Starting phenix.real_space_refine on Fri Feb 6 07:33:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9p_49175/02_2026/9n9p_49175.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9p_49175/02_2026/9n9p_49175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n9p_49175/02_2026/9n9p_49175.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9p_49175/02_2026/9n9p_49175.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n9p_49175/02_2026/9n9p_49175.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9p_49175/02_2026/9n9p_49175.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 Mg 1 5.21 5 S 87 5.16 5 C 14675 2.51 5 N 3973 2.21 5 O 4438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23175 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1800 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain: "B" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1800 Classifications: {'peptide': 229} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 218} Chain: "C" Number of atoms: 9424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1191, 9424 Classifications: {'peptide': 1191} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1139} Chain breaks: 1 Chain: "D" Number of atoms: 9264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1176, 9264 Classifications: {'peptide': 1176} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 50, 'TRANS': 1123} Chain breaks: 2 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 885 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 19575 SG CYS D 825 66.793 28.490 87.792 1.00 62.96 S ATOM 20146 SG CYS D 899 66.180 32.067 88.072 1.00 45.39 S ATOM 20192 SG CYS D 906 67.524 30.644 85.062 1.00 34.31 S ATOM 20212 SG CYS D 909 64.083 30.513 85.432 1.00 63.62 S Time building chain proxies: 5.01, per 1000 atoms: 0.22 Number of scatterers: 23175 At special positions: 0 Unit cell: (129.876, 160.29, 164.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 87 16.00 Mg 1 11.99 O 4438 8.00 N 3973 7.00 C 14675 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: 2.24 Conformation dependent library (CDL) restraints added in 924.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 909 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 825 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 899 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 906 " Number of angles added : 6 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5456 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 39 sheets defined 42.8% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 32 through 49 removed outlier: 3.691A pdb=" N THR A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 84 Processing helix chain 'A' and resid 113 through 116 Processing helix chain 'A' and resid 209 through 226 Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'B' and resid 1 through 6 removed outlier: 3.705A pdb=" N LEU B 4 " --> pdb=" O MET B 1 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASN B 5 " --> pdb=" O ALA B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 49 removed outlier: 4.374A pdb=" N LEU B 49 " --> pdb=" O LEU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.751A pdb=" N GLN B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 removed outlier: 3.798A pdb=" N GLN B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS B 117 " --> pdb=" O GLY B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 117' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 209 through 226 Processing helix chain 'B' and resid 227 through 229 No H-bonds generated for 'chain 'B' and resid 227 through 229' Processing helix chain 'C' and resid 24 through 36 removed outlier: 4.479A pdb=" N SER C 30 " --> pdb=" O ILE C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 56 removed outlier: 3.605A pdb=" N ASN C 56 " --> pdb=" O THR C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 106 through 110 removed outlier: 3.535A pdb=" N GLU C 110 " --> pdb=" O PRO C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 211 through 219 removed outlier: 3.704A pdb=" N PHE C 219 " --> pdb=" O ILE C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 313 removed outlier: 3.660A pdb=" N HIS C 308 " --> pdb=" O TYR C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 337 through 350 removed outlier: 3.594A pdb=" N ILE C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 370 Processing helix chain 'C' and resid 381 through 397 Processing helix chain 'C' and resid 415 through 442 Processing helix chain 'C' and resid 448 through 453 removed outlier: 3.504A pdb=" N LEU C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 469 removed outlier: 3.707A pdb=" N VAL C 461 " --> pdb=" O THR C 457 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN C 469 " --> pdb=" O PHE C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 488 Processing helix chain 'C' and resid 504 through 509 removed outlier: 3.708A pdb=" N ARG C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 607 through 611 removed outlier: 3.694A pdb=" N ILE C 611 " --> pdb=" O PRO C 608 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 629 removed outlier: 3.864A pdb=" N ILE C 629 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 635 Processing helix chain 'C' and resid 636 through 648 removed outlier: 3.867A pdb=" N ARG C 648 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 674 removed outlier: 4.074A pdb=" N ARG C 674 " --> pdb=" O ALA C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 700 through 707 Processing helix chain 'C' and resid 784 through 789 Processing helix chain 'C' and resid 860 through 871 Processing helix chain 'C' and resid 904 through 942 Processing helix chain 'C' and resid 965 through 970 Processing helix chain 'C' and resid 986 through 1020 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1091 through 1107 Processing helix chain 'C' and resid 1119 through 1131 Processing helix chain 'C' and resid 1133 through 1135 No H-bonds generated for 'chain 'C' and resid 1133 through 1135' Processing helix chain 'C' and resid 1166 through 1170 Processing helix chain 'C' and resid 1199 through 1210 Processing helix chain 'C' and resid 1211 through 1220 Processing helix chain 'C' and resid 1225 through 1239 removed outlier: 3.638A pdb=" N ALA C1230 " --> pdb=" O VAL C1226 " (cutoff:3.500A) Processing helix chain 'C' and resid 1248 through 1261 Processing helix chain 'D' and resid 22 through 29 Processing helix chain 'D' and resid 54 through 59 Processing helix chain 'D' and resid 73 through 77 removed outlier: 3.617A pdb=" N TYR D 76 " --> pdb=" O ARG D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 96 removed outlier: 3.542A pdb=" N VAL D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 114 removed outlier: 3.731A pdb=" N PHE D 113 " --> pdb=" O HIS D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 125 Processing helix chain 'D' and resid 127 through 136 Processing helix chain 'D' and resid 163 through 174 Processing helix chain 'D' and resid 175 through 180 removed outlier: 4.318A pdb=" N GLN D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 175 through 180' Processing helix chain 'D' and resid 194 through 204 removed outlier: 3.676A pdb=" N ARG D 204 " --> pdb=" O ASP D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 223 through 247 removed outlier: 3.586A pdb=" N GLN D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASN D 246 " --> pdb=" O GLU D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 253 Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 280 through 303 removed outlier: 3.921A pdb=" N ASP D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 326 Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 353 through 359 removed outlier: 3.815A pdb=" N LEU D 359 " --> pdb=" O PHE D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 394 Processing helix chain 'D' and resid 394 through 405 Processing helix chain 'D' and resid 410 through 421 Processing helix chain 'D' and resid 422 through 434 removed outlier: 3.603A pdb=" N TRP D 426 " --> pdb=" O GLU D 422 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN D 431 " --> pdb=" O ASP D 427 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS D 434 " --> pdb=" O GLU D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 449 No H-bonds generated for 'chain 'D' and resid 447 through 449' Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'D' and resid 470 through 475 Processing helix chain 'D' and resid 490 through 501 Processing helix chain 'D' and resid 521 through 532 Processing helix chain 'D' and resid 551 through 561 Processing helix chain 'D' and resid 592 through 599 Processing helix chain 'D' and resid 602 through 606 Processing helix chain 'D' and resid 613 through 628 Processing helix chain 'D' and resid 629 through 652 removed outlier: 3.557A pdb=" N GLY D 651 " --> pdb=" O PHE D 647 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 686 Processing helix chain 'D' and resid 690 through 720 Processing helix chain 'D' and resid 721 through 724 Processing helix chain 'D' and resid 725 through 733 Processing helix chain 'D' and resid 738 through 747 Processing helix chain 'D' and resid 779 through 816 removed outlier: 3.862A pdb=" N HIS D 788 " --> pdb=" O PHE D 784 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY D 789 " --> pdb=" O ILE D 785 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ALA D 802 " --> pdb=" O ALA D 798 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ASP D 803 " --> pdb=" O LEU D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 845 through 851 Processing helix chain 'D' and resid 876 through 886 Processing helix chain 'D' and resid 895 through 899 Processing helix chain 'D' and resid 906 through 911 Processing helix chain 'D' and resid 925 through 941 Proline residue: D 937 - end of helix Processing helix chain 'D' and resid 1139 through 1149 Processing helix chain 'D' and resid 1218 through 1226 Processing helix chain 'D' and resid 1227 through 1246 removed outlier: 4.044A pdb=" N GLN D1246 " --> pdb=" O VAL D1242 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1263 removed outlier: 4.266A pdb=" N PHE D1255 " --> pdb=" O ASN D1251 " (cutoff:3.500A) Processing helix chain 'D' and resid 1284 through 1295 Processing helix chain 'D' and resid 1317 through 1330 Processing helix chain 'D' and resid 1351 through 1358 removed outlier: 3.544A pdb=" N GLN D1358 " --> pdb=" O ARG D1354 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1369 Processing helix chain 'D' and resid 1370 through 1382 Processing helix chain 'D' and resid 1389 through 1397 removed outlier: 3.910A pdb=" N ASN