Starting phenix.real_space_refine on Sat Jun 28 12:50:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b1d_44074/06_2025/9b1d_44074.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b1d_44074/06_2025/9b1d_44074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b1d_44074/06_2025/9b1d_44074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b1d_44074/06_2025/9b1d_44074.map" model { file = "/net/cci-nas-00/data/ceres_data/9b1d_44074/06_2025/9b1d_44074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b1d_44074/06_2025/9b1d_44074.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 70 5.49 5 Mg 8 5.21 5 S 126 5.16 5 C 20729 2.51 5 N 5725 2.21 5 O 6487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 33147 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 5827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5827 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 20, 'TRANS': 689} Chain breaks: 2 Chain: "B" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1152 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 129} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3335 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 25, 'TRANS': 385} Chain breaks: 1 Chain: "D" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1518 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 9, 'TRANS': 177} Chain breaks: 2 Chain: "E" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3281 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 17, 'TRANS': 408} Chain breaks: 1 Chain: "F" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3410 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 10, 'TRANS': 432} Chain: "G" Number of atoms: 3334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3334 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 18, 'TRANS': 415} Chain: "H" Number of atoms: 3393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3393 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 430} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 3351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3351 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 18, 'TRANS': 417} Chain: "J" Number of atoms: 3279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3279 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 10, 'TRANS': 415} Chain breaks: 2 Chain: "Y" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "Z" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11562 SG CYS D 244 69.502 53.828 107.911 1.00103.14 S ATOM 11582 SG CYS D 247 67.720 56.223 110.307 1.00 91.55 S ATOM 11698 SG CYS D 264 70.939 57.208 108.747 1.00 94.81 S ATOM 11723 SG CYS D 268 70.928 54.543 111.441 1.00114.42 S ATOM 11642 SG CYS D 256 76.400 46.895 103.756 1.00114.11 S ATOM 11663 SG CYS D 259 74.873 44.033 103.525 1.00117.74 S Time building chain proxies: 19.56, per 1000 atoms: 0.59 Number of scatterers: 33147 At special positions: 0 Unit cell: (188.49, 162.74, 148.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 126 16.00 P 70 15.00 Mg 8 11.99 O 6487 8.00 N 5725 7.00 C 20729 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.34 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 247 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 264 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 268 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 244 " pdb=" ZN D 302 " pdb="ZN ZN D 302 " - pdb=" SG CYS D 259 " pdb="ZN ZN D 302 " - pdb=" NE2 HIS D 272 " pdb="ZN ZN D 302 " - pdb=" SG CYS D 256 " Number of angles added : 6 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7594 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 31 sheets defined 48.9% alpha, 10.9% beta 25 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 13.02 Creating SS restraints... Processing helix chain 'A' and resid 697 through 713 Processing helix chain 'A' and resid 726 through 742 Processing helix chain 'A' and resid 753 through 768 Processing helix chain 'A' and resid 779 through 788 Processing helix chain 'A' and resid 802 through 814 removed outlier: 6.290A pdb=" N HIS A 811 " --> pdb=" O VAL A 807 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER A 812 " --> pdb=" O GLN A 808 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 813 " --> pdb=" O ASP A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 834 through 842 removed outlier: 4.268A pdb=" N ASN A 842 " --> pdb=" O GLN A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 871 removed outlier: 3.875A pdb=" N LEU A 863 " --> pdb=" O ASN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 904 removed outlier: 4.743A pdb=" N ARG A 896 " --> pdb=" O GLN A 892 " (cutoff:3.500A) Proline residue: A 897 - end of helix Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 933 through 938 removed outlier: 3.780A pdb=" N VAL A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 970 removed outlier: 4.318A pdb=" N THR A 970 " --> pdb=" O SER A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 996 through 999 Processing helix chain 'A' and resid 1015 through 1017 No H-bonds generated for 'chain 'A' and resid 1015 through 1017' Processing helix chain 'A' and resid 1018 through 1036 removed outlier: 3.828A pdb=" N LYS A1031 " --> pdb=" O LYS A1027 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASN A1032 " --> pdb=" O LEU A1028 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A1035 " --> pdb=" O LYS A1031 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASN A1036 " --> pdb=" O ASN A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1054 removed outlier: 4.055A pdb=" N ASP A1053 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1055 through 1065 Processing helix chain 'A' and resid 1067 through 1090 Processing helix chain 'A' and resid 1099 through 1131 Processing helix chain 'A' and resid 1137 through 1146 Processing helix chain 'A' and resid 1158 through 1163 Processing helix chain 'A' and resid 1165 through 1173 Processing helix chain 'A' and resid 1173 through 1181 Processing helix chain 'A' and resid 1190 through 1196 removed outlier: 4.250A pdb=" N LYS A1194 " --> pdb=" O LEU A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1220 Processing helix chain 'A' and resid 1224 through 1233 removed outlier: 3.506A pdb=" N ILE A1233 " --> pdb=" O THR A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1244 removed outlier: 4.086A pdb=" N GLN A1242 " --> pdb=" O LYS A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1262 removed outlier: 3.675A pdb=" N ILE A1253 " --> pdb=" O GLN A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1285 Processing helix chain 'A' and resid 1297 through 1311 Processing helix chain 'A' and resid 1322 through 1326 removed outlier: 3.528A pdb=" N GLY A1325 " --> pdb=" O ARG A1322 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A1326 " --> pdb=" O SER A1323 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1322 through 1326' Processing helix chain 'A' and resid 1344 through 1356 removed outlier: 3.798A pdb=" N ASP A1348 " --> pdb=" O ASN A1344 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N CYS A1355 " --> pdb=" O CYS A1351 " (cutoff:3.500A) Processing helix chain 'A' and resid 1374 through 1395 removed outlier: 4.219A pdb=" N ASN A1378 " --> pdb=" O THR A1374 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 279 Processing helix chain 'B' and resid 298 through 316 Processing helix chain 'B' and resid 605 through 615 removed outlier: 3.807A pdb=" N PHE B 614 " --> pdb=" O ASN B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 665 removed outlier: 3.618A pdb=" N ASN B 665 " --> pdb=" O SER B 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 49 Processing helix chain 'C' and resid 68 through 82 removed outlier: 3.842A pdb=" N GLU C 72 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASN C 82 " --> pdb=" O TYR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 122 Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.792A pdb=" N PHE C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.575A pdb=" N LYS C 141 " --> pdb=" O PRO C 138 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR C 143 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 235 Processing helix chain 'C' and resid 241 through 252 Processing helix chain 'C' and resid 259 through 266 Processing helix chain 'C' and resid 308 through 313 removed outlier: 3.960A pdb=" N ILE C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 319 through 324 Processing helix chain 'C' and resid 329 through 341 Processing helix chain 'C' and resid 345 through 352 Processing helix chain 'C' and resid 358 through 362 Processing helix chain 'C' and resid 364 through 377 removed outlier: 3.661A pdb=" N GLN C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 405 removed outlier: 4.406A pdb=" N TRP C 397 " --> pdb=" O ALA C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 413 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 423 through 431 removed outlier: 4.229A pdb=" N CYS C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N THR C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 107 Processing helix chain 'D' and resid 109 through 114 Proline residue: D 114 - end of helix Processing helix chain 'D' and resid 115 through 125 removed outlier: 4.023A pdb=" N LEU D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 134 Processing helix chain 'D' and resid 168 through 179 Processing helix chain 'D' and resid 192 through 202 Processing helix chain 'D' and resid 207 through 214 Processing helix chain 'D' and resid 218 through 227 Processing helix chain 'D' and resid 265 through 276 Processing helix chain 'E' and resid 51 through 68 removed outlier: 3.666A pdb=" N LYS E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 97 Processing helix chain 'E' and resid 108 through 111 removed outlier: 3.718A pdb=" N TYR E 111 " --> pdb=" O SER E 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 108 through 111' Processing helix chain 'E' and resid 116 through 128 Processing helix chain 'E' and resid 182 through 192 Processing helix chain 'E' and resid 217 through 219 No H-bonds generated for 'chain 'E' and resid 217 through 219' Processing helix chain 'E' and resid 249 through 258 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'E' and resid 281 through 298 removed outlier: 3.533A pdb=" N ARG E 285 " --> pdb=" O THR E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 316 Processing helix chain 'E' and resid 317 through 329 removed outlier: 3.582A pdb=" N LYS E 326 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU E 329 " --> pdb=" O ASN E 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 365 Processing helix chain 'E' and resid 376 through 391 Processing helix chain 'E' and resid 396 through 410 Processing helix chain 'E' and resid 411 through 418 Processing helix chain 'E' and resid 418 through 429 Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 448 through 457 Processing helix chain 'F' and resid 47 through 64 removed outlier: 3.529A pdb=" N GLY F 64 " --> pdb=" O MET F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 93 Processing helix chain 'F' and resid 104 through 106 No H-bonds generated for 'chain 'F' and resid 104 through 106' Processing helix chain 'F' and resid 112 through 123 Processing helix chain 'F' and resid 172 through 183 Processing helix chain 'F' and resid 241 through 250 removed outlier: 4.199A pdb=" N ARG F 250 " --> pdb=" O VAL F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 260 removed outlier: 4.163A pdb=" N PHE F 258 " --> pdb=" O PHE F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 283 removed outlier: 3.594A pdb=" N ARG F 270 " --> pdb=" O ARG F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 301 Processing helix chain 'F' and resid 302 through 313 Processing helix chain 'F' and resid 344 through 350 removed outlier: 3.797A pdb=" N ARG F 350 " --> pdb=" O ASP F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 375 Processing helix chain 'F' and resid 380 through 394 Processing helix chain 'F' and resid 395 through 413 removed outlier: 4.343A pdb=" N SER F 404 " --> pdb=" O SER F 400 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL F 405 " --> pdb=" O ASN F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 419 through 430 Processing helix chain 'F' and resid 432 through 443 Processing helix chain 'F' and resid 444 through 447 Processing helix chain 'G' and resid 51 through 68 removed outlier: 3.505A pdb=" N LYS G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 97 Processing helix chain 'G' and resid 108 through 111 Processing helix chain 'G' and resid 116 through 129 removed outlier: 3.612A pdb=" N ILE G 129 " --> pdb=" O PHE G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 192 removed outlier: 4.352A pdb=" N SER G 188 " --> pdb=" O THR G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 219 No H-bonds generated for 'chain 'G' and resid 217 through 219' Processing helix chain 'G' and resid 249 through 258 Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'G' and resid 281 through 298 Processing helix chain 'G' and resid 313 through 316 Processing helix chain 'G' and resid 317 through 328 Processing helix chain 'G' and resid 360 through 365 Processing helix chain 'G' and resid 376 through 391 Processing helix chain 'G' and resid 396 through 410 Processing helix chain 'G' and resid 411 through 429 removed outlier: 3.544A pdb=" N ALA G 415 " --> pdb=" O SER G 411 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA G 420 " --> pdb=" O LEU G 416 " (cutoff:3.500A) Proline residue: G 421 - end of helix Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 448 through 455 Processing helix chain 'H' and resid 47 through 64 Processing helix chain 'H' and resid 80 through 93 Processing helix chain 'H' and resid 104 through 107 Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 172 through 183 Processing helix chain 'H' and resid 206 through 212 removed outlier: 4.477A pdb=" N ARG H 210 " --> pdb=" O ALA H 207 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR H 212 " --> pdb=" O SER H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 250 removed outlier: 3.938A pdb=" N ARG H 250 " --> pdb=" O VAL H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 260 removed outlier: 3.903A pdb=" N ALA H 256 " --> pdb=" O GLN H 252 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE H 258 " --> pdb=" O PHE H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 283 Processing helix chain 'H' and resid 298 through 301 Processing helix chain 'H' and resid 302 through 313 removed outlier: 3.725A pdb=" N ARG H 311 " --> pdb=" O SER H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 350 removed outlier: 3.583A pdb=" N ARG H 350 " --> pdb=" O ASP H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 375 Processing helix chain 'H' and resid 380 through 394 Processing helix chain 'H' and resid 395 through 413 removed outlier: 3.600A pdb=" N SER H 399 " --> pdb=" O SER H 395 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N SER H 404 " --> pdb=" O SER H 400 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL H 405 " --> pdb=" O ASN H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 419 through 430 Processing helix chain 'H' and resid 432 through 443 Processing helix chain 'H' and resid 444 through 447 removed outlier: 3.637A pdb=" N TYR H 447 " --> pdb=" O GLU H 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 444 through 447' Processing helix chain 'I' and resid 51 through 68 removed outlier: 3.622A pdb=" N LYS I 68 " --> pdb=" O LEU I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 84 through 97 Processing helix chain 'I' and resid 108 through 111 Processing helix chain 'I' and resid 116 through 127 Processing helix chain 'I' and resid 154 through 158 removed outlier: 3.905A pdb=" N GLY I 158 " --> pdb=" O PRO I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 193 Processing helix chain 'I' and resid 217 through 219 No H-bonds generated for 'chain 'I' and resid 217 through 219' Processing helix chain 'I' and resid 249 through 258 Processing helix chain 'I' and resid 264 through 273 Processing helix chain 'I' and resid 281 through 298 Processing helix chain 'I' and resid 312 through 316 Processing helix chain 'I' and resid 317 through 328 removed outlier: 3.567A pdb=" N LYS I 326 " --> pdb=" O THR I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 365 Processing helix chain 'I' and resid 376 through 391 Processing helix chain 'I' and resid 396 through 410 Processing helix chain 'I' and resid 411 through 429 removed outlier: 3.618A pdb=" N ALA I 415 " --> pdb=" O SER I 411 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA I 420 " --> pdb=" O LEU I 416 " (cutoff:3.500A) Proline residue: I 421 - end of helix Processing helix chain 'I' and resid 435 through 446 Processing helix chain 'I' and resid 448 through 457 Processing helix chain 'J' and resid 47 through 64 Processing helix chain 'J' and resid 80 through 93 Processing helix chain 'J' and resid 102 through 106 removed outlier: 3.839A pdb=" N ILE J 106 " --> pdb=" O GLY J 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 124 removed outlier: 3.652A pdb=" N SER J 124 " --> pdb=" O ALA J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 183 Processing helix chain 'J' and resid 241 through 250 removed outlier: 4.007A pdb=" N ARG J 250 " --> pdb=" O VAL J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 254 No H-bonds generated for 'chain 'J' and resid 252 through 254' Processing helix chain 'J' and resid 255 through 260 Processing helix chain 'J' and resid 266 through 284 Processing helix chain 'J' and resid 297 through 301 Processing helix chain 'J' and resid 302 through 315 removed outlier: 3.687A pdb=" N ARG J 311 " --> pdb=" O SER J 307 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU J 314 " --> pdb=" O ASN J 310 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP J 315 " --> pdb=" O ARG J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 350 removed outlier: 3.613A pdb=" N ARG J 350 " --> pdb=" O ASP J 346 " (cutoff:3.500A) Processing helix chain 'J' and resid 360 through 375 Processing helix chain 'J' and resid 380 through 394 Processing helix chain 'J' and resid 395 through 413 removed outlier: 3.789A pdb=" N ILE J 403 " --> pdb=" O SER J 399 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N SER J 404 " --> pdb=" O SER J 400 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL J 405 " --> pdb=" O ASN J 401 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG J 413 " --> pdb=" O ILE J 409 " (cutoff:3.500A) Processing helix chain 'J' and resid 419 through 430 Processing helix chain 'J' and resid 432 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 717 through 719 removed outlier: 3.766A pdb=" N GLY A 717 " --> pdb=" O ARG A 848 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLN A 819 " --> pdb=" O THR A 845 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 847 " --> pdb=" O GLN A 819 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU A 749 " --> pdb=" O VAL A 822 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N HIS A 748 " --> pdb=" O CYS A 799 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N VAL A 801 " --> pdb=" O HIS A 748 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE A 750 " --> pdb=" O VAL A 801 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 874 through 876 removed outlier: 3.530A pdb=" N ILE A 876 " --> pdb=" O LYS A 879 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 944 through 951 removed outlier: 5.792A pdb=" N LEU A1266 " --> pdb=" O ILE A1337 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA A1265 " --> pdb=" O PHE A1317 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU A1319 " --> pdb=" O ALA A1265 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE A1267 " --> pdb=" O LEU A1319 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N MET A1290 " --> pdb=" O ILE A1318 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N SER A1320 " --> pdb=" O MET A1290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1008 through 1009 removed outlier: 5.923A pdb=" N PHE A1008 " --> pdb=" O VAL A1188 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 286 through 296 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 588 through 598 current: chain 'F' and resid 154 through 161 removed outlier: 4.521A pdb=" N GLY F 156 " --> pdb=" O LEU F 171 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 166 through 171 current: chain 'F' and resid 199 through 204 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 199 through 204 current: chain 'G' and resid 161 through 172 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 175 through 181 current: chain 'G' and resid 209 through 215 removed outlier: 5.461A pdb=" N VAL G 230 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ARG G 214 " --> pdb=" O VAL G 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 635 through 640 removed outlier: 6.920A pdb=" N ILE H 145 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N HIS B 638 " --> pdb=" O ILE H 143 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE H 143 " --> pdb=" O HIS B 638 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ILE B 640 " --> pdb=" O VAL H 141 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N VAL H 141 " --> pdb=" O ILE B 640 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL H 140 " --> pdb=" O LYS H 161 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LYS H 161 " --> pdb=" O VAL H 140 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU H 142 " --> pdb=" O THR H 159 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY H 156 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET H 165 " --> pdb=" O THR H 162 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 165 through 171 current: chain 'H' and resid 199 through 204 Processing sheet with id=AA7, first strand: chain 'C' and resid 15 through 19 Processing sheet with id=AA8, first