026 (p) cc_final: 0.8767 (t) REVERT: A 25 LYS cc_start: 0.9096 (mtpt) cc_final: 0.8488 (mtpp) REVERT: B 7 GLU cc_start: 0.4471 (OUTLIER) cc_final: 0.3941 (mp0) REVERT: B 51 MET cc_start: 0.7655 (ttt) cc_final: 0.7344 (ttt) REVERT: B 77 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7485 (m-30) REVERT: C 8 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.8115 (mttm) REVERT: C 9 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8582 (mtpp) REVERT: C 97 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8376 (mmt90) REVERT: C 245 ARG cc_start: 0.8580 (ttm170) cc_final: 0.8053 (ttm170) REVERT: C 270 THR cc_start: 0.2048 (OUTLIER) cc_final: 0.1786 (p) REVERT: C 299 LYS cc_start: 0.7168 (OUTLIER) cc_final: 0.6590 (ptmt) REVERT: C 332 ARG cc_start: 0.7020 (mmt-90) cc_final: 0.6719 (mmm-85) REVERT: C 529 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8226 (mtt-85) REVERT: C 626 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: C 915 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8506 (t70) REVERT: C 919 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8597 (mtp85) REVERT: C 954 LYS cc_start: 0.8628 (tmmt) cc_final: 0.8411 (tttt) REVERT: C 1057 LYS cc_start: 0.9429 (OUTLIER) cc_final: 0.9150 (ttpt) REVERT: C 1134 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7167 (mm-40) REVERT: C 1321 GLU cc_start: 0.8099 (tp30) cc_final: 0.7737 (tp30) REVERT: D 44 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8142 (mt) REVERT: D 172 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.5050 (m-80) REVERT: D 255 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7913 (mt) REVERT: D 368 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8682 (tp) REVERT: D 422 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8887 (mp) REVERT: D 619 ILE cc_start: 0.9259 (tt) cc_final: 0.8970 (tp) REVERT: D 654 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.8922 (mp) REVERT: D 678 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6245 (tmm160) REVERT: D 781 LYS cc_start: 0.8701 (tptt) cc_final: 0.8105 (mttt) REVERT: D 788 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8329 (tp) REVERT: D 827 GLU cc_start: 0.6536 (tp30) cc_final: 0.6254 (tp30) REVERT: D 832 LYS cc_start: 0.7849 (mmmt) cc_final: 0.7230 (mmmt) REVERT: D 875 ASN cc_start: 0.7551 (OUTLIER) cc_final: 0.7275 (t0) REVERT: D 929 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: D 999 TYR cc_start: 0.0218 (OUTLIER) cc_final: -0.0465 (m-80) REVERT: D 1023 HIS cc_start: 0.3259 (OUTLIER) cc_final: 0.1984 (p-80) REVERT: D 1140 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8727 (tpp80) REVERT: D 1279 GLN cc_start: 0.7296 (tt0) cc_final: 0.6877 (tt0) REVERT: D 1325 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.8283 (p90) REVERT: E 56 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: F 131 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6799 (pp30) REVERT: F 266 PHE cc_start: 0.7266 (OUTLIER) cc_final: 0.6525 (t80) REVERT: F 316 PHE cc_start: 0.2400 (OUTLIER) cc_final: 0.1508 (m-80) REVERT: F 322 MET cc_start: 0.2606 (tpt) cc_final: 0.1987 (mmm) REVERT: F 446 GLN cc_start: 0.9481 (OUTLIER) cc_final: 0.9190 (pm20) REVERT: F 507 MET cc_start: 0.8966 (ttp) cc_final: 0.8700 (ttm) REVERT: F 561 MET cc_start: 0.8454 (tpp) cc_final: 0.7872 (tpp) REVERT: F 579 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.7459 (tp40) REVERT: F 589 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7101 (mp10) outliers start: 350 outliers final: 268 residues processed: 744 average time/residue: 0.1959 time to fit residues: 241.1384 Evaluate side-chains 737 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 304 poor density : 433 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 38 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 12 THR Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 38 ILE Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 116 THR Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU 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 14 VAL Chi-restraints excluded: chain A residue 22 THR 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 111 THR Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 195 ARG Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 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 58 GLU 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 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 178 SER 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 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 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 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS 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 366 ILE 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 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 487 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 529 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 672 GLU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 748 ILE 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 802 VAL Chi-restraints excluded: chain C residue 843 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 948 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1029 LEU 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 1058 ARG Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1077 SER 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 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1167 GLU 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 1295 SER Chi-restraints excluded: chain C residue 1308 ILE Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain C residue 1339 LEU 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 44 ILE Chi-restraints excluded: chain D residue 46 TYR Chi-restraints excluded: chain D residue 83 VAL 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 210 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 255 LEU 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 347 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 354 VAL 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 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 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 474 LEU 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 531 LYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 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 654 ILE Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 664 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 680 ASN Chi-restraints excluded: chain D residue 685 ILE 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 737 ILE Chi-restraints excluded: chain D residue 743 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 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 857 LEU Chi-restraints excluded: chain D residue 875 ASN 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 925 GLU Chi-restraints excluded: chain D residue 929 GLN 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 1023 HIS Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1140 ARG Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1234 VAL 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 1321 SER 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 E residue 4 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 109 GLU 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 229 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 316 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 365 MET 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 412 LEU Chi-restraints excluded: chain F residue 429 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 485 GLU Chi-restraints excluded: chain F residue 525 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 604 SER Chi-restraints excluded: chain F residue 609 SER Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: [196, 78, 173, 6, 309, 400, 39, 336, 63, 408, 97] chunk 196 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 173 optimal weight: 10.0000 chunk 6 optimal weight: 0.1980 chunk 309 optimal weight: 0.7980 chunk 400 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 336 optimal weight: 40.0000 chunk 63 optimal weight: 7.9990 chunk 408 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 24 GLN ** I 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN B 93 GLN C 31 GLN ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.148446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114301 restraints weight = 58241.