D1393 " --> pdb=" O GLY D1389 " (cutoff:3.500A) Processing helix chain 'D' and resid 1402 through 1410 removed outlier: 3.928A pdb=" N MET D1406 " --> pdb=" O GLY D1403 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG D1407 " --> pdb=" O THR D1404 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ASP D1408 " --> pdb=" O GLY D1405 " (cutoff:3.500A) Processing helix chain 'D' and resid 1417 through 1432 Processing helix chain 'E' and resid 3 through 7 removed outlier: 3.780A pdb=" N THR E 7 " --> pdb=" O LEU E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 27 through 58 Processing helix chain 'E' and resid 70 through 82 Processing helix chain 'E' and resid 85 through 96 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 6.650A pdb=" N VAL A 12 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ARG A 27 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N MET A 14 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLU A 25 " --> pdb=" O MET A 14 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP A 16 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLU A 21 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR A 204 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LYS A 23 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE A 202 " --> pdb=" O LYS A 23 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLU A 25 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE A 200 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG A 27 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU A 198 " --> pdb=" O ARG A 27 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N THR A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL A 189 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 7.319A pdb=" N ASN A 141 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ILE A 59 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU A 143 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 57 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 145 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 111 removed outlier: 6.857A pdb=" N LEU A 110 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 17 removed outlier: 6.615A pdb=" N LYS B 23 " --> pdb=" O ILE B 15 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER B 17 " --> pdb=" O GLU B 21 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU B 21 " --> pdb=" O SER B 17 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU B 196 " --> pdb=" O PRO B 28 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N THR B 193 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ARG B 188 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N TYR B 195 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN B 186 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LYS B 197 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE B 184 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL B 199 " --> pdb=" O TYR B 182 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N TYR B 182 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLU B 201 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL B 180 " --> pdb=" O GLU B 201 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 203 " --> pdb=" O LYS B 178 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 105 removed outlier: 7.316A pdb=" N ASN B 141 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE B 59 " --> pdb=" O ASN B 141 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLU B 143 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL B 57 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 145 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AA9, first strand: chain 'B' and resid 109 through 111 removed outlier: 6.870A pdb=" N LEU B 110 " --> pdb=" O ILE B 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.350A pdb=" N VAL C 9 " --> pdb=" O GLY C1111 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 5.354A pdb=" N LEU C 68 " --> pdb=" O TYR C 103 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TYR C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N PHE C 70 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS C 101 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL C 94 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N THR C 123 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N LEU C 96 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 133 through 135 Processing sheet with id=AB5, first strand: chain 'C' and resid 411 through 414 removed outlier: 6.492A pdb=" N SER C 144 " --> pdb=" O SER C 491 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 151 through 158 removed outlier: 5.253A pdb=" N TYR C 166 " --> pdb=" O THR C 182 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 192 " --> pdb=" O LYS C 196 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 540 through 541 Processing sheet with id=AB8, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AB9, first strand: chain 'C' and resid 595 through 596 Processing sheet with id=AC1, first strand: chain 'C' and resid 712 through 716 removed outlier: 6.833A pdb=" N LYS C 692 " --> pdb=" O VAL C 688 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N VAL C 688 " --> pdb=" O LYS C 692 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR C 694 " --> pdb=" O GLU C 686 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 719 through 722 removed outlier: 5.619A pdb=" N LYS C 719 " --> pdb=" O LEU C 731 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU C 731 " --> pdb=" O LYS C 719 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 753 through 754 Processing sheet with id=AC4, first strand: chain 'C' and resid 1137 through 1138 removed outlier: 7.072A pdb=" N ILE C 780 " --> pdb=" O ARG C1060 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL C1062 " --> pdb=" O ILE C 780 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE C 782 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N ILE C1078 " --> pdb=" O ASN C 763 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS C 765 " --> pdb=" O ILE C1078 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LEU C1080 " --> pdb=" O LYS C 765 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA C 767 " --> pdb=" O LEU C1080 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR C1154 " --> pdb=" O PHE C 768 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 810 through 811 removed outlier: 4.050A pdb=" N LYS C1030 " --> pdb=" O VAL C 804 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASP C 806 " --> pdb=" O ILE C1028 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE C1028 " --> pdb=" O ASP C 806 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 894 " --> pdb=" O TYR C1035 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA C1037 " --> pdb=" O VAL C 892 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL C 892 " --> pdb=" O ALA C1037 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LYS C1039 " --> pdb=" O GLY C 890 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLY C 890 " --> pdb=" O LYS C1039 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 813 through 814 Processing sheet with id=AC7, first strand: chain 'C' and resid 846 through 848 removed outlier: 6.991A pdb=" N LEU C 882 " --> pdb=" O LEU C 847 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 956 through 958 removed outlier: 6.621A pdb=" N VAL C 949 " --> pdb=" O VAL C 957 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1172 through 1174 removed outlier: 7.746A pdb=" N ALA D 463 " --> pdb=" O PRO D 386 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1197 through 1198 Processing sheet with id=AD2, first strand: chain 'C' and resid 1263 through 1268 removed outlier: 3.573A pdb=" N SER D 17 " --> pdb=" O ARG C1266 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 30 through 33 removed outlier: 7.480A pdb=" N HIS D 100 " --> pdb=" O ARG D 31 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU D 33 " --> pdb=" O HIS D 100 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASN D 102 " --> pdb=" O GLU D 33 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS D 257 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 10.508A pdb=" N VAL D 105 " --> pdb=" O ILE D 255 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N ILE D 255 " --> pdb=" O VAL D 105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 161 through 162 removed outlier: 6.400A pdb=" N ILE D 190 " --> pdb=" O ILE D 143 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 269 through 271 Processing sheet with id=AD6, first strand: chain 'D' and resid 548 through 549 removed outlier: 3.502A pdb=" N THR D 574 " --> pdb=" O LYS D 586 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 831 through 834 removed outlier: 4.667A pdb=" N VAL D 854 " --> pdb=" O ARG D 894 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 836 through 838 removed outlier: 6.765A pdb=" N LEU D 836 " --> pdb=" O VAL D 843 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 859 through 860 Processing sheet with id=AE1, first strand: chain 'D' and resid 1281 through 1283 removed outlier: 6.670A pdb=" N THR D1344 " --> pdb=" O GLN D1269 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 1314 through 1316 removed outlier: 6.874A pdb=" N THR D1336 " --> pdb=" O GLU D1301 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1412 through 1416 1051 hydrogen bonds defined for protein. 2961 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.02 Time building geometry restraints manager: 2.