strand: chain 'C' and resid 40 through 42 Processing sheet with id=AA9, first strand: chain 'C' and resid 147 through 151 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 147 through 151 current: chain 'C' and resid 198 through 204 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 207 through 208 current: chain 'C' and resid 384 through 388 Processing sheet with id=AB1, first strand: chain 'C' and resid 286 through 288 removed outlier: 3.609A pdb=" N TYR C 286 " --> pdb=" O VAL C 275 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 5 through 7 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 5 through 7 current: chain 'E' and resid 166 through 171 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 176 through 181 current: chain 'E' and resid 208 through 215 removed outlier: 5.498A pdb=" N VAL E 230 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG E 214 " --> pdb=" O VAL E 230 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 21 current: chain 'D' and resid 262 through 263 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 262 through 263 current: chain 'J' and resid 155 through 161 removed outlier: 3.576A pdb=" N THR J 167 " --> pdb=" O ILE J 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 166 through 170 current: chain 'J' and resid 199 through 204 Processing sheet with id=AB4, first strand: chain 'E' and resid 44 through 45 Processing sheet with id=AB5, first strand: chain 'E' and resid 102 through 106 removed outlier: 6.235A pdb=" N CYS E 103 " --> pdb=" O PHE E 309 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASP E 311 " --> pdb=" O CYS E 103 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU E 105 " --> pdb=" O ASP E 311 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU E 308 " --> pdb=" O VAL E 337 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ALA E 339 " --> pdb=" O LEU E 308 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE E 310 " --> pdb=" O ALA E 339 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY E 79 " --> pdb=" O SER E 340 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA E 74 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N VAL E 370 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU E 76 " --> pdb=" O VAL E 370 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR E 372 " --> pdb=" O LEU E 76 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA E 78 " --> pdb=" O THR E 372 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 40 through 41 Processing sheet with id=AB7, first strand: chain 'F' and resid 98 through 102 removed outlier: 6.247A pdb=" N THR F 99 " --> pdb=" O PHE F 294 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ASP F 296 " --> pdb=" O THR F 99 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE F 101 " --> pdb=" O ASP F 296 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU F 293 " --> pdb=" O MET F 322 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ALA F 324 " --> pdb=" O LEU F 293 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE F 295 " --> pdb=" O ALA F 324 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA F 70 " --> pdb=" O ILE F 352 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ILE F 354 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU F 72 " --> pdb=" O ILE F 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 330 through 331 Processing sheet with id=AB9, first strand: chain 'G' and resid 44 through 45 Processing sheet with id=AC1, first strand: chain 'G' and resid 102 through 106 removed outlier: 6.410A pdb=" N CYS G 103 " --> pdb=" O PHE G 309 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ASP G 311 " --> pdb=" O CYS G 103 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N LEU G 105 " --> pdb=" O ASP G 311 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA G 339 " --> pdb=" O ILE G 310 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY G 79 " --> pdb=" O SER G 340 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 344 through 346 removed outlier: 3.664A pdb=" N THR G 345 " --> pdb=" O SER G 355 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 40 through 41 Processing sheet with id=AC4, first strand: chain 'H' and resid 98 through 102 removed outlier: 6.299A pdb=" N THR H 99 " --> pdb=" O PHE H 294 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ASP H 296 " --> pdb=" O THR H 99 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ILE H 101 " --> pdb=" O ASP H 296 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU H 293 " --> pdb=" O MET H 322 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA H 324 " --> pdb=" O LEU H 293 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE H 295 " --> pdb=" O ALA H 324 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA H 70 " --> pdb=" O ILE H 352 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE H 354 " --> pdb=" O ALA H 70 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU H 72 " --> pdb=" O ILE H 354 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 330 through 331 Processing sheet with id=AC6, first strand: chain 'I' and resid 44 through 45 Processing sheet with id=AC7, first strand: chain 'I' and resid 102 through 106 removed outlier: 6.334A pdb=" N CYS I 103 " --> pdb=" O PHE I 309 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N ASP I 311 " --> pdb=" O CYS I 103 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU I 105 " --> pdb=" O ASP I 311 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU I 308 " --> pdb=" O VAL I 337 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA I 339 " --> pdb=" O LEU I 308 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE I 310 " --> pdb=" O ALA I 339 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA I 74 " --> pdb=" O LEU I 368 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL I 370 " --> pdb=" O ALA I 74 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU I 76 " --> pdb=" O VAL I 370 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 129 through 151 removed outlier: 6.148A pdb=" N GLY I 169 " --> pdb=" O THR I 145 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU I 147 " --> pdb=" O ILE I 167 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE I 167 " --> pdb=" O LEU I 147 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N HIS I 165 " --> pdb=" O PRO I 149 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASP I 151 " --> pdb=" O ILE I 163 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE I 163 " --> pdb=" O ASP I 151 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 175 through 181 current: chain 'I' and resid 208 through 215 removed outlier: 6.167A pdb=" N VAL I 230 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ARG I 214 " --> pdb=" O VAL I 230 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 345 through 346 Processing sheet with id=AD1, first strand: chain 'I' and resid 394 through 395 removed outlier: 7.408A pdb=" N GLN I 394 " --> pdb=" O ILE I 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'J' and resid 40 through 41 Processing sheet with id=AD3, first strand: chain 'J' and resid 98 through 101 removed outlier: 6.399A pdb=" N THR J 99 " --> pdb=" O PHE J 294 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU J 293 " --> pdb=" O MET J 322 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA J 324 " --> pdb=" O LEU J 293 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE J 295 " --> pdb=" O ALA J 324 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA J 70 " --> pdb=" O ILE J 352 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE J 354 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU J 72 " --> pdb=" O ILE J 354 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 330 through 331 removed outlier: 3.556A pdb=" N SER J 330 " --> pdb=" O SER J 339 " (cutoff:3.500A) 1396 hydrogen bonds defined for protein. 4020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 64 hydrogen bonds 128 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 13.65 Time building geometry restraints manager: 10.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 11010 1.36 - 1.51: 8754 1.51 - 1.66: 13788 1.66 - 1.80: 145 1.80 - 1.95: 60 Bond restraints: 33757 Sorted by residual: bond pdb=" C3' DA Z 44 " pdb=" O3' DA Z 44 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.08e+00 bond pdb=" C4 ADP J 501 " pdb=" C5 ADP J 501 " ideal model delta sigma weight residual 1.490 1.461 0.029 2.00e-02 2.50e+03 2.03e+00 bond pdb=" C3' DA Y 90 " pdb=" O3' DA Y 90 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.02e+00 bond pdb=" C4 ADP H 502 " pdb=" C5 ADP H 502 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.77e+00 bond pdb=" C4 ADP I 901 " pdb=" C5 ADP I 901 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 33752 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 45056 1.53 - 3.06: 653 3.06 - 4.60: 98 4.60 - 6.13: 38 6.13 - 7.66: 2 Bond angle restraints: 45847 Sorted by residual: angle pdb=" C LYS F 94 " pdb=" N ASP F 95 " pdb=" CA ASP F 95 " ideal model delta sigma weight residual 121.54 126.32 -4.78 1.91e+00 2.74e-01 6.27e+00 angle pdb=" C3' DA Y 90 " pdb=" O3' DA Y 90 " pdb=" P DA Y 91 " ideal model delta sigma weight residual 120.20 123.78 -3.58 1.50e+00 4.44e-01 5.71e+00 angle pdb=" C VAL I 359 " pdb=" N PRO I 360 " pdb=" CA PRO I 360 " ideal model delta sigma weight residual 119.66 121.40 -1.74 7.30e-01 1.88e+00 5.67e+00 angle pdb=" C4' DT Z 50 " pdb=" O4' DT Z 50 " pdb=" C1' DT Z 50 " ideal model delta sigma weight residual 109.70 106.17 3.53 1.50e+00 4.44e-01 5.52e+00 angle pdb=" N LEU D 184 " pdb=" CA LEU D 184 " pdb=" C LEU D 184 " ideal model delta sigma weight residual 108.39 113.22 -4.83 2.10e+00 2.27e-01 5.30e+00 ... (remaining 45842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 19980 35.86 - 71.72: 544 71.72 - 107.58: 45 107.58 - 143.44: 3 143.44 - 179.30: 3 Dihedral angle restraints: 20575 sinusoidal: 8846 harmonic: 11729 Sorted by residual: dihedral pdb=" O2A ADP H 502 " pdb=" O3A ADP H 502 " pdb=" PA ADP H 502 " pdb=" PB ADP H 502 " ideal model delta sinusoidal sigma weight residual -60.00 72.74 -132.74 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" O2A ADP F 502 " pdb=" O3A ADP F 502 " pdb=" PA ADP F 502 " pdb=" PB ADP F 502 " ideal model delta sinusoidal sigma weight residual -60.00 65.82 -125.82 1 2.00e+01 2.50e-03 3.80e+01 dihedral pdb=" C5' ADP I 901 " pdb=" O5' ADP I 901 " pdb=" PA ADP I 901 " pdb=" O2A ADP I 901 " ideal model delta sinusoidal sigma weight residual -60.00 -155.39 95.39 1 2.00e+01 2.50e-03 2.63e+01 ... (remaining 20572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 4155 0.047 - 0.094: 949 0.094 - 0.141: 233 0.141 - 0.188: 6 0.188 - 0.235: 1 Chirality restraints: 5344 Sorted by residual: chirality pdb=" CB ILE G 332 " pdb=" CA ILE G 332 " pdb=" CG1 ILE G 332 " pdb=" CG2 ILE G 332 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE E 332 " pdb=" CA ILE E 332 " pdb=" CG1 ILE E 332 " pdb=" CG2 ILE E 332 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CB VAL G 265 " pdb=" CA VAL G 265 " pdb=" CG1 VAL G 265 " pdb=" CG2 VAL G 265 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.24e-01 ... (remaining 5341 not shown) Planarity restraints: 5653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 341 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO C 342 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 342 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 342 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 752 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO A 753 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 753 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 753 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC Y 95 " -0.027 2.00e-02 2.50e+03 1.33e-02 3.98e+00 pdb=" N1 DC Y 95 " 0.026 2.00e-02 2.50e+03 pdb=" C2 DC Y 95 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC Y 95 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DC Y 95 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC Y 95 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC Y 95 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DC Y 95 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC Y 95 " 0.005 2.00e-02 2.50e+03 ... (remaining 5650 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 148 2.47 - 3.08: 22518 3.08 - 3.68: 50930 3.68 - 4.29: 73469 4.29 - 4.90: 121457 Nonbonded interactions: 268522 Sorted by model distance: nonbonded pdb=" OD1 ASN D 258 " pdb="ZN ZN D 302 " model vdw 1.862 2.230 nonbonded pdb=" O2B AGS C 501 " pdb="MG MG C 502 " model vdw 1.862 2.170 nonbonded pdb=" OG1 THR F 82 " pdb="MG MG F 501 " model vdw 1.938 2.170 nonbonded pdb=" O3G AGS E 901 " pdb="MG MG E 902 " model vdw 1.939 2.170 nonbonded pdb="MG MG H 501 " pdb=" O2B ADP H 502 " model vdw 1.983 2.170 ... (remaining 268517 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 'E' and resid 22 through 455) selection = (chain 'G' and (resid 22 through 151 or resid 163 through 455)) selection = (chain 'I' and (resid 22 through 151 or resid 163 through 455)) } ncs_group { reference = (chain 'F' and (resid 17 through 148 or resid 153 or (resid 154 and (name N or n \ ame CA or name C or name O or name CB )) or resid 155 through 205 or resid 222 t \ hrough 459)) selection = (chain 'H' and (resid 17 through 148 or resid 153 through 205 or resid 222 throu \ gh 459)) selection = (chain 'J' and (resid 17 through 148 or resid 153 or (resid 154 and (name N or n \ ame CA or name C or name O or name CB )) or resid 155 through 459)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.300 Check model and map are aligned: 0.280 Set scattering table: 0.330 Process input model: 90.590 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.003 0.075 33764 Z= 0.148 Angle : 0.499 7.661 45853 Z= 0.260 Chirality : 0.041 0.235 5344 Planarity : 0.003 0.056 5653 Dihedral : 15.990 179.304 12981 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.13), residues: 4008 helix: 1.60 (0.12), residues: 1820 sheet: 0.75 (0.20), residues: 678 loop : -0.31 (0.16), residues: 1510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 864 HIS 0.004 0.001 HIS G 357 PHE 0.016 0.001 PHE B 609 TYR 0.015 0.001 TYR G 323 ARG 0.005 0.000 ARG H 266 Details of bonding type rmsd hydrogen bonds : bond 0.15069 ( 1460) hydrogen bonds : angle 5.26953 ( 4148) metal coordination : bond 0.00634 ( 7) metal coordination : angle 2.03265 ( 6) covalent geometry : bond 0.00329 (33757) covalent geometry : angle 0.49802 (45847) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1363 time to evaluate : 3.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 738 LEU cc_start: 0.8230 (mt) cc_final: 0.8025 (mt) REVERT: A 745 TRP cc_start: 0.6778 (m100) cc_final: 0.6477 (m-10) REVERT: A 756 VAL cc_start: 0.8508 (t) cc_final: 0.8276 (m) REVERT: A 763 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7514 (mm-30) REVERT: A 821 MET cc_start: 0.7998 (ttt) cc_final: 0.7789 (ttt) REVERT: A 825 GLU cc_start: 0.7478 (mm-30) cc_final: 0.6957 (mm-30) REVERT: A 829 ILE cc_start: 0.8496 (pt) cc_final: 0.8072 (tt) REVERT: A 838 GLN cc_start: 0.8330 (mm110) cc_final: 0.8095 (mm110) REVERT: A 841 LEU cc_start: 0.8349 (tp) cc_final: 0.8019 (tp) REVERT: A 863 LEU cc_start: 0.9003 (tp) cc_final: 0.8748 (tp) REVERT: A 864 TRP cc_start: 0.7954 (t60) cc_final: 0.7631 (t60) REVERT: A 870 LEU cc_start: 0.8644 (mm) cc_final: 0.7931 (mm) REVERT: A 871 MET cc_start: 0.7906 (mmp) cc_final: 0.6927 (mmp) REVERT: A 899 ASP cc_start: 0.7287 (t0) cc_final: 0.6681 (t0) REVERT: A 930 LEU cc_start: 0.7497 (tp) cc_final: 0.7253 (tp) REVERT: A 946 GLU cc_start: 0.7032 (pp20) cc_final: 0.6531 (pp20) REVERT: A 1000 GLU cc_start: 0.6653 (tp30) cc_final: 0.6415 (tp30) REVERT: A 1052 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8252 (mtmt) REVERT: A 1073 GLU cc_start: 0.7815 (pt0) cc_final: 0.7560 (pt0) REVERT: A 1099 ASP cc_start: 0.7806 (t0) cc_final: 0.7553 (t0) REVERT: A 1109 LYS cc_start: 0.8238 (tmtt) cc_final: 0.7899 (tttp) REVERT: A 1111 LYS cc_start: 0.8201 (ttmm) cc_final: 0.7974 (ttmm) REVERT: A 1133 ARG cc_start: 0.8217 (ptp-110) cc_final: 0.7928 (ptp-110) REVERT: A 1146 LYS cc_start: 0.7964 (ttmm) cc_final: 0.7680 (ttmm) REVERT: A 1161 GLU cc_start: 0.7123 (tp30) cc_final: 0.6799 (tp30) REVERT: A 1202 ASP cc_start: 0.7616 (p0) cc_final: 0.7030 (p0) REVERT: A 1238 LYS cc_start: 0.7865 (mppt) cc_final: 0.7563 (mtmm) REVERT: A 1245 CYS cc_start: 0.7874 (t) cc_final: 0.7458 (t) REVERT: A 1290 MET cc_start: 0.6997 (mtt) cc_final: 0.6432 (mtt) REVERT: A 1350 GLN cc_start: 0.7852 (pp30) cc_final: 0.7452 (pp30) REVERT: A 1394 ILE cc_start: 0.7438 (mm) cc_final: 0.7145 (mm) REVERT: B 269 ASN cc_start: 0.7645 (m110) cc_final: 0.7289 (m110) REVERT: B 596 LEU cc_start: 0.8305 (mp) cc_final: 0.8092 (mp) REVERT: C 7 VAL cc_start: 0.9007 (p) cc_final: 0.8685 (m) REVERT: C 17 PHE cc_start: 0.8286 (p90) cc_final: 0.8026 (p90) REVERT: C 44 ASN cc_start: 0.8673 (t0) cc_final: 0.8213 (t0) REVERT: C 59 ARG cc_start: 0.8371 (mtt90) cc_final: 0.8168 (mtt90) REVERT: C 70 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7407 (mp0) REVERT: C 71 LEU cc_start: 0.8542 (pt) cc_final: 0.8244 (pt) REVERT: C 74 CYS cc_start: 0.8635 (m) cc_final: 0.8321 (m) REVERT: C 95 LYS cc_start: 0.9031 (ttmm) cc_final: 0.8609 (ttmm) REVERT: C 103 GLU cc_start: 0.7501 (pm20) cc_final: 0.7245 (pm20) REVERT: C 106 MET cc_start: 0.8203 (mmm) cc_final: 0.7839 (mmm) REVERT: C 117 GLN cc_start: 0.8875 (tt0) cc_final: 0.8577 (tt0) REVERT: C 122 GLU cc_start: 0.7921 (tp30) cc_final: 0.7559 (tp30) REVERT: C 126 ASP cc_start: 0.5718 (p0) cc_final: 0.5455 (p0) REVERT: C 184 TYR cc_start: 0.8699 (p90) cc_final: 0.8483 (p90) REVERT: C 192 ASP cc_start: 0.8001 (t0) cc_final: 0.7747 (t0) REVERT: C 222 PHE cc_start: 0.8583 (t80) cc_final: 0.8149 (t80) REVERT: C 239 MET cc_start: 0.7340 (tmm) cc_final: 0.6589 (tmm) REVERT: C 240 ASP cc_start: 0.7868 (t0) cc_final: 0.7440 (t0) REVERT: C 250 GLU cc_start: 0.7839 (tp30) cc_final: 0.7532 (tp30) REVERT: C 265 LYS cc_start: 0.8350 (mmpt) cc_final: 0.7906 (mmpt) REVERT: C 269 LYS cc_start: 0.8641 (tppt) cc_final: 0.8285 (tppt) REVERT: C 278 ASP cc_start: 0.8016 (t0) cc_final: 0.7812 (t0) REVERT: C 316 THR cc_start: 0.8846 (t) cc_final: 0.8616 (m) REVERT: C 324 GLN cc_start: 0.8526 (mp-120) cc_final: 0.8317 (mp10) REVERT: C 336 GLU cc_start: 0.8403 (tt0) cc_final: 0.7973 (tt0) REVERT: C 340 MET cc_start: 0.8391 (mmm) cc_final: 0.8082 (mmm) REVERT: C 359 ASN cc_start: 0.8454 (m-40) cc_final: 0.8196 (m110) REVERT: C 402 GLN cc_start: 0.9101 (mm110) cc_final: 0.8899 (mm110) REVERT: C 416 ARG cc_start: 0.8137 (ttt90) cc_final: 0.7603 (ttt180) REVERT: C 421 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7910 (mt-10) REVERT: C 435 GLN cc_start: 0.8858 (mm110) cc_final: 0.8546 (mm-40) REVERT: D 98 SER cc_start: 0.8955 (t) cc_final: 0.8742 (t) REVERT: D 103 MET cc_start: 0.8548 (ttm) cc_final: 0.8178 (ttm) REVERT: D 106 ASN cc_start: 0.8809 (t0) cc_final: 0.8591 (t0) REVERT: D 119 LEU cc_start: 0.8883 (tt) cc_final: 0.8628 (tt) REVERT: D 124 THR cc_start: 0.8703 (m) cc_final: 0.8476 (p) REVERT: D 136 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7896 (mtmm) REVERT: D 173 ARG cc_start: 0.8834 (mtt90) cc_final: 0.8150 (mtt90) REVERT: D 219 LEU cc_start: 0.9010 (mm) cc_final: 0.8760 (mp) REVERT: D 228 ASN cc_start: 0.8436 (m110) cc_final: 0.7928 (m110) REVERT: D 241 ILE cc_start: 0.8811 (mt) cc_final: 0.8577 (mt) REVERT: D 250 TYR cc_start: 0.8684 (p90) cc_final: 0.8462 (p90) REVERT: D 262 LYS cc_start: 0.8636 (mttm) cc_final: 0.8330 (mmmm) REVERT: E 45 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7398 (mm-30) REVERT: E 69 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8426 (mtpp) REVERT: E 117 LYS cc_start: 0.7687 (ptpp) cc_final: 0.7453 (ptpt) REVERT: E 118 THR cc_start: 0.8383 (m) cc_final: 0.7178 (t) REVERT: E 132 ARG cc_start: 0.7706 (ttm170) cc_final: 0.7423 (ttm-80) REVERT: E 134 LYS cc_start: 0.8110 (mtmm) cc_final: 0.7807 (mtmm) REVERT: E 193 LYS cc_start: 0.8436 (mmmt) cc_final: 0.8154 (mmmt) REVERT: E 210 LYS cc_start: 0.8424 (tptt) cc_final: 0.8079 (tptm) REVERT: E 218 TYR cc_start: 0.8731 (m-80) cc_final: 0.8522 (m-80) REVERT: E 253 ASP cc_start: 0.7814 (m-30) cc_final: 0.7546 (m-30) REVERT: E 266 ILE cc_start: 0.8166 (mt) cc_final: 0.7882 (mt) REVERT: E 273 LEU cc_start: 0.7661 (tp) cc_final: 0.7460 (tp) REVERT: E 276 LYS cc_start: 0.8137 (mttp) cc_final: 0.7934 (mttp) REVERT: E 312 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7812 (mm-30) REVERT: E 351 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7571 (mt-10) REVERT: E 366 ARG cc_start: 0.7922 (mpt-90) cc_final: 0.7633 (mtt90) REVERT: E 438 ASP cc_start: 0.7473 (m-30) cc_final: 0.7026 (m-30) REVERT: E 441 GLU cc_start: 0.7843 (tp30) cc_final: 0.7207 (tp30) REVERT: F 32 ASP cc_start: 0.7871 (m-30) cc_final: 0.7653 (m-30) REVERT: F 59 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8326 (mmtp) REVERT: F 142 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7550 (mt-10) REVERT: F 155 GLN cc_start: 0.8002 (tt0) cc_final: 0.7763 (tt0) REVERT: F 185 LEU cc_start: 0.8169 (mt) cc_final: 0.7914 (mm) REVERT: F 192 ILE cc_start: 0.8174 (mm) cc_final: 0.7947 (mm) REVERT: F 193 ASP cc_start: 0.7528 (t0) cc_final: 0.6965 (t0) REVERT: F 229 LEU cc_start: 0.8672 (tt) cc_final: 0.8417 (tt) REVERT: F 231 LYS cc_start: 0.8616 (ptpt) cc_final: 0.8298 (ptpp) REVERT: F 232 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7473 (mtp85) REVERT: F 276 LYS cc_start: 0.8137 (tppt) cc_final: 0.7900 (tppt) REVERT: F 287 GLU cc_start: 0.7840 (tt0) cc_final: 0.7585 (tt0) REVERT: F 315 ASP cc_start: 0.7922 (t0) cc_final: 0.7700 (t0) REVERT: F 317 PHE cc_start: 0.8150 (m-80) cc_final: 0.7929 (m-10) REVERT: F 349 ASP cc_start: 0.7659 (t70) cc_final: 0.7327 (t70) REVERT: F 389 LYS cc_start: 0.8339 (tttm) cc_final: 0.8070 (tttm) REVERT: F 393 GLU cc_start: 0.7817 (tp30) cc_final: 0.7528 (tp30) REVERT: F 405 VAL cc_start: 0.8464 (t) cc_final: 0.8226 (m) REVERT: F 412 LYS cc_start: 0.7210 (tptm) cc_final: 0.6927 (tptt) REVERT: F 442 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7606 (mt-10) REVERT: F 444 GLU cc_start: 0.7889 (tt0) cc_final: 0.7668 (tt0) REVERT: G 36 ASP cc_start: 0.7535 (p0) cc_final: 0.7196 (p0) REVERT: G 44 VAL cc_start: 0.8496 (p) cc_final: 0.8240 (t) REVERT: G 69 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7931 (mtpp) REVERT: G 134 LYS cc_start: 0.8163 (mtmm) cc_final: 0.7901 (mtmm) REVERT: G 171 LYS cc_start: 0.8262 (ptmm) cc_final: 0.8058 (ptmm) REVERT: G 198 ASP cc_start: 0.7161 (m-30) cc_final: 0.6646 (m-30) REVERT: G 199 VAL cc_start: 0.8919 (p) cc_final: 0.8668 (m) REVERT: G 210 LYS cc_start: 0.8118 (tppt) cc_final: 0.7631 (tppt) REVERT: G 216 ASP cc_start: 0.7700 (m-30) cc_final: 0.7299 (m-30) REVERT: G 234 LYS cc_start: 0.8419 (mttm) cc_final: 0.8145 (mttm) REVERT: G 240 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7897 (mtmm) REVERT: G 242 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7868 (mt-10) REVERT: G 246 ASP cc_start: 0.7594 (p0) cc_final: 0.7371 (p0) REVERT: G 251 ASP cc_start: 0.7683 (m-30) cc_final: 0.7475 (m-30) REVERT: G 260 GLN cc_start: 0.7882 (tp40) cc_final: 0.7593 (tp40) REVERT: G 269 MET cc_start: 0.7680 (mpp) cc_final: 0.7273 (mpp) REVERT: G 287 GLU cc_start: 0.7842 (tp30) cc_final: 0.7213 (tp30) REVERT: G 294 LYS cc_start: 0.8733 (ttpt) cc_final: 0.8425 (tttp) REVERT: G 295 TYR cc_start: 0.8478 (m-80) cc_final: 0.8221 (m-80) REVERT: G 427 GLN cc_start: 0.8011 (tm-30) cc_final: 0.7705 (tm-30) REVERT: G 433 GLU cc_start: 0.7426 (mp0) cc_final: 0.7130 (mp0) REVERT: G 443 LYS cc_start: 0.8503 (ttmt) cc_final: 0.8268 (ttmt) REVERT: G 451 ARG cc_start: 0.7747 (mtm180) cc_final: 0.7511 (mtm110) REVERT: G 452 SER cc_start: 0.8119 (m) cc_final: 0.7827 (m) REVERT: H 115 GLU cc_start: 0.8224 (tp30) cc_final: 0.7928 (mm-30) REVERT: H 144 GLN cc_start: 0.7424 (tt0) cc_final: 0.7203 (tt0) REVERT: H 157 LYS cc_start: 0.7991 (mtmm) cc_final: 0.7626 (mtmm) REVERT: H 166 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7387 (tp30) REVERT: H 167 THR cc_start: 0.8359 (m) cc_final: 0.7952 (m) REVERT: H 175 MET cc_start: 0.8266 (tpp) cc_final: 0.7760 (tpp) REVERT: H 176 ILE cc_start: 0.8503 (mt) cc_final: 0.8279 (mt) REVERT: H 185 LEU cc_start: 0.7988 (mt) cc_final: 0.7399 (mt) REVERT: H 188 ASP cc_start: 0.7445 (m-30) cc_final: 0.7161 (m-30) REVERT: H 198 LYS cc_start: 0.7599 (tptp) cc_final: 0.7308 (tptp) REVERT: H 199 ILE cc_start: 0.8708 (mt) cc_final: 0.8276 (mt) REVERT: H 211 ASP cc_start: 0.7872 (m-30) cc_final: 0.7545 (m-30) REVERT: H 252 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7610 (mm-40) REVERT: H 265 ILE cc_start: 0.8322 (mt) cc_final: 0.8035 (mp) REVERT: H 271 ASP cc_start: 0.7585 (m-30) cc_final: 0.7116 (m-30) REVERT: H 330 SER cc_start: 0.8643 (p) cc_final: 0.8372 (t) REVERT: H 331 LYS cc_start: 0.8334 (ttmm) cc_final: 0.8031 (ttmm) REVERT: H 336 ASN cc_start: 0.7841 (p0) cc_final: 0.7639 (p0) REVERT: H 349 ASP cc_start: 0.8041 (t0) cc_final: 0.7708 (t0) REVERT: H 374 GLU cc_start: 0.7955 (tp30) cc_final: 0.7583 (tp30) REVERT: H 438 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8029 (ttmt) REVERT: H 444 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7655 (mt-10) REVERT: I 52 ILE cc_start: 0.8164 (mm) cc_final: 0.7227 (mm) REVERT: I 56 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7784 (mt-10) REVERT: I 123 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7610 (mt-10) REVERT: I 127 ARG cc_start: 0.7944 (ttm170) cc_final: 0.7737 (ttm170) REVERT: I 133 ILE cc_start: 0.8793 (tt) cc_final: 0.8565 (pt) REVERT: I 138 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7651 (mt-10) REVERT: I 182 ASP cc_start: 0.7995 (m-30) cc_final: 0.7418 (m-30) REVERT: I 187 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7527 (mt-10) REVERT: I 203 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7459 (mt-10) REVERT: I 210 LYS cc_start: 0.8101 (ttpt) cc_final: 0.7858 (ttpt) REVERT: I 223 ASP cc_start: 0.7427 (p0) cc_final: 0.6580 (p0) REVERT: I 258 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7592 (mtm-85) REVERT: I 268 MET cc_start: 0.7323 (ttp) cc_final: 0.7116 (ttp) REVERT: I 279 GLU cc_start: 0.7608 (pt0) cc_final: 0.7380 (pt0) REVERT: I 325 ASN cc_start: 0.8078 (m110) cc_final: 0.7867 (m110) REVERT: I 417 GLN cc_start: 0.8095 (mt0) cc_final: 0.7883 (mt0) REVERT: J 26 ILE cc_start: 0.8605 (mt) cc_final: 0.8357 (mt) REVERT: J 128 LYS cc_start: 0.8359 (mtpp) cc_final: 0.8046 (mtpp) REVERT: J 157 LYS cc_start: 0.8429 (mttm) cc_final: 0.8168 (mttm) REVERT: J 170 GLU cc_start: 0.7206 (mp0) cc_final: 0.6702 (mp0) REVERT: J 268 GLU cc_start: 0.8004 (pm20) cc_final: 0.7388 (mp0) REVERT: J 297 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7463 (mm-30) REVERT: J 299 HIS cc_start: 0.8533 (p90) cc_final: 0.8267 (p-80) REVERT: J 310 ASN cc_start: 0.8039 (m-40) cc_final: 0.7701 (m110) REVERT: J 346 ASP cc_start: 0.7393 (t70) cc_final: 0.6870 (t70) REVERT: J 350 ARG cc_start: 0.7833 (ttm110) cc_final: 0.7504 (ttm110) REVERT: J 357 LYS cc_start: 0.7954 (mmpt) cc_final: 0.7749 (mmpt) REVERT: J 363 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7506 (mt-10) REVERT: J 365 LYS cc_start: 0.8291 (ttmt) cc_final: 0.8074 (ttmt) REVERT: J 385 ASP cc_start: 0.7878 (t70) cc_final: 0.7596 (t70) REVERT: J 389 LYS cc_start: 0.8374 (ptmm) cc_final: 0.8047 (ptmm) REVERT: J 393 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7490 (mt-10) REVERT: J 405 VAL cc_start: 0.8371 (t) cc_final: 0.8076 (m) REVERT: J 411 MET cc_start: 0.7962 (mtt) cc_final: 0.7726 (mtm) REVERT: J 438 LYS cc_start: 0.8114 (tmtt) cc_final: 0.7878 (tmtt) REVERT: J 450 ASP cc_start: 0.8044 (t70) cc_final: 0.7812 (t70) REVERT: J 451 GLN cc_start: 0.8596 (mm-40) cc_final: 0.8330 (mm-40) outliers start: 0 outliers final: 0 residues processed: 1363 average time/residue: 0.5376 time to fit residues: 1111.8183 Evaluate side-chains 1252 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1252 time to evaluate : 3.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 341 optimal weight: 0.0980 chunk 306 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 317 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 193 optimal weight: 0.2980 chunk 236 optimal weight: 0.9980 chunk 367 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1012 HIS A1216 ASN A1356 HIS C 196 ASN C 319 HIS D 109 ASN E 256 ASN E 263 GLN F 401 ASN G 124 ASN G 256 ASN H 441 GLN J 252 GLN J 408 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111070 restraints weight = 55050.844| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.23 r_work: 0.3269 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33764 Z= 0.153 Angle : 0.578 9.889 45853 Z= 0.298 Chirality : 0.043 0.178 5344 Planarity : 0.004 0.053 5653 Dihedral : 14.388 174.947 5012 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.66 % Allowed : 11.95 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.13), residues: 4008 helix: 1.60 (0.12), residues: 1841 sheet: 0.69 (0.20), residues: 685 loop : -0.33 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 837 HIS 0.010 0.001 HIS A1012 PHE 0.022 0.001 PHE B 259 TYR 0.020 0.001 TYR G 186 ARG 0.006 0.000 ARG I 43 Details of bonding type rmsd hydrogen bonds : bond 0.04688 ( 1460) hydrogen bonds : angle 4.40876 ( 4148) metal coordination : bond 0.00711 ( 7) metal coordination : angle 2.58532 ( 6) covalent geometry : bond 0.00341 (33757) covalent geometry : angle 0.57776 (45847) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1341 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 1282 time to evaluate : 5.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 LEU cc_start: 0.8170 (mt) cc_final: 0.7895 (mt) REVERT: A 745 TRP cc_start: 0.7024 (m100) cc_final: 0.6611 (m-10) REVERT: A 752 VAL cc_start: 0.7760 (OUTLIER) cc_final: 0.7527 (t) REVERT: A 762 MET cc_start: 0.8363 (mmt) cc_final: 0.8114 (mmt) REVERT: A 763 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 765 LYS cc_start: 0.8831 (ptpt) cc_final: 0.8613 (ptpt) REVERT: A 797 HIS cc_start: 0.7856 (m90) cc_final: 0.7487 (m90) REVERT: A 821 MET cc_start: 0.8135 (ttt) cc_final: 0.7844 (ttt) REVERT: A 825 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7143 (mm-30) REVERT: A 828 ASN cc_start: 0.8000 (m-40) cc_final: 0.7776 (t0) REVERT: A 829 ILE cc_start: 0.8498 (pt) cc_final: 0.8204 (tt) REVERT: A 838 GLN cc_start: 0.8689 (mm110) cc_final: 0.8333 (mm110) REVERT: A 863 LEU cc_start: 0.9129 (tp) cc_final: 0.8836 (tp) REVERT: A 870 LEU cc_start: 0.8707 (mm) cc_final: 0.8147 (mm) REVERT: A 871 MET cc_start: 0.8044 (mmp) cc_final: 0.7369 (mmp) REVERT: A 896 ARG cc_start: 0.7213 (tpm170) cc_final: 0.6596 (tpm170) REVERT: A 946 GLU cc_start: 0.7000 (pp20) cc_final: 0.6549 (pp20) REVERT: A 1000 GLU cc_start: 0.6917 (tp30) cc_final: 0.6627 (tp30) REVERT: A 1022 GLU cc_start: 0.7720 (tt0) cc_final: 0.7444 (tt0) REVERT: A 1052 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8292 (mtmt) REVERT: A 1069 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8141 (mmmt) REVERT: A 1099 ASP cc_start: 0.7971 (t0) cc_final: 0.7606 (t0) REVERT: A 1109 LYS cc_start: 0.8336 (tmtt) cc_final: 0.8096 (tttp) REVERT: A 1113 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7332 (tm-30) REVERT: A 1133 ARG cc_start: 0.8259 (ptp-110) cc_final: 0.8006 (ptp-110) REVERT: A 1146 LYS cc_start: 0.8006 (ttmm) cc_final: 0.7685 (ttmm) REVERT: A 1161 GLU cc_start: 0.7328 (tp30) cc_final: 0.6931 (tp30) REVERT: A 1202 ASP cc_start: 0.7735 (p0) cc_final: 0.7196 (p0) REVERT: A 1211 LEU cc_start: 0.8515 (mm) cc_final: 0.8268 (mp) REVERT: A 1225 HIS cc_start: 0.8709 (t70) cc_final: 0.8330 (t-90) REVERT: A 1238 LYS cc_start: 0.7992 (mppt) cc_final: 0.7717 (mtmm) REVERT: A 1245 CYS cc_start: 0.7876 (t) cc_final: 0.7294 (t) REVERT: A 1290 MET cc_start: 0.6949 (mtt) cc_final: 0.6417 (mtt) REVERT: A 1334 ASP cc_start: 0.7563 (t0) cc_final: 0.7140 (m-30) REVERT: A 1347 MET cc_start: 0.7195 (mmp) cc_final: 0.6197 (mmt) REVERT: A 1394 ILE cc_start: 0.7459 (mm) cc_final: 0.7223 (mm) REVERT: B 269 ASN cc_start: 0.8025 (m110) cc_final: 0.7616 (m110) REVERT: C 7 VAL cc_start: 0.8907 (p) cc_final: 0.8646 (m) REVERT: C 44 ASN cc_start: 0.8702 (t0) cc_final: 0.8334 (t0) REVERT: C 70 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7687 (mp0) REVERT: C 71 LEU cc_start: 0.8195 (pt) cc_final: 0.7988 (pt) REVERT: C 95 LYS cc_start: 0.8995 (ttmm) cc_final: 0.8781 (ttmm) REVERT: C 103 GLU cc_start: 0.7950 (pm20) cc_final: 0.7748 (pm20) REVERT: C 116 ASP cc_start: 0.7943 (m-30) cc_final: 0.7698 (m-30) REVERT: C 117 GLN cc_start: 0.8840 (tt0) cc_final: 0.8478 (tt0) REVERT: C 121 GLU cc_start: 0.8529 (mt-10) cc_final: 0.6435 (mt-10) REVERT: C 122 GLU cc_start: 0.8109 (tp30) cc_final: 0.7843 (tp30) REVERT: C 184 TYR cc_start: 0.8639 (p90) cc_final: 0.8391 (p90) REVERT: C 222 PHE cc_start: 0.8598 (t80) cc_final: 0.8238 (t80) REVERT: C 240 ASP cc_start: 0.8180 (t0) cc_final: 0.7741 (t0) REVERT: C 250 GLU cc_start: 0.7954 (tp30) cc_final: 0.7628 (tp30) REVERT: C 256 SER cc_start: 0.9148 (m) cc_final: 0.8646 (t) REVERT: C 267 LYS cc_start: 0.8519 (ptmm) cc_final: 0.8192 (ptmt) REVERT: C 278 ASP cc_start: 0.8122 (t0) cc_final: 0.7889 (t0) REVERT: C 308 ASP cc_start: 0.7993 (m-30) cc_final: 0.7485 (m-30) REVERT: C 336 GLU cc_start: 0.8298 (tt0) cc_final: 0.7781 (tt0) REVERT: C 337 SER cc_start: 0.8913 (t) cc_final: 0.8554 (p) REVERT: C 416 ARG cc_start: 0.8074 (ttt90) cc_final: 0.7855 (ttt90) REVERT: C 418 GLU cc_start: 0.8081 (tt0) cc_final: 0.7634 (tt0) REVERT: D 98 SER cc_start: 0.8936 (t) cc_final: 0.8705 (t) REVERT: D 103 MET cc_start: 0.8633 (ttm) cc_final: 0.8337 (ttm) REVERT: D 119 LEU cc_start: 0.8873 (tt) cc_final: 0.8668 (tt) REVERT: D 173 ARG cc_start: 0.8711 (mtt90) cc_final: 0.8061 (mtt90) REVERT: D 194 ARG cc_start: 0.7918 (ttt90) cc_final: 0.7691 (ttt90) REVERT: D 223 ASN cc_start: 0.8120 (t0) cc_final: 0.7866 (t0) REVERT: D 228 ASN cc_start: 0.8413 (m110) cc_final: 0.8114 (m110) REVERT: D 231 ASN cc_start: 0.8156 (OUTLIER) cc_final: 0.7731 (t0) REVERT: D 262 LYS cc_start: 0.8621 (mttm) cc_final: 0.8420 (mmmm) REVERT: E 45 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7541 (mm-30) REVERT: E 123 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7794 (mt-10) REVERT: E 134 LYS cc_start: 0.8300 (mtmm) cc_final: 0.8010 (mtmm) REVERT: E 253 ASP cc_start: 0.7821 (m-30) cc_final: 0.7554 (m-30) REVERT: E 264 ASP cc_start: 0.7368 (t0) cc_final: 0.7109 (t0) REVERT: E 273 LEU cc_start: 0.7766 (tp) cc_final: 0.7557 (tp) REVERT: E 312 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7861 (mm-30) REVERT: E 351 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7779 (mt-10) REVERT: E 379 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7604 (mt-10) REVERT: E 438 ASP cc_start: 0.7639 (m-30) cc_final: 0.7105 (m-30) REVERT: F 32 ASP cc_start: 0.8048 (m-30) cc_final: 0.7724 (m-30) REVERT: F 47 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8317 (mm-40) REVERT: F 142 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7545 (mt-10) REVERT: F 185 LEU cc_start: 0.8363 (mt) cc_final: 0.8096 (mm) REVERT: F 193 ASP cc_start: 0.7657 (t0) cc_final: 0.7091 (t0) REVERT: F 204 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7611 (mmm-85) REVERT: F 229 LEU cc_start: 0.8748 (tt) cc_final: 0.8362 (tp) REVERT: F 231 LYS cc_start: 0.8658 (ptpt) cc_final: 0.8431 (ptpt) REVERT: F 232 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7503 (mtp85) REVERT: F 261 ASP cc_start: 0.7726 (t0) cc_final: 0.7474 (t0) REVERT: F 287 GLU cc_start: 0.7988 (tt0) cc_final: 0.7764 (tt0) REVERT: F 302 ASP cc_start: 0.7542 (t0) cc_final: 0.7241 (t0) REVERT: F 315 ASP cc_start: 0.7793 (t0) cc_final: 0.7585 (t0) REVERT: F 317 PHE cc_start: 0.8213 (m-80) cc_final: 0.7985 (m-10) REVERT: F 349 ASP cc_start: 0.7752 (t70) cc_final: 0.7365 (t70) REVERT: F 389 LYS cc_start: 0.8424 (tttm) cc_final: 0.8166 (tttm) REVERT: F 393 GLU cc_start: 0.7857 (tp30) cc_final: 0.7578 (tp30) REVERT: F 412 LYS cc_start: 0.7438 (tptm) cc_final: 0.7227 (tptt) REVERT: F 413 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8077 (ttp80) REVERT: F 442 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7599 (mt-10) REVERT: F 444 GLU cc_start: 0.7827 (tt0) cc_final: 0.7592 (tt0) REVERT: G 52 ILE cc_start: 0.8043 (mm) cc_final: 0.7828 (mt) REVERT: G 69 LYS cc_start: 0.8334 (mtpp) cc_final: 0.7976 (mtpp) REVERT: G 99 LYS cc_start: 0.8342 (mmmt) cc_final: 0.8124 (mmmt) REVERT: G 116 LYS cc_start: 0.8448 (pttp) cc_final: 0.8138 (pttt) REVERT: G 134 LYS cc_start: 0.8228 (mtmm) cc_final: 0.7964 (mtmm) REVERT: G 194 VAL cc_start: 0.8711 (m) cc_final: 0.8474 (p) REVERT: G 198 ASP cc_start: 0.7407 (m-30) cc_final: 0.6858 (m-30) REVERT: G 199 VAL cc_start: 0.8995 (p) cc_final: 0.8737 (m) REVERT: G 210 LYS cc_start: 0.8196 (tppt) cc_final: 0.7676 (tppt) REVERT: G 216 ASP cc_start: 0.7859 (m-30) cc_final: 0.7434 (m-30) REVERT: G 234 LYS cc_start: 0.8386 (mttm) cc_final: 0.8109 (mttm) REVERT: G 240 LYS cc_start: 0.8375 (mtmm) cc_final: 0.8057 (mtmm) REVERT: G 287 GLU cc_start: 0.7853 (tp30) cc_final: 0.7146 (tp30) REVERT: G 406 MET cc_start: 0.8331 (mtm) cc_final: 0.8078 (mtm) REVERT: G 427 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7631 (tm-30) REVERT: G 431 ARG cc_start: 0.8018 (mtm-85) cc_final: 0.7737 (mtm110) REVERT: G 433 GLU cc_start: 0.7568 (mp0) cc_final: 0.7192 (mp0) REVERT: G 443 LYS cc_start: 0.8488 (ttmt) cc_final: 0.8213 (ttmt) REVERT: G 452 SER cc_start: 0.7960 (m) cc_final: 0.7632 (m) REVERT: H 49 GLN cc_start: 0.8040 (mm-40) cc_final: 0.7712 (mm110) REVERT: H 144 GLN cc_start: 0.7467 (tt0) cc_final: 0.7252 (tt0) REVERT: H 166 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7438 (tm-30) REVERT: H 175 MET cc_start: 0.8275 (tpp) cc_final: 0.7739 (tpp) REVERT: H 176 ILE cc_start: 0.8390 (mt) cc_final: 0.8174 (mt) REVERT: H 185 LEU cc_start: 0.7900 (mt) cc_final: 0.7366 (mt) REVERT: H 188 ASP cc_start: 0.7754 (m-30) cc_final: 0.7441 (m-30) REVERT: H 198 LYS cc_start: 0.7688 (tptp) cc_final: 0.7383 (tptp) REVERT: H 199 ILE cc_start: 0.8711 (mt) cc_final: 0.8304 (mt) REVERT: H 211 ASP cc_start: 0.8094 (m-30) cc_final: 0.7661 (m-30) REVERT: H 252 GLN cc_start: 0.8206 (mm-40) cc_final: 0.8005 (mm-40) REVERT: H 270 ARG cc_start: 0.8261 (mtt-85) cc_final: 0.8035 (mtt-85) REVERT: H 271 ASP cc_start: 0.7720 (m-30) cc_final: 0.7198 (m-30) REVERT: H 282 GLU cc_start: 0.8255 (tp30) cc_final: 0.8018 (tp30) REVERT: H 331 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8166 (ttmm) REVERT: H 336 ASN cc_start: 0.7954 (p0) cc_final: 0.7726 (p0) REVERT: H 349 ASP cc_start: 0.8129 (t0) cc_final: 0.7828 (t0) REVERT: H 374 GLU cc_start: 0.8133 (tp30) cc_final: 0.7737 (tp30) REVERT: H 438 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7942 (ttmt) REVERT: I 52 ILE cc_start: 0.8034 (mm) cc_final: 0.7637 (mm) REVERT: I 53 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8176 (mt-10) REVERT: I 127 ARG cc_start: 0.8154 (ttm170) cc_final: 0.7889 (ttm170) REVERT: I 133 ILE cc_start: 0.8906 (tt) cc_final: 0.8637 (pt) REVERT: I 138 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7476 (mt-10) REVERT: I 182 ASP cc_start: 0.7926 (m-30) cc_final: 0.7451 (m-30) REVERT: I 187 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7725 (mt-10) REVERT: I 210 LYS cc_start: 0.8300 (ttpt) cc_final: 0.8022 (ttpt) REVERT: I 258 ARG cc_start: 0.7834 (mtm-85) cc_final: 0.7610 (mtm-85) REVERT: I 268 MET cc_start: 0.7294 (ttp) cc_final: 0.7083 (ttp) REVERT: I 279 GLU cc_start: 0.7513 (pt0) cc_final: 0.7264 (pt0) REVERT: I 325 ASN cc_start: 0.8100 (m110) cc_final: 0.7888 (m110) REVERT: I 386 ARG cc_start: 0.8267 (mmm-85) cc_final: 0.7953 (mmm160) REVERT: I 406 MET cc_start: 0.8613 (ttp) cc_final: 0.8240 (ttm) REVERT: I 417 GLN cc_start: 0.8026 (mt0) cc_final: 0.7773 (mt0) REVERT: I 443 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8289 (mtpt) REVERT: J 36 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8077 (mm-40) REVERT: J 128 LYS cc_start: 0.8234 (mtpp) cc_final: 0.7916 (mtpp) REVERT: J 157 LYS cc_start: 0.8348 (mttm) cc_final: 0.8088 (mttm) REVERT: J 170 GLU cc_start: 0.7262 (mp0) cc_final: 0.6846 (mp0) REVERT: J 268 GLU cc_start: 0.7685 (pm20) cc_final: 0.6869 (mp0) REVERT: J 297 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7442 (mm-30) REVERT: J 350 ARG cc_start: 0.7908 (ttm110) cc_final: 0.7564 (ttm110) REVERT: J 357 LYS cc_start: 0.8155 (mmpt) cc_final: 0.7933 (mmpt) REVERT: J 361 GLU cc_start: 0.7593 (tt0) cc_final: 0.7303 (tm-30) REVERT: J 385 ASP cc_start: 0.7880 (t70) cc_final: 0.7674 (t70) REVERT: J 389 LYS cc_start: 0.8527 (ptmm) cc_final: 0.8237 (ptmm) REVERT: J 393 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7626 (mt-10) REVERT: J 405 VAL cc_start: 0.8160 (t) cc_final: 0.7883 (m) REVERT: J 438 LYS cc_start: 0.8218 (tmtt) cc_final: 0.8002 (tmtt) REVERT: J 451 GLN cc_start: 0.8517 (mm-40) cc_final: 0.8256 (mm-40) outliers start: 59 outliers final: 34 residues processed: 1300 average time/residue: 0.6302 time to fit residues: 1263.1841 Evaluate side-chains 1290 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 1253 time to evaluate : 4.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1076 ASN Chi-restraints excluded: chain A residue 1110 GLN Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 110 GLU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 429 LYS Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 406 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 362 GLN Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 414 LYS Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 443 LYS Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 132 GLU Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 252 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 380 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 176 optimal weight: 0.0980 chunk 384 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 331 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 435 GLN D 109 ASN E 256 ASN E 263 GLN F 446 GLN G 256 ASN ** H 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 GLN J 63 ASN J 248 ASN J 299 HIS J 310 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.128731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.108928 restraints weight = 55468.469| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.22 r_work: 0.3236 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 33764 Z= 0.248 Angle : 0.630 13.942 45853 Z= 0.323 Chirality : 0.045 0.205 5344 Planarity : 0.004 0.057 5653 Dihedral : 14.570 177.453 5012 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.65 % Allowed : 14.91 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.13), residues: 4008 helix: 1.46 (0.12), residues: 1831 sheet: 0.36 (0.19), residues: 711 loop : -0.44 (0.16), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 864 HIS 0.009 0.001 HIS C 97 PHE 0.018 0.002 PHE B 637 TYR 0.031 0.002 TYR C 143 ARG 0.009 0.001 ARG H 266 Details of bonding type rmsd hydrogen bonds : bond 0.05003 ( 1460) hydrogen bonds : angle 4.35014 ( 4148) metal coordination : bond 0.01073 ( 7) metal coordination : angle 3.26639 ( 6) covalent geometry : bond 0.00555 (33757) covalent geometry : angle 0.62878 (45847) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1269 time to evaluate : 3.