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111896 restraints weight = 77902.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.113182 restraints weight = 79655.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.113682 restraints weight = 46750.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114743 restraints weight = 40187.343| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 35836 Z= 0.200 Angle : 0.575 9.620 48882 Z= 0.306 Chirality : 0.041 0.174 5556 Planarity : 0.004 0.044 5994 Dihedral : 18.371 175.687 6101 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 39.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 9.25 % Allowed : 20.92 % Favored : 69.83 % 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: -4.01 (0.12), residues: 4130 helix: -2.15 (0.12), residues: 1535 sheet: -2.95 (0.24), residues: 397 loop : -3.05 (0.12), residues: 2198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 764 TYR 0.015 0.001 TYR C1018 PHE 0.025 0.001 PHE C 545 TRP 0.009 0.001 TRP F 433 HIS 0.003 0.001 HIS C 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00459 / 0.20 (35829) covalent geometry : angle 0.56880 / 0.31 (48876) hydrogen bonds : bond 0.05344 / 6.12 ( 948) hydrogen bonds : angle 5.76732 / 7.45 ( 2552) metal coordination : bond 0.01400 / 0.93 ( 7) metal coordination : angle 7.52268 / 14.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 329 poor density : 446 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 56 ASN cc_start: 0.7457 (p0) cc_final: 0.6464 (p0) REVERT: I 57 GLN cc_start: 0.6187 (mt0) cc_final: 0.5441 (tm-30) REVERT: I 89 MET cc_start: 0.8252 (mmm) cc_final: 0.7791 (mmm) REVERT: J 19 ASP cc_start: 0.5880 (t0) cc_final: 0.4182 (m-30) REVERT: J 64 ASP cc_start: 0.7407 (t70) cc_final: 0.7203 (t0) REVERT: J 115 ASN cc_start: 0.7086 (OUTLIER) cc_final: 0.6561 (t0) REVERT: J 184 LYS cc_start: 0.7895 (mtpt) cc_final: 0.6773 (tptm) REVERT: J 192 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6735 (mm-30) REVERT: J 195 SER cc_start: 0.8954 (p) cc_final: 0.8722 (t) REVERT: A 25 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8490 (mtpp) REVERT: B 7 GLU cc_start: 0.4501 (OUTLIER) cc_final: 0.3995 (mp0) REVERT: B 51 MET cc_start: 0.7579 (ttt) cc_final: 0.7265 (ttt) REVERT: B 77 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7356 (m-30) REVERT: C 8 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7882 (mttm) REVERT: C 9 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8597 (mtpp) REVERT: C 97 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8364 (mmt90) REVERT: C 245 ARG cc_start: 0.8492 (ttm170) cc_final: 0.8063 (ttm170) REVERT: C 270 THR cc_start: 0.1870 (OUTLIER) cc_final: 0.1597 (p) REVERT: C 299 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6497 (ptmt) REVERT: C 315 MET cc_start: 0.8421 (tpp) cc_final: 0.7667 (tmm) REVERT: C 484 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7192 (mt) REVERT: C 626 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7153 (mm-30) REVERT: C 761 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.8869 (mp10) REVERT: C 915 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8489 (t70) REVERT: C 919 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8496 (mtp85) REVERT: C 954 LYS cc_start: 0.8643 (tmmt) cc_final: 0.8434 (tttt) REVERT: C 1057 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9057 (ttpt) REVERT: C 1069 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8714 (mtp180) REVERT: C 1134 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.7158 (mm-40) REVERT: C 1321 GLU cc_start: 0.8055 (tp30) cc_final: 0.7730 (tp30) REVERT: D 44 ILE cc_start: 0.8375 (OUTLIER) cc_final: 0.8102 (mt) REVERT: D 172 PHE cc_start: 0.7185 (OUTLIER) cc_final: 0.5090 (m-80) REVERT: D 368 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8741 (tp) REVERT: D 422 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8922 (mp) REVERT: D 619 ILE cc_start: 0.9226 (tt) cc_final: 0.8954 (tp) REVERT: D 654 ILE cc_start: 0.9415 (OUTLIER) cc_final: 0.8945 (mp) REVERT: D 678 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.6171 (tmm160) REVERT: D 781 LYS cc_start: 0.8812 (tptt) cc_final: 0.8166 (mttt) REVERT: D 788 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8386 (tp) REVERT: D 827 GLU cc_start: 0.6430 (tp30) cc_final: 0.6159 (tp30) REVERT: D 832 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7328 (mmmt) REVERT: D 849 LEU cc_start: 0.6791 (OUTLIER) cc_final: 0.6112 (pp) REVERT: D 875 ASN cc_start: 0.7572 (OUTLIER) cc_final: 0.7299 (t0) REVERT: D 929 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7327 (pm20) REVERT: D 999 TYR cc_start: 0.0811 (OUTLIER) cc_final: 0.0078 (m-80) REVERT: D 1023 HIS cc_start: 0.3169 (OUTLIER) cc_final: 0.2098 (p-80) REVERT: D 1140 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8652 (tpp80) REVERT: D 1325 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8298 (p90) REVERT: E 56 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: F 131 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6836 (pt0) REVERT: F 266 PHE cc_start: 0.7108 (OUTLIER) cc_final: 0.6435 (t80) REVERT: F 316 PHE cc_start: 0.2606 (OUTLIER) cc_final: 0.1580 (m-80) REVERT: F 322 MET cc_start: 0.2572 (tpt) cc_final: 0.2048 (mmt) REVERT: F 507 MET cc_start: 0.8930 (ttp) cc_final: 0.8698 (ttm) REVERT: F 579 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7436 (tp40) REVERT: F 589 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7097 (mp10) outliers start: 329 outliers final: 265 residues processed: 722 average time/residue: 0.1982 time to fit residues: 235.5367 Evaluate side-chains 738 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 302 poor density : 436 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 38 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 92 TYR Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 12 THR 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 52 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 254 LEU 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 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 111 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 19 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 58 GLU 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 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 178 SER 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 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 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 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 232 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS 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 366 ILE Chi-restraints excluded: chain C residue 384 LEU 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 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 492 MET 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 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 724 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 761 GLN Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 843 THR Chi-restraints excluded: chain C residue 845 LEU 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 995 ASP Chi-restraints excluded: chain C residue 1019 ASP Chi-restraints excluded: chain C residue 1029 LEU 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 1060 ILE Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE 