Starting phenix.real_space_refine on Wed Feb 4 13:43:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lg9_63058/02_2026/9lg9_63058_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lg9_63058/02_2026/9lg9_63058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lg9_63058/02_2026/9lg9_63058_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lg9_63058/02_2026/9lg9_63058_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lg9_63058/02_2026/9lg9_63058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lg9_63058/02_2026/9lg9_63058.map" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.024 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: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 6922 2.51 5 N 1765 2.21 5 O 1902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s 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: 10647 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10607 Classifications: {'peptide': 1336} Link IDs: {'PTRANS': 50, 'TRANS': 1285} Chain breaks: 8 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'GDS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.04, per 1000 atoms: 0.19 Number of scatterers: 10647 At special positions: 0 Unit cell: (84.24, 110.24, 150.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1902 8.00 N 1765 7.00 C 6922 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: 0.65 Conformation dependent library (CDL) restraints added in 382.4 milliseconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2528 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 5 sheets defined 71.9% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.677A pdb=" N THR A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 60 removed outlier: 3.960A pdb=" N LEU A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N VAL A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 51 - end of helix removed outlier: 3.865A pdb=" N LEU A 55 " --> pdb=" O PRO A 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 94 removed outlier: 3.696A pdb=" N LEU A 89 " --> pdb=" O CYS A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 130 removed outlier: 3.577A pdb=" N VAL A 108 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 136 through 160 removed outlier: 4.530A pdb=" N TRP A 142 " --> pdb=" O MET A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.545A pdb=" N PHE A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 220 removed outlier: 3.825A pdb=" N THR A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.650A pdb=" N GLN A 234 " --> pdb=" O GLN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 312 through 322 Processing helix chain 'A' and resid 322 through 340 removed outlier: 4.122A pdb=" N MET A 327 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 355 removed outlier: 3.551A pdb=" N GLU A 344 " --> pdb=" O PHE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 408 removed outlier: 3.577A pdb=" N TYR A 364 " --> pdb=" O GLU A 360 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N HIS A 386 " --> pdb=" O HIS A 382 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 417 removed outlier: 3.757A pdb=" N SER A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 429 removed outlier: 4.252A pdb=" N MET A 427 " --> pdb=" O ILE A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.529A pdb=" N PHE A 434 " --> pdb=" O ASP A 430 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 439 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TYR A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 444 No H-bonds generated for 'chain 'A' and resid 442 through 444' Processing helix chain 'A' and resid 445 through 462 Processing helix chain 'A' and resid 465 through 511 Proline residue: A 478 - end of helix Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 520 through 555 removed outlier: 3.755A pdb=" N LYS A 527 " --> pdb=" O ALA A 523 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL A 538 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 571 Processing helix chain 'A' and resid 578 through 621 removed outlier: 4.513A pdb=" N VAL A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N PHE A 594 " --> pdb=" O ASN A 590 " (cutoff:3.500A) Proline residue: A 595 - end of helix Proline residue: A 600 - end of helix removed outlier: 3.831A pdb=" N VAL A 611 " --> pdb=" O VAL A 607 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 612 " --> pdb=" O GLN A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 692 removed outlier: 3.552A pdb=" N LEU A 688 " --> pdb=" O LYS