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 745 TRP cc_start: 0.7152 (m100) cc_final: 0.6540 (m-10) REVERT: A 752 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7738 (t) REVERT: A 761 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7571 (tm-30) REVERT: A 763 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7739 (mm-30) REVERT: A 765 LYS cc_start: 0.8716 (ptpt) cc_final: 0.8439 (ptpt) REVERT: A 797 HIS cc_start: 0.7976 (m90) cc_final: 0.7688 (m90) REVERT: A 821 MET cc_start: 0.8106 (ttt) cc_final: 0.7750 (ttt) REVERT: A 825 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7142 (mm-30) REVERT: A 829 ILE cc_start: 0.8483 (pt) cc_final: 0.8153 (tt) REVERT: A 837 TRP cc_start: 0.8076 (t60) cc_final: 0.7573 (t60) REVERT: A 841 LEU cc_start: 0.8332 (tt) cc_final: 0.8020 (tp) REVERT: A 862 GLU cc_start: 0.7984 (mp0) cc_final: 0.7339 (mp0) REVERT: A 870 LEU cc_start: 0.8765 (mm) cc_final: 0.8298 (mm) REVERT: A 871 MET cc_start: 0.8242 (mmp) cc_final: 0.7667 (mmp) REVERT: A 938 GLU cc_start: 0.7622 (tp30) cc_final: 0.7294 (tp30) REVERT: A 946 GLU cc_start: 0.6958 (pp20) cc_final: 0.6564 (pp20) REVERT: A 1000 GLU cc_start: 0.6949 (tp30) cc_final: 0.6654 (tp30) REVERT: A 1011 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: A 1022 GLU cc_start: 0.7766 (tt0) cc_final: 0.7416 (tt0) REVERT: A 1052 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8254 (mtmt) REVERT: A 1069 LYS cc_start: 0.8491 (mmmt) cc_final: 0.8109 (mmmt) REVERT: A 1073 GLU cc_start: 0.7994 (pt0) cc_final: 0.7776 (pt0) REVERT: A 1099 ASP cc_start: 0.7929 (t0) cc_final: 0.7586 (t0) REVERT: A 1109 LYS cc_start: 0.8424 (tmtt) cc_final: 0.8178 (tttp) REVERT: A 1113 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 1133 ARG cc_start: 0.8278 (ptp-110) cc_final: 0.8013 (ptp-110) REVERT: A 1146 LYS cc_start: 0.8012 (ttmm) cc_final: 0.7711 (ttmm) REVERT: A 1161 GLU cc_start: 0.7375 (tp30) cc_final: 0.6989 (tp30) REVERT: A 1202 ASP cc_start: 0.7773 (p0) cc_final: 0.7252 (p0) REVERT: A 1211 LEU cc_start: 0.8610 (mm) cc_final: 0.8361 (mp) REVERT: A 1238 LYS cc_start: 0.7939 (mppt) cc_final: 0.7669 (mtmm) REVERT: A 1245 CYS cc_start: 0.8018 (t) cc_final: 0.7472 (t) REVERT: A 1290 MET cc_start: 0.7014 (mtt) cc_final: 0.6495 (mtt) REVERT: A 1347 MET cc_start: 0.7241 (mmp) cc_final: 0.6364 (mmt) REVERT: A 1394 ILE cc_start: 0.7571 (mm) cc_final: 0.7322 (mm) REVERT: B 269 ASN cc_start: 0.8072 (m110) cc_final: 0.7687 (m110) REVERT: C 44 ASN cc_start: 0.8661 (t0) cc_final: 0.8325 (t0) REVERT: C 78 TYR cc_start: 0.8834 (t80) cc_final: 0.8593 (t80) REVERT: C 95 LYS cc_start: 0.9063 (ttmm) cc_final: 0.8787 (ttmm) REVERT: C 103 GLU cc_start: 0.7966 (pm20) cc_final: 0.7761 (pm20) REVERT: C 116 ASP cc_start: 0.7981 (m-30) cc_final: 0.7773 (m-30) REVERT: C 122 GLU cc_start: 0.8187 (tp30) cc_final: 0.7936 (tp30) REVERT: C 184 TYR cc_start: 0.8676 (p90) cc_final: 0.8413 (p90) REVERT: C 239 MET cc_start: 0.7969 (tpp) cc_final: 0.7544 (tpp) REVERT: C 240 ASP cc_start: 0.8133 (t0) cc_final: 0.7772 (t0) REVERT: C 250 GLU cc_start: 0.8042 (tp30) cc_final: 0.7733 (tp30) REVERT: C 256 SER cc_start: 0.9144 (m) cc_final: 0.8745 (t) REVERT: C 269 LYS cc_start: 0.8492 (tppt) cc_final: 0.8275 (tppt) REVERT: C 278 ASP cc_start: 0.8031 (t0) cc_final: 0.7818 (t70) REVERT: C 337 SER cc_start: 0.8917 (t) cc_final: 0.8598 (p) REVERT: C 435 GLN cc_start: 0.8784 (mm110) cc_final: 0.8563 (mm110) REVERT: D 103 MET cc_start: 0.8628 (ttm) cc_final: 0.8378 (ttm) REVERT: D 173 ARG cc_start: 0.8673 (mtt90) cc_final: 0.8057 (mtt90) REVERT: D 219 LEU cc_start: 0.8930 (mm) cc_final: 0.8679 (mp) REVERT: D 228 ASN cc_start: 0.8483 (m110) cc_final: 0.8112 (m110) REVERT: E 123 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7817 (mt-10) REVERT: E 134 LYS cc_start: 0.8222 (mtmm) cc_final: 0.7919 (mtmm) REVERT: E 135 GLU cc_start: 0.7554 (tt0) cc_final: 0.7232 (tt0) REVERT: E 241 LYS cc_start: 0.8523 (ptmt) cc_final: 0.8113 (ptmt) REVERT: E 253 ASP cc_start: 0.7847 (m-30) cc_final: 0.7600 (m-30) REVERT: E 263 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8608 (mt0) REVERT: E 264 ASP cc_start: 0.7445 (t0) cc_final: 0.7127 (t0) REVERT: E 266 ILE cc_start: 0.8325 (mt) cc_final: 0.8052 (mt) REVERT: E 312 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7813 (mm-30) REVERT: E 379 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7656 (mt-10) REVERT: E 438 ASP cc_start: 0.7640 (m-30) cc_final: 0.7110 (m-30) REVERT: F 32 ASP cc_start: 0.8043 (m-30) cc_final: 0.7688 (m-30) REVERT: F 142 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7586 (mt-10) REVERT: F 179 LEU cc_start: 0.8050 (mt) cc_final: 0.7821 (mt) REVERT: F 193 ASP cc_start: 0.7638 (t0) cc_final: 0.7093 (t0) REVERT: F 204 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7935 (mmm-85) REVERT: F 229 LEU cc_start: 0.8761 (tt) cc_final: 0.8489 (tt) REVERT: F 231 LYS cc_start: 0.8649 (ptpt) cc_final: 0.8412 (ptpp) REVERT: F 232 ARG cc_start: 0.7878 (mtp85) cc_final: 0.7549 (mtp85) REVERT: F 233 LYS cc_start: 0.8447 (ptmt) cc_final: 0.8195 (ptmt) REVERT: F 261 ASP cc_start: 0.7761 (t0) cc_final: 0.7515 (t0) REVERT: F 302 ASP cc_start: 0.7736 (t0) cc_final: 0.7373 (t0) REVERT: F 315 ASP cc_start: 0.7707 (t0) cc_final: 0.7494 (t0) REVERT: F 317 PHE cc_start: 0.8227 (m-80) cc_final: 0.8019 (m-10) REVERT: F 349 ASP cc_start: 0.7864 (t70) cc_final: 0.7546 (t70) REVERT: F 377 VAL cc_start: 0.8527 (t) cc_final: 0.8238 (p) REVERT: F 389 LYS cc_start: 0.8474 (tttm) cc_final: 0.8201 (tttm) REVERT: F 393 GLU cc_start: 0.7934 (tp30) cc_final: 0.7652 (tp30) REVERT: F 413 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8206 (ttp80) REVERT: F 442 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7581 (mt-10) REVERT: F 444 GLU cc_start: 0.7879 (tt0) cc_final: 0.7628 (tt0) REVERT: G 69 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8071 (mtpp) REVERT: G 116 LYS cc_start: 0.8515 (pttp) cc_final: 0.8306 (pttm) REVERT: G 134 LYS cc_start: 0.8249 (mtmm) cc_final: 0.7978 (mtmm) REVERT: G 194 VAL cc_start: 0.8714 (m) cc_final: 0.8472 (p) REVERT: G 198 ASP cc_start: 0.7380 (m-30) cc_final: 0.6841 (m-30) REVERT: G 199 VAL cc_start: 0.8968 (p) cc_final: 0.8719 (m) REVERT: G 210 LYS cc_start: 0.8237 (tppt) cc_final: 0.7702 (tppt) REVERT: G 216 ASP cc_start: 0.7962 (m-30) cc_final: 0.7556 (m-30) REVERT: G 234 LYS cc_start: 0.8419 (mttm) cc_final: 0.8131 (mttm) REVERT: G 240 LYS cc_start: 0.8397 (mtmm) cc_final: 0.8088 (mtmm) REVERT: G 287 GLU cc_start: 0.7880 (tp30) cc_final: 0.7107 (tp30) REVERT: G 294 LYS cc_start: 0.8773 (tttm) cc_final: 0.8403 (tttm) REVERT: G 406 MET cc_start: 0.8345 (mtm) cc_final: 0.8107 (mtm) REVERT: G 427 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7645 (tm-30) REVERT: G 433 GLU cc_start: 0.7604 (mp0) cc_final: 0.7317 (mp0) REVERT: G 443 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8246 (ttmt) REVERT: H 49 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7885 (mm110) REVERT: H 115 GLU cc_start: 0.8544 (tp30) cc_final: 0.8077 (mm-30) REVERT: H 144 GLN cc_start: 0.7503 (tt0) cc_final: 0.7299 (tt0) REVERT: H 157 LYS cc_start: 0.8098 (mtmm) cc_final: 0.7722 (mtmm) REVERT: H 165 MET cc_start: 0.8285 (tpt) cc_final: 0.8060 (tpt) REVERT: H 166 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7490 (tm-30) REVERT: H 175 MET cc_start: 0.8284 (tpp) cc_final: 0.7672 (tpp) REVERT: H 185 LEU cc_start: 0.7865 (mt) cc_final: 0.7444 (mt) REVERT: H 188 ASP cc_start: 0.7776 (m-30) cc_final: 0.7518 (m-30) REVERT: H 194 LYS cc_start: 0.8053 (tttt) cc_final: 0.7495 (mttt) REVERT: H 198 LYS cc_start: 0.7668 (tptp) cc_final: 0.7373 (tptp) REVERT: H 199 ILE cc_start: 0.8719 (mt) cc_final: 0.8353 (mt) REVERT: H 229 LEU cc_start: 0.8446 (mm) cc_final: 0.8220 (mm) REVERT: H 252 GLN cc_start: 0.8187 (mm-40) cc_final: 0.7930 (mm-40) REVERT: H 264 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6819 (mp0) REVERT: H 271 ASP cc_start: 0.7696 (m-30) cc_final: 0.7179 (m-30) REVERT: H 331 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8212 (ttmm) REVERT: H 336 ASN cc_start: 0.8002 (p0) cc_final: 0.7755 (p0) REVERT: H 349 ASP cc_start: 0.8147 (t0) cc_final: 0.7902 (t0) REVERT: H 374 GLU cc_start: 0.8103 (tp30) cc_final: 0.7687 (tp30) REVERT: H 438 LYS cc_start: 0.8323 (ttmt) cc_final: 0.8070 (ttmt) REVERT: I 52 ILE cc_start: 0.8206 (mm) cc_final: 0.7778 (mm) REVERT: I 127 ARG cc_start: 0.8101 (ttm170) cc_final: 0.7838 (ttm170) REVERT: I 133 ILE cc_start: 0.8925 (tt) cc_final: 0.8635 (pt) REVERT: I 135 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: I 138 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7490 (mt-10) REVERT: I 150 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7140 (mm-30) REVERT: I 182 ASP cc_start: 0.7928 (m-30) cc_final: 0.7421 (m-30) REVERT: I 187 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7802 (mt-10) REVERT: I 210 LYS cc_start: 0.8355 (ttpt) cc_final: 0.8094 (ttpt) REVERT: I 223 ASP cc_start: 0.7190 (p0) cc_final: 0.6169 (p0) REVERT: I 258 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7683 (mtm-85) REVERT: I 268 MET cc_start: 0.7422 (ttp) cc_final: 0.7160 (ttp) REVERT: I 279 GLU cc_start: 0.7492 (pt0) cc_final: 0.7229 (pt0) REVERT: I 290 LYS cc_start: 0.8453 (mttm) cc_final: 0.8228 (mttt) REVERT: I 312 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: I 313 VAL cc_start: 0.8830 (p) cc_final: 0.8562 (m) REVERT: I 317 ASP cc_start: 0.7537 (t70) cc_final: 0.7304 (t0) REVERT: I 386 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.7982 (mmm160) REVERT: I 392 ARG cc_start: 0.7936 (mtm180) cc_final: 0.7703 (mtt180) REVERT: I 406 MET cc_start: 0.8593 (ttp) cc_final: 0.8214 (ttm) REVERT: I 417 GLN cc_start: 0.8050 (mt0) cc_final: 0.7797 (mt0) REVERT: J 128 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7932 (mtpp) REVERT: J 145 ILE cc_start: 0.8494 (mm) cc_final: 0.8222 (mm) REVERT: J 157 LYS cc_start: 0.8404 (mttm) cc_final: 0.8158 (mttm) REVERT: J 170 GLU cc_start: 0.7337 (mp0) cc_final: 0.6630 (mp0) REVERT: J 248 ASN cc_start: 0.8563 (m110) cc_final: 0.8198 (m-40) REVERT: J 252 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.8091 (mt0) REVERT: J 268 GLU cc_start: 0.7853 (pm20) cc_final: 0.7061 (mp0) REVERT: J 297 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7432 (mm-30) REVERT: J 349 ASP cc_start: 0.8142 (t0) cc_final: 0.7889 (t0) REVERT: J 350 ARG cc_start: 0.7894 (ttm110) cc_final: 0.7558 (ttm110) REVERT: J 357 LYS cc_start: 0.8152 (mmpt) cc_final: 0.7921 (mmpt) REVERT: J 365 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7958 (ttmt) REVERT: J 385 ASP cc_start: 0.7879 (t70) cc_final: 0.7578 (t70) REVERT: J 389 LYS cc_start: 0.8548 (ptmm) cc_final: 0.8262 (ptmm) REVERT: J 393 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7642 (mt-10) REVERT: J 405 VAL cc_start: 0.8225 (t) cc_final: 0.7989 (m) REVERT: J 414 LYS cc_start: 0.8424 (mptt) cc_final: 0.8192 (mptt) REVERT: J 438 LYS cc_start: 0.8214 (tmtt) cc_final: 0.7963 (tmtt) REVERT: J 451 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8210 (mm-40) outliers start: 94 outliers final: 67 residues processed: 1295 average time/residue: 0.5671 time to fit residues: 1133.5557 Evaluate side-chains 1342 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 1269 time to evaluate : 3.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1076 ASN Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 400 MET Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 429 LYS Chi-restraints excluded: chain D residue 113 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 263 GLN Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 406 MET Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 65 THR Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain G residue 313 VAL Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain H residue 168 ILE Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 414 LYS Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 448 ILE Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 191 ARG Chi-restraints excluded: chain I residue 193 LYS Chi-restraints excluded: chain I residue 312 GLU Chi-restraints excluded: chain I residue 394 GLN Chi-restraints excluded: chain I residue 428 THR Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 238 THR Chi-restraints excluded: chain J residue 252 GLN Chi-restraints excluded: chain J residue 450 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 169 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 315 optimal weight: 0.0980 chunk 195 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 221 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 354 optimal weight: 1.9990 chunk 287 optimal weight: 4.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 702 GLN A1242 GLN D 109 ASN E 256 ASN E 325 ASN G 245 GLN G 256 ASN G 286 GLN H 274 ASN ** H 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 443 ASN ** I 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 63 ASN J 310 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.130269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.110352 restraints weight = 55300.442| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.24 r_work: 0.3259 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 33764 Z= 0.150 Angle : 0.593 13.096 45853 Z= 0.299 Chirality : 0.043 0.176 5344 Planarity : 0.004 0.058 5653 Dihedral : 14.513 177.198 5012 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.76 % Allowed : 17.27 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.13), residues: 4008 helix: 1.53 (0.12), residues: 1837 sheet: 0.30 (0.19), residues: 702 loop : -0.50 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 864 HIS 0.006 0.001 HIS C 319 PHE 0.032 0.001 PHE B 259 TYR 0.031 0.002 TYR C 143 ARG 0.008 0.000 ARG I 43 Details of bonding type rmsd hydrogen bonds : bond 0.04146 ( 1460) hydrogen bonds : angle 4.17973 ( 4148) metal coordination : bond 0.00740 ( 7) metal coordination : angle 4.13349 ( 6) covalent geometry : bond 0.00338 (33757) covalent geometry : angle 0.59081 (45847) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1373 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 1275 time to evaluate : 4.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 745 TRP cc_start: 0.7168 (m100) cc_final: 0.6690 (m-10) REVERT: A 752 VAL cc_start: 0.7916 (OUTLIER) cc_final: 0.7628 (t) REVERT: A 761 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7923 (tm-30) REVERT: A 763 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7706 (mm-30) REVERT: A 765 LYS cc_start: 0.8813 (ptpt) cc_final: 0.8475 (ptpp) REVERT: A 797 HIS cc_start: 0.7867 (m90) cc_final: 0.7655 (m90) REVERT: A 821 MET cc_start: 0.8102 (ttt) cc_final: 0.7724 (ttt) REVERT: A 825 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7156 (mm-30) REVERT: A 829 ILE cc_start: 0.8536 (pt) cc_final: 0.8159 (tt) REVERT: A 837 TRP cc_start: 0.8170 (t60) cc_final: 0.7793 (t60) REVERT: A 838 GLN cc_start: 0.8716 (mm110) cc_final: 0.8257 (mm110) REVERT: A 841 LEU cc_start: 0.8304 (tt) cc_final: 0.7966 (tp) REVERT: A 862 GLU cc_start: 0.8008 (mp0) cc_final: 0.7373 (mp0) REVERT: A 868 TYR cc_start: 0.7847 (t80) cc_final: 0.7516 (t80) REVERT: A 870 LEU cc_start: 0.8762 (mm) cc_final: 0.8531 (mm) REVERT: A 871 MET cc_start: 0.8073 (mmp) cc_final: 0.7759 (mmp) REVERT: A 926 ARG cc_start: 0.8245 (mtt180) cc_final: 0.7973 (mtp180) REVERT: A 946 GLU cc_start: 0.6942 (pp20) cc_final: 0.6562 (pp20) REVERT: A 1000 GLU cc_start: 0.6981 (tp30) cc_final: 0.6682 (tp30) REVERT: A 1011 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: A 1022 GLU cc_start: 0.7684 (tt0) cc_final: 0.7330 (tt0) REVERT: A 1052 LYS cc_start: 0.8542 (mtmt) cc_final: 0.8281 (mtmt) REVERT: A 1073 GLU cc_start: 0.7924 (pt0) cc_final: 0.7652 (pt0) REVERT: A 1079 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7548 (ttp80) REVERT: A 1099 ASP cc_start: 0.7956 (t0) cc_final: 0.7588 (t0) REVERT: A 1109 LYS cc_start: 0.8379 (tmtt) cc_final: 0.8115 (tttp) REVERT: A 1113 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7359 (tm-30) REVERT: A 1133 ARG cc_start: 0.8282 (ptp-110) cc_final: 0.8034 (ptp-110) REVERT: A 1146 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7740 (ttmm) REVERT: A 1161 GLU cc_start: 0.7377 (tp30) cc_final: 0.6978 (tp30) REVERT: A 1202 ASP cc_start: 0.7714 (p0) cc_final: 0.7222 (p0) REVERT: A 1211 LEU cc_start: 0.8568 (mm) cc_final: 0.8333 (mp) REVERT: A 1238 LYS cc_start: 0.7894 (mppt) cc_final: 0.7633 (mtmm) REVERT: A 1245 CYS cc_start: 0.7914 (t) cc_final: 0.7287 (t) REVERT: A 1290 MET cc_start: 0.7044 (mtt) cc_final: 0.6519 (mtt) REVERT: A 1330 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8128 (tt) REVERT: A 1394 ILE cc_start: 0.7575 (mm) cc_final: 0.7318 (mm) REVERT: B 269 ASN cc_start: 0.8027 (m110) cc_final: 0.7613 (m110) REVERT: C 7 VAL cc_start: 0.8909 (p) cc_final: 0.8548 (m) REVERT: C 44 ASN cc_start: 0.8696 (t0) cc_final: 0.8340 (t0) REVERT: C 57 PHE cc_start: 0.8036 (m-80) cc_final: 0.7793 (m-10) REVERT: C 116 ASP cc_start: 0.8007 (m-30) cc_final: 0.7758 (m-30) REVERT: C 122 GLU cc_start: 0.8106 (tp30) cc_final: 0.7869 (tp30) REVERT: C 184 TYR cc_start: 0.8662 (p90) cc_final: 0.8381 (p90) REVERT: C 240 ASP cc_start: 0.8286 (t0) cc_final: 0.7876 (t0) REVERT: C 250 GLU cc_start: 0.8066 (tp30) cc_final: 0.7721 (tp30) REVERT: C 256 SER cc_start: 0.9136 (m) cc_final: 0.8717 (t) REVERT: C 265 LYS cc_start: 0.8579 (mmpt) cc_final: 0.8216 (mmtt) REVERT: C 269 LYS cc_start: 0.8438 (tppt) cc_final: 0.8226 (tppt) REVERT: C 336 GLU cc_start: 0.8179 (tt0) cc_final: 0.7909 (tt0) REVERT: C 337 SER cc_start: 0.8913 (t) cc_final: 0.8580 (p) REVERT: D 173 ARG cc_start: 0.8687 (mtt90) cc_final: 0.8054 (mtt90) REVERT: D 228 ASN cc_start: 0.8441 (m110) cc_final: 0.8210 (m110) REVERT: D 250 TYR cc_start: 0.8578 (p90) cc_final: 0.7088 (p90) REVERT: E 99 LYS cc_start: 0.8527 (tttp) cc_final: 0.8305 (tptp) REVERT: E 123 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7830 (mt-10) REVERT: E 134 LYS cc_start: 0.8220 (mtmm) cc_final: 0.7910 (mtmm) REVERT: E 241 LYS cc_start: 0.8494 (ptmt) cc_final: 0.8063 (ptmt) REVERT: E 258 ARG cc_start: 0.8028 (ptp90) cc_final: 0.7608 (ptp90) REVERT: E 264 ASP cc_start: 0.7379 (t0) cc_final: 0.7153 (t0) REVERT: E 312 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7783 (mm-30) REVERT: E 379 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7545 (mt-10) REVERT: E 438 ASP cc_start: 0.7600 (m-30) cc_final: 0.7060 (m-30) REVERT: E 441 GLU cc_start: 0.7875 (tp30) cc_final: 0.7219 (tp30) REVERT: F 32 ASP cc_start: 0.8017 (m-30) cc_final: 0.7658 (m-30) REVERT: F 128 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8155 (mtmm) REVERT: F 142 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7583 (mt-10) REVERT: F 179 LEU cc_start: 0.7966 (mt) cc_final: 0.7755 (mt) REVERT: F 185 LEU cc_start: 0.8346 (mt) cc_final: 0.8124 (mm) REVERT: F 204 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7921 (mmm-85) REVERT: F 229 LEU cc_start: 0.8780 (tt) cc_final: 0.8445 (tp) REVERT: F 231 LYS cc_start: 0.8661 (ptpt) cc_final: 0.8422 (ptpp) REVERT: F 232 ARG cc_start: 0.7878 (mtp85) cc_final: 0.7517 (mtp85) REVERT: F 233 LYS cc_start: 0.8438 (ptmt) cc_final: 0.8192 (ptmt) REVERT: F 349 ASP cc_start: 0.7848 (t70) cc_final: 0.7521 (t70) REVERT: F 377 VAL cc_start: 0.8521 (t) cc_final: 0.8239 (p) REVERT: F 389 LYS cc_start: 0.8476 (tttm) cc_final: 0.8211 (tttm) REVERT: F 393 GLU cc_start: 0.7940 (tp30) cc_final: 0.7659 (tp30) REVERT: F 405 VAL cc_start: 0.8473 (t) cc_final: 0.8223 (m) REVERT: F 413 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8233 (ttp80) REVERT: F 442 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7565 (mt-10) REVERT: F 444 GLU cc_start: 0.7787 (tt0) cc_final: 0.7545 (tt0) REVERT: G 23 ARG cc_start: 0.8620 (mmm-85) cc_final: 0.8419 (mmm-85) REVERT: G 69 LYS cc_start: 0.8354 (mtpp) cc_final: 0.7991 (mtpp) REVERT: G 108 SER cc_start: 0.8398 (t) cc_final: 0.8177 (m) REVERT: G 134 LYS cc_start: 0.8224 (mtmm) cc_final: 0.7962 (mtmm) REVERT: G 194 VAL cc_start: 0.8719 (m) cc_final: 0.8461 (p) REVERT: G 198 ASP cc_start: 0.7440 (m-30) cc_final: 0.6874 (m-30) REVERT: G 199 VAL cc_start: 0.8900 (p) cc_final: 0.8667 (m) REVERT: G 210 LYS cc_start: 0.8255 (tppt) cc_final: 0.7706 (tppt) REVERT: G 216 ASP cc_start: 0.7882 (m-30) cc_final: 0.7478 (m-30) REVERT: G 234 LYS cc_start: 0.8374 (mttm) cc_final: 0.8091 (mttm) REVERT: G 240 LYS cc_start: 0.8368 (mtmm) cc_final: 0.8083 (mtmm) REVERT: G 269 MET cc_start: 0.7525 (mpp) cc_final: 0.7068 (mpp) REVERT: G 287 GLU cc_start: 0.7896 (tp30) cc_final: 0.7150 (tp30) REVERT: G 294 LYS cc_start: 0.8773 (tttm) cc_final: 0.8369 (tttm) REVERT: G 315 MET cc_start: 0.8338 (mmp) cc_final: 0.8132 (mmm) REVERT: G 427 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7599 (tm-30) REVERT: G 431 ARG cc_start: 0.7960 (mtm-85) cc_final: 0.7653 (mtm110) REVERT: G 433 GLU cc_start: 0.7586 (mp0) cc_final: 0.7237 (mp0) REVERT: G 435 VAL cc_start: 0.7897 (OUTLIER) cc_final: 0.7409 (m) REVERT: G 443 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8218 (ttmt) REVERT: H 49 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7753 (mm110) REVERT: H 59 LYS cc_start: 0.8813 (mmmm) cc_final: 0.8608 (mmtp) REVERT: H 115 GLU cc_start: 0.8452 (tp30) cc_final: 0.8010 (mm-30) REVERT: H 157 LYS cc_start: 0.8076 (mtmm) cc_final: 0.7774 (mtmm) REVERT: H 166 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7480 (tm-30) REVERT: H 175 MET cc_start: 0.8295 (tpp) cc_final: 0.7777 (tpp) REVERT: H 185 LEU cc_start: 0.7869 (mt) cc_final: 0.7386 (mt) REVERT: H 188 ASP cc_start: 0.7725 (m-30) cc_final: 0.7475 (m-30) REVERT: H 198 LYS cc_start: 0.7667 (tptp) cc_final: 0.7357 (tptp) REVERT: H 199 ILE cc_start: 0.8663 (mt) cc_final: 0.8254 (mt) REVERT: H 271 ASP cc_start: 0.7632 (m-30) cc_final: 0.7125 (m-30) REVERT: H 331 LYS cc_start: 0.8496 (ttmm) cc_final: 0.8235 (ttmm) REVERT: H 336 ASN cc_start: 0.7935 (p0) cc_final: 0.7675 (p0) REVERT: H 349 ASP cc_start: 0.8151 (t0) cc_final: 0.7896 (t0) REVERT: H 374 GLU cc_start: 0.8155 (tp30) cc_final: 0.7757 (tp30) REVERT: H 422 ASP cc_start: 0.7904 (m-30) cc_final: 0.7596 (m-30) REVERT: H 438 LYS cc_start: 0.8313 (ttmt) cc_final: 0.8029 (ttmt) REVERT: I 52 ILE cc_start: 0.8081 (mm) cc_final: 0.7669 (mm) REVERT: I 127 ARG cc_start: 0.8139 (ttm170) cc_final: 0.7917 (ttm170) REVERT: I 133 ILE cc_start: 0.8913 (tt) cc_final: 0.8620 (pt) REVERT: I 135 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7658 (pt0) REVERT: I 138 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7432 (mt-10) REVERT: I 150 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7160 (mm-30) REVERT: I 182 ASP cc_start: 0.7850 (m-30) cc_final: 0.7358 (m-30) REVERT: I 187 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7748 (mt-10) REVERT: I 210 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8069 (ttpt) REVERT: I 223 ASP cc_start: 0.7175 (p0) cc_final: 0.6216 (p0) REVERT: I 258 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7627 (mtm-85) REVERT: I 268 MET cc_start: 0.7344 (ttp) cc_final: 0.7086 (ttp) REVERT: I 279 GLU cc_start: 0.7509 (pt0) cc_final: 0.7189 (pt0) REVERT: I 313 VAL cc_start: 0.8832 (p) cc_final: 0.8582 (m) REVERT: I 386 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.8016 (mmm160) REVERT: I 392 ARG cc_start: 0.7959 (mtm180) cc_final: 0.7684 (mtm180) REVERT: I 401 ASP cc_start: 0.7821 (m-30) cc_final: 0.7378 (m-30) REVERT: I 406 MET cc_start: 0.8571 (ttp) cc_final: 0.8233 (ttm) REVERT: I 417 GLN cc_start: 0.8014 (mt0) cc_final: 0.7749 (mt0) REVERT: I 433 GLU cc_start: 0.7856 (pp20) cc_final: 0.7575 (pp20) REVERT: J 81 LYS cc_start: 0.8272 (mtmm) cc_final: 0.7936 (mttp) REVERT: J 128 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7892 (mtpp) REVERT: J 145 ILE cc_start: 0.8432 (mm) cc_final: 0.8163 (mm) REVERT: J 157 LYS cc_start: 0.8401 (mttm) cc_final: 0.8138 (mttm) REVERT: J 170 GLU cc_start: 0.7358 (mp0) cc_final: 0.6643 (mp0) REVERT: J 266 ARG cc_start: 0.6963 (mtm-85) cc_final: 0.6572 (mtm-85) REVERT: J 268 GLU cc_start: 0.7746 (pm20) cc_final: 0.6990 (mp0) REVERT: J 297 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7497 (mm-30) REVERT: J 349 ASP cc_start: 0.8139 (t0) cc_final: 0.7874 (t0) REVERT: J 350 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7644 (ttm110) REVERT: J 365 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7949 (ttmt) REVERT: J 385 ASP cc_start: 0.7869 (t70) cc_final: 0.7577 (t70) REVERT: J 389 LYS cc_start: 0.8489 (ptmm) cc_final: 0.8215 (ptmm) REVERT: J 393 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7609 (mt-10) REVERT: J 405 VAL cc_start: 0.8173 (t) cc_final: 0.7926 (m) REVERT: J 438 LYS cc_start: 0.8241 (tmtt) cc_final: 0.8002 (tmtt) REVERT: J 451 GLN cc_start: 0.8461 (mm-40) cc_final: 0.8212 (mm-40) outliers start: 98 outliers final: 60 residues processed: 1305 average time/residue: 0.5354 time to fit residues: 1065.3826 Evaluate side-chains 1317 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 1252 time to evaluate : 5.