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 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1167 GLU Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1192 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 1295 SER Chi-restraints excluded: chain C residue 1308 ILE Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain C residue 1339 LEU 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 44 ILE Chi-restraints excluded: chain D residue 46 TYR 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 146 VAL Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 229 GLN 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 347 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 354 VAL 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 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 453 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 474 LEU 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 531 LYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 564 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 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 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 743 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 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 857 LEU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 875 ASN 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 925 GLU Chi-restraints excluded: chain D residue 929 GLN 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 1023 HIS Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1041 ILE Chi-restraints excluded: chain D residue 1045 THR Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1140 ARG Chi-restraints excluded: chain D residue 1167 LYS 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 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 1321 SER 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 E residue 4 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 109 GLU 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 229 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 316 PHE Chi-restraints excluded: chain F residue 320 ILE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 365 MET 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 412 LEU Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 474 MET Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 525 ASP Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 558 VAL Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 587 ILE Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 598 LEU Chi-restraints excluded: chain F residue 604 SER Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: [410, 101, 59, 288, 178, 6, 147, 348, 196, 194, 159] chunk 410 optimal weight: 10.0000 chunk 101 optimal weight: 0.0980 chunk 59 optimal weight: 6.9990 chunk 288 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 6 optimal weight: 0.0370 chunk 147 optimal weight: 4.9990 chunk 348 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 194 optimal weight: 0.2980 chunk 159 optimal weight: 0.0030 overall best weight: 0.2870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 24 GLN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 273 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 600 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.151908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.116876 restraints weight = 58018.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.115977 restraints weight = 71412.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116531 restraints weight = 78768.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117473 restraints weight = 44573.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.118445 restraints weight = 36934.991| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35836 Z= 0.090 Angle : 0.487 11.313 48882 Z= 0.265 Chirality : 0.039 0.169 5556 Planarity : 0.003 0.041 5994 Dihedral : 18.045 175.863 6088 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 37.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 6.55 % Allowed : 23.64 % Favored : 69.81 % 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: -3.54 (0.12), residues: 4130 helix: -1.70 (0.13), residues: 1540 sheet: -2.78 (0.24), residues: 391 loop : -2.81 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 274 TYR 0.018 0.001 TYR C1018 PHE 0.022 0.001 PHE C 545 TRP 0.012 0.001 TRP D 33 HIS 0.009 0.001 HIS I 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00185 / 0.09 (35829) covalent geometry : angle 0.48366 / 0.26 (48876) hydrogen bonds : bond 0.04478 / 5.17 ( 948) hydrogen bonds : angle 5.18085 / 6.67 ( 2552) metal coordination : bond 0.00845 / 0.46 ( 7) metal coordination : angle 5.51002 / 10.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 472 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 56 ASN cc_start: 0.7270 (p0) cc_final: 0.6340 (p0) REVERT: I 57 GLN cc_start: 0.5996 (mt0) cc_final: 0.5373 (tm-30) REVERT: I 85 HIS cc_start: 0.6775 (m-70) cc_final: 0.5876 (m-70) REVERT: I 89 MET cc_start: 0.8093 (mmm) cc_final: 0.7627 (mmm) REVERT: I 112 THR cc_start: 0.7649 (m) cc_final: 0.7401 (t) REVERT: J 81 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7618 (mt-10) REVERT: J 103 MET cc_start: 0.7690 (mtt) cc_final: 0.7461 (mtt) REVERT: J 115 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.6825 (t0) REVERT: J 142 VAL cc_start: 0.8099 (OUTLIER) cc_final: 0.7892 (t) REVERT: J 184 LYS cc_start: 0.7833 (mtpt) cc_final: 0.6724 (tptm) REVERT: J 192 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6636 (mm-30) REVERT: J 195 SER cc_start: 0.8926 (p) cc_final: 0.8607 (t) REVERT: A 25 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8672 (ttmm) REVERT: B 51 MET cc_start: 0.7486 (ttt) cc_final: 0.7168 (ttt) REVERT: B 77 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7232 (m-30) REVERT: B 233 ASP cc_start: 0.6960 (OUTLIER) cc_final: 0.6523 (m-30) REVERT: C 8 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7851 (mttm) REVERT: C 9 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8592 (mtpp) REVERT: C 245 ARG cc_start: 0.8313 (ttm170) cc_final: 0.7934 (ttm170) REVERT: C 270 THR cc_start: 0.1843 (OUTLIER) cc_final: 0.1498 (p) REVERT: C 299 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6543 (ptmt) REVERT: C 315 MET cc_start: 0.8332 (tpp) cc_final: 0.7609 (tmm) REVERT: C 484 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7199 (mt) REVERT: C 626 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7121 (mm-30) REVERT: C 754 THR cc_start: 0.9076 (OUTLIER) cc_final: 0.8812 (p) REVERT: C 761 GLN cc_start: 0.9223 (OUTLIER) cc_final: 0.8875 (mp10) REVERT: C 919 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8387 (mtp85) REVERT: C 1033 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7059 (tmt170) REVERT: C 1057 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9000 (ttpt) REVERT: C 1134 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7273 (mm-40) REVERT: D 172 PHE cc_start: 0.7136 (OUTLIER) cc_final: 0.4973 (m-80) REVERT: D 368 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8624 (tp) REVERT: D 573 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.9003 (p) REVERT: D 619 ILE cc_start: 0.9242 (tt) cc_final: 0.9010 (tp) REVERT: D 654 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.8884 (mp) REVERT: D 678 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6009 (tmm160) REVERT: D 781 LYS cc_start: 0.8713 (tptt) cc_final: 0.8096 (mttt) REVERT: D 788 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8309 (tp) REVERT: D 849 LEU cc_start: 0.7037 (OUTLIER) cc_final: 0.6491 (pp) REVERT: D 867 GLN cc_start: 0.8537 (mm-40) cc_final: 0.7945 (tp40) REVERT: D 925 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8019 (tp30) REVERT: D 999 TYR cc_start: 0.1090 (OUTLIER) cc_final: 0.0399 (m-80) REVERT: D 1023 HIS cc_start: 0.3542 (OUTLIER) cc_final: 0.2240 (p-80) REVERT: D 1325 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8114 (p90) REVERT: E 56 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: E 61 ASN cc_start: 0.8401 (t0) cc_final: 0.8039 (t0) REVERT: F 266 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.6442 (t80) REVERT: F 316 PHE cc_start: 0.2833 (OUTLIER) cc_final: 0.2406 (m-80) REVERT: F 322 MET cc_start: 0.2183 (tpt) cc_final: 0.1789 (mmt) REVERT: F 507 MET cc_start: 0.8810 (ttp) cc_final: 0.8590 (ttm) REVERT: F 561 MET cc_start: 0.8439 (tpp) cc_final: 0.7514 (tpp) REVERT: F 579 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7254 (tp40) REVERT: F 589 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7075 (mp10) outliers start: 233 outliers final: 167 residues processed: 666 average time/residue: 0.2020 time to fit residues: 221.9363 Evaluate side-chains 646 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 445 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 53 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 207 MET Chi-restraints excluded: chain J residue 12 THR 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 52 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 115 ASN Chi-restraints excluded: chain J residue 142 VAL Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU 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 129 VAL Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 58 GLU 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 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 178 SER 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 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 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 311 CYS Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 366 ILE 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 443 ASP 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 524 ILE Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 699 LEU 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 843 THR Chi-restraints excluded: chain C residue 845 LEU 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 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 935 THR Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1029 LEU 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 1060 ILE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1134 GLN Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1192 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 1295 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 106 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 117 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 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 357 VAL Chi-restraints excluded: chain D residue 368 LEU 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 527 LEU 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 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 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 925 GLU Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1167 LYS 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 1307 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 41 GLU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 250 LEU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 316 PHE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 554 ARG Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 598 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: [204, 396, 238, 354, 397, 201, 45, 259, 232, 368, 87] chunk 204 optimal weight: 0.9990 chunk 396 optimal weight: 7.9990 chunk 238 optimal weight: 0.7980 chunk 354 optimal weight: 10.0000 chunk 397 optimal weight: 9.9990 chunk 201 optimal weight: 0.0570 chunk 45 optimal weight: 20.0000 chunk 259 optimal weight: 5.9990 chunk 232 optimal weight: 2.9990 chunk 368 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 24 GLN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 HIS ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 HIS ** 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 = 0.3819 r_free = 0.3819 target = 0.150816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116309 restraints weight = 57961.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.115160 restraints weight = 76271.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116021 restraints weight = 77725.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116670 restraints weight = 45139.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117908 restraints weight = 38340.195| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35836 Z= 0.125 Angle : 0.490 8.012 48882 Z= 0.264 Chirality : 0.039 0.163 5556 Planarity : 0.003 0.039 5994 Dihedral : 17.897 176.749 6049 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 37.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 6.27 % Allowed : 23.95 % Favored : 69.78 % 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: -3.39 (0.12), residues: 4130 helix: -1.53 (0.13), residues: 1540 sheet: -2.65 (0.25), residues: 389 loop : -2.76 (0.12), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 88 TYR 0.014 0.001 TYR C1018 PHE 0.023 0.001 PHE C 545 TRP 0.014 0.001 TRP F 433 HIS 0.004 0.001 HIS I 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (35829) covalent geometry : angle 0.48735 / 0.26 (48876) hydrogen bonds : bond 0.04355 / 5.03 ( 948) hydrogen bonds : angle 5.06804 / 6.53 ( 2552) metal coordination : bond 0.00928 / 0.58 ( 7) metal coordination : angle 4.82702 / 8.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 452 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 57 GLN cc_start: 0.5959 (mt0) cc_final: 0.5388 (tm-30) REVERT: I 85 HIS cc_start: 0.7292 (m-70) cc_final: 0.7040 (m-70) REVERT: I 89 MET cc_start: 0.8029 (mmm) cc_final: 0.7584 (mmm) REVERT: I 112 THR cc_start: 0.7603 (m) cc_final: 0.7395 (t) REVERT: J 81 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: J 103 MET cc_start: 0.7749 (mtt) cc_final: 0.7519 (mtt) REVERT: J 184 LYS cc_start: 0.7885 (mtpt) cc_final: 0.6785 (tptm) REVERT: J 192 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6636 (mm-30) REVERT: J 195 SER cc_start: 0.8926 (p) cc_final: 0.8604 (t) REVERT: A 25 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8674 (ttmm) REVERT: B 51 MET cc_start: 0.7497 (ttt) cc_final: 0.7181 (ttt) REVERT: B 233 ASP cc_start: 0.7004 (OUTLIER) cc_final: 0.6554 (m-30) REVERT: C 8 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7903 (mttm) REVERT: C 245 ARG cc_start: 0.8365 (ttm170) cc_final: 0.7990 (ttm170) REVERT: C 270 THR cc_start: 0.1746 (OUTLIER) cc_final: 0.1438 (p) REVERT: C 290 GLU cc_start: 0.5608 (pm20) cc_final: 0.5098 (mm-30) REVERT: C 299 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6381 (ptmt) REVERT: C 315 MET cc_start: 0.8363 (tpp) cc_final: 0.7582 (tmm) REVERT: C 484 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7221 (mt) REVERT: C 626 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7199 (mm-30) REVERT: C 754 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8841 (p) REVERT: C 761 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8896 (mp10) REVERT: C 919 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8393 (mtp85) REVERT: C 1033 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7095 (tmt170) REVERT: C 1057 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8960 (ttpt) REVERT: C 1134 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7382 (mm-40) REVERT: C 1151 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8326 (tp) REVERT: C 1230 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8066 (ttp) REVERT: C 1321 GLU cc_start: 0.8048 (tp30) cc_final: 0.7743 (tp30) REVERT: D 172 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.4942 (m-80) REVERT: D 619 ILE cc_start: 0.9235 (tt) cc_final: 0.8939 (tp) REVERT: D 654 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.8900 (mp) REVERT: D 678 ARG cc_start: 0.7487 (OUTLIER) cc_final: 0.6017 (tmm160) REVERT: D 781 LYS cc_start: 0.8725 (tptt) cc_final: 