A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 728 Processing helix chain 'A' and resid 733 through 744 removed outlier: 4.369A pdb=" N GLU A 742 " --> pdb=" O LYS A 738 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 743 " --> pdb=" O ALA A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 755 through 759 removed outlier: 3.658A pdb=" N ARG A 758 " --> pdb=" O SER A 755 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 759 " --> pdb=" O GLY A 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 755 through 759' Processing helix chain 'A' and resid 769 through 785 Processing helix chain 'A' and resid 799 through 810 Processing helix chain 'A' and resid 831 through 835 Processing helix chain 'A' and resid 851 through 859 Processing helix chain 'A' and resid 860 through 869 removed outlier: 4.015A pdb=" N TYR A 869 " --> pdb=" O PHE A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 970 removed outlier: 3.882A pdb=" N TYR A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 999 removed outlier: 4.045A pdb=" N LEU A 989 " --> pdb=" O HIS A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1007 Processing helix chain 'A' and resid 1010 through 1034 removed outlier: 4.144A pdb=" N PHE A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1057 Processing helix chain 'A' and resid 1060 through 1066 Processing helix chain 'A' and resid 1067 through 1077 removed outlier: 3.653A pdb=" N LEU A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1084 removed outlier: 3.515A pdb=" N ASP A1083 " --> pdb=" O LEU A1079 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1111 removed outlier: 3.736A pdb=" N PHE A1098 " --> pdb=" O MET A1094 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN A1099 " --> pdb=" O GLY A1095 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1146 removed outlier: 4.932A pdb=" N GLN A1138 " --> pdb=" O ALA A1134 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A1141 " --> pdb=" O ARG A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1160 removed outlier: 3.782A pdb=" N TYR A1151 " --> pdb=" O ARG A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1168 Processing helix chain 'A' and resid 1169 through 1220 removed outlier: 3.560A pdb=" N ALA A1187 " --> pdb=" O GLU A1183 " (cutoff:3.500A) Proline residue: A1190 - end of helix removed outlier: 3.513A pdb=" N ASN A1195 " --> pdb=" O SER A1191 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A1205 " --> pdb=" O ARG A1201 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A1210 " --> pdb=" O GLY A1206 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA A1217 " --> pdb=" O ALA A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1228 through 1238 removed outlier: 3.672A pdb=" N GLN A1238 " --> pdb=" O SER A1234 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1265 removed outlier: 3.680A pdb=" N ASN A1244 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N TRP A1245 " --> pdb=" O THR A1241 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL A1247 " --> pdb=" O LEU A1243 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A1254 " --> pdb=" O SER A1250 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A1261 " --> pdb=" O ILE A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1269 removed outlier: 3.846A pdb=" N THR A1269 " --> pdb=" O TYR A1266 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1266 through 1269' Processing helix chain 'A' and resid 1331 through 1340 removed outlier: 3.669A pdb=" N THR A1336 " --> pdb=" O LYS A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1368 Processing helix chain 'A' and resid 1382 through 1388 Processing helix chain 'A' and resid 1394 through 1405 Processing helix chain 'A' and resid 1407 through 1412 Processing helix chain 'A' and resid 1416 through 1420 removed outlier: 3.863A pdb=" N HIS A1420 " --> pdb=" O LYS A1417 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1446 removed outlier: 3.638A pdb=" N LYS A1446 " --> pdb=" O ALA A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1474 removed outlier: 3.975A pdb=" N GLN A1474 " --> pdb=" O THR A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 removed outlier: 3.878A pdb=" N ILE A1490 " --> pdb=" O ARG A1486 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP A1492 " --> pdb=" O ASN A1488 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR A1493 " --> pdb=" O THR A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1509 through 1514 Processing sheet with id=AA1, first strand: chain 'A' and resid 661 through 668 removed outlier: 7.039A