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1076 ASN Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 429 LYS Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 406 MET Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain G residue 245 GLN Chi-restraints excluded: chain G residue 279 GLU Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 414 LYS Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 448 ILE Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 135 GLU Chi-restraints excluded: chain I residue 191 ARG Chi-restraints excluded: chain I residue 193 LYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 339 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 122 optimal weight: 0.0070 chunk 169 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 196 optimal weight: 0.9980 chunk 376 optimal weight: 0.0370 chunk 304 optimal weight: 0.7980 chunk 359 optimal weight: 3.9990 chunk 150 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 312 optimal weight: 2.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS C 319 HIS C 324 GLN C 422 HIS D 109 ASN E 256 ASN G 286 GLN H 299 HIS J 47 GLN J 63 ASN J 252 GLN J 310 ASN J 408 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.130775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111007 restraints weight = 55394.998| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.23 r_work: 0.3274 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33764 Z= 0.133 Angle : 0.585 14.235 45853 Z= 0.295 Chirality : 0.042 0.180 5344 Planarity : 0.004 0.062 5653 Dihedral : 14.445 174.739 5012 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.82 % Allowed : 18.57 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.13), residues: 4008 helix: 1.58 (0.12), residues: 1842 sheet: 0.29 (0.19), residues: 702 loop : -0.46 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 864 HIS 0.010 0.001 HIS C 422 PHE 0.024 0.001 PHE B 259 TYR 0.032 0.001 TYR C 143 ARG 0.010 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.03894 ( 1460) hydrogen bonds : angle 4.08880 ( 4148) metal coordination : bond 0.00563 ( 7) metal coordination : angle 4.18591 ( 6) covalent geometry : bond 0.00299 (33757) covalent geometry : angle 0.58348 (45847) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1374 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 1274 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 LEU cc_start: 0.8231 (mm) cc_final: 0.7959 (mt) REVERT: A 745 TRP cc_start: 0.7139 (m100) cc_final: 0.6715 (m-10) REVERT: A 752 VAL cc_start: 0.7899 (OUTLIER) cc_final: 0.7628 (t) REVERT: A 763 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7638 (mm-30) REVERT: A 821 MET cc_start: 0.8049 (ttt) cc_final: 0.7668 (ttt) REVERT: A 828 ASN cc_start: 0.8397 (m-40) cc_final: 0.8174 (m-40) REVERT: A 829 ILE cc_start: 0.8586 (pt) cc_final: 0.8249 (tt) REVERT: A 837 TRP cc_start: 0.8187 (t60) cc_final: 0.7766 (t60) REVERT: A 838 GLN cc_start: 0.8642 (mm110) cc_final: 0.8054 (mm110) REVERT: A 841 LEU cc_start: 0.8374 (tt) cc_final: 0.7993 (tp) REVERT: A 847 ARG cc_start: 0.7459 (mmp80) cc_final: 0.7202 (mmp80) REVERT: A 862 GLU cc_start: 0.7965 (mp0) cc_final: 0.7162 (mp0) REVERT: A 868 TYR cc_start: 0.7821 (t80) cc_final: 0.7531 (t80) REVERT: A 870 LEU cc_start: 0.8730 (mm) cc_final: 0.8519 (mm) REVERT: A 871 MET cc_start: 0.8055 (mmp) cc_final: 0.7775 (mmp) REVERT: A 946 GLU cc_start: 0.6912 (pp20) cc_final: 0.6532 (pp20) REVERT: A 1000 GLU cc_start: 0.6950 (tp30) cc_final: 0.6663 (tp30) REVERT: A 1022 GLU cc_start: 0.7660 (tt0) cc_final: 0.7329 (tt0) REVERT: A 1052 LYS cc_start: 0.8498 (mtmt) cc_final: 0.8263 (mtmt) REVERT: A 1073 GLU cc_start: 0.7968 (pt0) cc_final: 0.7706 (pt0) REVERT: A 1079 ARG cc_start: 0.7868 (tpp80) cc_final: 0.7550 (ttp80) REVERT: A 1099 ASP cc_start: 0.7973 (t0) cc_final: 0.7600 (t0) REVERT: A 1109 LYS cc_start: 0.8360 (tmtt) cc_final: 0.8112 (tttp) REVERT: A 1113 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7266 (tm-30) REVERT: A 1133 ARG cc_start: 0.8272 (ptp-110) cc_final: 0.8015 (ptp-110) REVERT: A 1146 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7652 (ttmm) REVERT: A 1202 ASP cc_start: 0.7744 (p0) cc_final: 0.7243 (p0) REVERT: A 1211 LEU cc_start: 0.8563 (mm) cc_final: 0.8319 (mp) REVERT: A 1238 LYS cc_start: 0.7874 (mppt) cc_final: 0.7616 (mtmm) REVERT: A 1245 CYS cc_start: 0.7917 (t) cc_final: 0.7319 (t) REVERT: A 1290 MET cc_start: 0.6957 (mtt) cc_final: 0.6432 (mtt) REVERT: A 1330 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8212 (tt) REVERT: A 1347 MET cc_start: 0.7162 (mmp) cc_final: 0.6216 (mmt) REVERT: A 1352 GLN cc_start: 0.8021 (tm-30) cc_final: 0.7814 (tm-30) REVERT: A 1394 ILE cc_start: 0.7545 (mm) cc_final: 0.7182 (mm) REVERT: B 269 ASN cc_start: 0.8050 (m110) cc_final: 0.7668 (m110) REVERT: C 7 VAL cc_start: 0.8904 (p) cc_final: 0.8591 (m) REVERT: C 44 ASN cc_start: 0.8651 (t0) cc_final: 0.8290 (t0) REVERT: C 57 PHE cc_start: 0.8004 (m-80) cc_final: 0.7721 (m-10) REVERT: C 71 LEU cc_start: 0.8325 (pt) cc_final: 0.8106 (pp) REVERT: C 110 GLU cc_start: 0.8040 (pm20) cc_final: 0.7765 (mp0) REVERT: C 116 ASP cc_start: 0.7952 (m-30) cc_final: 0.7726 (m-30) REVERT: C 122 GLU cc_start: 0.8169 (tp30) cc_final: 0.7944 (tp30) REVERT: C 153 LYS cc_start: 0.8732 (ttmm) cc_final: 0.8458 (mttm) REVERT: C 184 TYR cc_start: 0.8665 (p90) cc_final: 0.8371 (p90) REVERT: C 240 ASP cc_start: 0.8223 (t0) cc_final: 0.7823 (t0) REVERT: C 250 GLU cc_start: 0.8079 (tp30) cc_final: 0.7715 (tp30) REVERT: C 256 SER cc_start: 0.9121 (m) cc_final: 0.8801 (t) REVERT: C 265 LYS cc_start: 0.8562 (mmpt) cc_final: 0.8181 (mmtt) REVERT: C 269 LYS cc_start: 0.8455 (tppt) cc_final: 0.8250 (tppt) REVERT: C 337 SER cc_start: 0.8910 (t) cc_final: 0.8550 (p) REVERT: D 173 ARG cc_start: 0.8644 (mtt90) cc_final: 0.8070 (mtt90) REVERT: D 222 LYS cc_start: 0.8689 (tppp) cc_final: 0.8233 (tppp) REVERT: D 228 ASN cc_start: 0.8446 (m110) cc_final: 0.8216 (m-40) REVERT: D 250 TYR cc_start: 0.8587 (p90) cc_final: 0.7567 (p90) REVERT: E 99 LYS cc_start: 0.8488 (tttp) cc_final: 0.8247 (tptp) REVERT: E 123 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7921 (mt-10) REVERT: E 134 LYS cc_start: 0.8191 (mtmm) cc_final: 0.7896 (mtmm) REVERT: E 137 LYS cc_start: 0.8290 (mmtp) cc_final: 0.7942 (mmtp) REVERT: E 182 ASP cc_start: 0.8039 (m-30) cc_final: 0.7814 (m-30) REVERT: E 241 LYS cc_start: 0.8521 (ptmt) cc_final: 0.8090 (ptmt) REVERT: E 264 ASP cc_start: 0.7386 (t0) cc_final: 0.7177 (t0) REVERT: E 312 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7751 (mm-30) REVERT: E 379 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7561 (mt-10) REVERT: E 438 ASP cc_start: 0.7604 (m-30) cc_final: 0.7063 (m-30) REVERT: E 441 GLU cc_start: 0.7914 (tp30) cc_final: 0.7255 (tp30) REVERT: F 32 ASP cc_start: 0.7990 (m-30) cc_final: 0.7662 (m-30) REVERT: F 128 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8165 (mtmm) REVERT: F 142 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7532 (mt-10) REVERT: F 179 LEU cc_start: 0.8017 (mt) cc_final: 0.7810 (mt) REVERT: F 185 LEU cc_start: 0.8374 (mt) cc_final: 0.8153 (mm) REVERT: F 204 ARG cc_start: 0.8161 (mmm160) cc_final: 0.7906 (mmm-85) REVERT: F 231 LYS cc_start: 0.8650 (ptpt) cc_final: 0.8411 (ptpp) REVERT: F 232 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7512 (mtp85) REVERT: F 264 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7235 (mt-10) REVERT: F 349 ASP cc_start: 0.7859 (t70) cc_final: 0.7535 (t70) REVERT: F 377 VAL cc_start: 0.8567 (t) cc_final: 0.8291 (p) REVERT: F 389 LYS cc_start: 0.8428 (tttm) cc_final: 0.8169 (tttm) REVERT: F 393 GLU cc_start: 0.7948 (tp30) cc_final: 0.7668 (tp30) REVERT: F 405 VAL cc_start: 0.8510 (t) cc_final: 0.8251 (m) REVERT: F 413 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8291 (ttp80) REVERT: F 438 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7360 (mtpp) REVERT: F 442 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7584 (mt-10) REVERT: F 444 GLU cc_start: 0.7813 (tt0) cc_final: 0.7579 (tt0) REVERT: G 69 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7928 (mtpp) REVERT: G 85 LYS cc_start: 0.8295 (mtmm) cc_final: 0.8078 (mtmm) REVERT: G 134 LYS cc_start: 0.8211 (mtmm) cc_final: 0.7959 (mtmm) REVERT: G 194 VAL cc_start: 0.8734 (m) cc_final: 0.8472 (p) REVERT: G 198 ASP cc_start: 0.7462 (m-30) cc_final: 0.6957 (m-30) REVERT: G 199 VAL cc_start: 0.8893 (p) cc_final: 0.8669 (m) REVERT: G 210 LYS cc_start: 0.8276 (tppt) cc_final: 0.7727 (tppt) REVERT: G 216 ASP cc_start: 0.7942 (m-30) cc_final: 0.7561 (m-30) REVERT: G 234 LYS cc_start: 0.8439 (mttm) cc_final: 0.8148 (mttm) REVERT: G 239 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8267 (mtmm) REVERT: G 240 LYS cc_start: 0.8346 (mtmm) cc_final: 0.8054 (mtmm) REVERT: G 269 MET cc_start: 0.7557 (mpp) cc_final: 0.7110 (mpp) REVERT: G 287 GLU cc_start: 0.7808 (tp30) cc_final: 0.7070 (tp30) REVERT: G 406 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8059 (mtp) REVERT: G 427 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7561 (tm-30) REVERT: G 431 ARG cc_start: 0.7953 (mtm-85) cc_final: 0.7624 (mtm110) REVERT: G 433 GLU cc_start: 0.7563 (mp0) cc_final: 0.7232 (mp0) REVERT: G 435 VAL cc_start: 0.7840 (OUTLIER) cc_final: 0.7294 (m) REVERT: G 443 LYS cc_start: 0.8548 (ttmt) cc_final: 0.8215 (ttmt) REVERT: H 115 GLU cc_start: 0.8481 (tp30) cc_final: 0.8223 (mm-30) REVERT: H 128 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8147 (mtmm) REVERT: H 157 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7755 (mtmm) REVERT: H 166 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7582 (tm-30) REVERT: H 175 MET cc_start: 0.8285 (tpp) cc_final: 0.7796 (tpp) REVERT: H 185 LEU cc_start: 0.7886 (mt) cc_final: 0.7464 (mt) REVERT: H 188 ASP cc_start: 0.7703 (m-30) cc_final: 0.7476 (m-30) REVERT: H 198 LYS cc_start: 0.7662 (tptp) cc_final: 0.7349 (tptp) REVERT: H 199 ILE cc_start: 0.8688 (mt) cc_final: 0.8273 (mt) REVERT: H 271 ASP cc_start: 0.7630 (m-30) cc_final: 0.7118 (m-30) REVERT: H 331 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8174 (ttmm) REVERT: H 336 ASN cc_start: 0.7993 (p0) cc_final: 0.7733 (p0) REVERT: H 349 ASP cc_start: 0.8115 (t0) cc_final: 0.7861 (t0) REVERT: H 374 GLU cc_start: 0.8113 (tp30) cc_final: 0.7700 (tp30) REVERT: H 422 ASP cc_start: 0.7898 (m-30) cc_final: 0.7598 (m-30) REVERT: H 438 LYS cc_start: 0.8326 (ttmt) cc_final: 0.8035 (ttmt) REVERT: I 52 ILE cc_start: 0.8090 (mm) cc_final: 0.7697 (mm) REVERT: I 127 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7851 (ttm170) REVERT: I 133 ILE cc_start: 0.8901 (tt) cc_final: 0.8630 (pt) REVERT: I 135 GLU cc_start: 0.8004 (tt0) cc_final: 0.7754 (pt0) REVERT: I 136 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8529 (p) REVERT: I 138 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7371 (mt-10) REVERT: I 150 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7227 (mm-30) REVERT: I 174 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8646 (mmmm) REVERT: I 182 ASP cc_start: 0.7843 (m-30) cc_final: 0.7328 (m-30) REVERT: I 187 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7712 (mt-10) REVERT: I 210 LYS cc_start: 0.8325 (ttpt) cc_final: 0.8077 (ttpt) REVERT: I 223 ASP cc_start: 0.7134 (p0) cc_final: 0.6208 (p0) REVERT: I 249 LEU cc_start: 0.8234 (mt) cc_final: 0.8010 (mp) REVERT: I 258 ARG cc_start: 0.7867 (mtm-85) cc_final: 0.7634 (mtm-85) REVERT: I 268 MET cc_start: 0.7310 (ttp) cc_final: 0.7062 (ttp) REVERT: I 279 GLU cc_start: 0.7556 (pt0) cc_final: 0.7224 (pt0) REVERT: I 302 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7775 (mm-30) REVERT: I 313 VAL cc_start: 0.8758 (p) cc_final: 0.8530 (m) REVERT: I 386 ARG cc_start: 0.8231 (mmm-85) cc_final: 0.8022 (mmm160) REVERT: I 392 ARG cc_start: 0.7874 (mtm180) cc_final: 0.7575 (mtm180) REVERT: I 401 ASP cc_start: 0.7815 (m-30) cc_final: 0.7322 (m-30) REVERT: I 406 MET cc_start: 0.8530 (ttp) cc_final: 0.8206 (ttm) REVERT: I 417 GLN cc_start: 0.8006 (mt0) cc_final: 0.7739 (mt0) REVERT: I 438 ASP cc_start: 0.7863 (m-30) cc_final: 0.7449 (m-30) REVERT: J 78 SER cc_start: 0.8440 (t) cc_final: 0.8199 (t) REVERT: J 81 LYS cc_start: 0.8241 (mtmm) cc_final: 0.7904 (mttp) REVERT: J 124 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8569 (p) REVERT: J 128 LYS cc_start: 0.8255 (mtpp) cc_final: 0.7895 (mtpp) REVERT: J 157 LYS cc_start: 0.8358 (mttm) cc_final: 0.8086 (mttm) REVERT: J 170 GLU cc_start: 0.7355 (mp0) cc_final: 0.6662 (mp0) REVERT: J 245 ASP cc_start: 0.7900 (t0) cc_final: 0.7628 (m-30) REVERT: J 266 ARG cc_start: 0.6951 (mtm-85) cc_final: 0.6606 (mtm-85) REVERT: J 268 GLU cc_start: 0.7691 (pm20) cc_final: 0.6922 (mp0) REVERT: J 297 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7487 (mm-30) REVERT: J 349 ASP cc_start: 0.8177 (t0) cc_final: 0.7897 (t0) REVERT: J 350 ARG cc_start: 0.7913 (ttm110) cc_final: 0.7582 (ttm110) REVERT: J 361 GLU cc_start: 0.7586 (tt0) cc_final: 0.7352 (tm-30) REVERT: J 365 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7960 (ttmt) REVERT: J 385 ASP cc_start: 0.7869 (t70) cc_final: 0.7578 (t70) REVERT: J 389 LYS cc_start: 0.8494 (ptmm) cc_final: 0.8215 (ptmm) REVERT: J 393 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7605 (mt-10) REVERT: J 405 VAL cc_start: 0.8185 (t) cc_final: 0.7950 (m) REVERT: J 438 LYS cc_start: 0.8214 (tmtt) cc_final: 0.7960 (tmtt) REVERT: J 451 GLN cc_start: 0.8469 (mm-40) cc_final: 0.8227 (mm-40) outliers start: 100 outliers final: 65 residues processed: 1307 average time/residue: 0.5188 time to fit residues: 1028.7913 Evaluate side-chains 1313 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 1242 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 832 PHE Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 280 GLN Chi-restraints excluded: chain C residue 332 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 429 LYS Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 406 MET Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 406 MET Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 414 LYS Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 448 ILE Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 193 LYS Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 124 SER Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 288 ILE Chi-restraints excluded: chain J residue 339 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 19 optimal weight: 3.9990 chunk 302 optimal weight: 1.9990 chunk 246 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 197 optimal weight: 0.0670 chunk 208 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 366 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN A1012 HIS A1167 GLN A1270 GLN C 319 HIS C 324 GLN C 435 GLN D 109 ASN E 256 ASN E 263 GLN G 245 GLN G 286 GLN H 272 GLN ** I 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 250 HIS J 63 ASN J 310 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.130271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.110414 restraints weight = 55429.180| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.24 r_work: 0.3259 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 33764 Z= 0.163 Angle : 0.599 14.775 45853 Z= 0.302 Chirality : 0.043 0.183 5344 Planarity : 0.004 0.063 5653 Dihedral : 14.442 174.195 5012 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.27 % Allowed : 19.16 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.13), residues: 4008 helix: 1.54 (0.12), residues: 1842 sheet: 0.29 (0.19), residues: 713 loop : -0.51 (0.16), residues: 1453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.002 TRP A 864 HIS 0.009 0.001 HIS A1012 PHE 0.035 0.001 PHE B 259 TYR 0.033 0.002 TYR C 143 ARG 0.010 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 1460) hydrogen bonds : angle 4.11621 ( 4148) metal coordination : bond 0.00699 ( 7) metal coordination : angle 4.23816 ( 6) covalent geometry : bond 0.00368 (33757) covalent geometry : angle 0.59723 (45847) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1362 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 1246 time to evaluate : 3.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 ARG cc_start: 0.7615 (mmt90) cc_final: 0.7375 (mpt180) REVERT: A 707 LEU cc_start: 0.8255 (mm) cc_final: 0.7991 (mt) REVERT: A 745 TRP cc_start: 0.7141 (m100) cc_final: 0.6660 (m-10) REVERT: A 752 VAL cc_start: 0.7894 (OUTLIER) cc_final: 0.7651 (t) REVERT: A 761 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7932 (pp20) REVERT: A 763 GLU cc_start: 0.8102 (mm-30) cc_final: 0.7779 (mm-30) REVERT: A 797 HIS cc_start: 0.7084 (m90) cc_final: 0.6661 (m90) REVERT: A 821 MET cc_start: 0.8032 (ttt) cc_final: 0.7696 (ttt) REVERT: A 828 ASN cc_start: 0.8395 (m-40) cc_final: 0.8112 (m-40) REVERT: A 829 ILE cc_start: 0.8597 (pt) cc_final: 0.8234 (tt) REVERT: A 837 TRP cc_start: 0.8283 (t60) cc_final: 0.7725 (t60) REVERT: A 838 GLN cc_start: 0.8668 (mm110) cc_final: 0.8046 (mm110) REVERT: A 841 LEU cc_start: 0.8465 (tt) cc_final: 0.8027 (tp) REVERT: A 847 ARG cc_start: 0.7345 (mmp80) cc_final: 0.7093 (mmp80) REVERT: A 862 GLU cc_start: 0.8028 (mp0) cc_final: 0.7215 (mp0) REVERT: A 864 TRP cc_start: 0.8112 (t60) cc_final: 0.7592 (t60) REVERT: A 868 TYR cc_start: 0.7809 (t80) cc_final: 0.6885 (t80) REVERT: A 870 LEU cc_start: 0.8830 (mm) cc_final: 0.8581 (mm) REVERT: A 871 MET cc_start: 0.7999 (mmp) cc_final: 0.7644 (mmp) REVERT: A 946 GLU cc_start: 0.6914 (pp20) cc_final: 0.6535 (pp20) REVERT: A 1000 GLU cc_start: 0.7006 (tp30) cc_final: 0.6704 (tp30) REVERT: A 1011 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: A 1022 GLU cc_start: 0.7703 (tt0) cc_final: 0.7387 (tt0) REVERT: A 1052 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8277 (mtmt) REVERT: A 1073 GLU cc_start: 0.7934 (pt0) cc_final: 0.7677 (pt0) REVERT: A 1079 ARG cc_start: 0.7864 (tpp80) cc_final: 0.7511 (ttp80) REVERT: A 1099 ASP cc_start: 0.7925 (t0) cc_final: 0.7559 (t0) REVERT: A 1109 LYS cc_start: 0.8391 (tmtt) cc_final: 0.8135 (tttp) REVERT: A 1113 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7326 (tm-30) REVERT: A 1133 ARG cc_start: 0.8249 (ptp-110) cc_final: 0.7984 (ptp-110) REVERT: A 1146 LYS cc_start: 0.8035 (ttmm) cc_final: 0.7684 (ttmm) REVERT: A 1161 GLU cc_start: 0.7318 (tp30) cc_final: 0.6912 (tp30) REVERT: A 1202 ASP cc_start: 0.7741 (p0) cc_final: 0.7243 (p0) REVERT: A 1245 CYS cc_start: 0.7930 (t) cc_final: 0.7298 (t) REVERT: A 1290 MET cc_start: 0.7003 (mtt) cc_final: 0.6478 (mtt) REVERT: A 1330 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8155 (tt) REVERT: A 1334 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7181 (m-30) REVERT: A 1347 MET cc_start: 0.7162 (mmp) cc_final: 0.6682 (mmm) REVERT: A 1394 ILE cc_start: 0.7602 (mm) cc_final: 0.7243 (mm) REVERT: B 269 ASN cc_start: 0.8062 (m110) cc_final: 0.7662 (m110) REVERT: C 7 VAL cc_start: 0.8954 (p) cc_final: 0.8642 (m) REVERT: C 44 ASN cc_start: 0.8684 (t0) cc_final: 0.8314 (t0) REVERT: C 57 PHE cc_start: 0.8011 (m-80) cc_final: 0.7739 (m-10) REVERT: C 77 ASP cc_start: 0.8292 (m-30) cc_final: 0.8088 (m-30) REVERT: C 183 ASP cc_start: 0.8713 (p0) cc_final: 0.7981 (p0) REVERT: C 184 TYR cc_start: 0.8692 (p90) cc_final: 0.8352 (p90) REVERT: C 240 ASP cc_start: 0.8260 (t0) cc_final: 0.7836 (t0) REVERT: C 250 GLU cc_start: 0.7954 (tp30) cc_final: 0.7564 (tp30) REVERT: C 256 SER cc_start: 0.9160 (m) cc_final: 0.8841 (t) REVERT: C 265 LYS cc_start: 0.8603 (mmpt) cc_final: 0.8242 (mmtt) REVERT: C 269 LYS cc_start: 0.8491 (tppt) cc_final: 0.8278 (tppt) REVERT: C 337 SER cc_start: 0.8913 (t) cc_final: 0.8557 (p) REVERT: C 398 