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7770 1.34 - 1.46: 4593 1.46 - 1.58: 11039 1.58 - 1.70: 0 1.70 - 1.81: 156 Bond restraints: 23558 Sorted by residual: bond pdb=" CB GLU C 935 " pdb=" CG GLU C 935 " ideal model delta sigma weight residual 1.520 1.561 -0.041 3.00e-02 1.11e+03 1.87e+00 bond pdb=" CB GLU D 668 " pdb=" CG GLU D 668 " ideal model delta sigma weight residual 1.520 1.556 -0.036 3.00e-02 1.11e+03 1.46e+00 bond pdb=" CG1 ILE A 222 " pdb=" CD1 ILE A 222 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.33e+00 bond pdb=" CA GLY C1111 " pdb=" C GLY C1111 " ideal model delta sigma weight residual 1.520 1.512 0.008 7.30e-03 1.88e+04 1.13e+00 bond pdb=" CB GLU D 33 " pdb=" CG GLU D 33 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.06e+00 ... (remaining 23553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 31505 2.43 - 4.86: 256 4.86 - 7.28: 24 7.28 - 9.71: 5 9.71 - 12.14: 2 Bond angle restraints: 31792 Sorted by residual: angle pdb=" C ASP D 629 " pdb=" N VAL D 630 " pdb=" CA VAL D 630 " ideal model delta sigma weight residual 120.33 123.57 -3.24 8.00e-01 1.56e+00 1.64e+01 angle pdb=" CA GLU D 33 " pdb=" CB GLU D 33 " pdb=" CG GLU D 33 " ideal model delta sigma weight residual 114.10 121.39 -7.29 2.00e+00 2.50e-01 1.33e+01 angle pdb=" CA LEU C1261 " pdb=" CB LEU C1261 " pdb=" CG LEU C1261 " ideal model delta sigma weight residual 116.30 128.44 -12.14 3.50e+00 8.16e-02 1.20e+01 angle pdb=" CA ILE C 582 " pdb=" CB ILE C 582 " pdb=" CG1 ILE C 582 " ideal model delta sigma weight residual 110.40 116.01 -5.61 1.70e+00 3.46e-01 1.09e+01 angle pdb=" CA LEU D1277 " pdb=" CB LEU D1277 " pdb=" CG LEU D1277 " ideal model delta sigma weight residual 116.30 127.77 -11.47 3.50e+00 8.16e-02 1.07e+01 ... (remaining 31787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 12964 17.87 - 35.74: 1200 35.74 - 53.60: 279 53.60 - 71.47: 48 71.47 - 89.34: 15 Dihedral angle restraints: 14506 sinusoidal: 6034 harmonic: 8472 Sorted by residual: dihedral pdb=" CA SER A 47 " pdb=" C SER A 47 " pdb=" N SER A 48 " pdb=" CA SER A 48 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA SER B 47 " pdb=" C SER B 47 " pdb=" N SER B 48 " pdb=" CA SER B 48 " ideal model delta harmonic sigma weight residual -180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA MET B 142 " pdb=" C MET B 142 " pdb=" N GLU B 143 " pdb=" CA GLU B 143 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 14503 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3213 0.073 - 0.145: 379 0.145 - 0.218: 3 0.218 - 0.290: 0 0.290 - 0.363: 1 Chirality restraints: 3596 Sorted by residual: chirality pdb=" CG LEU C 933 " pdb=" CB LEU C 933 " pdb=" CD1 LEU C 933 " pdb=" CD2 LEU C 933 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CA ILE C 577 " pdb=" N ILE C 577 " pdb=" C ILE C 577 " pdb=" CB ILE C 577 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA ILE D 255 " pdb=" N ILE D 255 " pdb=" C ILE D 255 " pdb=" CB ILE D 255 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.05e-01 ... (remaining 3593 not shown) Planarity restraints: 4142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 926 " 0.013 2.00e-02 2.50e+03 1.83e-02 5.84e+00 pdb=" CG PHE C 926 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 926 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 926 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE C 926 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 926 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 926 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 385 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO D 386 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 386 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 386 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 603 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C GLU D 603 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU D 603 " 0.010 2.00e-02 2.50e+03 pdb=" N GLN D 604 " 0.009 2.00e-02 2.50e+03 ... (remaining 4139 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 212 2.60 - 3.18: 18963 3.18 - 3.75: 35644 3.75 - 4.33: 49909 4.33 - 4.90: 83209 Nonbonded interactions: 187937 Sorted by model distance: nonbonded pdb=" OD1 ASP D 481 " pdb="MG MG D1501 " model vdw 2.028 2.170 nonbonded pdb=" OD1 ASP D 479 " pdb="MG MG D1501 " model vdw 2.111 2.170 nonbonded pdb=" OH TYR A 33 " pdb=" OG SER B 48 " model vdw 2.173 3.040 nonbonded pdb=" O GLN B 191 " pdb=" NZ LYS D 387 " model vdw 2.189 3.120 nonbonded pdb=" NH2 ARG C 488 " pdb=" O SER C 536 " model vdw 2.191 3.120 ... (remaining 187932 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 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: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.780 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 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 0.131 23562 Z= 0.129 Angle : 0.584 24.016 31798 Z= 0.310 Chirality : 0.043 0.363 3596 Planarity : 0.004 0.062 4142 Dihedral : 14.617 89.338 9050 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.33 % Allowed : 16.72 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.16), residues: 2917 helix: 1.93 (0.16), residues: 1089 sheet: 0.83 (0.27), residues: 353 loop : 0.84 (0.17), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 27 TYR 0.021 0.001 TYR A 182 PHE 0.042 0.001 PHE C 926 TRP 0.009 0.001 TRP C 771 HIS 0.010 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00260 (23558) covalent geometry : angle 0.56066 (31792) hydrogen bonds : bond 0.16186 ( 1051) hydrogen bonds : angle 6.13570 ( 2961) metal coordination : bond 0.07074 ( 4) metal coordination : angle 11.83373 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 425 time to evaluate : 0.865 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: A 147 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7894 (mt-10) REVERT: A 185 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7831 (mt-10) REVERT: B 116 GLN cc_start: 0.7487 (tp40) cc_final: 0.7282 (tp40) REVERT: B 148 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7871 (ttmm) REVERT: B 200 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7520 (m-80) REVERT: C 84 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7201 (mt-10) REVERT: C 375 MET cc_start: 0.5805 (mmm) cc_final: 0.5414 (mmm) REVERT: C 390 LYS cc_start: 0.6814 (tmtm) cc_final: 0.6538 (tmtm) REVERT: C 394 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6099 (mp0) REVERT: C 422 GLN cc_start: 0.7969 (mm-40) cc_final: 0.7727 (mp10) REVERT: C 509 ASP cc_start: 0.8182 (t0) cc_final: 0.7891 (t0) REVERT: C 560 ASP cc_start: 0.7444 (t0) cc_final: 0.6961 (p0) REVERT: C 563 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7137 (pp20) REVERT: C 642 MET cc_start: 0.8229 (mtm) cc_final: 0.7900 (mpp) REVERT: C 696 LYS cc_start: 0.8245 (tttt) cc_final: 0.8031 (mtpt) REVERT: C 755 LYS cc_start: 0.8624 (mttt) cc_final: 0.8404 (mmtm) REVERT: C 784 GLU cc_start: 0.7882 (tt0) cc_final: 0.7624 (pt0) REVERT: C 893 ILE cc_start: 0.7545 (pt) cc_final: 0.7022 (pp) REVERT: C 995 ASP cc_start: 0.7933 (m-30) cc_final: 0.7622 (t0) REVERT: C 1057 ILE cc_start: 0.8467 (mm) cc_final: 0.8190 (tp) REVERT: C 1244 GLU cc_start: 0.7898 (pm20) cc_final: 0.7654 (pm20) REVERT: D 134 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.7005 (mm) REVERT: D 137 TYR cc_start: 0.7318 (m-80) cc_final: 0.7068 (m-80) REVERT: D 140 TYR cc_start: 0.6485 (m-80) cc_final: 0.6062 (m-80) REVERT: D 313 LYS cc_start: 0.7297 (mttt) cc_final: 0.7082 (mttm) REVERT: D 326 ASN cc_start: 0.7643 (t0) cc_final: 0.7358 (t0) REVERT: D 415 LYS cc_start: 0.7952 (mttt) cc_final: 0.7692 (mtpt) REVERT: D 451 ILE cc_start: 0.7869 (mt) cc_final: 0.7665 (tt) REVERT: D 492 GLU cc_start: 0.7761 (tp30) cc_final: 0.7416 (tp30) REVERT: D 553 GLU cc_start: 0.7718 (tt0) cc_final: 0.7425 (tt0) REVERT: D 618 ARG cc_start: 0.7783 (ttp80) cc_final: 0.7227 (ttp80) REVERT: D 666 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.6921 (tttp) REVERT: D 792 LYS cc_start: 0.7169 (mtmt) cc_final: 0.6863 (mppt) REVERT: D 832 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: D 844 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7679 (mm-30) REVERT: D 879 ASP cc_start: 0.8112 (m-30) cc_final: 0.7883 (m-30) REVERT: D 880 VAL cc_start: 0.8116 (t) cc_final: 0.7801 (t) REVERT: D 881 LYS cc_start: 0.7816 (mttt) cc_final: 0.7542 (ttmm) REVERT: D 884 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6971 (mt-10) REVERT: D 890 LYS cc_start: 0.7912 (mttt) cc_final: 0.7583 (mttt) REVERT: D 924 GLU cc_start: 0.7146 (tp30) cc_final: 0.6859 (tp30) REVERT: D 1145 THR cc_start: 0.8410 (m) cc_final: 0.7989 (p) REVERT: D 1244 ARG cc_start: 0.7854 (ttp-110) cc_final: 0.7324 (mtm110) REVERT: D 1263 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8506 (ttt) REVERT: D 1277 LEU cc_start: 0.8361 (tm) cc_final: 0.8148 (tt) REVERT: D 1377 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7877 (mm-30) REVERT: D 1406 MET cc_start: 0.8143 (mmm) cc_final: 0.6835 (mtm) outliers start: 34 outliers final: 16 residues processed: 438 average time/residue: 0.6971 time to fit residues: 346.7926 Evaluate side-chains 439 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 415 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain B residue 60 ASP Chi-restraints excluded: chain B residue 75 ASP Chi-restraints excluded: chain B residue 148 LYS Chi-restraints excluded: chain B residue 167 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 563 GLU Chi-restraints excluded: chain C residue 1126 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 300 MET Chi-restraints excluded: chain D residue 603 GLU Chi-restraints excluded: chain D residue 627 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain D residue 832 GLU Chi-restraints excluded: chain D residue 1263 MET Chi-restraints excluded: chain D residue 1271 SER Chi-restraints excluded: chain D residue 1408 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN C1054 ASN C1147 GLN D1254 HIS D1313 GLN D1398 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.170085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.141930 restraints weight = 33390.357| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.22 r_work: 0.3704 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23562 Z= 0.210 Angle : 0.563 10.352 31798 Z= 0.297 Chirality : 0.045 0.165 3596 Planarity : 0.004 0.044 4142 Dihedral : 5.714 107.737 3234 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.20 % Allowed : 13.62 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.16), residues: 2917 helix: 1.69 (0.16), residues: 1127 sheet: 0.39 (0.27), residues: 369 loop : 0.78 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 27 TYR 0.019 0.002 TYR D 695 PHE 0.033 0.002 PHE C 926 TRP 0.011 0.002 TRP C 177 HIS 0.012 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00492 (23558) covalent geometry : angle 0.56157 (31792) hydrogen bonds : bond 0.04598 ( 1051) hydrogen bonds : angle 4.98685 ( 2961) metal coordination : bond 0.00863 ( 4) metal coordination : angle 3.33783 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 449 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 58 ARG cc_start: 0.7819 (ttp-110) cc_final: 0.7553 (ttp80) REVERT: B 59 ILE cc_start: 0.7752 (OUTLIER) cc_final: 0.7516 (mt) REVERT: B 116 GLN cc_start: 0.7528 (tp40) cc_final: 0.7283 (tp40) REVERT: B 200 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7782 (t80) REVERT: C 13 SER cc_start: 0.8354 (m) cc_final: 0.8106 (p) REVERT: C 362 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6397 (tpp80) REVERT: C 375 MET cc_start: 0.5883 (mmm) cc_final: 0.5424 (mmm) REVERT: C 509 ASP cc_start: 0.8113 (t0) cc_final: 0.7617 (t0) REVERT: C 553 LYS cc_start: 0.7758 (tttt) cc_final: 