0.8081 (mttt) REVERT: D 788 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8314 (tp) REVERT: D 849 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6410 (pp) REVERT: D 867 GLN cc_start: 0.8532 (mm-40) cc_final: 0.7975 (tp40) REVERT: D 999 TYR cc_start: 0.1174 (OUTLIER) cc_final: 0.0466 (m-80) REVERT: D 1023 HIS cc_start: 0.3566 (OUTLIER) cc_final: 0.2293 (p-80) REVERT: D 1325 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.8265 (p90) REVERT: E 56 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: E 61 ASN cc_start: 0.8433 (t0) cc_final: 0.8086 (t0) REVERT: F 266 PHE cc_start: 0.6808 (OUTLIER) cc_final: 0.6363 (t80) REVERT: F 316 PHE cc_start: 0.2877 (OUTLIER) cc_final: 0.2433 (m-80) REVERT: F 322 MET cc_start: 0.2124 (tpt) cc_final: 0.1814 (mmt) REVERT: F 561 MET cc_start: 0.8457 (tpp) cc_final: 0.8227 (tpp) REVERT: F 589 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7079 (mp10) outliers start: 223 outliers final: 175 residues processed: 628 average time/residue: 0.1991 time to fit residues: 205.7965 Evaluate side-chains 647 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 444 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 38 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE Chi-restraints excluded: chain I residue 207 MET 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 52 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 207 MET Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU 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 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 58 GLU 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 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 178 SER 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 8 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 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS 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 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 492 MET Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 749 ASP 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 865 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 905 ILE 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 979 LEU Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1029 LEU 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 1077 SER Chi-restraints excluded: chain C residue 1082 ILE 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 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1192 GLU Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1339 LEU 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 106 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 172 PHE Chi-restraints excluded: chain D residue 210 SER 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 347 VAL Chi-restraints excluded: chain D residue 357 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 527 LEU Chi-restraints excluded: chain D residue 564 VAL 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 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 769 VAL Chi-restraints excluded: chain D residue 788 LEU Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 986 ASP Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1023 HIS Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1041 ILE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1167 LYS 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 1279 GLN Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 109 GLU 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 250 LEU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 316 PHE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 429 THR Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 609 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: [157, 175, 225, 30, 372, 326, 186, 321, 337, 1, 33] chunk 157 optimal weight: 0.0670 chunk 175 optimal weight: 4.9990 chunk 225 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 372 optimal weight: 0.7980 chunk 326 optimal weight: 30.0000 chunk 186 optimal weight: 8.9990 chunk 321 optimal weight: 2.9990 chunk 337 optimal weight: 0.3980 chunk 1 optimal weight: 50.0000 chunk 33 optimal weight: 9.9990 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 24 GLN I 45 ASN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN B 147 GLN ** C 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 677 ASN ** C1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 365 GLN D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.152695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114459 restraints weight = 58001.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.113715 restraints weight = 50866.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.114107 restraints weight = 56108.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.114698 restraints weight = 35476.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115962 restraints weight = 30323.757| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35836 Z= 0.091 Angle : 0.461 8.804 48882 Z= 0.250 Chirality : 0.039 0.312 5556 Planarity : 0.003 0.038 5994 Dihedral : 17.645 176.862 6014 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 36.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.95 % Allowed : 25.47 % Favored : 69.58 % 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: -3.04 (0.13), residues: 4130 helix: -1.20 (0.13), residues: 1551 sheet: -2.52 (0.26), residues: 351 loop : -2.60 (0.12), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 407 TYR 0.013 0.001 TYR F 148 PHE 0.020 0.001 PHE C 545 TRP 0.013 0.001 TRP J 166 HIS 0.009 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00193 / 0.09 (35829) covalent geometry : angle 0.45898 / 0.25 (48876) hydrogen bonds : bond 0.03864 / 4.49 ( 948) hydrogen bonds : angle 4.74612 / 6.11 ( 2552) metal coordination : bond 0.00736 / 0.43 ( 7) metal coordination : angle 3.87947 / 7.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 476 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 57 GLN cc_start: 0.6194 (mt0) cc_final: 0.5632 (tm-30) REVERT: I 89 MET cc_start: 0.8154 (mmm) cc_final: 0.7629 (mmm) REVERT: I 110 TRP cc_start: 0.7423 (m-10) cc_final: 0.6582 (m-10) REVERT: I 112 THR cc_start: 0.7616 (m) cc_final: 0.7415 (t) REVERT: J 81 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: J 103 MET cc_start: 0.7749 (mtt) cc_final: 0.7496 (mtt) REVERT: J 160 TYR cc_start: 0.8057 (m-80) cc_final: 0.7760 (m-80) REVERT: J 184 LYS cc_start: 0.7705 (mtpt) cc_final: 0.6557 (tptm) REVERT: J 192 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6647 (mm-30) REVERT: J 195 SER cc_start: 0.8916 (p) cc_final: 0.8571 (t) REVERT: A 25 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8648 (ttmm) REVERT: B 27 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8129 (m) REVERT: B 51 MET cc_start: 0.7583 (ttt) cc_final: 0.7274 (ttt) REVERT: B 233 ASP cc_start: 0.6937 (OUTLIER) cc_final: 0.6450 (m-30) REVERT: C 8 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7953 (mttm) REVERT: C 245 ARG cc_start: 0.8417 (ttm170) cc_final: 0.8024 (ttm170) REVERT: C 270 THR cc_start: 0.1920 (OUTLIER) cc_final: 0.1649 (p) REVERT: C 290 GLU cc_start: 0.5533 (pm20) cc_final: 0.5134 (mm-30) REVERT: C 299 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6450 (ptmt) REVERT: C 484 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7149 (mt) REVERT: C 626 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7142 (mm-30) REVERT: C 754 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8792 (p) REVERT: C 761 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8877 (mp10) REVERT: C 919 ARG cc_start: 0.9064 (OUTLIER) cc_final: 0.8428 (mtp85) REVERT: C 957 LYS cc_start: 0.8382 (pttt) cc_final: 0.8026 (pttp) REVERT: C 1033 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.7087 (tmt170) REVERT: C 1057 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8932 (ttpt) REVERT: C 1230 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8150 (ttp) REVERT: C 1321 GLU cc_start: 0.8057 (tp30) cc_final: 0.7737 (tp30) REVERT: D 172 PHE cc_start: 0.7117 (OUTLIER) cc_final: 0.4900 (m-80) REVERT: D 619 ILE cc_start: 0.9241 (tt) cc_final: 0.9030 (tp) REVERT: D 654 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.8864 (mp) REVERT: D 678 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.5806 (tmm160) REVERT: D 781 LYS cc_start: 0.8853 (tptt) cc_final: 0.8011 (ttpt) REVERT: D 849 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6461 (pp) REVERT: D 867 GLN cc_start: 0.8562 (mm-40) cc_final: 0.7917 (tp40) REVERT: D 999 TYR cc_start: 0.0742 (OUTLIER) cc_final: 0.0437 (m-80) REVERT: D 1189 MET cc_start: 0.6161 (ppp) cc_final: 0.5689 (ppp) REVERT: D 1325 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8215 (p90) REVERT: E 11 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6771 (mt-10) REVERT: E 56 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: E 61 ASN cc_start: 0.8461 (t0) cc_final: 0.8152 (t0) REVERT: F 266 PHE cc_start: 0.6827 (OUTLIER) cc_final: 0.6308 (t80) REVERT: F 316 PHE cc_start: 0.2716 (OUTLIER) cc_final: 0.1702 (m-80) REVERT: F 322 MET cc_start: 0.1098 (tpt) cc_final: 0.0830 (mmt) REVERT: F 589 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7171 (mp10) outliers start: 176 outliers final: 138 residues processed: 614 average time/residue: 0.1990 time to fit residues: 201.6602 Evaluate side-chains 618 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 455 time to evaluate : 0.961 ------------------------------------------------------------------------------- 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 53 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE 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 52 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 96 ASP Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR 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 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 178 SER 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 8 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 311 CYS 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 443 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 699 LEU 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 857 VAL 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 919 ARG Chi-restraints excluded: chain C residue 924 VAL Chi-restraints excluded: chain C residue 948 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 995 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 1060 ILE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1295 SER 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 105 ILE Chi-restraints excluded: chain D residue 106 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 172 PHE Chi-restraints excluded: chain D residue 244 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 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 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 664 ILE Chi-restraints excluded: chain D residue 678 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 769 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1167 LYS Chi-restraints excluded: chain D residue 1234 VAL Chi-restraints excluded: chain D residue 1235 ASN Chi-restraints excluded: chain D residue 1250 ASP 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 E residue 46 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 134 VAL Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 316 PHE Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 589 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: [215, 231, 175, 205, 243, 406, 12, 283, 372, 200, 34] chunk 215 optimal weight: 0.0870 chunk 231 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 243 optimal weight: 9.9990 chunk 406 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 283 optimal weight: 7.9990 chunk 372 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 24 GLN ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN B 132 HIS ** C 165 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 677 ASN C1336 ASN D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.151375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.113336 restraints weight = 57804.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.112374 restraints weight = 49189.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112756 restraints weight = 56414.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.113425 restraints weight = 35604.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114128 restraints weight = 30294.836| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35836 Z= 0.129 Angle : 0.479 6.871 48882 Z= 0.257 Chirality : 0.039 0.148 5556 Planarity : 0.003 0.039 5994 Dihedral : 17.593 177.349 5982 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 37.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 5.45 % Allowed : 25.25 % Favored : 69.30 % 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: -2.97 (0.13), residues: 4130 helix: -1.14 (0.13), residues: 1555 sheet: -2.48 (0.26), residues: 352 loop : -2.57 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1373 TYR 0.012 0.001 TYR F 148 PHE 0.023 0.001 PHE C 545 TRP 0.013 0.001 TRP F 433 HIS 0.007 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (35829) covalent geometry : angle 0.47758 / 0.26 (48876) hydrogen bonds : bond 0.03948 / 4.57 ( 948) hydrogen bonds : angle 4.76682 / 6.13 ( 2552) metal coordination : bond 0.00857 / 0.57 ( 7) metal coordination : angle 3.82681 / 7.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 456 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 19 ASP cc_start: 0.7573 (t0) cc_final: 0.7329 (m-30) REVERT: I 57 GLN cc_start: 0.6213 (mt0) cc_final: 0.5635 (tm-30) REVERT: I 89 MET cc_start: 0.8192 (mmm) cc_final: 0.7648 (mmm) REVERT: I 109 ASP cc_start: 0.7767 (t0) cc_final: 0.7251 (t70) REVERT: I 110 TRP cc_start: 0.7424 (m-10) cc_final: 0.6511 (m-10) REVERT: I 112 THR cc_start: 0.7637 (m) cc_final: 0.7411 (t) REVERT: J 81 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7732 (mt-10) REVERT: J 103 MET cc_start: 0.7784 (mtt) cc_final: 0.7540 (mtt) REVERT: J 184 LYS cc_start: 0.7744 (mtpt) cc_final: 0.6606 (tptm) REVERT: J 192 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.6671 (mm-30) REVERT: J 195 SER cc_start: 0.8919 (p) cc_final: 0.8594 (t) REVERT: A 25 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8450 (mttp) REVERT: B 27 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8157 (m) REVERT: B 51 MET cc_start: 0.7583 (ttt) cc_final: 0.7288 (ttt) REVERT: B 233 ASP cc_start: 0.7010 (OUTLIER) cc_final: 0.6495 (m-30) REVERT: C 8 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8043 (mttm) REVERT: C 163 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6101 (pttt) REVERT: C 245 ARG cc_start: 0.8436 (ttm170) cc_final: 0.8021 (ttm170) REVERT: C 270 THR cc_start: 0.1644 (OUTLIER) cc_final: 0.1356 (p) REVERT: C 290 GLU cc_start: 0.5538 (pm20) cc_final: 0.5176 (mm-30) REVERT: C 299 LYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6359 (ptmt) REVERT: C 315 MET cc_start: 0.8385 (tpp) cc_final: 0.7601 (tmm) REVERT: C 484 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7178 (mt) REVERT: C 626 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: C 754 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8817 (p) REVERT: C 761 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8920 (mp10) REVERT: C 915 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8463 (t70) REVERT: C 919 ARG cc_start: 0.9093 (OUTLIER) cc_final: 0.8493 (mtp85) REVERT: C 1033 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7190 (tmt170) REVERT: C 1057 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9019 (ttpt) REVERT: C 1230 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8194 (ttp) REVERT: C 1321 GLU cc_start: 0.8099 (tp30) cc_final: 0.7794 (tp30) REVERT: D 172 