pdb=" N HIS A 662 " --> pdb=" O THR A 650 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR A 650 " --> pdb=" O HIS A 662 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ILE A 664 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 646 " --> pdb=" O VAL A 702 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL A 702 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASN A 648 " --> pdb=" O GLY A 700 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 700 " --> pdb=" O ASN A 648 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR A 650 " --> pdb=" O VAL A 698 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 708 through 711 removed outlier: 6.300A pdb=" N TYR A 789 " --> pdb=" O LEU A 823 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL A 825 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A 791 " --> pdb=" O VAL A 825 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N LEU A 673 " --> pdb=" O VAL A 837 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE A 839 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA A 675 " --> pdb=" O ILE A 839 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1309 through 1316 removed outlier: 5.875A pdb=" N LYS A1310 " --> pdb=" O LEU A1299 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A1299 " --> pdb=" O LYS A1310 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL A1314 " --> pdb=" O ARG A1295 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG A1295 " --> pdb=" O VAL A1314 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE A1316 " --> pdb=" O GLU A1293 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU A1293 " --> pdb=" O ILE A1316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1309 through 1316 removed outlier: 5.875A pdb=" N LYS A1310 " --> pdb=" O LEU A1299 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU A1299 " --> pdb=" O LYS A1310 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL A1314 " --> pdb=" O ARG A1295 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ARG A1295 " --> pdb=" O VAL A1314 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE A1316 " --> pdb=" O GLU A1293 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N GLU A1293 " --> pdb=" O ILE A1316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1369 through 1372 removed outlier: 6.390A pdb=" N LEU A1450 " --> pdb=" O LEU A1481 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ILE A1483 " --> pdb=" O LEU A1450 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A1452 " --> pdb=" O ILE A1483 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLY A1323 " --> pdb=" O ILE A1497 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU A1499 " --> pdb=" O GLY A1323 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A1325 " --> pdb=" O LEU A1499 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL A1496 " --> pdb=" O TRP A1507 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N TRP A1507 " --> pdb=" O VAL A1496 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A1498 " --> pdb=" O GLN A1505 " (cutoff:3.500A) 661 hydrogen bonds defined for protein. 1953 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: 1.65 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 3424 1.37 - 1.53: 6721 1.53 - 1.70: 644 1.70 - 1.86: 93 1.86 - 2.02: 1 Bond restraints: 10883 Sorted by residual: bond pdb=" N VAL A1289 " pdb=" CA VAL A1289 " ideal model delta sigma weight residual 1.460 1.492 -0.032 8.60e-03 1.35e+04 1.41e+01 bond pdb=" N TRP A1286 " pdb=" CA TRP A1286 " ideal model delta sigma weight residual 1.462 1.487 -0.025 7.70e-03 1.69e+04 1.05e+01 bond pdb=" N ILE A 576 " pdb=" CA ILE A 576 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.15e-02 7.56e+03 1.04e+01 bond pdb=" N ILE A1355 " pdb=" CA ILE A1355 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N LEU A1224 " pdb=" CA LEU A1224 " ideal model delta sigma weight residual 1.454 1.490 -0.037 1.23e-02 6.61e+03 8.86e+00 ... (remaining 10878 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 14227 2.23 - 4.46: 503 4.46 - 6.69: 32 6.69 - 8.92: 10 8.92 - 11.15: 1 Bond angle restraints: 14773 Sorted by residual: angle pdb=" N VAL A1289 " pdb=" CA VAL A1289 " pdb=" C VAL A1289 " ideal model delta sigma weight residual 113.71 107.64 6.07 9.50e-01 1.11e+00 4.09e+01 angle pdb=" C VAL A1229 " pdb=" CA VAL A1229 " pdb=" CB VAL A1229 " ideal model delta sigma weight residual 111.29 103.60 7.69 1.64e+00 3.72e-01 2.20e+01 angle pdb=" N ALA A1115 " pdb=" CA ALA A1115 " pdb=" C ALA A1115 " ideal model delta sigma weight