0.7539 (mmmm) REVERT: C 695 ILE cc_start: 0.8303 (mt) cc_final: 0.8095 (mt) REVERT: C 696 LYS cc_start: 0.8002 (tttt) cc_final: 0.7728 (mtpt) REVERT: C 755 LYS cc_start: 0.8640 (mttt) cc_final: 0.8380 (mmtp) REVERT: C 893 ILE cc_start: 0.7656 (pt) cc_final: 0.7136 (pp) REVERT: C 947 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.5982 (mp10) REVERT: C 995 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7571 (t0) REVERT: C 1039 LYS cc_start: 0.8390 (ttpp) cc_final: 0.7928 (ttpp) REVERT: C 1048 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8203 (mtm) REVERT: C 1057 ILE cc_start: 0.8534 (mm) cc_final: 0.8256 (tt) REVERT: C 1218 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7871 (OUTLIER) REVERT: C 1234 GLU cc_start: 0.8018 (tp30) cc_final: 0.7817 (tp30) REVERT: C 1243 PRO cc_start: 0.8816 (Cg_endo) cc_final: 0.8534 (Cg_exo) REVERT: C 1244 GLU cc_start: 0.7974 (pm20) cc_final: 0.7749 (pm20) REVERT: D 134 ILE cc_start: 0.7392 (mm) cc_final: 0.7176 (tp) REVERT: D 137 TYR cc_start: 0.7414 (m-80) cc_final: 0.7190 (m-80) REVERT: D 138 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.7008 (mp0) REVERT: D 140 TYR cc_start: 0.6745 (m-80) cc_final: 0.6277 (m-80) REVERT: D 242 GLU cc_start: 0.7645 (tp30) cc_final: 0.7435 (tp30) REVERT: D 303 LYS cc_start: 0.5884 (OUTLIER) cc_final: 0.5113 (mmmm) REVERT: D 326 ASN cc_start: 0.7674 (t0) cc_final: 0.7387 (t0) REVERT: D 415 LYS cc_start: 0.7983 (mttt) cc_final: 0.7702 (mtpt) REVERT: D 492 GLU cc_start: 0.7805 (tp30) cc_final: 0.7426 (tp30) REVERT: D 512 ASN cc_start: 0.8058 (p0) cc_final: 0.7564 (p0) REVERT: D 553 GLU cc_start: 0.7735 (tt0) cc_final: 0.7298 (tt0) REVERT: D 607 TYR cc_start: 0.8408 (t80) cc_final: 0.8149 (t80) REVERT: D 618 ARG cc_start: 0.7785 (ttp80) cc_final: 0.7244 (ttp80) REVERT: D 666 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7085 (tttp) REVERT: D 681 MET cc_start: 0.7391 (tpp) cc_final: 0.6963 (mpp) REVERT: D 792 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6917 (ttmt) REVERT: D 822 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7944 (t) REVERT: D 832 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7762 (tt0) REVERT: D 844 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7650 (mm-30) REVERT: D 880 VAL cc_start: 0.8158 (t) cc_final: 0.7835 (t) REVERT: D 881 LYS cc_start: 0.7809 (mttt) cc_final: 0.7521 (ttmm) REVERT: D 884 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7072 (mt-10) REVERT: D 890 LYS cc_start: 0.8072 (mttt) cc_final: 0.7755 (mttt) REVERT: D 1145 THR cc_start: 0.8443 (m) cc_final: 0.8015 (p) outliers start: 107 outliers final: 45 residues processed: 503 average time/residue: 0.6651 time to fit residues: 382.7449 Evaluate side-chains 489 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 432 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 655 ARG Chi-restraints excluded: chain C residue 658 SER Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 840 GLU Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 947 GLN Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 995 ASP Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain C residue 1218 ILE Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain D residue 792 LYS Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 832 GLU Chi-restraints excluded: chain D residue 857 HIS Chi-restraints excluded: chain D residue 919 MET Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1359 THR Chi-restraints excluded: chain D residue 1408 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 42 optimal weight: 3.9990 chunk 254 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 222 optimal weight: 0.8980 chunk 209 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 46 optimal weight: 0.0040 chunk 237 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 64 HIS ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN C1147 GLN D1381 ASN D1398 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.170600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.142407 restraints weight = 33425.126| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.24 r_work: 0.3718 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23562 Z= 0.139 Angle : 0.506 10.842 31798 Z= 0.265 Chirality : 0.043 0.156 3596 Planarity : 0.004 0.059 4142 Dihedral : 4.590 58.317 3200 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.61 % Allowed : 14.72 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.16), residues: 2917 helix: 1.84 (0.16), residues: 1121 sheet: 0.31 (0.27), residues: 367 loop : 0.79 (0.17), residues: 1429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 27 TYR 0.017 0.001 TYR C 191 PHE 0.031 0.001 PHE C 926 TRP 0.007 0.001 TRP C 177 HIS 0.011 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00322 (23558) covalent geometry : angle 0.50409 (31792) hydrogen bonds : bond 0.04135 ( 1051) hydrogen bonds : angle 4.73173 ( 2961) metal coordination : bond 0.00760 ( 4) metal coordination : angle 3.07280 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 433 time to evaluate : 0.951 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: B 58 ARG cc_start: 0.7838 (ttp-110) cc_final: 0.7587 (ttp80) REVERT: B 59 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.7517 (mt) REVERT: B 116 GLN cc_start: 0.7508 (tp40) cc_final: 0.7235 (tp40) REVERT: B 197 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7765 (tttm) REVERT: B 200 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7739 (t80) REVERT: C 13 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.8111 (p) REVERT: C 32 GLN cc_start: 0.7926 (mt0) cc_final: 0.7700 (mp10) REVERT: C 197 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7186 (mtpp) REVERT: C 362 ARG cc_start: 0.6823 (OUTLIER) cc_final: 0.6349 (tpp80) REVERT: C 375 MET cc_start: 0.5957 (mmm) cc_final: 0.5488 (mmm) REVERT: C 509 ASP cc_start: 0.8171 (t0) cc_final: 0.7706 (t0) REVERT: C 551 TYR cc_start: 0.8072 (m-10) cc_final: 0.7701 (m-10) REVERT: C 553 LYS cc_start: 0.7687 (tttt) cc_final: 0.7416 (tppp) REVERT: C 657 GLU cc_start: 0.8075 (tt0) cc_final: 0.7846 (pt0) REVERT: C 696 LYS cc_start: 0.8064 (tttt) cc_final: 0.7657 (mtpp) REVERT: C 755 LYS cc_start: 0.8602 (mttt) cc_final: 0.8308 (mmmt) REVERT: C 768 PHE cc_start: 0.7905 (m-10) cc_final: 0.7667 (m-10) REVERT: C 784 GLU cc_start: 0.7874 (tt0) cc_final: 0.7563 (pt0) REVERT: C 947 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.6003 (mp10) REVERT: C 985 THR cc_start: 0.6353 (OUTLIER) cc_final: 0.6122 (p) REVERT: C 995 ASP cc_start: 0.7896 (m-30) cc_final: 0.7511 (t0) REVERT: C 999 ASN cc_start: 0.8600 (m-40) cc_final: 0.8302 (m-40) REVERT: C 1039 LYS cc_start: 0.8416 (ttpp) cc_final: 0.7978 (ttpp) REVERT: C 1048 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8180 (mtm) REVERT: C 1057 ILE cc_start: 0.8576 (mm) cc_final: 0.8289 (tt) REVERT: C 1243 PRO cc_start: 0.8789 (Cg_endo) cc_final: 0.8509 (Cg_exo) REVERT: C 1244 GLU cc_start: 0.7954 (pm20) cc_final: 0.7706 (pm20) REVERT: D 33 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6958 (tm-30) REVERT: D 134 ILE cc_start: 0.7399 (mm) cc_final: 0.7091 (mp) REVERT: D 138 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.6871 (mp0) REVERT: D 140 TYR cc_start: 0.6575 (m-80) cc_final: 0.6108 (m-80) REVERT: D 303 LYS cc_start: 0.5776 (OUTLIER) cc_final: 0.5049 (mmmm) REVERT: D 326 ASN cc_start: 0.7656 (t0) cc_final: 0.7344 (t0) REVERT: D 377 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7081 (mp0) REVERT: D 382 GLU cc_start: 0.7513 (mt-10) cc_final: 0.7296 (mt-10) REVERT: D 415 LYS cc_start: 0.7910 (mttt) cc_final: 0.7644 (mtpt) REVERT: D 553 GLU cc_start: 0.7756 (tt0) cc_final: 0.7333 (tt0) REVERT: D 607 TYR cc_start: 0.8418 (t80) cc_final: 0.8207 (t80) REVERT: D 618 ARG cc_start: 0.7780 (ttp80) cc_final: 0.7223 (ttp80) REVERT: D 666 LYS cc_start: 0.7562 (OUTLIER) cc_final: 0.7108 (tttp) REVERT: D 681 MET cc_start: 0.7407 (tpp) cc_final: 0.7067 (mpp) REVERT: D 792 LYS cc_start: 0.7257 (OUTLIER) cc_final: 0.6871 (ttmt) REVERT: D 822 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7894 (t) REVERT: D 832 GLU cc_start: 0.8268 (tt0) cc_final: 0.7922 (tt0) REVERT: D 844 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7559 (mm-30) REVERT: D 880 VAL cc_start: 0.8183 (t) cc_final: 0.7874 (t) REVERT: D 881 LYS cc_start: 0.7792 (mttt) cc_final: 0.7525 (ttmm) REVERT: D 884 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7080 (mt-10) REVERT: D 890 LYS cc_start: 0.8090 (mttt) cc_final: 0.7729 (mttt) REVERT: D 1145 THR cc_start: 0.8420 (m) cc_final: 0.8000 (p) REVERT: D 1270 ASP cc_start: 0.7165 (t0) cc_final: 0.6889 (t70) REVERT: D 1399 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8220 (mttm) outliers start: 92 outliers final: 43 residues processed: 480 average time/residue: 0.6792 time to fit residues: 372.1746 Evaluate side-chains 478 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 421 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 655 ARG Chi-restraints excluded: chain C residue 658 SER Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 782 ILE Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 947 GLN Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 985 THR Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 627 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 792 LYS Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 857 HIS Chi-restraints excluded: chain D residue 1359 THR Chi-restraints excluded: chain D residue 1399 LYS Chi-restraints excluded: chain D residue 1408 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 103 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 121 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 281 optimal weight: 3.9990 chunk 159 optimal weight: 0.2980 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 207 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 223 HIS ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 745 GLN C 999 ASN C1054 ASN C1147 GLN D 109 HIS ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1398 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.170576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.142295 restraints weight = 33421.526| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.24 r_work: 0.3722 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23562 Z= 0.128 Angle : 0.496 10.369 31798 Z= 0.259 Chirality : 0.043 0.172 3596 Planarity : 0.004 0.062 4142 Dihedral : 4.328 59.035 3195 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.65 % Allowed : 15.62 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.16), residues: 2917 helix: 1.87 (0.16), residues: 1126 sheet: 