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.4899 (m-80) REVERT: D 619 ILE cc_start: 0.9243 (tt) cc_final: 0.9036 (tp) REVERT: D 654 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8872 (mp) REVERT: D 678 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.5901 (tmm160) REVERT: D 781 LYS cc_start: 0.8859 (tptt) cc_final: 0.8044 (ttpt) REVERT: D 849 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6320 (pp) REVERT: D 867 GLN cc_start: 0.8569 (mm-40) cc_final: 0.7966 (tp40) REVERT: D 999 TYR cc_start: 0.0951 (OUTLIER) cc_final: 0.0495 (m-80) REVERT: D 1325 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.8294 (p90) REVERT: E 56 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: E 61 ASN cc_start: 0.8491 (t0) cc_final: 0.8190 (t0) REVERT: F 266 PHE cc_start: 0.6755 (OUTLIER) cc_final: 0.6290 (t80) REVERT: F 316 PHE cc_start: 0.2774 (OUTLIER) cc_final: 0.1717 (m-80) REVERT: F 322 MET cc_start: 0.1079 (tpt) cc_final: 0.0827 (mmt) REVERT: F 507 MET cc_start: 0.8708 (ttp) cc_final: 0.8508 (ttm) REVERT: F 579 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.7345 (tp40) REVERT: F 589 GLN cc_start: 0.8038 (OUTLIER) cc_final: 0.7192 (mp10) outliers start: 194 outliers final: 156 residues processed: 610 average time/residue: 0.1979 time to fit residues: 198.7619 Evaluate side-chains 635 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 451 time to evaluate : 1.201 ------------------------------------------------------------------------------- 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 38 ILE Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE 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 52 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU 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 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR 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 98 VAL 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 178 SER 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 8 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 311 CYS 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 443 ASP Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 472 GLU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 672 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 754 THR Chi-restraints excluded: chain C residue 761 GLN Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 857 VAL 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 948 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 995 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 1060 ILE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1336 ASN Chi-restraints excluded: chain C residue 1339 LEU 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 105 ILE Chi-restraints excluded: chain D residue 106 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 172 PHE Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 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 578 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 678 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 769 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1167 LYS 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 1279 GLN Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 109 GLU 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 266 PHE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 316 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 589 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: [190, 146, 388, 148, 227, 361, 329, 61, 416, 323, 164] chunk 190 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 388 optimal weight: 20.0000 chunk 148 optimal weight: 4.9990 chunk 227 optimal weight: 4.9990 chunk 361 optimal weight: 1.9990 chunk 329 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 416 optimal weight: 0.4980 chunk 323 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 165 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 677 ASN D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 HIS ** 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 = 0.3834 r_free = 0.3834 target = 0.151452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.113350 restraints weight = 58385.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112014 restraints weight = 52070.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112769 restraints weight = 55087.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.113186 restraints weight = 37267.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114240 restraints weight = 31402.453| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 35836 Z= 0.129 Angle : 0.592 59.121 48882 Z= 0.335 Chirality : 0.039 0.362 5556 Planarity : 0.003 0.041 5994 Dihedral : 17.593 177.331 5981 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 38.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 5.40 % Allowed : 25.25 % Favored : 69.36 % Cbeta Deviations : 0.03 % 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: -2.96 (0.13), residues: 4130 helix: -1.12 (0.13), residues: 1555 sheet: -2.47 (0.27), residues: 352 loop : -2.57 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1373 TYR 0.012 0.001 TYR C1018 PHE 0.023 0.001 PHE C 545 TRP 0.012 0.001 TRP F 433 HIS 0.008 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (35829) covalent geometry : angle 0.59088 / 0.34 (48876) hydrogen bonds : bond 0.03946 / 4.56 ( 948) hydrogen bonds : angle 4.76120 / 6.12 ( 2552) metal coordination : bond 0.00807 / 0.51 ( 7) metal coordination : angle 3.81846 / 7.07 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8260 Ramachandran restraints generated. 4130 Oldfield, 0 Emsley, 4130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 453 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 19 ASP cc_start: 0.7613 (t0) cc_final: 0.7364 (m-30) REVERT: I 57 GLN cc_start: 0.6257 (mt0) cc_final: 0.5665 (tm-30) REVERT: I 89 MET cc_start: 0.8206 (mmm) cc_final: 0.7652 (mmm) REVERT: I 109 ASP cc_start: 0.7782 (t0) cc_final: 0.7251 (t70) REVERT: I 110 TRP cc_start: 0.7418 (m-10) cc_final: 0.6504 (m-10) REVERT: I 112 THR cc_start: 0.7641 (m) cc_final: 0.7417 (t) REVERT: J 81 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7729 (mt-10) REVERT: J 103 MET cc_start: 0.7779 (mtt) cc_final: 0.7533 (mtt) REVERT: J 184 LYS cc_start: 0.7716 (mtpt) cc_final: 0.6575 (tptm) REVERT: J 192 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6686 (mm-30) REVERT: J 195 SER cc_start: 0.8930 (p) cc_final: 0.8604 (t) REVERT: A 25 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8444 (mttp) REVERT: B 27 THR cc_start: 0.8503 (OUTLIER) cc_final: 0.8155 (m) REVERT: B 51 MET cc_start: 0.7578 (ttt) cc_final: 0.7276 (ttt) REVERT: B 233 ASP cc_start: 0.7012 (OUTLIER) cc_final: 0.6494 (m-30) REVERT: C 8 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8047 (mttm) REVERT: C 163 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6104 (pttt) REVERT: C 245 ARG cc_start: 0.8444 (ttm170) cc_final: 0.8018 (ttm170) REVERT: C 270 THR cc_start: 0.1671 (OUTLIER) cc_final: 0.1386 (p) REVERT: C 290 GLU cc_start: 0.5538 (pm20) cc_final: 0.5182 (mm-30) REVERT: C 299 LYS cc_start: 0.6885 (OUTLIER) cc_final: 0.6358 (ptmt) REVERT: C 315 MET cc_start: 0.8441 (tpp) cc_final: 0.7620 (tmm) REVERT: C 484 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7173 (mt) REVERT: C 626 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7288 (mm-30) REVERT: C 754 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8810 (p) REVERT: C 761 GLN cc_start: 0.9279 (OUTLIER) cc_final: 0.8918 (mp10) REVERT: C 915 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8463 (t70) REVERT: C 919 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8489 (mtp85) REVERT: C 1033 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.7186 (tmt170) REVERT: C 1057 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9009 (ttpt) REVERT: C 1230 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8178 (ttp) REVERT: C 1321 