GLU cc_start: 0.8539 (tt0) cc_final: 0.8009 (tm-30) REVERT: C 418 GLU cc_start: 0.8244 (tt0) cc_final: 0.7739 (tm-30) REVERT: C 422 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.6730 (m170) REVERT: D 173 ARG cc_start: 0.8713 (mtt90) cc_final: 0.8144 (mtt90) REVERT: D 212 LEU cc_start: 0.8846 (mm) cc_final: 0.8625 (mt) REVERT: D 222 LYS cc_start: 0.8747 (tppp) cc_final: 0.8290 (tppp) REVERT: D 228 ASN cc_start: 0.8492 (m110) cc_final: 0.8244 (m110) REVERT: D 250 TYR cc_start: 0.8591 (p90) cc_final: 0.7193 (p90) REVERT: E 45 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7434 (mm-30) REVERT: E 99 LYS cc_start: 0.8556 (tttp) cc_final: 0.8313 (tptp) REVERT: E 123 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7875 (mt-10) REVERT: E 134 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7899 (mtmm) REVERT: E 137 LYS cc_start: 0.8296 (mmtp) cc_final: 0.7956 (mmtp) REVERT: E 182 ASP cc_start: 0.8122 (m-30) cc_final: 0.7865 (m-30) REVERT: E 241 LYS cc_start: 0.8522 (ptmt) cc_final: 0.8070 (ptmt) REVERT: E 243 ILE cc_start: 0.8551 (pp) cc_final: 0.8220 (pt) REVERT: E 312 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7797 (mm-30) REVERT: E 379 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7552 (mt-10) REVERT: E 438 ASP cc_start: 0.7561 (m-30) cc_final: 0.7040 (m-30) REVERT: E 441 GLU cc_start: 0.7901 (tp30) cc_final: 0.7253 (tp30) REVERT: F 32 ASP cc_start: 0.8014 (m-30) cc_final: 0.7676 (m-30) REVERT: F 128 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8284 (mtmm) REVERT: F 142 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7590 (mt-10) REVERT: F 185 LEU cc_start: 0.8356 (mt) cc_final: 0.8126 (mm) REVERT: F 204 ARG cc_start: 0.8179 (mmm160) cc_final: 0.7920 (mmm-85) REVERT: F 229 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8416 (tp) REVERT: F 231 LYS cc_start: 0.8645 (ptpt) cc_final: 0.8392 (ptpt) REVERT: F 232 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7497 (mtp85) REVERT: F 251 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8423 (m) REVERT: F 264 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7210 (mt-10) REVERT: F 349 ASP cc_start: 0.7865 (t70) cc_final: 0.7565 (t70) REVERT: F 365 LYS cc_start: 0.8496 (ttpp) cc_final: 0.8192 (ttmm) REVERT: F 377 VAL cc_start: 0.8572 (t) cc_final: 0.8301 (p) REVERT: F 389 LYS cc_start: 0.8438 (tttm) cc_final: 0.8178 (tttm) REVERT: F 393 GLU cc_start: 0.7956 (tp30) cc_final: 0.7684 (tp30) REVERT: F 405 VAL cc_start: 0.8487 (t) cc_final: 0.8228 (m) REVERT: F 413 ARG cc_start: 0.8481 (ttp80) cc_final: 0.8243 (ttp80) REVERT: F 438 LYS cc_start: 0.7870 (mtpp) cc_final: 0.7354 (mtpp) REVERT: F 442 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7583 (mt-10) REVERT: F 444 GLU cc_start: 0.7786 (tt0) cc_final: 0.7544 (tt0) REVERT: G 36 ASP cc_start: 0.7679 (p0) cc_final: 0.7439 (p0) REVERT: G 69 LYS cc_start: 0.8377 (mtpp) cc_final: 0.7988 (mtpp) REVERT: G 134 LYS cc_start: 0.8214 (mtmm) cc_final: 0.7951 (mtmm) REVERT: G 194 VAL cc_start: 0.8726 (m) cc_final: 0.8470 (p) REVERT: G 198 ASP cc_start: 0.7479 (m-30) cc_final: 0.6938 (m-30) REVERT: G 199 VAL cc_start: 0.8870 (OUTLIER) cc_final: 0.8645 (m) REVERT: G 210 LYS cc_start: 0.8281 (tppt) cc_final: 0.7729 (tppt) REVERT: G 216 ASP cc_start: 0.7899 (m-30) cc_final: 0.7506 (m-30) REVERT: G 234 LYS cc_start: 0.8348 (mttm) cc_final: 0.8069 (mttm) REVERT: G 240 LYS cc_start: 0.8405 (mtmm) cc_final: 0.8132 (mtmm) REVERT: G 269 MET cc_start: 0.7433 (mpp) cc_final: 0.7052 (mpp) REVERT: G 287 GLU cc_start: 0.7911 (tp30) cc_final: 0.7166 (tp30) REVERT: G 294 LYS cc_start: 0.8800 (tttm) cc_final: 0.8432 (tttm) REVERT: G 406 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.8001 (mtp) REVERT: G 431 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7636 (mtm110) REVERT: G 433 GLU cc_start: 0.7569 (mp0) cc_final: 0.7234 (mp0) REVERT: G 435 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.7421 (m) REVERT: G 443 LYS cc_start: 0.8567 (ttmt) cc_final: 0.8196 (ttmt) REVERT: H 62 GLN cc_start: 0.8482 (mt0) cc_final: 0.8159 (mt0) REVERT: H 128 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8176 (mtmm) REVERT: H 157 LYS cc_start: 0.8048 (mtmm) cc_final: 0.7772 (mtmm) REVERT: H 166 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7609 (tm-30) REVERT: H 175 MET cc_start: 0.8310 (tpp) cc_final: 0.7790 (tpp) REVERT: H 185 LEU cc_start: 0.7908 (mt) cc_final: 0.7549 (mt) REVERT: H 198 LYS cc_start: 0.7654 (tptp) cc_final: 0.7342 (tptp) REVERT: H 199 ILE cc_start: 0.8679 (mt) cc_final: 0.8254 (mt) REVERT: H 270 ARG cc_start: 0.8293 (mtt-85) cc_final: 0.7858 (mtt90) REVERT: H 271 ASP cc_start: 0.7655 (m-30) cc_final: 0.7138 (m-30) REVERT: H 336 ASN cc_start: 0.7932 (p0) cc_final: 0.7634 (p0) REVERT: H 349 ASP cc_start: 0.8119 (t0) cc_final: 0.7877 (t0) REVERT: H 374 GLU cc_start: 0.8191 (tp30) cc_final: 0.7793 (tp30) REVERT: H 422 ASP cc_start: 0.7909 (m-30) cc_final: 0.7624 (m-30) REVERT: H 438 LYS cc_start: 0.8334 (ttmt) cc_final: 0.8033 (ttmt) REVERT: I 52 ILE cc_start: 0.8078 (mm) cc_final: 0.7684 (mm) REVERT: I 127 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7884 (ttm170) REVERT: I 133 ILE cc_start: 0.8915 (tt) cc_final: 0.8615 (pt) REVERT: I 135 GLU cc_start: 0.8002 (tt0) cc_final: 0.7755 (pt0) REVERT: I 136 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8545 (p) REVERT: I 138 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7359 (mt-10) REVERT: I 182 ASP cc_start: 0.7821 (m-30) cc_final: 0.7315 (m-30) REVERT: I 187 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7790 (mt-10) REVERT: I 210 LYS cc_start: 0.8329 (ttpt) cc_final: 0.8073 (ttpt) REVERT: I 223 ASP cc_start: 0.7199 (p0) cc_final: 0.6246 (p0) REVERT: I 258 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7611 (mtm-85) REVERT: I 268 MET cc_start: 0.7244 (ttp) cc_final: 0.6951 (ttp) REVERT: I 279 GLU cc_start: 0.7558 (pt0) cc_final: 0.7199 (pt0) REVERT: I 313 VAL cc_start: 0.8797 (p) cc_final: 0.8574 (m) REVERT: I 386 ARG cc_start: 0.8228 (mmm-85) cc_final: 0.8028 (mmm160) REVERT: I 392 ARG cc_start: 0.7921 (mtm180) cc_final: 0.7618 (mtm180) REVERT: I 401 ASP cc_start: 0.7823 (m-30) cc_final: 0.7355 (m-30) REVERT: I 406 MET cc_start: 0.8526 (ttp) cc_final: 0.8176 (ttm) REVERT: I 417 GLN cc_start: 0.7989 (mt0) cc_final: 0.7719 (mt0) REVERT: I 438 ASP cc_start: 0.7832 (m-30) cc_final: 0.7391 (m-30) REVERT: J 78 SER cc_start: 0.8446 (t) cc_final: 0.8203 (t) REVERT: J 81 LYS cc_start: 0.8277 (mtmm) cc_final: 0.7956 (mttp) REVERT: J 128 LYS cc_start: 0.8231 (mtpp) cc_final: 0.7873 (mtpp) REVERT: J 145 ILE cc_start: 0.8410 (mm) cc_final: 0.8194 (mm) REVERT: J 170 GLU cc_start: 0.7407 (mp0) cc_final: 0.6688 (mp0) REVERT: J 245 ASP cc_start: 0.7889 (t0) cc_final: 0.7623 (m-30) REVERT: J 266 ARG cc_start: 0.7017 (mtm-85) cc_final: 0.6633 (mtm-85) REVERT: J 268 GLU cc_start: 0.7734 (pm20) cc_final: 0.7012 (mp0) REVERT: J 295 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.8061 (mt) REVERT: J 349 ASP cc_start: 0.8129 (t0) cc_final: 0.7869 (t0) REVERT: J 350 ARG cc_start: 0.7887 (ttm110) cc_final: 0.7565 (ttm110) REVERT: J 357 LYS cc_start: 0.8124 (mmpt) cc_final: 0.7854 (mmpt) REVERT: J 365 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7958 (ttmt) REVERT: J 385 ASP cc_start: 0.7922 (t70) cc_final: 0.7623 (t70) REVERT: J 389 LYS cc_start: 0.8480 (ptmm) cc_final: 0.8205 (ptmm) REVERT: J 393 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7617 (mt-10) REVERT: J 405 VAL cc_start: 0.8215 (t) cc_final: 0.7979 (m) REVERT: J 438 LYS cc_start: 0.8239 (tmtt) cc_final: 0.7988 (tmtt) REVERT: J 451 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8235 (mm-40) outliers start: 116 outliers final: 73 residues processed: 1284 average time/residue: 0.5350 time to fit residues: 1050.1032 Evaluate side-chains 1328 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1243 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 965 MET Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1334 ASP Chi-restraints excluded: chain A residue 1336 VAL Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 76 TRP Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 429 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 406 MET Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 281 LYS Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 406 MET Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain H residue 296 ASP Chi-restraints excluded: chain H residue 376 GLU Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 414 LYS Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain H residue 448 ILE Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 428 THR Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 295 ILE Chi-restraints excluded: chain J residue 339 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 102 optimal weight: 0.8980 chunk 223 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 271 optimal weight: 0.0770 chunk 281 optimal weight: 1.9990 chunk 352 optimal weight: 0.5980 chunk 277 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 240 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS C 319 HIS D 109 ASN E 256 ASN G 286 GLN H 441 GLN I 250 HIS I 325 ASN J 299 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.130897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111024 restraints weight = 55388.568| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.24 r_work: 0.3266 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33764 Z= 0.140 Angle : 0.598 15.447 45853 Z= 0.302 Chirality : 0.043 0.180 5344 Planarity : 0.004 0.060 5653 Dihedral : 14.402 172.916 5012 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.73 % Allowed : 20.23 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.13), residues: 4008 helix: 1.55 (0.12), residues: 1848 sheet: 0.27 (0.19), residues: 715 loop : -0.46 (0.16), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP A 864 HIS 0.009 0.001 HIS A1012 PHE 0.023 0.001 PHE B 259 TYR 0.033 0.001 TYR C 143 ARG 0.012 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 1460) hydrogen bonds : angle 4.05629 ( 4148) metal coordination : bond 0.00576 ( 7) metal coordination : angle 4.49895 ( 6) covalent geometry : bond 0.00319 (33757) covalent geometry : angle 0.59629 (45847) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1347 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 1250 time to evaluate : 3.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 LEU cc_start: 0.8252 (mm) cc_final: 0.7959 (mt) REVERT: A 745 TRP cc_start: 0.7090 (m100) cc_final: 0.6778 (m-10) REVERT: A 752 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7684 (t) REVERT: A 761 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7945 (pp20) REVERT: A 763 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7740 (mm-30) REVERT: A 821 MET cc_start: 0.8062 (ttt) cc_final: 0.7717 (ttt) REVERT: A 828 ASN cc_start: 0.8407 (m-40) cc_final: 0.8068 (m110) REVERT: A 829 ILE cc_start: 0.8579 (pt) cc_final: 0.8253 (tt) REVERT: A 837 TRP cc_start: 0.8261 (t60) cc_final: 0.7967 (t60) REVERT: A 838 GLN cc_start: 0.8645 (mm110) cc_final: 0.8016 (mm110) REVERT: A 847 ARG cc_start: 0.7315 (mmp80) cc_final: 0.7093 (mmp80) REVERT: A 862 GLU cc_start: 0.8014 (mp0) cc_final: 0.7248 (mp0) REVERT: A 864 TRP cc_start: 0.8044 (t60) cc_final: 0.7703 (t60) REVERT: A 868 TYR cc_start: 0.7819 (t80) cc_final: 0.7108 (t80) REVERT: A 870 LEU cc_start: 0.8853 (mm) cc_final: 0.8524 (mm) REVERT: A 871 MET cc_start: 0.8054 (mmp) cc_final: 0.7497 (mmp) REVERT: A 946 GLU cc_start: 0.6921 (pp20) cc_final: 0.6539 (pp20) REVERT: A 1000 GLU cc_start: 0.7031 (tp30) cc_final: 0.6734 (tp30) REVERT: A 1002 ARG cc_start: 0.8268 (mtp180) cc_final: 0.8007 (mtp180) REVERT: A 1022 GLU cc_start: 0.7669 (tt0) cc_final: 0.7329 (tt0) REVERT: A 1052 LYS cc_start: 0.8536 (mtmt) cc_final: 0.8309 (mtmt) REVERT: A 1073 GLU cc_start: 0.7889 (pt0) cc_final: 0.7623 (pt0) REVERT: A 1079 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7498 (ttp80) REVERT: A 1099 ASP cc_start: 0.7894 (t0) cc_final: 0.7522 (t0) REVERT: A 1109 LYS cc_start: 0.8378 (tmtt) cc_final: 0.8139 (tttp) REVERT: A 1113 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7323 (tm-30) REVERT: A 1133 ARG cc_start: 0.8244 (ptp-110) cc_final: 0.7996 (ptp-110) REVERT: A 1146 LYS cc_start: 0.8009 (ttmm) cc_final: 0.7733 (ttmm) REVERT: A 1245 CYS cc_start: 0.7924 (t) cc_final: 0.7338 (t) REVERT: A 1290 MET cc_start: 0.6981 (mtt) cc_final: 0.6430 (mtt) REVERT: A 1330 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8183 (tt) REVERT: A 1334 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7170 (m-30) REVERT: A 1347 MET cc_start: 0.7111 (mmp) cc_final: 0.6703 (mmm) REVERT: A 1352 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7944 (tm-30) REVERT: A 1394 ILE cc_start: 0.7578 (mm) cc_final: 0.7236 (mm) REVERT: B 269 ASN cc_start: 0.8028 (m110) cc_final: 0.7620 (m110) REVERT: C 7 VAL cc_start: 0.8911 (p) cc_final: 0.8607 (m) REVERT: C 44 ASN cc_start: 0.8647 (t0) cc_final: 0.8204 (t0) REVERT: C 57 PHE cc_start: 0.7982 (m-80) cc_final: 0.7722 (m-10) REVERT: C 77 ASP cc_start: 0.8259 (m-30) cc_final: 0.8042 (m-30) REVERT: C 146 GLU cc_start: 0.7891 (mp0) cc_final: 0.7572 (mp0) REVERT: C 183 ASP cc_start: 0.8740 (p0) cc_final: 0.7991 (p0) REVERT: C 184 TYR cc_start: 0.8702 (p90) cc_final: 0.8357 (p90) REVERT: C 240 ASP cc_start: 0.8277 (t0) cc_final: 0.7877 (t0) REVERT: C 250 GLU cc_start: 0.7963 (tp30) cc_final: 0.7587 (tp30) REVERT: C 256 SER cc_start: 0.9148 (m) cc_final: 0.8838 (t) REVERT: C 265 LYS cc_start: 0.8605 (mmpt) cc_final: 0.8228 (mmtt) REVERT: C 267 LYS cc_start: 0.8598 (ptmt) cc_final: 0.8289 (ptmm) REVERT: C 269 LYS cc_start: 0.8471 (tppt) cc_final: 0.8261 (tppt) REVERT: C 337 SER cc_start: 0.8908 (t) cc_final: 0.8558 (p) REVERT: C 398 GLU cc_start: 0.8534 (tt0) cc_final: 0.7998 (tm-30) REVERT: C 422 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.7510 (m170) REVERT: D 101 ARG cc_start: 0.8444 (tmt170) cc_final: 0.8183 (tmt170) REVERT: D 173 ARG cc_start: 0.8728 (mtt90) cc_final: 0.8146 (mtt90) REVERT: D 222 LYS cc_start: 0.8773 (tppp) cc_final: 0.8325 (tppp) REVERT: D 250 TYR cc_start: 0.8564 (p90) cc_final: 0.7156 (p90) REVERT: E 45 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7442 (mm-30) REVERT: E 123 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7880 (mt-10) REVERT: E 132 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7797 (mtt-85) REVERT: E 134 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7894 (mtmm) REVERT: E 137 LYS cc_start: 0.8279 (mmtp) cc_final: 0.7944 (mmtp) REVERT: E 182 ASP cc_start: 0.8101 (m-30) cc_final: 0.7858 (m-30) REVERT: E 225 GLU cc_start: 0.7790 (tt0) cc_final: 0.7491 (tp30) REVERT: E 241 LYS cc_start: 0.8528 (ptmt) cc_final: 0.8088 (ptmt) REVERT: E 312 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7764 (mm-30) REVERT: E 379 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7567 (mt-10) REVERT: E 438 ASP cc_start: 0.7497 (m-30) cc_final: 0.6977 (m-30) REVERT: E 441 GLU cc_start: 0.7910 (tp30) cc_final: 0.7250 (tp30) REVERT: F 32 ASP cc_start: 0.8003 (m-30) cc_final: 0.7670 (m-30) REVERT: F 128 LYS cc_start: 0.8639 (mtmt) cc_final: 0.8299 (mtmm) REVERT: F 131 GLU cc_start: 0.7321 (pt0) cc_final: 0.7081 (pt0) REVERT: F 142 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7656 (mt-10) REVERT: F 185 LEU cc_start: 0.8371 (mt) cc_final: 0.8142 (mm) REVERT: F 204 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7913 (mmm-85) REVERT: F 229 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8418 (tp) REVERT: F 231 LYS cc_start: 0.8645 (ptpt) cc_final: 0.8374 (ptpt) REVERT: F 232 ARG cc_start: 0.7849 (mtp85) cc_final: 0.7496 (mtp85) REVERT: F 251 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8395 (m) REVERT: F 264 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7184 (mt-10) REVERT: F 349 ASP cc_start: 0.7863 (t70) cc_final: 0.7561 (t70) REVERT: F 365 LYS cc_start: 0.8495 (ttpp) cc_final: 0.8187 (ttmm) REVERT: F 377 VAL cc_start: 0.8570 (t) cc_final: 0.8305 (p) REVERT: F 389 LYS cc_start: 0.8442 (tttm) cc_final: 0.8179 (tttm) REVERT: F 393 GLU cc_start: 0.7959 (tp30) cc_final: 0.7683 (tp30) REVERT: F 405 VAL cc_start: 0.8487 (t) cc_final: 0.8273 (m) REVERT: F 413 ARG cc_start: 0.8452 (ttp80) cc_final: 0.8213 (ttp80) REVERT: F 438 LYS cc_start: 0.7847 (mtpp) cc_final: 0.7365 (mtpp) REVERT: F 442 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7587 (mt-10) REVERT: F 444 GLU cc_start: 0.7746 (tt0) cc_final: 0.7512 (tt0) REVERT: G 69 LYS cc_start: 0.8305 (mtpp) cc_final: 0.7933 (mtpp) REVERT: G 134 LYS cc_start: 0.8190 (mtmm) cc_final: 0.7924 (mtmm) REVERT: G 194 VAL cc_start: 0.8726 (m) cc_final: 0.8490 (p) REVERT: G 199 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8651 (m) REVERT: G 210 LYS cc_start: 0.8274 (tppt) cc_final: 0.7722 (tppt) REVERT: G 216 ASP cc_start: 0.7896 (m-30) cc_final: 0.7516 (m-30) REVERT: G 234 LYS cc_start: 0.8312 (mttm) cc_final: 0.8040 (mttm) REVERT: G 240 LYS cc_start: 0.8395 (mtmm) cc_final: 0.8115 (mtmm) REVERT: G 267 SER cc_start: 0.8070 (m) cc_final: 0.7697 (p) REVERT: G 269 MET cc_start: 0.7464 (mpp) cc_final: 0.7113 (mpp) REVERT: G 287 GLU cc_start: 0.7900 (tp30) cc_final: 0.7133 (tp30) REVERT: G 294 LYS cc_start: 0.8774 (tttm) cc_final: 0.8405 (tttm) REVERT: G 315 MET cc_start: 0.8507 (mmm) cc_final: 0.8134 (mmp) REVERT: G 406 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7951 (mtp) REVERT: G 431 ARG cc_start: 0.7926 (mtm-85) cc_final: 0.7606 (mtm110) REVERT: G 433 GLU cc_start: 0.7578 (mp0) cc_final: 0.7236 (mp0) REVERT: G 435 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7348 (m) REVERT: G 443 LYS cc_start: 0.8529 (ttmt) cc_final: 0.8217 (ttmt) REVERT: H 115 GLU cc_start: 0.8530 (tp30) cc_final: 0.8234 (tp30) REVERT: H 128 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8163 (mtmm) REVERT: H 157 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7760 (mtmm) REVERT: H 166 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7550 (tm-30) REVERT: H 175 MET cc_start: 0.8315 (tpp) cc_final: 0.7815 (tpp) REVERT: H 198 LYS cc_start: 0.7674 (tptp) cc_final: 0.7362 (tptp) REVERT: H 199 ILE cc_start: 0.8685 (mt) cc_final: 0.8252 (mt) REVERT: H 270 ARG cc_start: 0.8281 (mtt-85) cc_final: 0.7939 (mtt90) REVERT: H 271 ASP cc_start: 0.7599 (m-30) cc_final: 0.7103 (m-30) REVERT: H 336 ASN cc_start: 0.7933 (p0) cc_final: 0.7631 (p0) REVERT: H 349 ASP cc_start: 0.8082 (t0) cc_final: 0.7831 (t0) REVERT: H 374 GLU cc_start: 0.8146 (tp30) cc_final: 0.7738 (tp30) REVERT: H 422 ASP cc_start: 0.7924 (m-30) cc_final: 0.7669 (m-30) REVERT: H 438 LYS cc_start: 0.8312 (ttmt) cc_final: 0.8038 (ttmt) REVERT: I 52 ILE cc_start: 0.8060 (mm) cc_final: 0.7670 (mm) REVERT: I 53 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7976 (mp0) REVERT: I 127 ARG cc_start: 0.8138 (ttm170) cc_final: 0.7899 (ttm170) REVERT: I 133 ILE cc_start: 0.8889 (tt) cc_final: 0.8629 (pt) REVERT: I 135 GLU cc_start: 0.7996 (tt0) cc_final: 0.7751 (pt0) REVERT: I 136 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8530 (p) REVERT: I 138 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7340 (mt-10) REVERT: I 182 ASP cc_start: 0.7798 (m-30) cc_final: 0.7294 (m-30) REVERT: I 187 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7777 (mt-10) REVERT: I 210 LYS cc_start: 0.8318 (ttpt) cc_final: 0.8068 (ttpt) REVERT: I 223 ASP cc_start: 0.7220 (p0) cc_final: 0.6276 (p0) REVERT: I 253 ASP cc_start: 0.7830 (m-30) cc_final: 0.7619 (m-30) REVERT: I 258 ARG cc_start: 0.7829 (mtm-85) cc_final: 0.7582 (mtm-85) REVERT: I 268 MET cc_start: 0.7270 (ttp) cc_final: 0.6970 (ttp) REVERT: I 279 GLU cc_start: 0.7508 (pt0) cc_final: 0.7154 (pt0) REVERT: I 302 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7828 (mm-30) REVERT: I 313 VAL cc_start: 0.8798 (p) cc_final: 0.8577 (m) REVERT: I 386 ARG cc_start: 0.8222 (mmm-85) cc_final: 0.7851 (mmm160) REVERT: I 392 ARG cc_start: 0.7927 (mtm180) cc_final: 0.7618 (mtm180) REVERT: I 401 ASP cc_start: 0.7832 (m-30) cc_final: 0.7365 (m-30) REVERT: I 406 MET cc_start: 0.8494 (ttp) cc_final: 0.8154 (ttm) REVERT: I 417 GLN cc_start: 0.8001 (mt0) cc_final: 0.7726 (mt0) REVERT: I 438 ASP cc_start: 0.7826 (m-30) cc_final: 0.7383 (m-30) REVERT: J 78 SER cc_start: 0.8424 (t) cc_final: 0.8182 (t) REVERT: J 81 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7925 (mttp) REVERT: J 128 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7875 (mtpp) REVERT: J 132 GLU cc_start: 0.6183 (tm-30) cc_final: 0.5797 (mm-30) REVERT: J 145 ILE cc_start: 0.8405 (mm) cc_final: 0.8182 (mm) REVERT: J 170 GLU cc_start: 0.7394 (mp0) cc_final: 0.6678 (mp0) REVERT: J 245 ASP cc_start: 0.7910 (t0) cc_final: 0.7613 (m-30) REVERT: J 266 ARG cc_start: 0.7028 (mtm-85) cc_final: 0.6666 (mtm-85) REVERT: J 268 GLU cc_start: 0.7692 (pm20) cc_final: 0.6978 (mp0) REVERT: J 295 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.8041 (mt) REVERT: J 297 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7376 (mm-30) REVERT: J 310 ASN cc_start: 0.8153 (m-40) cc_final: 0.7671 (m110) REVERT: J 346 ASP cc_start: 0.7397 (t70) cc_final: 0.6829 (t70) REVERT: J 349 ASP cc_start: 0.8108 (t0) cc_final: 0.7865 (t0) REVERT: J 350 ARG cc_start: 0.7897 (ttm110) cc_final: 0.7510 (ttm110) REVERT: J 357 LYS cc_start: 0.8139 (mmpt) cc_final: 0.7869 (mmpt) REVERT: J 362 GLN cc_start: 0.7737 (mp10) cc_final: 0.7349 (mp10) REVERT: J 365 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7926 (ttmt) REVERT: J 385 ASP cc_start: 0.7888 (t70) cc_final: 0.7591 (t70) REVERT: J 389 LYS cc_start: 0.8466 (ptmm) cc_final: 0.8207 (ptmm) REVERT: J 393 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7601 (mt-10) REVERT: J 405 VAL cc_start: 0.8189 (t) cc_final: 0.7960 (m) REVERT: J 414 LYS cc_start: 0.8383 (mptt) cc_final: 0.8182 (mptt) REVERT: J 438 LYS cc_start: 0.8217 (tmtt) cc_final: 0.7949 (tmtt) REVERT: J 451 GLN cc_start: 0.8494 (mm-40) cc_final: 0.8248 (mm-40) outliers start: 97 outliers final: 67 residues processed: 1284 average time/residue: 0.5381 time to fit residues: 1056.7011 Evaluate side-chains 1333 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 1255 time to evaluate : 3.