residual 114.56 108.91 5.65 1.27e+00 6.20e-01 1.98e+01 angle pdb=" N VAL A1205 " pdb=" CA VAL A1205 " pdb=" C VAL A1205 " ideal model delta sigma weight residual 111.58 106.96 4.62 1.06e+00 8.90e-01 1.90e+01 angle pdb=" CA ASN A 206 " pdb=" C ASN A 206 " pdb=" O ASN A 206 " ideal model delta sigma weight residual 120.47 117.48 2.99 6.90e-01 2.10e+00 1.87e+01 ... (remaining 14768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5705 17.92 - 35.85: 575 35.85 - 53.77: 152 53.77 - 71.69: 42 71.69 - 89.62: 11 Dihedral angle restraints: 6485 sinusoidal: 2585 harmonic: 3900 Sorted by residual: dihedral pdb=" CA HIS A 382 " pdb=" C HIS A 382 " pdb=" N GLN A 383 " pdb=" CA GLN A 383 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA ASN A 245 " pdb=" C ASN A 245 " pdb=" N LYS A 246 " pdb=" CA LYS A 246 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CG ARG A1472 " pdb=" CD ARG A1472 " pdb=" NE ARG A1472 " pdb=" CZ ARG A1472 " ideal model delta sinusoidal sigma weight residual -90.00 -40.17 -49.83 2 1.50e+01 4.44e-03 1.25e+01 ... (remaining 6482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1326 0.056 - 0.112: 284 0.112 - 0.167: 88 0.167 - 0.223: 19 0.223 - 0.279: 3 Chirality restraints: 1720 Sorted by residual: chirality pdb=" CA LEU A 462 " pdb=" N LEU A 462 " pdb=" C LEU A 462 " pdb=" CB LEU A 462 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA5 GDS A1601 " pdb=" C5 GDS A1601 " pdb=" CB5 GDS A1601 " pdb=" N5 GDS A1601 " both_signs ideal model delta sigma weight residual False 2.63 2.39 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL A 132 " pdb=" N VAL A 132 " pdb=" C VAL A 132 " pdb=" CB VAL A 132 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1717 not shown) Planarity restraints: 1831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG1 GDS A1601 " 0.019 2.00e-02 2.50e+03 2.27e-01 6.43e+02 pdb=" CD1 GDS A1601 " 0.067 2.00e-02 2.50e+03 pdb=" CA2 GDS A1601 " -0.264 2.00e-02 2.50e+03 pdb=" N2 GDS A1601 " 0.378 2.00e-02 2.50e+03 pdb=" O1 GDS A1601 " -0.199 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA5 GDS A1601 " -0.225 2.00e-02 2.50e+03 1.87e-01 4.38e+02 pdb=" CD6 GDS A1601 " 0.061 2.00e-02 2.50e+03 pdb=" CG6 GDS A1601 " -0.157 2.00e-02 2.50e+03 pdb=" N5 GDS A1601 " 0.310 2.00e-02 2.50e+03 pdb=" O6 GDS A1601 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 GDS A1601 " 0.041 2.00e-02 2.50e+03 9.71e-02 1.18e+02 pdb=" CA2 GDS A1601 " -0.091 2.00e-02 2.50e+03 pdb=" CA3 GDS A1601 " -0.119 2.00e-02 2.50e+03 pdb=" N3 GDS A1601 " 0.151 2.00e-02 2.50e+03 pdb=" O2 GDS A1601 " 0.017 2.00e-02 2.50e+03 ... (remaining 1828 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2907 2.81 - 3.34: 10896 3.34 - 3.86: 17713 3.86 - 4.38: 20317 4.38 - 4.90: 34811 Nonbonded interactions: 86644 Sorted by model distance: nonbonded pdb=" O ALA A 484 " pdb=" OG1 THR A 487 " model vdw 2.293 3.040 nonbonded pdb=" OD1 ASN A 992 " pdb=" OH TYR A1235 " model vdw 2.333 3.040 nonbonded pdb=" ND2 ASN A 719 " pdb=" OE2 GLU A1156 " model vdw 2.335 3.120 nonbonded pdb=" OG SER A 328 " pdb=" ND2 ASN A 442 " model vdw 2.343 3.120 nonbonded pdb=" NH1 ARG A1341 " pdb=" O ILE A1357 " model vdw 2.345 3.120 ... (remaining 86639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.370 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 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 : 0.006 0.039 10883 Z= 0.399 Angle : 0.860 11.152 14773 Z= 0.582 Chirality : 0.055 0.279 1720 Planarity : 0.010 0.227 1831 Dihedral : 16.174 89.617 3957 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.17 % Allowed : 16.01 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.52 (0.23), residues: 1318 helix: 0.19 (0.18), residues: 862 sheet: -0.48 (0.57), residues: 77 loop : -1.34 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 735 TYR 0.038 0.001 TYR A 490 PHE 0.028 0.001 PHE A 865 TRP 0.008 0.001 TRP A 22 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd covalent geometry : bond 0.00583 (10883) covalent geometry : angle 0.85972 (14773) hydrogen bonds : bond 0.20018 ( 659) hydrogen bonds : angle 7.33099 ( 1953) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 245 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 MET cc_start: 0.8166 (tpp) cc_final: 0.7944 (mmt) REVERT: A 364 TYR cc_start: 0.8496 (m-10) cc_final: 0.8157 (m-10) REVERT: A 495 MET cc_start: 0.8490 (tpp) cc_final: 0.8172 (tpp) REVERT: A 521 GLU cc_start: 0.6955 (mp0) cc_final: 0.6445 (mt-10) REVERT: A 537 LYS cc_start: 0.6691 (mmmt) cc_final: 0.6396 (mtpt) REVERT: A 959 LEU cc_start: 0.8872 (mt) cc_final: 0.8188 (tt) REVERT: A 1094 MET cc_start: 0.7765 (mmm) cc_final: 0.7078 (ttp) REVERT: A 1113 MET cc_start: 0.7117 (mmm) cc_final: 0.6830 (mmt) REVERT: A 1249 MET cc_start: 0.7971 (mmp) cc_final: 0.7732 (mmt) outliers start: 2 outliers final: 1 residues processed: 246 average time/residue: 0.0944 time to fit residues: 32.1298 Evaluate side-chains 151 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 811 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.0670 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 351 ASN A 432 GLN A 992 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.182455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.141045 restraints weight = 13256.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.143943 restraints weight = 7973.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.144761 restraints weight = 5788.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.145208 restraints weight = 4326.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.145675 restraints weight = 4193.059| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10883 Z= 0.153 Angle : 0.614 8.108 14773 Z= 0.315 Chirality : 0.041 0.158 1720 Planarity : 0.005 0.063 1831 Dihedral : 6.204 60.850 1478 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.64 % Allowed : 19.17 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.23), residues: 1318 helix: 1.06 (0.18), residues: 875 sheet: -0.31 (0.58), residues: 77 loop : -1.29 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1472 TYR 0.030 0.001 TYR A 518 PHE 0.040 0.002 PHE A 558 TRP 0.016 0.001 TRP A 94 HIS 0.005 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00324 (10883) covalent geometry : angle 0.61420 (14773) hydrogen bonds : bond 0.05305 ( 659) hydrogen bonds : angle 4.70763 ( 1953) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7180 (t0) cc_final: 0.6957 (t0) REVERT: A 118 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.8002 (mt) REVERT: A 338 MET cc_start: 0.8292 (tpp) cc_final: 0.7970 (mmt) REVERT: A 346 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8267 (tt) REVERT: A 495 MET cc_start: 0.8499 (tpp) cc_final: 0.7977 (tmm) REVERT: A 537 LYS cc_start: 0.6637 (mmmt) cc_final: 0.6414 (mtpt) REVERT: A 804 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8550 (tppt) REVERT: A 959 LEU cc_start: 0.8842 (mt) cc_final: 0.8181 (tt) REVERT: A 966 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7357 (mtt) REVERT: A 1094 MET cc_start: 0.7284 (mmm) cc_final: 0.6878 (ptm) REVERT: A 1495 ARG cc_start: 0.7304 (mtp180) cc_final: 0.7032 (mtp180) outliers start: 31 outliers final: 16 residues processed: 179 average time/residue: 0.0906 time to fit residues: 23.0998 Evaluate side-chains 161 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 54 PHE Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 483 MET Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1278 GLN Chi-restraints excluded: chain A residue 1404 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 31 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 122 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 125 GLN A1276 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.178180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.135398 restraints weight = 13403.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.137952 restraints weight = 8032.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.139141 restraints weight = 5401.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.139133 restraints weight = 4201.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139569 restraints weight = 4150.838| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10883 Z= 0.166 Angle : 0.600 7.686 14773 Z= 0.303 Chirality : 0.042 0.223 1720 Planarity : 0.004 0.059 1831 Dihedral : 5.959 58.664 1478 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.00 % Allowed : 19.93 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.23), residues: 1318 helix: 1.28 (0.18), residues: 875 sheet: -0.20 (0.58), residues: 78 loop : -1.20 (0.29), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 758 TYR 0.034 0.001 TYR A 518 PHE 0.034 0.001 PHE A 558 TRP 0.018 0.001 TRP A 82 HIS 0.005 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00377 (10883) covalent geometry : angle 0.60027 (14773) hydrogen bonds : bond 0.04819 ( 659) hydrogen bonds : angle 4.49137 ( 1953) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 ASN cc_start: 0.7208 (t0) cc_final: 0.6973 (t0) REVERT: A 158 MET cc_start: 0.7522 (mmp) cc_final: 0.7301 (mtt) REVERT: A 315 LYS cc_start: 0.7947 (ttmm) cc_final: 0.7496 (mptt) REVERT: A 495 MET cc_start: 0.8497 (tpp) cc_final: 0.8004 (tmm) REVERT: A 537 LYS cc_start: 0.6765 (mmmt) cc_final: 0.6555 (mtpt) REVERT: A 720 ILE cc_start: 0.8235 (tp) cc_final: 0.8030 (pt) REVERT: A 804 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8563 (tppt) REVERT: A 959 LEU cc_start: 0.8838 (mt) cc_final: 0.8145 (tt) REVERT: A 966 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7374 (mtt) REVERT: A 1094 MET cc_start: 0.7519 (mmm) cc_final: 0.6600 (ptm) REVERT: A 1407 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7564 (tt) outliers start: 47 outliers final: 22 residues processed: 177 average time/residue: 0.0902 time to fit residues: 22.9506 Evaluate side-chains 163 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1407 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 106 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 59 optimal weight: 0.7980 chunk 81 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 ASN A 801 HIS A 985 HIS A1468 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.177366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.136050 restraints weight = 13598.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.137765 restraints weight = 8448.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138468 restraints weight = 7015.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.139205 restraints weight = 5428.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.139538 restraints weight = 4832.691| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10883 Z= 0.154 Angle : 0.592 9.850 14773 Z= 0.294 Chirality : 0.041 0.246 1720 Planarity : 0.004 0.056 1831 Dihedral : 5.796 59.979 1478 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.09 % Allowed : 20.61 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.92 (0.23), residues: 1318 helix: 1.40 (0.18), residues: 874 sheet: -0.15 (0.58), residues: 78 loop : -1.09 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 758 TYR 0.028 0.001 TYR A 518 PHE 0.014 0.001 PHE A 175 TRP 0.019 0.001 TRP A 94 HIS 0.007 0.001 HIS A 801 Details of bonding type rmsd covalent geometry : bond 0.00347 (10883) covalent geometry : angle 0.59228 (14773) hydrogen bonds : bond 0.04510 ( 659) hydrogen bonds : angle 4.43641 ( 1953) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LYS cc_start: 0.7884 (ttmm) cc_final: 0.7422 (mptt) REVERT: A 495 MET cc_start: 0.8518 (tpp) cc_final: 0.8009 (tmm) REVERT: A 503 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7614 (pttp) REVERT: A 537 LYS cc_start: 0.6788 (mmmt) cc_final: 0.6548 (mtpt) REVERT: A 742 GLU cc_start: 0.8610 (pm20) cc_final: 0.8230 (pm20) REVERT: A 804 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8514 (tppt) REVERT: A 959 LEU cc_start: 0.8834 (mt) cc_final: 0.8145 (tt) REVERT: A 966 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7292 (mtt) REVERT: A 1449 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7371 (mp) REVERT: A 1478 CYS cc_start: 0.7531 (m) cc_final: 0.7323 (m) outliers start: 48 outliers final: 32 residues processed: 182 average time/residue: 0.0971 time to fit residues: 25.3784 Evaluate side-chains 167 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 132 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1397 GLU Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1449 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 0.0980 chunk 114 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1420 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.176312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134591 restraints weight = 13396.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137864 restraints weight = 8749.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.138932 restraints weight = 5518.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.138848 restraints weight = 4726.