GLU cc_start: 0.8086 (tp30) cc_final: 0.7790 (tp30) REVERT: D 172 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.4904 (m-80) REVERT: D 619 ILE cc_start: 0.9250 (tt) cc_final: 0.9050 (tp) REVERT: D 654 ILE cc_start: 0.9290 (OUTLIER) cc_final: 0.8867 (mp) REVERT: D 678 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.5898 (tmm160) REVERT: D 781 LYS cc_start: 0.8850 (tptt) cc_final: 0.8039 (ttpt) REVERT: D 849 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6317 (pp) REVERT: D 867 GLN cc_start: 0.8608 (mm-40) cc_final: 0.7959 (tp40) REVERT: D 999 TYR cc_start: 0.0924 (OUTLIER) cc_final: 0.0476 (m-80) REVERT: D 1189 MET cc_start: 0.6188 (ppp) cc_final: 0.5746 (ppp) REVERT: D 1325 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8293 (p90) REVERT: E 56 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.6938 (mp0) REVERT: E 61 ASN cc_start: 0.8498 (t0) cc_final: 0.8192 (t0) REVERT: F 266 PHE cc_start: 0.6787 (OUTLIER) cc_final: 0.6293 (t80) REVERT: F 316 PHE cc_start: 0.2753 (OUTLIER) cc_final: 0.1711 (m-80) REVERT: F 322 MET cc_start: 0.1070 (tpt) cc_final: 0.0818 (mmt) REVERT: F 561 MET cc_start: 0.8609 (tpp) cc_final: 0.8327 (tpp) REVERT: F 579 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7362 (tp40) REVERT: F 589 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7189 (mp10) outliers start: 192 outliers final: 162 residues processed: 605 average time/residue: 0.2058 time to fit residues: 205.1162 Evaluate side-chains 643 residues out of total 3578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 453 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 53 LEU Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 75 ILE 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 52 ASP Chi-restraints excluded: chain J residue 66 GLU Chi-restraints excluded: chain J residue 81 GLU Chi-restraints excluded: chain J residue 98 GLU Chi-restraints excluded: chain J residue 183 LEU Chi-restraints excluded: chain J residue 192 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 254 LEU Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 13 LEU 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 168 ILE Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 200 LYS Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 27 THR 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 98 VAL 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 178 SER 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 8 LYS Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 161 LYS Chi-restraints excluded: chain C residue 163 LYS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 287 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 311 CYS 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 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 484 LEU Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 622 ASN Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 672 GLU Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 699 LEU 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 857 VAL 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 948 ILE Chi-restraints excluded: chain C residue 979 LEU Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1018 TYR 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 1060 ILE Chi-restraints excluded: chain C residue 1077 SER Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1158 LYS Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1292 THR Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 39 LYS Chi-restraints excluded: chain D residue 44 ILE 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 105 ILE Chi-restraints excluded: chain D residue 106 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 172 PHE Chi-restraints excluded: chain D residue 210 SER Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 306 LEU Chi-restraints excluded: chain D residue 316 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 578 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 654 ILE Chi-restraints excluded: chain D residue 678 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 769 VAL Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 907 HIS Chi-restraints excluded: chain D residue 999 TYR Chi-restraints excluded: chain D residue 1020 TRP Chi-restraints excluded: chain D residue 1034 PHE Chi-restraints excluded: chain D residue 1068 THR Chi-restraints excluded: chain D residue 1082 ASP Chi-restraints excluded: chain D residue 1167 LYS 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 1250 ASP Chi-restraints excluded: chain D residue 1265 THR Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1279 GLN Chi-restraints excluded: chain D residue 1307 LEU Chi-restraints excluded: chain D residue 1325 PHE Chi-restraints excluded: chain D residue 1353 VAL Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 90 GLU Chi-restraints excluded: chain F residue 109 GLU 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 266 PHE Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 301 ASN Chi-restraints excluded: chain F residue 316 PHE Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 341 LEU Chi-restraints excluded: chain F residue 365 MET Chi-restraints excluded: chain F residue 384 LEU Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 452 ILE Chi-restraints excluded: chain F residue 458 GLU Chi-restraints excluded: chain F residue 485 GLU Chi-restraints excluded: chain F residue 551 LEU Chi-restraints excluded: chain F residue 579 GLN Chi-restraints excluded: chain F residue 589 GLN Chi-restraints excluded: chain F residue 611 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 423 random chunks: [413, 303, 88, 330, 119, 57, 137, 70, 151, 282, 342] chunk 413 optimal weight: 0.0770 chunk 303 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 330 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 137 optimal weight: 0.0670 chunk 70 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 282 optimal weight: 3.9990 chunk 342 optimal weight: 1.9990 overall best weight: 0.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 165 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 677 ASN D 865 HIS ** D 875 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 ASN ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 600 HIS ** 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 = 0.3834 r_free = 0.3834 target = 0.151523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113636 restraints weight = 58132.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.112642 restraints weight = 52886.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113069 restraints weight = 57869.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113661 restraints weight = 37644.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.114253 restraints weight = 31745.026| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.133 35836 Z= 0.127 Angle : 0.590 58.181 48882 Z= 0.334 Chirality : 0.039 0.338 5556 Planarity : 0.003 0.040 5994 Dihedral : 17.593 177.332 5981 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 38.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 5.45 % Allowed : 25.19 % Favored : 69.36 % Cbeta Deviations : 0.03 % 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: -2.96 (0.13), residues: 4130 helix: -1.12 (0.13), residues: 1555 sheet: -2.47 (0.27), residues: 352 loop : -2.57 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1373 TYR 0.012 0.001 TYR C1018 PHE 0.022 0.001 PHE C 545 TRP 0.011 0.001 TRP F 433 HIS 0.008 0.001 HIS C 165 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (35829) covalent geometry : angle 0.58873 / 0.33 (48876) hydrogen bonds : bond 0.03945 / 4.56 ( 948) hydrogen bonds : angle 4.76107 / 6.12 ( 2552) metal coordination : bond 0.00805 / 0.51 ( 7) metal coordination : angle 3.81812 / 7.07 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5925.06 seconds wall clock time: 103 minutes 5.74 seconds (6185.74 seconds total)