0.17 (0.27), residues: 374 loop : 0.83 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 598 TYR 0.017 0.001 TYR C 189 PHE 0.030 0.001 PHE C 926 TRP 0.006 0.001 TRP C 771 HIS 0.006 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00298 (23558) covalent geometry : angle 0.49466 (31792) hydrogen bonds : bond 0.03875 ( 1051) hydrogen bonds : angle 4.61753 ( 2961) metal coordination : bond 0.00680 ( 4) metal coordination : angle 2.71532 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 426 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7492 (tt0) cc_final: 0.7289 (tt0) REVERT: A 185 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7574 (mt-10) REVERT: B 59 ILE cc_start: 0.7734 (OUTLIER) cc_final: 0.7523 (mt) REVERT: B 116 GLN cc_start: 0.7494 (tp40) cc_final: 0.7219 (tp40) REVERT: B 143 GLU cc_start: 0.7217 (tt0) cc_final: 0.6993 (tt0) REVERT: B 197 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7753 (tttm) REVERT: B 200 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7715 (t80) REVERT: C 13 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.8103 (p) REVERT: C 32 GLN cc_start: 0.7910 (mt0) cc_final: 0.7672 (mp10) REVERT: C 197 LYS cc_start: 0.7701 (mtpp) cc_final: 0.7106 (mtpp) REVERT: C 362 ARG cc_start: 0.6799 (OUTLIER) cc_final: 0.6352 (tpp80) REVERT: C 375 MET cc_start: 0.5938 (mmm) cc_final: 0.5414 (mmm) REVERT: C 509 ASP cc_start: 0.8136 (t0) cc_final: 0.7696 (t0) REVERT: C 553 LYS cc_start: 0.7753 (tttt) cc_final: 0.7484 (tppp) REVERT: C 616 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8350 (p) REVERT: C 657 GLU cc_start: 0.8079 (tt0) cc_final: 0.7843 (pt0) REVERT: C 696 LYS cc_start: 0.8062 (tttt) cc_final: 0.7643 (mtpp) REVERT: C 755 LYS cc_start: 0.8615 (mttt) cc_final: 0.8323 (mmmt) REVERT: C 768 PHE cc_start: 0.7929 (m-10) cc_final: 0.7650 (m-10) REVERT: C 784 GLU cc_start: 0.7846 (tt0) cc_final: 0.7540 (pt0) REVERT: C 897 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6945 (tp) REVERT: C 921 ASP cc_start: 0.8523 (t0) cc_final: 0.8279 (t0) REVERT: C 1039 LYS cc_start: 0.8389 (ttpp) cc_final: 0.7955 (ttpp) REVERT: C 1048 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8196 (mtm) REVERT: C 1057 ILE cc_start: 0.8545 (mm) cc_final: 0.8274 (tt) REVERT: C 1234 GLU cc_start: 0.8122 (tp30) cc_final: 0.7885 (tp30) REVERT: C 1243 PRO cc_start: 0.8797 (Cg_endo) cc_final: 0.8543 (Cg_exo) REVERT: C 1244 GLU cc_start: 0.7952 (pm20) cc_final: 0.7680 (pm20) REVERT: D 33 GLU cc_start: 0.7236 (tm-30) cc_final: 0.6892 (tm-30) REVERT: D 134 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7130 (mp) REVERT: D 138 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: D 303 LYS cc_start: 0.5733 (OUTLIER) cc_final: 0.5058 (mmmm) REVERT: D 326 ASN cc_start: 0.7681 (t0) cc_final: 0.7364 (t0) REVERT: D 377 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7043 (mp0) REVERT: D 415 LYS cc_start: 0.7891 (mttt) cc_final: 0.7646 (mtpt) REVERT: D 492 GLU cc_start: 0.7807 (tp30) cc_final: 0.7540 (tp30) REVERT: D 507 ILE cc_start: 0.8798 (mt) cc_final: 0.8592 (mm) REVERT: D 530 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7720 (ptp) REVERT: D 553 GLU cc_start: 0.7777 (tt0) cc_final: 0.7347 (tt0) REVERT: D 618 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7206 (ttp80) REVERT: D 666 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7105 (tttp) REVERT: D 681 MET cc_start: 0.7385 (tpp) cc_final: 0.7090 (mpp) REVERT: D 792 LYS cc_start: 0.7237 (OUTLIER) cc_final: 0.6867 (ttmt) REVERT: D 822 THR cc_start: 0.8158 (OUTLIER) cc_final: 0.7889 (t) REVERT: D 832 GLU cc_start: 0.8240 (tt0) cc_final: 0.7953 (tt0) REVERT: D 880 VAL cc_start: 0.8203 (t) cc_final: 0.7880 (t) REVERT: D 881 LYS cc_start: 0.7789 (mttt) cc_final: 0.7533 (ttmm) REVERT: D 884 GLU cc_start: 0.7416 (mt-10) cc_final: 0.7090 (mt-10) REVERT: D 890 LYS cc_start: 0.8092 (mttt) cc_final: 0.7719 (mttt) REVERT: D 1145 THR cc_start: 0.8413 (m) cc_final: 0.7986 (p) REVERT: D 1244 ARG cc_start: 0.8035 (ttm-80) cc_final: 0.7663 (mtm110) REVERT: D 1399 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8207 (mttm) outliers start: 93 outliers final: 41 residues processed: 477 average time/residue: 0.6859 time to fit residues: 373.4588 Evaluate side-chains 471 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 414 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 167 SER Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 42 ASP Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 474 PHE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 658 SER Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain C residue 1072 ASP Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 792 LYS Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 857 HIS Chi-restraints excluded: chain D residue 1359 THR Chi-restraints excluded: chain D residue 1399 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 192 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 13 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 118 optimal weight: 0.0010 chunk 55 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.2070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 224 HIS C 634 HIS C1054 ASN C1147 GLN D1398 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.168299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.140159 restraints weight = 33112.152| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.23 r_work: 0.3688 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23562 Z= 0.216 Angle : 0.563 11.068 31798 Z= 0.295 Chirality : 0.045 0.169 3596 Planarity : 0.004 0.060 4142 Dihedral : 4.594 58.189 3193 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.96 % Allowed : 16.09 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.16), residues: 2917 helix: 1.67 (0.16), residues: 1121 sheet: 0.23 (0.27), residues: 379 loop : 0.64 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 27 TYR 0.027 0.002 TYR C 551 PHE 0.028 0.002 PHE C 926 TRP 0.008 0.002 TRP C 177 HIS 0.006 0.001 HIS C 147 Details of bonding type rmsd covalent geometry : bond 0.00513 (23558) covalent geometry : angle 0.56219 (31792) hydrogen bonds : bond 0.04485 ( 1051) hydrogen bonds : angle 4.79207 ( 2961) metal coordination : bond 0.01230 ( 4) metal coordination : angle 1.93187 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 437 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7507 (tt0) cc_final: 0.7212 (tt0) REVERT: A 185 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7575 (mt-10) REVERT: B 59 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7518 (mt) REVERT: B 116 GLN cc_start: 0.7563 (tp40) cc_final: 0.7252 (tp40) REVERT: B 197 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7971 (tttm) REVERT: C 13 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.8126 (p) REVERT: C 197 LYS cc_start: 0.7775 (mtpp) cc_final: 0.7333 (mtpp) REVERT: C 362 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6306 (tpp80) REVERT: C 375 MET cc_start: 0.5898 (mmm) cc_final: 0.5436 (mmm) REVERT: C 390 LYS cc_start: 0.7137 (OUTLIER) cc_final: 0.6770 (tmtm) REVERT: C 394 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6363 (mp0) REVERT: C 509 ASP cc_start: 0.8187 (t0) cc_final: 0.7878 (t0) REVERT: C 553 LYS cc_start: 0.7942 (tttt) cc_final: 0.7717 (mmmm) REVERT: C 657 GLU cc_start: 0.8049 (tt0) cc_final: 0.7792 (pt0) REVERT: C 696 LYS cc_start: 0.8059 (tttt) cc_final: 0.7794 (ttmm) REVERT: C 755 LYS cc_start: 0.8598 (mttt) cc_final: 0.8308 (mmmt) REVERT: C 784 GLU cc_start: 0.7827 (tt0) cc_final: 0.7528 (pt0) REVERT: C 893 ILE cc_start: 0.7765 (pt) cc_final: 0.7231 (pp) REVERT: C 935 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7375 (tt0) REVERT: C 947 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.6056 (mp10) REVERT: C 1048 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8162 (mtm) REVERT: C 1057 ILE cc_start: 0.8557 (mm) cc_final: 0.8257 (tt) REVERT: C 1244 GLU cc_start: 0.8093 (pm20) cc_final: 0.7536 (pm20) REVERT: D 33 GLU cc_start: 0.7222 (tm-30) cc_final: 0.6825 (tm-30) REVERT: D 134 ILE cc_start: 0.7464 (mm) cc_final: 0.7192 (tt) REVERT: D 137 TYR cc_start: 0.7569 (m-80) cc_final: 0.7348 (m-80) REVERT: D 138 GLU cc_start: 0.7211 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: D 229 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7309 (tp30) REVERT: D 252 GLU cc_start: 0.8016 (pm20) cc_final: 0.7766 (pm20) REVERT: D 303 LYS cc_start: 0.5863 (OUTLIER) cc_final: 0.4993 (mmmm) REVERT: D 306 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6480 (mm-30) REVERT: D 326 ASN cc_start: 0.7740 (t0) cc_final: 0.7414 (t0) REVERT: D 415 LYS cc_start: 0.7952 (mttt) cc_final: 0.7696 (mtpt) REVERT: D 457 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7544 (mtmm) REVERT: D 553 GLU cc_start: 0.7816 (tt0) cc_final: 0.7415 (tt0) REVERT: D 598 ASN cc_start: 0.7845 (m-40) cc_final: 0.7627 (m110) REVERT: D 618 ARG cc_start: 0.7739 (ttp80) cc_final: 0.7170 (ttp80) REVERT: D 639 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7983 (mttp) REVERT: D 666 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7219 (tttp) REVERT: D 681 MET cc_start: 0.7455 (tpp) cc_final: 0.6991 (mpp) REVERT: D 772 SER cc_start: 0.8601 (p) cc_final: 0.8394 (t) REVERT: D 792 LYS cc_start: 0.7302 (OUTLIER) cc_final: 0.7002 (ttmt) REVERT: D 822 THR cc_start: 0.8192 (OUTLIER) cc_final: 0.7935 (t) REVERT: D 832 GLU cc_start: 0.8282 (tt0) cc_final: 0.7994 (tt0) REVERT: D 880 VAL cc_start: 0.8169 (t) cc_final: 0.7847 (t) REVERT: D 881 LYS cc_start: 0.7821 (mttt) cc_final: 0.7521 (ttmm) REVERT: D 884 GLU cc_start: 0.7454 (mt-10) cc_final: 0.7112 (mt-10) REVERT: D 890 LYS cc_start: 0.8186 (mttt) cc_final: 0.7769 (mttt) REVERT: D 1145 THR cc_start: 0.8499 (m) cc_final: 0.8052 (p) REVERT: D 1270 ASP cc_start: 0.7184 (t0) cc_final: 0.6969 (t70) REVERT: D 1399 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8253 (mttm) outliers start: 101 outliers final: 53 residues processed: 488 average time/residue: 0.6884 time to fit residues: 385.4043 Evaluate side-chains 497 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 428 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLN Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 474 PHE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 614 THR Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 655 ARG Chi-restraints excluded: chain C residue 658 SER Chi-restraints excluded: chain C residue 665 LEU Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 840 GLU Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 947 GLN Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 256 MET Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 