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1334 ASP Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 76 TRP Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 422 HIS Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 429 LYS Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 406 MET Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 201 LYS Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 346 THR Chi-restraints excluded: chain G residue 406 MET Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain H residue 296 ASP Chi-restraints excluded: chain H residue 376 GLU Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 414 LYS Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain I residue 336 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 295 ILE Chi-restraints excluded: chain J residue 339 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 84 optimal weight: 0.0070 chunk 114 optimal weight: 0.0970 chunk 22 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 394 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 202 optimal weight: 8.9990 chunk 349 optimal weight: 0.0870 chunk 184 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS C 319 HIS D 109 ASN E 256 ASN G 286 GLN H 49 GLN I 250 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.111886 restraints weight = 55464.979| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.24 r_work: 0.3283 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 33764 Z= 0.122 Angle : 0.600 15.772 45853 Z= 0.300 Chirality : 0.042 0.170 5344 Planarity : 0.004 0.060 5653 Dihedral : 14.327 169.551 5012 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.65 % Allowed : 21.19 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.13), residues: 4008 helix: 1.64 (0.12), residues: 1834 sheet: 0.36 (0.19), residues: 702 loop : -0.43 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A 864 HIS 0.008 0.001 HIS A1012 PHE 0.024 0.001 PHE B 259 TYR 0.034 0.001 TYR C 143 ARG 0.014 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 1460) hydrogen bonds : angle 4.01440 ( 4148) metal coordination : bond 0.00443 ( 7) metal coordination : angle 4.39053 ( 6) covalent geometry : bond 0.00277 (33757) covalent geometry : angle 0.59763 (45847) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 1267 time to evaluate : 3.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 LEU cc_start: 0.8253 (mm) cc_final: 0.7958 (mt) REVERT: A 752 VAL cc_start: 0.7908 (OUTLIER) cc_final: 0.7646 (t) REVERT: A 761 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7984 (tm-30) REVERT: A 763 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7771 (mm-30) REVERT: A 821 MET cc_start: 0.8020 (ttt) cc_final: 0.7683 (ttt) REVERT: A 828 ASN cc_start: 0.8403 (m-40) cc_final: 0.8075 (m-40) REVERT: A 829 ILE cc_start: 0.8563 (pt) cc_final: 0.8240 (tt) REVERT: A 837 TRP cc_start: 0.8241 (t60) cc_final: 0.7995 (t60) REVERT: A 838 GLN cc_start: 0.8631 (mm110) cc_final: 0.8004 (mm110) REVERT: A 862 GLU cc_start: 0.7972 (mp0) cc_final: 0.7228 (mp0) REVERT: A 864 TRP cc_start: 0.8021 (t60) cc_final: 0.7696 (t60) REVERT: A 868 TYR cc_start: 0.7790 (t80) cc_final: 0.7115 (t80) REVERT: A 870 LEU cc_start: 0.8865 (mm) cc_final: 0.8578 (mm) REVERT: A 871 MET cc_start: 0.8028 (mmp) cc_final: 0.7567 (mmp) REVERT: A 946 GLU cc_start: 0.6902 (pp20) cc_final: 0.6522 (pp20) REVERT: A 1000 GLU cc_start: 0.7062 (tp30) cc_final: 0.6773 (tp30) REVERT: A 1002 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7997 (mtp180) REVERT: A 1022 GLU cc_start: 0.7637 (tt0) cc_final: 0.7300 (tt0) REVERT: A 1073 GLU cc_start: 0.7962 (pt0) cc_final: 0.7690 (pt0) REVERT: A 1079 ARG cc_start: 0.7885 (tpp80) cc_final: 0.7503 (ttp80) REVERT: A 1099 ASP cc_start: 0.7836 (t0) cc_final: 0.7449 (t0) REVERT: A 1109 LYS cc_start: 0.8358 (tmtt) cc_final: 0.8118 (tmtp) REVERT: A 1113 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7292 (tm-30) REVERT: A 1133 ARG cc_start: 0.8255 (ptp-110) cc_final: 0.8009 (ptp-110) REVERT: A 1146 LYS cc_start: 0.8016 (ttmm) cc_final: 0.7705 (ttmm) REVERT: A 1211 LEU cc_start: 0.8540 (mm) cc_final: 0.8297 (mp) REVERT: A 1245 CYS cc_start: 0.7897 (t) cc_final: 0.7308 (t) REVERT: A 1290 MET cc_start: 0.6950 (mtt) cc_final: 0.6426 (mtt) REVERT: A 1301 ARG cc_start: 0.7780 (ttm110) cc_final: 0.7559 (ttm110) REVERT: A 1330 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8170 (tt) REVERT: A 1347 MET cc_start: 0.7011 (mmp) cc_final: 0.6656 (mmm) REVERT: A 1352 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7885 (tm-30) REVERT: A 1394 ILE cc_start: 0.7497 (mm) cc_final: 0.7121 (mm) REVERT: B 269 ASN cc_start: 0.7967 (m110) cc_final: 0.7559 (m110) REVERT: B 297 MET cc_start: 0.7953 (mmm) cc_final: 0.7746 (mmm) REVERT: C 7 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8590 (m) REVERT: C 44 ASN cc_start: 0.8620 (t0) cc_final: 0.8181 (t0) REVERT: C 57 PHE cc_start: 0.8026 (m-80) cc_final: 0.7777 (m-10) REVERT: C 77 ASP cc_start: 0.8282 (m-30) cc_final: 0.8069 (m-30) REVERT: C 128 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8122 (tp) REVERT: C 146 GLU cc_start: 0.7914 (mp0) cc_final: 0.7618 (mp0) REVERT: C 183 ASP cc_start: 0.8722 (p0) cc_final: 0.7987 (p0) REVERT: C 184 TYR cc_start: 0.8695 (p90) cc_final: 0.8350 (p90) REVERT: C 240 ASP cc_start: 0.8255 (t0) cc_final: 0.7870 (t0) REVERT: C 250 GLU cc_start: 0.7952 (tp30) cc_final: 0.7557 (tp30) REVERT: C 256 SER cc_start: 0.9149 (m) cc_final: 0.8884 (t) REVERT: C 265 LYS cc_start: 0.8615 (mmpt) cc_final: 0.8195 (mmtt) REVERT: C 267 LYS cc_start: 0.8618 (ptmt) cc_final: 0.8290 (ptmm) REVERT: C 337 SER cc_start: 0.8883 (t) cc_final: 0.8551 (p) REVERT: C 398 GLU cc_start: 0.8531 (tt0) cc_final: 0.8169 (tm-30) REVERT: C 418 GLU cc_start: 0.8152 (tt0) cc_final: 0.7311 (tm-30) REVERT: C 421 GLU cc_start: 0.7708 (pp20) cc_final: 0.7034 (pp20) REVERT: D 173 ARG cc_start: 0.8705 (mtt90) cc_final: 0.8124 (mtt90) REVERT: D 250 TYR cc_start: 0.8551 (p90) cc_final: 0.7626 (p90) REVERT: D 251 ASP cc_start: 0.8084 (m-30) cc_final: 0.7800 (m-30) REVERT: E 45 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7415 (mm-30) REVERT: E 123 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7886 (mt-10) REVERT: E 124 ASN cc_start: 0.8880 (m-40) cc_final: 0.8571 (m-40) REVERT: E 134 LYS cc_start: 0.8212 (mtmm) cc_final: 0.7888 (mtmm) REVERT: E 137 LYS cc_start: 0.8295 (mmtp) cc_final: 0.7950 (mmtp) REVERT: E 182 ASP cc_start: 0.8088 (m-30) cc_final: 0.7866 (m-30) REVERT: E 230 VAL cc_start: 0.8613 (m) cc_final: 0.8397 (p) REVERT: E 241 LYS cc_start: 0.8541 (ptmt) cc_final: 0.8107 (ptmt) REVERT: E 277 LYS cc_start: 0.8338 (mttt) cc_final: 0.8095 (mtmt) REVERT: E 312 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7764 (mm-30) REVERT: E 438 ASP cc_start: 0.7487 (m-30) cc_final: 0.6962 (m-30) REVERT: E 441 GLU cc_start: 0.7929 (tp30) cc_final: 0.7274 (tp30) REVERT: F 32 ASP cc_start: 0.7998 (m-30) cc_final: 0.7663 (m-30) REVERT: F 128 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8319 (mtmm) REVERT: F 131 GLU cc_start: 0.7320 (pt0) cc_final: 0.7058 (pt0) REVERT: F 142 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7639 (mt-10) REVERT: F 155 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7765 (pt0) REVERT: F 185 LEU cc_start: 0.8349 (mt) cc_final: 0.8129 (mm) REVERT: F 204 ARG cc_start: 0.8126 (mmm160) cc_final: 0.7899 (mmm-85) REVERT: F 229 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8378 (tp) REVERT: F 231 LYS cc_start: 0.8647 (ptpt) cc_final: 0.8387 (ptpt) REVERT: F 232 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7518 (mtp85) REVERT: F 235 VAL cc_start: 0.8735 (t) cc_final: 0.8481 (m) REVERT: F 251 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8357 (m) REVERT: F 264 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7011 (mt-10) REVERT: F 349 ASP cc_start: 0.7863 (t70) cc_final: 0.7568 (t70) REVERT: F 377 VAL cc_start: 0.8543 (t) cc_final: 0.8278 (p) REVERT: F 389 LYS cc_start: 0.8423 (tttm) cc_final: 0.8169 (tttm) REVERT: F 393 GLU cc_start: 0.7964 (tp30) cc_final: 0.7683 (tp30) REVERT: F 405 VAL cc_start: 0.8493 (t) cc_final: 0.8236 (m) REVERT: F 413 ARG cc_start: 0.8407 (ttp80) cc_final: 0.8143 (ttp80) REVERT: F 438 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7353 (mtpp) REVERT: F 442 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7579 (mt-10) REVERT: F 443 ASN cc_start: 0.8141 (m-40) cc_final: 0.7923 (m-40) REVERT: F 444 GLU cc_start: 0.7746 (tt0) cc_final: 0.7507 (tt0) REVERT: G 69 LYS cc_start: 0.8325 (mtpp) cc_final: 0.7929 (mtpp) REVERT: G 134 LYS cc_start: 0.8172 (mtmm) cc_final: 0.7929 (mtmm) REVERT: G 198 ASP cc_start: 0.7647 (m-30) cc_final: 0.7244 (m-30) REVERT: G 199 VAL cc_start: 0.8829 (OUTLIER) cc_final: 0.8622 (m) REVERT: G 210 LYS cc_start: 0.8276 (tppt) cc_final: 0.7730 (tppt) REVERT: G 216 ASP cc_start: 0.7893 (m-30) cc_final: 0.7612 (m-30) REVERT: G 234 LYS cc_start: 0.8338 (mttm) cc_final: 0.8068 (mttm) REVERT: G 240 LYS cc_start: 0.8428 (mtmm) cc_final: 0.8150 (mtmm) REVERT: G 267 SER cc_start: 0.8048 (m) cc_final: 0.7671 (p) REVERT: G 269 MET cc_start: 0.7412 (mpp) cc_final: 0.7076 (mpp) REVERT: G 287 GLU cc_start: 0.7867 (tp30) cc_final: 0.7111 (tp30) REVERT: G 294 LYS cc_start: 0.8759 (tttm) cc_final: 0.8384 (tttm) REVERT: G 315 MET cc_start: 0.8538 (mmm) cc_final: 0.8261 (mmp) REVERT: G 400 LEU cc_start: 0.8549 (tp) cc_final: 0.8247 (mp) REVERT: G 406 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7872 (mtp) REVERT: G 418 LEU cc_start: 0.8607 (tp) cc_final: 0.8284 (tt) REVERT: G 433 GLU cc_start: 0.7622 (mp0) cc_final: 0.7330 (mp0) REVERT: G 435 VAL cc_start: 0.7842 (OUTLIER) cc_final: 0.7402 (m) REVERT: G 443 LYS cc_start: 0.8514 (ttmt) cc_final: 0.8221 (ttmt) REVERT: H 115 GLU cc_start: 0.8530 (tp30) cc_final: 0.8239 (tp30) REVERT: H 128 LYS cc_start: 0.8523 (ttmm) cc_final: 0.8168 (mtmm) REVERT: H 157 LYS cc_start: 0.8042 (mtmm) cc_final: 0.7803 (mtmm) REVERT: H 166 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7597 (tm-30) REVERT: H 175 MET cc_start: 0.8287 (tpp) cc_final: 0.7782 (tpp) REVERT: H 198 LYS cc_start: 0.7696 (tptp) cc_final: 0.7397 (tptp) REVERT: H 199 ILE cc_start: 0.8686 (mt) cc_final: 0.8277 (mt) REVERT: H 270 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.7905 (mtt90) REVERT: H 271 ASP cc_start: 0.7640 (m-30) cc_final: 0.7150 (m-30) REVERT: H 300 MET cc_start: 0.8336 (tpp) cc_final: 0.7941 (mpp) REVERT: H 336 ASN cc_start: 0.7916 (p0) cc_final: 0.7622 (p0) REVERT: H 349 ASP cc_start: 0.8075 (t0) cc_final: 0.7808 (t0) REVERT: H 374 GLU cc_start: 0.8141 (tp30) cc_final: 0.7752 (tp30) REVERT: H 422 ASP cc_start: 0.7901 (m-30) cc_final: 0.7646 (m-30) REVERT: H 438 LYS cc_start: 0.8322 (ttmt) cc_final: 0.8056 (ttmt) REVERT: I 52 ILE cc_start: 0.8012 (mm) cc_final: 0.7631 (mm) REVERT: I 53 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7986 (mp0) REVERT: I 127 ARG cc_start: 0.8140 (ttm170) cc_final: 0.7890 (ttm170) REVERT: I 133 ILE cc_start: 0.8881 (tt) cc_final: 0.8617 (pt) REVERT: I 135 GLU cc_start: 0.7980 (tt0) cc_final: 0.7751 (pt0) REVERT: I 136 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8510 (p) REVERT: I 138 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7304 (mt-10) REVERT: I 182 ASP cc_start: 0.7792 (m-30) cc_final: 0.7302 (m-30) REVERT: I 187 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7769 (mt-10) REVERT: I 210 LYS cc_start: 0.8321 (ttpt) cc_final: 0.8096 (ttpt) REVERT: I 249 LEU cc_start: 0.8140 (mt) cc_final: 0.7666 (mp) REVERT: I 253 ASP cc_start: 0.7783 (m-30) cc_final: 0.7569 (m-30) REVERT: I 258 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7596 (mtm-85) REVERT: I 268 MET cc_start: 0.7227 (ttp) cc_final: 0.6955 (ttp) REVERT: I 279 GLU cc_start: 0.7514 (pt0) cc_final: 0.7149 (pt0) REVERT: I 302 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7852 (mm-30) REVERT: I 313 VAL cc_start: 0.8835 (p) cc_final: 0.8598 (m) REVERT: I 386 ARG cc_start: 0.8188 (mmm-85) cc_final: 0.7807 (mmm160) REVERT: I 392 ARG cc_start: 0.7969 (mtm180) cc_final: 0.7625 (mtm180) REVERT: I 401 ASP cc_start: 0.7831 (m-30) cc_final: 0.7363 (m-30) REVERT: I 406 MET cc_start: 0.8478 (ttp) cc_final: 0.8202 (ttm) REVERT: I 417 GLN cc_start: 0.7999 (mt0) cc_final: 0.7713 (mt0) REVERT: I 431 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7640 (mtm-85) REVERT: I 438 ASP cc_start: 0.7815 (m-30) cc_final: 0.7210 (m-30) REVERT: I 451 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7414 (mtp85) REVERT: J 78 SER cc_start: 0.8401 (t) cc_final: 0.8163 (t) REVERT: J 81 LYS cc_start: 0.8230 (mtmm) cc_final: 0.8016 (mtmm) REVERT: J 128 LYS cc_start: 0.8227 (mtpp) cc_final: 0.7868 (mtpp) REVERT: J 132 GLU cc_start: 0.6195 (tm-30) cc_final: 0.5804 (mm-30) REVERT: J 145 ILE cc_start: 0.8431 (mm) cc_final: 0.8182 (mm) REVERT: J 170 GLU cc_start: 0.7387 (mp0) cc_final: 0.6963 (mp0) REVERT: J 171 LEU cc_start: 0.8672 (mp) cc_final: 0.8403 (mt) REVERT: J 245 ASP cc_start: 0.7871 (t0) cc_final: 0.7590 (m-30) REVERT: J 266 ARG cc_start: 0.6988 (mtm-85) cc_final: 0.6626 (mtm-85) REVERT: J 268 GLU cc_start: 0.7623 (pm20) cc_final: 0.6900 (mp0) REVERT: J 295 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.8026 (mt) REVERT: J 297 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7463 (mm-30) REVERT: J 310 ASN cc_start: 0.8185 (m-40) cc_final: 0.7743 (m110) REVERT: J 346 ASP cc_start: 0.7388 (t70) cc_final: 0.6837 (t70) REVERT: J 350 ARG cc_start: 0.7907 (ttm110) cc_final: 0.7544 (ttm110) REVERT: J 357 LYS cc_start: 0.8142 (mmpt) cc_final: 0.7853 (mmpt) REVERT: J 362 GLN cc_start: 0.7737 (mp10) cc_final: 0.7433 (mp10) REVERT: J 365 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7929 (ttmt) REVERT: J 380 SER cc_start: 0.8776 (t) cc_final: 0.8461 (t) REVERT: J 385 ASP cc_start: 0.7892 (t70) cc_final: 0.7585 (t70) REVERT: J 389 LYS cc_start: 0.8444 (ptmm) cc_final: 0.8161 (ptmm) REVERT: J 393 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7583 (mt-10) REVERT: J 405 VAL cc_start: 0.8181 (t) cc_final: 0.7940 (m) REVERT: J 438 LYS cc_start: 0.8221 (tmtt) cc_final: 0.7960 (tmtt) REVERT: J 451 GLN cc_start: 0.8500 (mm-40) cc_final: 0.8250 (mm-40) outliers start: 94 outliers final: 64 residues processed: 1296 average time/residue: 0.5562 time to fit residues: 1102.8591 Evaluate side-chains 1343 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1266 time to evaluate : 3.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 779 SER Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1002 ARG Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain A residue 1354 ARG Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 209 TYR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 429 LYS Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 406 MET Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 155 GLN Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 288 ILE Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 406 MET Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain H residue 296 ASP Chi-restraints excluded: chain H residue 376 GLU Chi-restraints excluded: chain H residue 414 LYS Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 238 THR Chi-restraints excluded: chain J residue 295 ILE Chi-restraints excluded: chain J residue 339 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 303 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 372 optimal weight: 9.9990 chunk 187 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.0050 chunk 272 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS A1101 ASN C 319 HIS D 109 ASN E 256 ASN G 286 GLN H 49 GLN H 272 GLN H 310 ASN ** H 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 250 HIS J 299 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.131075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.111135 restraints weight = 55532.900| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.24 r_work: 0.3269 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33764 Z= 0.152 Angle : 0.621 15.975 45853 Z= 0.313 Chirality : 0.043 0.200 5344 Planarity : 0.004 0.060 5653 Dihedral : 14.326 169.665 5012 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.40 % Allowed : 22.06 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.13), residues: 4008 helix: 1.60 (0.12), residues: 1836 sheet: 0.34 (0.19), residues: 709 loop : -0.46 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 745 HIS 0.009 0.001 HIS A1012 PHE 0.023 0.001 PHE B 637 TYR 0.035 0.001 TYR C 143 ARG 0.012 0.000 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.03830 ( 1460) hydrogen bonds : angle 4.04596 ( 4148) metal coordination : bond 0.00590 ( 7) metal coordination : angle 4.45800 ( 6) covalent geometry : bond 0.00347 (33757) covalent geometry : angle 0.61859 (45847) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 1281 time to evaluate : 3.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 707 LEU cc_start: 0.8318 (mm) cc_final: 0.8022 (mt) REVERT: A 752 VAL cc_start: 0.7921 (OUTLIER) cc_final: 0.7667 (t) REVERT: A 763 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7727 (mm-30) REVERT: A 765 LYS cc_start: 0.8768 (pttm) cc_final: 0.8566 (pttt) REVERT: A 821 MET cc_start: 0.8084 (ttt) cc_final: 0.7727 (ttt) REVERT: A 828 ASN cc_start: 0.8415 (m-40) cc_final: 0.8099 (m-40) REVERT: A 829 ILE cc_start: 0.8552 (pt) cc_final: 0.8245 (tt) REVERT: A 837 TRP cc_start: 0.8234 (t60) cc_final: 0.8017 (t60) REVERT: A 838 GLN cc_start: 0.8630 (mm110) cc_final: 0.8319 (mm-40) REVERT: A 862 GLU cc_start: 0.8029 (mp0) cc_final: 0.7293 (mp0) REVERT: A 864 TRP cc_start: 0.7975 (t60) cc_final: 0.7708 (t60) REVERT: A 870 LEU cc_start: 0.8836 (mm) cc_final: 0.8573 (mm) REVERT: A 871 MET cc_start: 0.8064 (mmp) cc_final: 0.7604 (mmp) REVERT: A 894 PHE cc_start: 0.7532 (m-80) cc_final: 0.7223 (m-10) REVERT: A 946 GLU cc_start: 0.6908 (pp20) cc_final: 0.6521 (pp20) REVERT: A 1000 GLU cc_start: 0.7053 (tp30) cc_final: 0.6777 (tp30) REVERT: A 1002 ARG cc_start: 0.8268 (mtp180) cc_final: 0.8024 (mtp180) REVERT: A 1022 GLU cc_start: 0.7687 (tt0) cc_final: 0.7345 (tt0) REVERT: A 1073 GLU cc_start: 0.7946 (pt0) cc_final: 0.7687 (pt0) REVERT: A 1079 ARG cc_start: 0.7927 (tpp80) cc_final: 0.7537 (ttp80) REVERT: A 1109 LYS cc_start: 0.8414 (tmtt) cc_final: 0.8173 (tmtp) REVERT: A 1113 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7314 (tm-30) REVERT: A 1133 ARG cc_start: 0.8242 (ptp-110) cc_final: 0.8002 (ptp-110) REVERT: A 1146 LYS cc_start: 0.8015 (ttmm) cc_final: 0.7685 (ttmm) REVERT: A 1161 GLU cc_start: 0.7303 (tp30) cc_final: 0.6909 (tp30) REVERT: A 1245 CYS cc_start: 0.7912 (t) cc_final: 0.7340 (t) REVERT: A 1290 MET cc_start: 0.6961 (mtt) cc_final: 0.6436 (mtt) REVERT: A 1330 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8197 (tt) REVERT: A 1347 MET cc_start: 0.7025 (mmp) cc_final: 0.6725 (mmm) REVERT: A 1394 ILE cc_start: 0.7483 (mm) cc_final: 0.7108 (mm) REVERT: B 269 ASN cc_start: 0.8024 (m110) cc_final: 0.7618 (m110) REVERT: C 7 VAL cc_start: 0.8905 (OUTLIER) cc_final: 0.8610 (m) REVERT: C 44 ASN cc_start: 0.8638 (t0) cc_final: 0.8182 (t0) REVERT: C 57 PHE cc_start: 0.8032 (m-80) cc_final: 0.7763 (m-10) REVERT: C 77 ASP cc_start: 0.8314 (m-30) cc_final: 0.8106 (m-30) REVERT: C 95 LYS cc_start: 0.8993 (ttmm) cc_final: 0.8662 (ttmm) REVERT: C 184 TYR cc_start: 0.8723 (p90) cc_final: 0.8419 (p90) REVERT: C 240 ASP cc_start: 0.8350 (t0) cc_final: 0.7951 (t0) REVERT: C 250 GLU cc_start: 0.7995 (tp30) cc_final: 0.7578 (tp30) REVERT: C 256 SER cc_start: 0.9146 (OUTLIER) cc_final: 0.8934 (t) REVERT: C 265 LYS cc_start: 0.8626 (mmpt) cc_final: 0.8197 (mmtt) REVERT: C 332 GLU cc_start: 0.7926 (mp0) cc_final: 0.7588 (mp0) REVERT: C 337 SER cc_start: 0.8905 (t) cc_final: 0.8547 (p) REVERT: C 398 GLU cc_start: 0.8550 (tt0) cc_final: 0.8001 (tm-30) REVERT: C 435 GLN cc_start: 0.8654 (mm110) cc_final: 0.8419 (mm110) REVERT: D 173 ARG cc_start: 0.8708 (mtt90) cc_final: 0.8169 (mtt90) REVERT: D 222 LYS cc_start: 0.8772 (tppp) cc_final: 0.8280 (tppp) REVERT: D 250 TYR cc_start: 0.8600 (p90) cc_final: 0.7661 (p90) REVERT: D 251 ASP cc_start: 0.8085 (m-30) cc_final: 0.7773 (m-30) REVERT: E 45 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7418 (mm-30) REVERT: E 113 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8580 (t) REVERT: E 123 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7855 (mt-10) REVERT: E 134 LYS cc_start: 0.8236 (mtmm) cc_final: 0.7916 (mtmm) REVERT: E 137 LYS cc_start: 0.8312 (mmtp) cc_final: 0.7968 (mmtp) REVERT: E 182 ASP cc_start: 0.8106 (m-30) cc_final: 0.7874 (m-30) REVERT: E 230 VAL cc_start: 0.8608 (m) cc_final: 0.8398 (p) REVERT: E 241 LYS cc_start: 0.8551 (ptmt) cc_final: 0.8131 (ptmt) REVERT: E 277 LYS cc_start: 0.8329 (mttt) cc_final: 0.8072 (mtmt) REVERT: E 312 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7783 (mm-30) REVERT: E 438 ASP cc_start: 0.7492 (m-30) cc_final: 0.6975 (m-30) REVERT: E 441 GLU cc_start: 0.7916 (tp30) cc_final: 0.7265 (tp30) REVERT: F 32 ASP cc_start: 0.7988 (m-30) cc_final: 0.7653 (m-30) REVERT: F 128 LYS cc_start: 0.8643 (mtmt) cc_final: 0.8314 (mtmm) REVERT: F 131 GLU cc_start: 0.7336 (pt0) cc_final: 0.7080 (pt0) REVERT: F 142 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7541 (mt-10) REVERT: F 155 GLN cc_start: 0.8121 (tt0) cc_final: 0.7755 (pt0) REVERT: F 185 LEU cc_start: 0.8359 (mt) cc_final: 0.8128 (mm) REVERT: F 204 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7919 (mmm-85) REVERT: F 221 PHE cc_start: 0.8466 (m-80) cc_final: 0.8092 (m-10) REVERT: F 229 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8393 (tp) REVERT: F 231 LYS cc_start: 0.8639 (ptpt) cc_final: 0.8361 (ptpt) REVERT: F 232 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7518 (mtp85) REVERT: F 235 VAL cc_start: 0.8729 (t) cc_final: 0.8468 (m) REVERT: F 