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139204 restraints weight = 4303.273| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10883 Z= 0.148 Angle : 0.574 9.857 14773 Z= 0.285 Chirality : 0.041 0.242 1720 Planarity : 0.004 0.040 1831 Dihedral : 5.682 59.060 1478 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.26 % Allowed : 21.04 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.23), residues: 1318 helix: 1.48 (0.18), residues: 871 sheet: 0.01 (0.59), residues: 78 loop : -1.01 (0.30), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 758 TYR 0.022 0.001 TYR A 518 PHE 0.016 0.001 PHE A 175 TRP 0.013 0.001 TRP A 94 HIS 0.006 0.001 HIS A1420 Details of bonding type rmsd covalent geometry : bond 0.00335 (10883) covalent geometry : angle 0.57373 (14773) hydrogen bonds : bond 0.04351 ( 659) hydrogen bonds : angle 4.30898 ( 1953) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 140 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 PHE cc_start: 0.8450 (t80) cc_final: 0.8173 (t80) REVERT: A 315 LYS cc_start: 0.7841 (ttmm) cc_final: 0.7379 (mptt) REVERT: A 495 MET cc_start: 0.8498 (tpp) cc_final: 0.8056 (tmm) REVERT: A 503 LYS cc_start: 0.7893 (mtmm) cc_final: 0.7615 (pttp) REVERT: A 537 LYS cc_start: 0.6825 (mmmt) cc_final: 0.6607 (mtpt) REVERT: A 959 LEU cc_start: 0.8820 (mt) cc_final: 0.8138 (tt) REVERT: A 966 MET cc_start: 0.7590 (OUTLIER) cc_final: 0.7256 (mtt) REVERT: A 1113 MET cc_start: 0.6980 (ttm) cc_final: 0.6779 (ttp) REVERT: A 1179 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7518 (tt) REVERT: A 1452 LEU cc_start: 0.8271 (mm) cc_final: 0.8070 (mp) REVERT: A 1475 PHE cc_start: 0.6136 (OUTLIER) cc_final: 0.5558 (t80) outliers start: 50 outliers final: 37 residues processed: 173 average time/residue: 0.0999 time to fit residues: 25.1432 Evaluate side-chains 174 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1397 GLU Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1475 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 46 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.173475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.131389 restraints weight = 13716.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.133521 restraints weight = 9076.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134345 restraints weight = 6995.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.134881 restraints weight = 5233.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.134833 restraints weight = 5033.145| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10883 Z= 0.184 Angle : 0.609 10.180 14773 Z= 0.303 Chirality : 0.042 0.243 1720 Planarity : 0.004 0.040 1831 Dihedral : 5.725 58.239 1478 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.20 % Allowed : 20.36 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.98 (0.23), residues: 1318 helix: 1.39 (0.18), residues: 876 sheet: -0.08 (0.57), residues: 83 loop : -0.94 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 758 TYR 0.031 0.002 TYR A 518 PHE 0.017 0.001 PHE A 175 TRP 0.021 0.002 TRP A1275 HIS 0.004 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00428 (10883) covalent geometry : angle 0.60949 (14773) hydrogen bonds : bond 0.04539 ( 659) hydrogen bonds : angle 4.36780 ( 1953) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 149 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 PHE cc_start: 0.8535 (t80) cc_final: 0.8250 (t80) REVERT: A 118 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7808 (mt) REVERT: A 315 LYS cc_start: 0.7844 (ttmm) cc_final: 0.7334 (mptt) REVERT: A 495 MET cc_start: 0.8463 (tpp) cc_final: 0.8051 (tmm) REVERT: A 503 LYS cc_start: 0.7809 (mtmm) cc_final: 0.7550 (pttp) REVERT: A 537 LYS cc_start: 0.6944 (mmmt) cc_final: 0.6700 (mtpt) REVERT: A 598 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8464 (tp) REVERT: A 662 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.6961 (m90) REVERT: A 804 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8578 (tppt) REVERT: A 959 LEU cc_start: 0.8856 (mt) cc_final: 0.8123 (tt) REVERT: A 966 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7244 (mtt) REVERT: A 1113 MET cc_start: 0.7114 (ttm) cc_final: 0.6880 (ttp) REVERT: A 1179 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7556 (tt) REVERT: A 1434 ARG cc_start: 0.8176 (mpp80) cc_final: 0.7642 (mpp80) REVERT: A 1475 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.5632 (t80) outliers start: 61 outliers final: 41 residues processed: 190 average time/residue: 0.1061 time to fit residues: 28.9971 Evaluate side-chains 187 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 139 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 664 ILE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1397 GLU Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1439 LEU Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1514 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 18 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 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 23 ASN A 533 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.175557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133282 restraints weight = 13571.