306 GLU Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 441 ASN Chi-restraints excluded: chain D residue 603 GLU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 639 LYS Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain D residue 682 MET Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 766 ILE Chi-restraints excluded: chain D residue 792 LYS Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 857 HIS Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1359 THR Chi-restraints excluded: chain D residue 1399 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 245 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 256 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 223 HIS B 82 ASN ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN C1147 GLN ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1398 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.169105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.141217 restraints weight = 33325.590| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.24 r_work: 0.3698 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3543 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 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 : 0.004 0.044 23562 Z= 0.150 Angle : 0.516 10.913 31798 Z= 0.270 Chirality : 0.043 0.204 3596 Planarity : 0.004 0.062 4142 Dihedral : 4.389 59.390 3191 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.69 % Allowed : 16.48 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.16), residues: 2917 helix: 1.70 (0.16), residues: 1129 sheet: 0.21 (0.28), residues: 360 loop : 0.66 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 27 TYR 0.021 0.001 TYR D 695 PHE 0.038 0.001 PHE C1198 TRP 0.007 0.001 TRP D 426 HIS 0.004 0.001 HIS C 147 Details of bonding type rmsd covalent geometry : bond 0.00354 (23558) covalent geometry : angle 0.51561 (31792) hydrogen bonds : bond 0.04021 ( 1051) hydrogen bonds : angle 4.66810 ( 2961) metal coordination : bond 0.00770 ( 4) metal coordination : angle 2.12327 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 429 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7533 (tt0) cc_final: 0.7254 (tt0) REVERT: A 185 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7746 (mt-10) REVERT: B 59 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7493 (mt) REVERT: B 116 GLN cc_start: 0.7523 (tp40) cc_final: 0.7217 (tp40) REVERT: B 197 LYS cc_start: 0.8364 (OUTLIER) cc_final: 0.7857 (tttm) REVERT: C 13 SER cc_start: 0.8340 (OUTLIER) cc_final: 0.8098 (p) REVERT: C 197 LYS cc_start: 0.7780 (mtpp) cc_final: 0.7263 (mtpp) REVERT: C 362 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.6293 (tpp80) REVERT: C 375 MET cc_start: 0.5874 (mmm) cc_final: 0.5447 (mmm) REVERT: C 509 ASP cc_start: 0.8195 (t0) cc_final: 0.7980 (t0) REVERT: C 553 LYS cc_start: 0.7859 (tttt) cc_final: 0.7614 (tptp) REVERT: C 657 GLU cc_start: 0.8021 (tt0) cc_final: 0.7764 (pt0) REVERT: C 696 LYS cc_start: 0.8108 (tttt) cc_final: 0.7786 (ttmm) REVERT: C 755 LYS cc_start: 0.8603 (mttt) cc_final: 0.8344 (mmtp) REVERT: C 784 GLU cc_start: 0.7848 (tt0) cc_final: 0.7536 (pt0) REVERT: C 893 ILE cc_start: 0.7674 (pt) cc_final: 0.7136 (pp) REVERT: C 921 ASP cc_start: 0.8533 (t0) cc_final: 0.8293 (t0) REVERT: C 923 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7059 (tm-30) REVERT: C 1048 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8186 (mtm) REVERT: C 1057 ILE cc_start: 0.8583 (mm) cc_final: 0.8279 (tt) REVERT: C 1244 GLU cc_start: 0.8122 (pm20) cc_final: 0.7557 (pm20) REVERT: D 33 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6720 (tm-30) REVERT: D 94 ARG cc_start: 0.8627 (mtp-110) cc_final: 0.8396 (mtp-110) REVERT: D 134 ILE cc_start: 0.7433 (OUTLIER) cc_final: 0.7154 (mp) REVERT: D 212 TYR cc_start: 0.7953 (m-10) cc_final: 0.7444 (m-10) REVERT: D 229 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7295 (tp30) REVERT: D 252 GLU cc_start: 0.7955 (pm20) cc_final: 0.7709 (pm20) REVERT: D 303 LYS cc_start: 0.5733 (OUTLIER) cc_final: 0.5043 (mmmm) REVERT: D 326 ASN cc_start: 0.7640 (t0) cc_final: 0.7303 (t0) REVERT: D 377 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7212 (mp0) REVERT: D 415 LYS cc_start: 0.7930 (mttt) cc_final: 0.7674 (mtpt) REVERT: D 492 GLU cc_start: 0.7821 (tp30) cc_final: 0.7526 (tp30) REVERT: D 553 GLU cc_start: 0.7842 (tt0) cc_final: 0.7435 (tt0) REVERT: D 618 ARG cc_start: 0.7751 (ttp80) cc_final: 0.7196 (ttp80) REVERT: D 639 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7954 (mttp) REVERT: D 666 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.7171 (tttp) REVERT: D 681 MET cc_start: 0.7492 (tpp) cc_final: 0.7053 (mpp) REVERT: D 792 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.7072 (mppt) REVERT: D 822 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7896 (t) REVERT: D 832 GLU cc_start: 0.8259 (tt0) cc_final: 0.7954 (tt0) REVERT: D 880 VAL cc_start: 0.8186 (t) cc_final: 0.7852 (t) REVERT: D 881 LYS cc_start: 0.7819 (mttt) cc_final: 0.7516 (ttmm) REVERT: D 884 GLU cc_start: 0.7461 (mt-10) cc_final: 0.7128 (mt-10) REVERT: D 890 LYS cc_start: 0.8174 (mttt) cc_final: 0.7693 (mttt) REVERT: D 1145 THR cc_start: 0.8477 (m) cc_final: 0.8035 (p) REVERT: D 1270 ASP cc_start: 0.7184 (t0) cc_final: 0.6977 (t70) REVERT: D 1313 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7313 (tt0) outliers start: 94 outliers final: 49 residues processed: 481 average time/residue: 0.6832 time to fit residues: 375.6358 Evaluate side-chains 483 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 422 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 474 PHE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 655 ARG Chi-restraints excluded: chain C residue 658 SER Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain C residue 1091 ILE Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 571 LYS Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 639 LYS Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain D residue 742 ILE Chi-restraints excluded: chain D residue 792 LYS Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 857 HIS Chi-restraints excluded: chain D residue 1313 GLN Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1359 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 246 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 0.1980 chunk 207 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 276 optimal weight: 0.4980 chunk 263 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 82 ASN B 158 ASN C1147 GLN D 598 ASN ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 932 GLN D1398 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.169534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.141575 restraints weight = 33302.025| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.23 r_work: 0.3711 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23562 Z= 0.127 Angle : 0.510 11.031 31798 Z= 0.265 Chirality : 0.043 0.175 3596 Planarity : 0.004 0.060 4142 Dihedral : 4.286 59.705 3191 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.22 % Allowed : 17.50 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.16), residues: 2917 helix: 1.74 (0.16), residues: 1136 sheet: 0.19 (0.28), residues: 359 loop : 0.66 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 27 TYR 0.026 0.001 TYR C 551 PHE 0.033 0.001 PHE C1198 TRP 0.007 0.001 TRP D 253 HIS 0.004 0.001 HIS D 788 Details of bonding type rmsd covalent geometry : bond 0.00297 (23558) covalent geometry : angle 0.50942 (31792) hydrogen bonds : bond 0.03767 ( 1051) hydrogen bonds : angle 4.58376 ( 2961) metal coordination : bond 0.00589 ( 4) metal coordination : angle 2.23368 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 422 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7491 (tt0) cc_final: 0.7212 (tt0) REVERT: A 146 ILE cc_start: 0.7102 (mt) cc_final: 0.6877 (mt) REVERT: A 185 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7700 (mt-10) REVERT: A 223 HIS cc_start: 0.7909 (t-90) cc_final: 0.7703 (t-90) REVERT: B 26 PHE cc_start: 0.8360 (t80) cc_final: 0.8102 (t80) REVERT: B 59 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7466 (mt) REVERT: B 116 GLN cc_start: 0.7505 (tp40) cc_final: 0.7193 (tp40) REVERT: B 197 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7806 (tttm) REVERT: B 200 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7511 (m-80) REVERT: C 13 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8105 (p) REVERT: C 197 LYS cc_start: 0.7767 (mtpp) cc_final: 0.7329 (mtpp) REVERT: C 362 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6470 (tpp80) REVERT: C 375 MET cc_start: 0.5928 (mmm) cc_final: 0.5697 (mmm) REVERT: C 509 ASP cc_start: 0.8170 (t0) cc_final: 0.7925 (t0) REVERT: C 657 GLU cc_start: 0.8047 (tt0) cc_final: 0.7792 (pt0) REVERT: C 696 LYS cc_start: 0.8075 (tttt) cc_final: 0.7771 (ttmm) REVERT: C 755 LYS cc_start: 0.8592 (mttt) cc_final: 0.8344 (mmtp) REVERT: C 784 GLU cc_start: 0.7863 (tt0) cc_final: 0.7548 (pt0) REVERT: C 893 ILE cc_start: 0.7636 (pt) cc_final: 0.7073 (pp) REVERT: C 921 ASP cc_start: 0.8512 (t0) cc_final: 0.8263 (t0) REVERT: C 923 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: C 935 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7390 (tt0) REVERT: C 956 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7122 (tm-30) REVERT: C 1048 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8240 (mtm) REVERT: C 1057 ILE cc_start: 0.8568 (mm) cc_final: 0.8281 (tt) REVERT: C 1244 GLU cc_start: 0.8120 (pm20) cc_final: 0.7542 (pm20) REVERT: D 33 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6813 (tm-30) REVERT: D 94 ARG cc_start: 0.8643 (mtp-110) cc_final: 0.8422 (mtp-110) REVERT: D 134 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.7173 (mp) REVERT: D 140 TYR cc_start: 0.6500 (m-80) cc_final: 0.6060 (m-80) REVERT: D 229 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7270 (tp30) REVERT: D 252 GLU cc_start: 0.7942 (pm20) cc_final: 0.7703 (pm20) REVERT: D 303 LYS cc_start: 0.5667 (OUTLIER) cc_final: 0.5071 (mmmm) REVERT: D 326 ASN cc_start: 0.7707 (t0) cc_final: 0.7380 (t0) REVERT: D 377 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7153 (mp0) REVERT: D 415 LYS cc_start: 0.7854 (mttt) cc_final: 0.7621 (mtpt) REVERT: D 492 GLU cc_start: 0.7806 (tp30) cc_final: 0.7477 (tp30) REVERT: D 553 GLU cc_start: 0.7807 (tt0) cc_final: 0.7345 (mt-10) REVERT: D 618 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7187 (ttp80) REVERT: D 666 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7107 (tttp) REVERT: D 681 MET cc_start: 0.7476 (tpp) cc_final: 0.7033 (mpp) REVERT: D 772 SER cc_start: 0.8546 (p) cc_final: 0.8294 (t) REVERT: D 792 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.7010 (mppt) REVERT: D 822 THR cc_start: 0.8117 (OUTLIER) cc_final: 0.7858 (t) REVERT: D 832 GLU cc_start: 0.8241 (tt0) cc_final: 0.7932 (tt0) REVERT: D 880 VAL cc_start: 0.8187 (t) cc_final: 0.7849 (t) REVERT: D 881 LYS cc_start: 0.7853 (mttt) cc_final: 0.7585 (ttmm) REVERT: D 884 GLU cc_start: 0.7436 (mt-10) cc_final: 0.7100 (mt-10) REVERT: D 890 LYS cc_start: 0.8121 (mttt) cc_final: 0.7711 (mttt) REVERT: D 1145 THR cc_start: 0.8459 (m) cc_final: 0.8009 (p) REVERT: D 1244 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7800 (mtm110) REVERT: D 1313 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7263 (tt0) outliers start: 82 outliers final: 46 residues processed: 466 average time/residue: 0.6933 time to fit residues: 368.7583 Evaluate side-chains 476 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 417 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain B residue 226 MET Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 655 ARG Chi-restraints excluded: chain C residue 658 SER Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 713 LYS Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 923 GLU Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 571 LYS Chi-restraints excluded: chain D residue 603 GLU Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 664 LYS Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain D residue 682 MET Chi-restraints excluded: chain D residue 792 LYS Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 857 HIS Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 1313 GLN Chi-restraints excluded: chain D residue 1359 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 219 optimal weight: 1.9990 chunk 258 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 286 optimal weight: 40.0000 chunk 95 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 231 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN B 82 ASN C 419 GLN ** C 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 ASN C1147 GLN D 598 ASN D 932 GLN D1398 HIS E 27 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.166135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.138261 restraints weight = 33128.578| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.22 r_work: 0.3654 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3492 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 23562 Z= 0.330 Angle : 0.662 11.958 31798 Z= 0.345 Chirality : 0.050 0.251 3596 Planarity : 0.005 0.058 4142 Dihedral : 4.881 57.770 3191 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.69 % Allowed : 17.43 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.16), residues: 2917 helix: 1.20 (0.15), residues: 1138 sheet: 0.01 (0.26), residues: 377 loop : 0.34 (0.17), residues: 1402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 27 TYR 0.031 0.002 TYR C 551 PHE 0.034 0.003 PHE C1198 TRP 0.010 0.002 TRP C 177 HIS 0.007 0.002 HIS C 998 Details of bonding type rmsd covalent geometry : bond 0.00787 (23558) covalent geometry : angle 0.66129 (31792) hydrogen bonds : bond 0.05069 ( 1051) hydrogen bonds : angle 5.01332 ( 2961) metal coordination : bond 0.01868 ( 4) metal coordination : angle 2.32311 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 429 time to evaluate : 0.934 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: A 25 GLU cc_start: 0.7488 (tt0) cc_final: 0.7195 (tt0) REVERT: B 59 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7565 (mt) REVERT: B 116 GLN cc_start: 0.7635 (tp40) cc_final: 0.7305 (tp40) REVERT: B 197 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8196 (tttm) REVERT: C 13 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8173 (p) REVERT: C 197 LYS cc_start: 0.8023 (mtpp) cc_final: 0.7609 (mtpp) REVERT: C 362 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6524 (tpp80) REVERT: C 375 MET cc_start: 0.6061 (mmm) cc_final: 0.5799 (mmm) REVERT: C 390 LYS cc_start: 0.7158 (OUTLIER) cc_final: 0.6884 (tmtm) REVERT: C 394 GLU cc_start: 0.6684 (mp0) cc_final: 0.6280 (mp0) REVERT: C 423 GLN cc_start: 0.7275 (mp10) cc_final: 0.6977 (mp10) REVERT: C 509 ASP cc_start: 0.8210 (t0) cc_final: 0.7886 (t0) REVERT: C 553 LYS cc_start: 0.8122 (tttp) cc_final: 0.7885 (mmmm) REVERT: C 696 LYS cc_start: 0.8040 (tttt) cc_final: 0.7780 (ttmm) REVERT: C 755 LYS cc_start: 0.8573 (mttt) cc_final: 0.8310 (mmpt) REVERT: C 784 GLU cc_start: 0.7826 (tt0) cc_final: 0.7501 (pt0) REVERT: C 893 ILE cc_start: 0.7765 (pt) cc_final: 0.7261 (pp) REVERT: C 921 ASP cc_start: 0.8593 (t0) cc_final: 0.8340 (t0) REVERT: C 923 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.7184 (tm-30) REVERT: C 935 GLU cc_start: 0.7786 (tm-30) cc_final: 0.7497 (tt0) REVERT: C 1008 GLN cc_start: 0.7288 (mt0) cc_final: 0.7077 (mt0) REVERT: C 1048 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8217 (mtm) REVERT: C 1057 ILE cc_start: 0.8570 (mm) cc_final: 0.8253 (tt) REVERT: C 1161 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8292 (mt) REVERT: C 1244 GLU cc_start: 0.8231 (pm20) cc_final: 0.7644 (pm20) REVERT: D 33 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6761 (tm-30) REVERT: D 115 SER cc_start: 0.8058 (p) cc_final: 0.7160 (m) REVERT: D 134 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7098 (tt) REVERT: D 140 TYR cc_start: 0.6802 (m-80) cc_final: 0.6508 (m-80) REVERT: D 229 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7294 (tp30) REVERT: D 252 GLU cc_start: 0.8072 (pm20) cc_final: 0.7868 (pm20) REVERT: D 303 LYS cc_start: 0.5830 (OUTLIER) cc_final: 0.4995 (mmmm) REVERT: D 326 ASN cc_start: 0.7805 (t0) cc_final: 0.7464 (t0) REVERT: D 349 LYS cc_start: 0.7726 (ptpp) cc_final: 0.7512 (ptpp) REVERT: D 377 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7210 (mp0) REVERT: D 379 LYS cc_start: 0.8148 (mttt) cc_final: 0.7919 (mtpp) REVERT: D 553 GLU cc_start: 0.7762 (tt0) cc_final: 0.7444 (tt0) REVERT: D 618 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7247 (ttp80) REVERT: D 639 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8013 (mttp) REVERT: D 666 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7215 (tttp) REVERT: D 681 MET cc_start: 0.7601 (tpp) cc_final: 0.7238 (mmm) REVERT: D 792 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.6950 (mppt) REVERT: D 822 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7953 (t) REVERT: D 832 GLU cc_start: 0.8258 (tt0) cc_final: 0.8012 (tt0) REVERT: D 881 LYS cc_start: 0.7897 (mttt) cc_final: 0.7573 (ttmm) REVERT: D 884 GLU cc_start: 0.7409 (mt-10) cc_final: 0.7060 (mt-10) REVERT: D 890 LYS cc_start: 0.8195 (mttt) cc_final: 0.7738 (mttt) REVERT: E 97 ASP cc_start: 0.6990 (t0) cc_final: 0.6779 (m-30) outliers start: 94 outliers final: 53 residues processed: 476 average time/residue: 0.6762 time to fit residues: 367.6864 Evaluate side-chains 495 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 428 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 197 LYS Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 390 LYS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 474 PHE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 655 ARG Chi-restraints excluded: chain C residue 658 SER Chi-restraints excluded: chain C residue 688 VAL Chi-restraints excluded: chain C residue 694 THR Chi-restraints excluded: chain C residue 713 LYS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 923 GLU Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain C residue 1097 THR Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 105 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 123 LEU Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 424 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 639 LYS Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain D residue 682 MET Chi-restraints excluded: chain D residue 792 LYS Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 857 HIS Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 1277 LEU Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1359 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 201 optimal weight: 0.7980 chunk 37 optimal weight: 0.0770 chunk 230 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 135 optimal weight: 7.9990 chunk 245 optimal weight: 0.8980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN C1054 ASN ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN D1398 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.168620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.140950 restraints weight = 33282.175| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.23 r_work: 0.3695 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23562 Z= 0.145 Angle : 0.557 12.723 31798 Z= 0.288 Chirality : 0.044 0.221 3596 Planarity : 0.004 0.062 4142 Dihedral : 4.530 59.796 3191 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.94 % Allowed : 18.33 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 2917 helix: 1.57 (0.16), residues: 1122 sheet: 0.03 (0.27), residues: 375 loop : 0.51 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 27 TYR 0.039 0.002 TYR C 551 PHE 0.031 0.002 PHE C 926 TRP 0.010 0.002 TRP D 426 HIS 0.004 0.001 HIS D 788 Details of bonding type rmsd covalent geometry : bond 0.00344 (23558) covalent geometry : angle 0.55601 (31792) hydrogen bonds : bond 0.04014 ( 1051) hydrogen bonds : angle 4.73581 ( 2961) metal coordination : bond 0.00639 ( 4) metal coordination : angle 2.10969 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 432 time to evaluate : 0.889 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: A 25 GLU cc_start: 0.7470 (tt0) cc_final: 0.7133 (tt0) REVERT: B 59 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7468 (mt) REVERT: B 116 GLN cc_start: 0.7559 (tp40) cc_final: 0.7225 (tp40) REVERT: B 200 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7518 (m-80) REVERT: C 13 SER cc_start: 0.8373 (OUTLIER) cc_final: 0.8133 (p) REVERT: C 197 LYS cc_start: 0.7968 (mtpp) cc_final: 0.7548 (mtpp) REVERT: C 362 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6490 (tpp80) REVERT: C 375 MET cc_start: 0.6061 (mmm) cc_final: 0.5811 (mmm) REVERT: C 423 GLN cc_start: 0.7161 (mp10) cc_final: 0.6921 (mp10) REVERT: C 509 ASP cc_start: 0.8187 (t0) cc_final: 0.7906 (t0) REVERT: C 687 TYR cc_start: 0.8184 (t80) cc_final: 0.7335 (t80) REVERT: C 696 LYS cc_start: 0.8065 (tttt) cc_final: 0.7799 (ttmm) REVERT: C 755 LYS cc_start: 0.8567 (mttt) cc_final: 0.8307 (mmpt) REVERT: C 784 GLU cc_start: 0.7891 (tt0) cc_final: 0.7616 (pt0) REVERT: C 893 ILE cc_start: 0.7680 (pt) cc_final: 0.7140 (pp) REVERT: C 921 ASP cc_start: 0.8489 (t0) cc_final: 0.8245 (t0) REVERT: C 935 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7430 (tt0) REVERT: C 1048 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8183 (mtm) REVERT: C 1057 ILE cc_start: 0.8555 (mm) cc_final: 0.8268 (tt) REVERT: C 1161 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8161 (mt) REVERT: C 1244 GLU cc_start: 0.8189 (pm20) cc_final: 0.7613 (pm20) REVERT: C 1269 GLU cc_start: 0.5780 (mp0) cc_final: 0.5575 (mp0) REVERT: D 33 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6819 (tm-30) REVERT: D 94 ARG cc_start: 0.8614 (mtp-110) cc_final: 0.8405 (mtp-110) REVERT: D 115 SER cc_start: 0.8009 (p) cc_final: 0.7106 (m) REVERT: D 134 ILE cc_start: 0.7274 (OUTLIER) cc_final: 0.6962 (mp) REVERT: D 140 TYR cc_start: 0.6644 (m-80) cc_final: 0.6214 (m-80) REVERT: D 229 GLU cc_start: 0.7682 (tm-30) cc_final: 0.7270 (tp30) REVERT: D 252 GLU cc_start: 0.7997 (pm20) cc_final: 0.7770 (pm20) REVERT: D 303 LYS cc_start: 0.5670 (OUTLIER) cc_final: 0.5132 (mmmm) REVERT: D 326 ASN cc_start: 0.7681 (t0) cc_final: 0.7343 (t0) REVERT: D 349 LYS cc_start: 0.7710 (ptpp) cc_final: 0.7476 (ptpp) REVERT: D 415 LYS cc_start: 0.7895 (mttt) cc_final: 0.7649 (mtpt) REVERT: D 457 LYS cc_start: 0.7941 (mtmm) cc_final: 0.7547 (ptpp) REVERT: D 553 GLU cc_start: 0.7776 (tt0) cc_final: 0.7556 (tt0) REVERT: D 618 ARG cc_start: 0.7729 (ttp80) cc_final: 0.7153 (ttp80) REVERT: D 666 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7129 (tttm) REVERT: D 681 MET cc_start: 0.7555 (tpp) cc_final: 0.7191 (mmm) REVERT: D 749 ARG cc_start: 0.7966 (ttt-90) cc_final: 0.7690 (ttt-90) REVERT: D 792 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6915 (mppt) REVERT: D 822 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7905 (t) REVERT: D 832 GLU cc_start: 0.8260 (tt0) cc_final: 0.7979 (tt0) REVERT: D 880 VAL cc_start: 0.8232 (t) cc_final: 0.7903 (t) REVERT: D 881 LYS cc_start: 0.7850 (mttt) cc_final: 0.7551 (ttmm) REVERT: D 884 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7106 (mt-10) REVERT: D 890 LYS cc_start: 0.8175 (mttt) cc_final: 0.7721 (mttt) REVERT: D 1244 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7843 (mtm110) REVERT: D 1391 LYS cc_start: 0.8092 (mtpp) cc_final: 0.7877 (ttmt) REVERT: E 97 ASP cc_start: 0.6976 (t0) cc_final: 0.6764 (m-30) outliers start: 75 outliers final: 43 residues processed: 470 average time/residue: 0.6720 time to fit residues: 360.2989 Evaluate side-chains 480 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 426 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 367 LYS Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 655 ARG Chi-restraints excluded: chain C residue 658 SER Chi-restraints excluded: chain C residue 713 LYS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 840 GLU Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain D residue 682 MET Chi-restraints excluded: chain D residue 792 LYS Chi-restraints excluded: chain D residue 814 VAL Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 857 HIS Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1359 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 3 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 162 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 254 optimal weight: 1.9990 chunk 252 optimal weight: 0.3980 chunk 269 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN B 158 ASN C 473 GLN C 514 HIS C1054 ASN C1147 GLN D 773 ASN D 903 GLN D 932 GLN D1398 HIS E 27 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.169564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.142007 restraints weight = 33319.025| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 2.25 r_work: 0.3705 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23562 Z= 0.131 Angle : 0.557 11.534 31798 Z= 0.288 Chirality : 0.044 0.294 3596 Planarity : 0.004 0.063 4142 Dihedral : 4.402 59.486 3191 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.35 % Allowed : 19.35 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.16), residues: 2917 helix: 1.72 (0.16), residues: 1120 sheet: 0.01 (0.27), residues: 372 loop : 0.54 (0.17), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 27 TYR 0.031 0.001 TYR D 137 PHE 0.028 0.001 PHE B 26 TRP 0.020 0.001 TRP D 111 HIS 0.004 0.001 HIS D 788 Details of bonding type rmsd covalent geometry : bond 0.00310 (23558) covalent geometry : angle 0.55653 (31792) hydrogen bonds : bond 0.03811 ( 1051) hydrogen bonds : angle 4.64620 ( 2961) metal coordination : bond 0.00583 ( 4) metal coordination : angle 2.25006 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 414 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 GLU cc_start: 0.7488 (tt0) cc_final: 0.7119 (tt0) REVERT: B 59 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7489 (mt) REVERT: B 116 GLN cc_start: 0.7550 (tp40) cc_final: 0.7228 (tp40) REVERT: B 200 PHE cc_start: 0.8012 (OUTLIER) cc_final: 0.7711 (t80) REVERT: C 13 SER cc_start: 0.8357 (OUTLIER) cc_final: 0.8127 (p) REVERT: C 197 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7545 (mtpp) REVERT: C 362 ARG cc_start: 0.6824 (OUTLIER) cc_final: 0.6553 (tpp80) REVERT: C 375 MET cc_start: 0.6041 (mmm) cc_final: 0.5803 (mmm) REVERT: C 509 ASP cc_start: 0.8179 (t0) cc_final: 0.7745 (t0) REVERT: C 696 LYS cc_start: 0.8102 (tttt) cc_final: 0.7833 (ttmm) REVERT: C 755 LYS cc_start: 0.8559 (mttt) cc_final: 0.8257 (mmmt) REVERT: C 893 ILE cc_start: 0.7663 (pt) cc_final: 0.7062 (pp) REVERT: C 921 ASP cc_start: 0.8454 (t0) cc_final: 0.8213 (t0) REVERT: C 923 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7111 (tm-30) REVERT: C 935 GLU cc_start: 0.7716 (tm-30) cc_final: 0.7376 (tt0) REVERT: C 1048 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8268 (mtm) REVERT: C 1057 ILE cc_start: 0.8553 (mm) cc_final: 0.8275 (tt) REVERT: C 1244 GLU cc_start: 0.8093 (pm20) cc_final: 0.7514 (pm20) REVERT: D 33 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6765 (tm-30) REVERT: D 115 SER cc_start: 0.8015 (p) cc_final: 0.7115 (m) REVERT: D 134 ILE cc_start: 0.7189 (OUTLIER) cc_final: 0.6864 (tt) REVERT: D 229 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7349 (tp30) REVERT: D 252 GLU cc_start: 0.7980 (pm20) cc_final: 0.7754 (pm20) REVERT: D 303 LYS cc_start: 0.5667 (tptp) cc_final: 0.5165 (mmmm) REVERT: D 326 ASN cc_start: 0.7680 (t0) cc_final: 0.7338 (t0) REVERT: D 349 LYS cc_start: 0.7716 (ptpp) cc_final: 0.7497 (ptpp) REVERT: D 415 LYS cc_start: 0.7836 (mttt) cc_final: 0.7600 (mtpt) REVERT: D 457 LYS cc_start: 0.7944 (mtmm) cc_final: 0.7582 (ptpp) REVERT: D 492 GLU cc_start: 0.7748 (tp30) cc_final: 0.7541 (tp30) REVERT: D 553 GLU cc_start: 0.7826 (tt0) cc_final: 0.7610 (tt0) REVERT: D 666 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7106 (tttp) REVERT: D 681 MET cc_start: 0.7543 (tpp) cc_final: 0.7127 (mpp) REVERT: D 792 LYS cc_start: 0.7193 (OUTLIER) cc_final: 0.6891 (tppt) REVERT: D 822 THR cc_start: 0.8142 (OUTLIER) cc_final: 0.7894 (t) REVERT: D 832 GLU cc_start: 0.8276 (tt0) cc_final: 0.8001 (tt0) REVERT: D 880 VAL cc_start: 0.8255 (t) cc_final: 0.7931 (t) REVERT: D 881 LYS cc_start: 0.7838 (mttt) cc_final: 0.7539 (ttmm) REVERT: D 884 GLU cc_start: 0.7447 (mt-10) cc_final: 0.7115 (mt-10) REVERT: D 890 LYS cc_start: 0.8187 (mttt) cc_final: 0.7733 (mttt) REVERT: D 1244 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7870 (mtm110) outliers start: 60 outliers final: 38 residues processed: 445 average time/residue: 0.6860 time to fit residues: 346.8826 Evaluate side-chains 453 residues out of total 2548 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 405 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 120 SER Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 200 PHE Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 35 PHE Chi-restraints excluded: chain C residue 156 GLN Chi-restraints excluded: chain C residue 362 ARG Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 462 ILE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 565 ILE Chi-restraints excluded: chain C residue 616 VAL Chi-restraints excluded: chain C residue 655 ARG Chi-restraints excluded: chain C residue 658 SER Chi-restraints excluded: chain C residue 713 LYS Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 804 VAL Chi-restraints excluded: chain C residue 923 GLU Chi-restraints excluded: chain C residue 945 THR Chi-restraints excluded: chain C residue 950 ILE Chi-restraints excluded: chain C residue 1002 ILE Chi-restraints excluded: chain C residue 1048 MET Chi-restraints excluded: chain C residue 1132 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 254 MET Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 666 LYS Chi-restraints excluded: chain D residue 682 MET Chi-restraints excluded: chain D residue 792 LYS Chi-restraints excluded: chain D residue 822 THR Chi-restraints excluded: chain D residue 857 HIS Chi-restraints excluded: chain D residue 876 SER Chi-restraints excluded: chain D residue 1333 THR Chi-restraints excluded: chain D residue 1359 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 290 random chunks: chunk 187 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 234 optimal weight: 0.7980 chunk 56 optimal weight: 0.0010 chunk 287 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS B 82 ASN B 158 ASN C1054 ASN C1147 GLN D 903 GLN ** D1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1398 HIS E 27 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.169604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.142003 restraints weight = 33294.442| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.22 r_work: 0.3702 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23562 Z= 0.136 Angle : 0.563 15.039 31798 Z= 0.289 Chirality : 0.044 0.379 3596 Planarity : 0.004 0.062 4142 Dihedral : 4.372 58.915 3191 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.51 % Allowed : 19.35 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.16), residues: 2917 helix: 1.75 (0.16), residues: 1119 sheet: 0.02 (0.27), residues: 381 loop : 0.55 (0.17), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 27 TYR 0.020 0.001 TYR C 551 PHE 0.027 0.001 PHE D1287 TRP 0.018 0.002 TRP D 111 HIS 0.004 0.001 HIS D 788 Details of bonding type rmsd covalent geometry : bond 0.00321 (23558) covalent geometry : angle 0.56268 (31792) hydrogen bonds : bond 0.03796 ( 1051) hydrogen bonds : angle 4.61544 ( 2961) metal coordination : bond 0.00640 ( 4) metal coordination : angle 2.10328 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9799.68 seconds wall clock time: 167 minutes 25.81 seconds (10045.81 seconds total)