251 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8413 (m) REVERT: F 264 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7010 (mt-10) REVERT: F 349 ASP cc_start: 0.7893 (t70) cc_final: 0.7618 (t70) REVERT: F 365 LYS cc_start: 0.8546 (ttpp) cc_final: 0.8234 (ttmm) REVERT: F 377 VAL cc_start: 0.8561 (t) cc_final: 0.8276 (p) REVERT: F 389 LYS cc_start: 0.8402 (tttm) cc_final: 0.8144 (tttm) REVERT: F 393 GLU cc_start: 0.7922 (tp30) cc_final: 0.7646 (tp30) REVERT: F 405 VAL cc_start: 0.8578 (t) cc_final: 0.8319 (m) REVERT: F 413 ARG cc_start: 0.8421 (ttp80) cc_final: 0.8153 (ttp80) REVERT: F 438 LYS cc_start: 0.7844 (mtpp) cc_final: 0.7366 (mtpp) REVERT: F 442 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7537 (mt-10) REVERT: F 444 GLU cc_start: 0.7757 (tt0) cc_final: 0.7519 (tt0) REVERT: G 69 LYS cc_start: 0.8340 (mtpp) cc_final: 0.7963 (mtpp) REVERT: G 134 LYS cc_start: 0.8143 (mtmm) cc_final: 0.7893 (mtmm) REVERT: G 198 ASP cc_start: 0.7697 (m-30) cc_final: 0.7449 (m-30) REVERT: G 210 LYS cc_start: 0.8280 (tppt) cc_final: 0.7723 (tppt) REVERT: G 216 ASP cc_start: 0.7900 (m-30) cc_final: 0.7628 (m-30) REVERT: G 234 LYS cc_start: 0.8356 (mttm) cc_final: 0.8093 (mttm) REVERT: G 246 ASP cc_start: 0.7537 (p0) cc_final: 0.7321 (p0) REVERT: G 267 SER cc_start: 0.8032 (m) cc_final: 0.7650 (p) REVERT: G 269 MET cc_start: 0.7449 (mpp) cc_final: 0.7109 (mpp) REVERT: G 287 GLU cc_start: 0.7881 (tp30) cc_final: 0.7114 (tp30) REVERT: G 294 LYS cc_start: 0.8776 (tttm) cc_final: 0.8410 (tttm) REVERT: G 315 MET cc_start: 0.8521 (mmm) cc_final: 0.8245 (mmp) REVERT: G 406 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7844 (mtp) REVERT: G 418 LEU cc_start: 0.8591 (tp) cc_final: 0.8273 (tt) REVERT: G 433 GLU cc_start: 0.7578 (mp0) cc_final: 0.7258 (mp0) REVERT: G 435 VAL cc_start: 0.7870 (OUTLIER) cc_final: 0.7435 (m) REVERT: G 443 LYS cc_start: 0.8543 (ttmt) cc_final: 0.8222 (ttmt) REVERT: H 62 GLN cc_start: 0.8470 (mt0) cc_final: 0.8139 (mt0) REVERT: H 115 GLU cc_start: 0.8548 (tp30) cc_final: 0.8264 (tp30) REVERT: H 128 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8192 (mtmm) REVERT: H 157 LYS cc_start: 0.8036 (mtmm) cc_final: 0.7792 (mtmm) REVERT: H 166 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7688 (tm-30) REVERT: H 175 MET cc_start: 0.8286 (tpp) cc_final: 0.7775 (tpp) REVERT: H 198 LYS cc_start: 0.7693 (tptp) cc_final: 0.7388 (tptp) REVERT: H 199 ILE cc_start: 0.8686 (mt) cc_final: 0.8287 (mt) REVERT: H 270 ARG cc_start: 0.8279 (mtt-85) cc_final: 0.7931 (mtt90) REVERT: H 271 ASP cc_start: 0.7652 (m-30) cc_final: 0.7164 (m-30) REVERT: H 300 MET cc_start: 0.8341 (tpp) cc_final: 0.8058 (mpp) REVERT: H 336 ASN cc_start: 0.7906 (p0) cc_final: 0.7614 (p0) REVERT: H 349 ASP cc_start: 0.8090 (t0) cc_final: 0.7816 (t0) REVERT: H 374 GLU cc_start: 0.8083 (tp30) cc_final: 0.7707 (tp30) REVERT: H 422 ASP cc_start: 0.7921 (m-30) cc_final: 0.7685 (m-30) REVERT: H 438 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8057 (ttmt) REVERT: I 52 ILE cc_start: 0.8060 (mm) cc_final: 0.7707 (mm) REVERT: I 53 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7995 (mp0) REVERT: I 127 ARG cc_start: 0.8094 (ttm170) cc_final: 0.7862 (ttm170) REVERT: I 133 ILE cc_start: 0.8884 (tt) cc_final: 0.8621 (pt) REVERT: I 135 GLU cc_start: 0.7998 (tt0) cc_final: 0.7764 (pt0) REVERT: I 182 ASP cc_start: 0.7816 (m-30) cc_final: 0.7288 (m-30) REVERT: I 187 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7759 (mt-10) REVERT: I 210 LYS cc_start: 0.8333 (ttpt) cc_final: 0.8094 (ttpt) REVERT: I 258 ARG cc_start: 0.7846 (mtm-85) cc_final: 0.7621 (mtm-85) REVERT: I 268 MET cc_start: 0.7263 (ttp) cc_final: 0.6986 (ttp) REVERT: I 279 GLU cc_start: 0.7543 (pt0) cc_final: 0.7180 (pt0) REVERT: I 302 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7831 (mm-30) REVERT: I 313 VAL cc_start: 0.8834 (p) cc_final: 0.8619 (m) REVERT: I 386 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7813 (mmm160) REVERT: I 392 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7621 (mtm180) REVERT: I 401 ASP cc_start: 0.7837 (m-30) cc_final: 0.7367 (m-30) REVERT: I 406 MET cc_start: 0.8545 (ttp) cc_final: 0.8242 (ttm) REVERT: I 417 GLN cc_start: 0.8001 (mt0) cc_final: 0.7720 (mt0) REVERT: I 438 ASP cc_start: 0.7825 (m-30) cc_final: 0.7394 (m-30) REVERT: J 78 SER cc_start: 0.8437 (t) cc_final: 0.8191 (t) REVERT: J 81 LYS cc_start: 0.8258 (mtmm) cc_final: 0.7923 (mttp) REVERT: J 128 LYS cc_start: 0.8235 (mtpp) cc_final: 0.7881 (mtpp) REVERT: J 132 GLU cc_start: 0.6194 (tm-30) cc_final: 0.5883 (tm-30) REVERT: J 145 ILE cc_start: 0.8417 (mm) cc_final: 0.8188 (mm) REVERT: J 170 GLU cc_start: 0.7467 (mp0) cc_final: 0.7031 (mp0) REVERT: J 171 LEU cc_start: 0.8694 (mp) cc_final: 0.8420 (mt) REVERT: J 245 ASP cc_start: 0.7877 (t0) cc_final: 0.7589 (m-30) REVERT: J 266 ARG cc_start: 0.7083 (mtm-85) cc_final: 0.6677 (mtm-85) REVERT: J 268 GLU cc_start: 0.7695 (pm20) cc_final: 0.6984 (mp0) REVERT: J 295 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.8043 (mt) REVERT: J 297 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7478 (mm-30) REVERT: J 346 ASP cc_start: 0.7420 (t70) cc_final: 0.6940 (t0) REVERT: J 350 ARG cc_start: 0.7899 (ttm110) cc_final: 0.7497 (ttm110) REVERT: J 365 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7939 (ttmt) REVERT: J 380 SER cc_start: 0.8766 (t) cc_final: 0.8453 (t) REVERT: J 385 ASP cc_start: 0.7884 (t70) cc_final: 0.7587 (t70) REVERT: J 389 LYS cc_start: 0.8457 (ptmm) cc_final: 0.8172 (ptmm) REVERT: J 393 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7569 (mt-10) REVERT: J 405 VAL cc_start: 0.8205 (t) cc_final: 0.7967 (m) REVERT: J 438 LYS cc_start: 0.8219 (tmtt) cc_final: 0.7959 (tmtt) REVERT: J 451 GLN cc_start: 0.8491 (mm-40) cc_final: 0.8242 (mm-40) outliers start: 85 outliers final: 63 residues processed: 1309 average time/residue: 0.5269 time to fit residues: 1052.9062 Evaluate side-chains 1345 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 1272 time to evaluate : 3.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1219 GLU Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 256 SER Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 429 LYS Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 302 GLU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 406 MET Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 406 MET Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain H residue 296 ASP Chi-restraints excluded: chain H residue 376 GLU Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 414 LYS Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain I residue 108 SER Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 238 THR Chi-restraints excluded: chain J residue 295 ILE Chi-restraints excluded: chain J residue 339 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 240 optimal weight: 2.9990 chunk 363 optimal weight: 0.0770 chunk 245 optimal weight: 0.9980 chunk 288 optimal weight: 4.9990 chunk 317 optimal weight: 1.9990 chunk 299 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS A1098 GLN A1101 ASN ** C 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 HIS C 324 GLN C 352 ASN D 109 ASN E 245 GLN E 256 ASN G 286 GLN H 441 GLN I 250 HIS J 299 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.130719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110875 restraints weight = 55368.326| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.21 r_work: 0.3267 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33764 Z= 0.193 Angle : 0.657 15.982 45853 Z= 0.331 Chirality : 0.044 0.258 5344 Planarity : 0.004 0.060 5653 Dihedral : 14.413 177.403 5012 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.31 % Allowed : 22.57 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.13), residues: 4008 helix: 1.49 (0.12), residues: 1838 sheet: 0.21 (0.19), residues: 716 loop : -0.50 (0.16), residues: 1454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.003 TRP A 745 HIS 0.009 0.001 HIS A1012 PHE 0.023 0.001 PHE B 259 TYR 0.037 0.002 TYR C 143 ARG 0.011 0.001 ARG C 375 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 1460) hydrogen bonds : angle 4.14305 ( 4148) metal coordination : bond 0.00739 ( 7) metal coordination : angle 4.40652 ( 6) covalent geometry : bond 0.00438 (33757) covalent geometry : angle 0.65474 (45847) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8016 Ramachandran restraints generated. 4008 Oldfield, 0 Emsley, 4008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 1272 time to evaluate : 3.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 752 VAL cc_start: 0.8006 (OUTLIER) cc_final: 0.7748 (t) REVERT: A 763 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7752 (mm-30) REVERT: A 821 MET cc_start: 0.8049 (ttt) cc_final: 0.7716 (ttt) REVERT: A 828 ASN cc_start: 0.8424 (m-40) cc_final: 0.8097 (m-40) REVERT: A 829 ILE cc_start: 0.8543 (pt) cc_final: 0.8234 (tt) REVERT: A 838 GLN cc_start: 0.8646 (mm110) cc_final: 0.8313 (mm-40) REVERT: A 862 GLU cc_start: 0.7979 (mp0) cc_final: 0.7286 (mp0) REVERT: A 870 LEU cc_start: 0.8855 (mm) cc_final: 0.8583 (mm) REVERT: A 871 MET cc_start: 0.8099 (mmp) cc_final: 0.7767 (mmp) REVERT: A 894 PHE cc_start: 0.7495 (m-80) cc_final: 0.7195 (m-10) REVERT: A 899 ASP cc_start: 0.7664 (t0) cc_final: 0.7453 (t0) REVERT: A 903 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7990 (mm-30) REVERT: A 946 GLU cc_start: 0.6948 (pp20) cc_final: 0.6580 (pp20) REVERT: A 1000 GLU cc_start: 0.6995 (tp30) cc_final: 0.6717 (tp30) REVERT: A 1002 ARG cc_start: 0.8241 (mtp180) cc_final: 0.7973 (mtp180) REVERT: A 1022 GLU cc_start: 0.7760 (tt0) cc_final: 0.7509 (tt0) REVERT: A 1073 GLU cc_start: 0.7919 (pt0) cc_final: 0.7643 (pt0) REVERT: A 1079 ARG cc_start: 0.7953 (tpp80) cc_final: 0.7586 (ttp80) REVERT: A 1133 ARG cc_start: 0.8274 (ptp-110) cc_final: 0.8013 (ptp-110) REVERT: A 1146 LYS cc_start: 0.7957 (ttmm) cc_final: 0.7649 (ttmm) REVERT: A 1161 GLU cc_start: 0.7382 (tp30) cc_final: 0.6969 (tp30) REVERT: A 1245 CYS cc_start: 0.8008 (t) cc_final: 0.7529 (t) REVERT: A 1290 MET cc_start: 0.7011 (mtt) cc_final: 0.6491 (mtt) REVERT: A 1330 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8204 (tt) REVERT: A 1347 MET cc_start: 0.6977 (mmp) cc_final: 0.6724 (mmm) REVERT: A 1394 ILE cc_start: 0.7460 (mm) cc_final: 0.7096 (mm) REVERT: B 269 ASN cc_start: 0.8105 (m110) cc_final: 0.7660 (m110) REVERT: B 297 MET cc_start: 0.7951 (mmm) cc_final: 0.7713 (mmm) REVERT: C 7 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8624 (m) REVERT: C 44 ASN cc_start: 0.8617 (t0) cc_final: 0.8181 (t0) REVERT: C 57 PHE cc_start: 0.8054 (m-80) cc_final: 0.7787 (m-10) REVERT: C 77 ASP cc_start: 0.8307 (m-30) cc_final: 0.8104 (m-30) REVERT: C 95 LYS cc_start: 0.8993 (ttmm) cc_final: 0.8654 (ttmm) REVERT: C 184 TYR cc_start: 0.8727 (p90) cc_final: 0.8429 (p90) REVERT: C 240 ASP cc_start: 0.8303 (t0) cc_final: 0.7889 (t0) REVERT: C 250 GLU cc_start: 0.7980 (tp30) cc_final: 0.7590 (tp30) REVERT: C 265 LYS cc_start: 0.8621 (mmpt) cc_final: 0.8177 (mmtt) REVERT: C 332 GLU cc_start: 0.7946 (mp0) cc_final: 0.7596 (mp0) REVERT: C 337 SER cc_start: 0.8900 (t) cc_final: 0.8558 (p) REVERT: C 398 GLU cc_start: 0.8469 (tt0) cc_final: 0.7961 (tm-30) REVERT: C 421 GLU cc_start: 0.7915 (pp20) cc_final: 0.7590 (pp20) REVERT: C 435 GLN cc_start: 0.8656 (mm110) cc_final: 0.8450 (mm110) REVERT: D 250 TYR cc_start: 0.8621 (p90) cc_final: 0.7614 (p90) REVERT: E 45 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7392 (mm-30) REVERT: E 113 VAL cc_start: 0.8831 (OUTLIER) cc_final: 0.8611 (t) REVERT: E 123 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7904 (mt-10) REVERT: E 134 LYS cc_start: 0.8239 (mtmm) cc_final: 0.7951 (mtmm) REVERT: E 137 LYS cc_start: 0.8275 (mmtp) cc_final: 0.7974 (mmtp) REVERT: E 182 ASP cc_start: 0.8091 (m-30) cc_final: 0.7838 (m-30) REVERT: E 241 LYS cc_start: 0.8555 (ptmt) cc_final: 0.8135 (ptmt) REVERT: E 260 GLN cc_start: 0.7510 (tp40) cc_final: 0.7152 (tp40) REVERT: E 277 LYS cc_start: 0.8326 (mttt) cc_final: 0.8095 (mtmt) REVERT: E 312 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7758 (mm-30) REVERT: E 438 ASP cc_start: 0.7491 (m-30) cc_final: 0.6993 (m-30) REVERT: E 441 GLU cc_start: 0.7969 (tp30) cc_final: 0.7348 (tp30) REVERT: F 32 ASP cc_start: 0.7971 (m-30) cc_final: 0.7664 (m-30) REVERT: F 128 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8357 (mtmm) REVERT: F 131 GLU cc_start: 0.7362 (pt0) cc_final: 0.7146 (pt0) REVERT: F 142 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7498 (mt-10) REVERT: F 155 GLN cc_start: 0.8167 (tt0) cc_final: 0.7764 (pt0) REVERT: F 204 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7943 (mmm-85) REVERT: F 221 PHE cc_start: 0.8486 (m-80) cc_final: 0.8118 (m-10) REVERT: F 231 LYS cc_start: 0.8649 (ptpt) cc_final: 0.8393 (ptpt) REVERT: F 232 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7459 (mtp85) REVERT: F 251 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8525 (m) REVERT: F 264 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7063 (mt-10) REVERT: F 349 ASP cc_start: 0.7910 (t70) cc_final: 0.7664 (t70) REVERT: F 377 VAL cc_start: 0.8583 (t) cc_final: 0.8298 (p) REVERT: F 389 LYS cc_start: 0.8470 (tttm) cc_final: 0.8206 (tttm) REVERT: F 393 GLU cc_start: 0.7912 (tp30) cc_final: 0.7633 (tp30) REVERT: F 405 VAL cc_start: 0.8565 (t) cc_final: 0.8307 (m) REVERT: F 413 ARG cc_start: 0.8489 (ttp80) cc_final: 0.8214 (ttp80) REVERT: F 438 LYS cc_start: 0.7878 (mtpp) cc_final: 0.7392 (mtpp) REVERT: F 442 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7594 (mt-10) REVERT: F 444 GLU cc_start: 0.7839 (tt0) cc_final: 0.7612 (tt0) REVERT: G 23 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8322 (mmm-85) REVERT: G 69 LYS cc_start: 0.8394 (mtpp) cc_final: 0.8047 (mtpp) REVERT: G 134 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7883 (mtmm) REVERT: G 198 ASP cc_start: 0.7758 (m-30) cc_final: 0.7446 (m-30) REVERT: G 210 LYS cc_start: 0.8263 (tppt) cc_final: 0.7706 (tppt) REVERT: G 216 ASP cc_start: 0.7925 (m-30) cc_final: 0.7653 (m-30) REVERT: G 234 LYS cc_start: 0.8438 (mttm) cc_final: 0.8173 (mttm) REVERT: G 246 ASP cc_start: 0.7541 (p0) cc_final: 0.7334 (p0) REVERT: G 269 MET cc_start: 0.7391 (mpp) cc_final: 0.7025 (mpp) REVERT: G 287 GLU cc_start: 0.7885 (tp30) cc_final: 0.7135 (tp30) REVERT: G 294 LYS cc_start: 0.8804 (tttm) cc_final: 0.8464 (tttm) REVERT: G 315 MET cc_start: 0.8517 (mmm) cc_final: 0.8240 (mmp) REVERT: G 406 MET cc_start: 0.8229 (mtm) cc_final: 0.7978 (mtp) REVERT: G 433 GLU cc_start: 0.7605 (mp0) cc_final: 0.7349 (mp0) REVERT: G 435 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.7546 (m) REVERT: G 443 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8249 (ttpt) REVERT: H 128 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8206 (mtmm) REVERT: H 166 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7686 (tm-30) REVERT: H 175 MET cc_start: 0.8263 (tpp) cc_final: 0.7691 (tpp) REVERT: H 270 ARG cc_start: 0.8318 (mtt-85) cc_final: 0.7913 (mtt90) REVERT: H 271 ASP cc_start: 0.7653 (m-30) cc_final: 0.7165 (m-30) REVERT: H 300 MET cc_start: 0.8299 (tpp) cc_final: 0.8007 (mpp) REVERT: H 336 ASN cc_start: 0.7929 (p0) cc_final: 0.7623 (p0) REVERT: H 349 ASP cc_start: 0.8092 (t0) cc_final: 0.7837 (t0) REVERT: H 374 GLU cc_start: 0.8109 (tp30) cc_final: 0.7733 (tp30) REVERT: H 438 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8065 (ttmt) REVERT: I 52 ILE cc_start: 0.8153 (mm) cc_final: 0.7764 (mm) REVERT: I 53 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8004 (mp0) REVERT: I 127 ARG cc_start: 0.8091 (ttm170) cc_final: 0.7829 (ttm170) REVERT: I 135 GLU cc_start: 0.7991 (tt0) cc_final: 0.7780 (pt0) REVERT: I 138 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7371 (mt-10) REVERT: I 182 ASP cc_start: 0.7838 (m-30) cc_final: 0.7312 (m-30) REVERT: I 187 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7797 (mt-10) REVERT: I 210 LYS cc_start: 0.8337 (ttpt) cc_final: 0.8097 (ttpt) REVERT: I 223 ASP cc_start: 0.7361 (p0) cc_final: 0.6457 (p0) REVERT: I 243 ILE cc_start: 0.8751 (mt) cc_final: 0.8532 (mm) REVERT: I 268 MET cc_start: 0.7274 (ttp) cc_final: 0.6994 (ttp) REVERT: I 279 GLU cc_start: 0.7526 (pt0) cc_final: 0.7168 (pt0) REVERT: I 386 ARG cc_start: 0.8203 (mmm-85) cc_final: 0.7839 (mmm160) REVERT: I 392 ARG cc_start: 0.7879 (mtm180) cc_final: 0.7603 (mtm180) REVERT: I 401 ASP cc_start: 0.7842 (m-30) cc_final: 0.7376 (m-30) REVERT: I 406 MET cc_start: 0.8498 (ttp) cc_final: 0.8160 (ttm) REVERT: I 438 ASP cc_start: 0.7839 (m-30) cc_final: 0.7428 (m-30) REVERT: J 81 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7976 (mttp) REVERT: J 128 LYS cc_start: 0.8232 (mtpp) cc_final: 0.7872 (mtpp) REVERT: J 132 GLU cc_start: 0.6139 (tm-30) cc_final: 0.5824 (tm-30) REVERT: J 145 ILE cc_start: 0.8411 (mm) cc_final: 0.8188 (mm) REVERT: J 170 GLU cc_start: 0.7370 (mp0) cc_final: 0.6668 (mp0) REVERT: J 171 LEU cc_start: 0.8695 (mp) cc_final: 0.8452 (mt) REVERT: J 245 ASP cc_start: 0.7826 (t0) cc_final: 0.7547 (m-30) REVERT: J 266 ARG cc_start: 0.7122 (mtm-85) cc_final: 0.6734 (mtm-85) REVERT: J 268 GLU cc_start: 0.7668 (pm20) cc_final: 0.6926 (mp0) REVERT: J 297 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7406 (mm-30) REVERT: J 346 ASP cc_start: 0.7467 (t70) cc_final: 0.7008 (t0) REVERT: J 365 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7955 (ttmt) REVERT: J 380 SER cc_start: 0.8765 (t) cc_final: 0.8459 (t) REVERT: J 385 ASP cc_start: 0.7886 (t70) cc_final: 0.7595 (t70) REVERT: J 389 LYS cc_start: 0.8461 (ptmm) cc_final: 0.8172 (ptmm) REVERT: J 393 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7581 (mt-10) REVERT: J 405 VAL cc_start: 0.8186 (t) cc_final: 0.7960 (m) REVERT: J 438 LYS cc_start: 0.8213 (tmtt) cc_final: 0.7945 (tmtt) REVERT: J 451 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8238 (mm-40) outliers start: 82 outliers final: 64 residues processed: 1301 average time/residue: 0.5457 time to fit residues: 1087.7149 Evaluate side-chains 1333 residues out of total 3551 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 1263 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 752 VAL Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 822 VAL Chi-restraints excluded: chain A residue 827 HIS Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1018 TYR Chi-restraints excluded: chain A residue 1074 GLU Chi-restraints excluded: chain A residue 1077 LYS Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1330 LEU Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 50 LYS Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 429 LYS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 200 LYS Chi-restraints excluded: chain D residue 228 ASN Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain E residue 38 SER Chi-restraints excluded: chain E residue 63 ASP Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 336 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 406 MET Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 113 LYS Chi-restraints excluded: chain F residue 149 ILE Chi-restraints excluded: chain F residue 158 LEU Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain F residue 239 VAL Chi-restraints excluded: chain F residue 251 THR Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 110 LEU Chi-restraints excluded: chain G residue 139 VAL Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain G residue 242 GLU Chi-restraints excluded: chain G residue 243 ILE Chi-restraints excluded: chain G residue 277 LYS Chi-restraints excluded: chain G residue 435 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 60 MET Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 296 ASP Chi-restraints excluded: chain H residue 376 GLU Chi-restraints excluded: chain H residue 385 ASP Chi-restraints excluded: chain H residue 414 LYS Chi-restraints excluded: chain H residue 417 THR Chi-restraints excluded: chain I residue 237 VAL Chi-restraints excluded: chain J residue 66 ILE Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain J residue 130 LYS Chi-restraints excluded: chain J residue 158 LEU Chi-restraints excluded: chain J residue 179 LEU Chi-restraints excluded: chain J residue 238 THR Chi-restraints excluded: chain J residue 339 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 369 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 349 optimal weight: 0.9990 chunk 302 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 260 optimal weight: 0.7980 chunk 168 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 107 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1012 HIS A1101 ASN ** A1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 HIS E 256 ASN G 286 GLN H 441 GLN J 299 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.130172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.110485 restraints weight = 55430.049| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.21 r_work: 0.3265 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33764 Z= 0.185 Angle : 0.667 14.830 45853 Z= 0.335 Chirality : 0.045 0.304 5344 Planarity : 0.004 0.061 5653 Dihedral : 14.433 177.477 5012 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.25 % Allowed : 22.88 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.13), residues: 4008 helix: 1.44 (0.12), residues: 1825 sheet: 0.22 (0.19), residues: 712 loop : -0.54 (0.16), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.004 TRP A 745 HIS 0.009 0.001 HIS A1012 PHE 0.027 0.001 PHE B 259 TYR 0.037 0.002 TYR C 143 ARG 0.016 0.001 ARG J 350 Details of bonding type rmsd hydrogen bonds : bond 0.04162 ( 1460) hydrogen bonds : angle 4.16283 ( 4148) metal coordination : bond 0.00704 ( 7) metal coordination : angle 4.47758 ( 6) covalent geometry : bond 0.00421 (33757) covalent geometry : angle 0.66535 (45847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26427.90 seconds wall clock time: 452 minutes 48.09 seconds (27168.09 seconds total)