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.135807 restraints weight = 9250.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136970 restraints weight = 6396.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137152 restraints weight = 5261.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.137935 restraints weight = 4894.387| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10883 Z= 0.144 Angle : 0.587 11.198 14773 Z= 0.291 Chirality : 0.041 0.159 1720 Planarity : 0.004 0.041 1831 Dihedral : 5.603 57.780 1478 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.34 % Allowed : 22.40 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.13 (0.23), residues: 1318 helix: 1.53 (0.18), residues: 880 sheet: -0.13 (0.57), residues: 83 loop : -0.92 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1045 TYR 0.025 0.001 TYR A 518 PHE 0.015 0.001 PHE A 558 TRP 0.031 0.001 TRP A1275 HIS 0.002 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00326 (10883) covalent geometry : angle 0.58727 (14773) hydrogen bonds : bond 0.04309 ( 659) hydrogen bonds : angle 4.28657 ( 1953) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 PHE cc_start: 0.8535 (t80) cc_final: 0.8122 (t80) REVERT: A 67 MET cc_start: 0.5870 (mmm) cc_final: 0.5477 (mtp) REVERT: A 315 LYS cc_start: 0.7803 (ttmm) cc_final: 0.7322 (mptt) REVERT: A 495 MET cc_start: 0.8454 (tpp) cc_final: 0.8059 (tmm) REVERT: A 503 LYS cc_start: 0.7854 (mtmm) cc_final: 0.7566 (pttp) REVERT: A 537 LYS cc_start: 0.6880 (mmmt) cc_final: 0.6650 (mtpt) REVERT: A 662 HIS cc_start: 0.7514 (OUTLIER) cc_final: 0.6911 (m90) REVERT: A 804 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8589 (tppt) REVERT: A 959 LEU cc_start: 0.8785 (mt) cc_final: 0.8082 (tt) REVERT: A 966 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7321 (mtt) REVERT: A 1113 MET cc_start: 0.7092 (ttm) cc_final: 0.6862 (ttp) REVERT: A 1179 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7558 (tt) REVERT: A 1449 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7401 (mp) REVERT: A 1475 PHE cc_start: 0.6197 (OUTLIER) cc_final: 0.5735 (t80) outliers start: 51 outliers final: 37 residues processed: 184 average time/residue: 0.0992 time to fit residues: 26.2881 Evaluate side-chains 186 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1449 ILE Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1514 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 120 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.176054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.133687 restraints weight = 13561.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134962 restraints weight = 9324.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136561 restraints weight = 7047.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136844 restraints weight = 5266.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.136982 restraints weight = 4743.786| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10883 Z= 0.138 Angle : 0.579 9.180 14773 Z= 0.285 Chirality : 0.041 0.157 1720 Planarity : 0.004 0.042 1831 Dihedral : 5.535 57.861 1478 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.34 % Allowed : 22.06 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.20 (0.23), residues: 1318 helix: 1.57 (0.18), residues: 882 sheet: -0.16 (0.56), residues: 83 loop : -0.88 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1045 TYR 0.023 0.001 TYR A 518 PHE 0.018 0.001 PHE A1126 TRP 0.018 0.001 TRP A1275 HIS 0.005 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00314 (10883) covalent geometry : angle 0.57942 (14773) hydrogen bonds : bond 0.04186 ( 659) hydrogen bonds : angle 4.22181 ( 1953) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 146 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LYS cc_start: 0.7803 (ttmm) cc_final: 0.7296 (mptt) REVERT: A 378 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8298 (m) REVERT: A 416 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7750 (mmtt) REVERT: A 495 MET cc_start: 0.8452 (tpp) cc_final: 0.8053 (tmm) REVERT: A 537 LYS cc_start: 0.6821 (mmmt) cc_final: 0.6609 (mtpt) REVERT: A 598 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8438 (tp) REVERT: A 662 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.7032 (m90) REVERT: A 804 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8595 (tppt) REVERT: A 959 LEU cc_start: 0.8725 (mt) cc_final: 0.8003 (tt) REVERT: A 966 MET cc_start: 0.7710 (OUTLIER) cc_final: 0.7379 (mtt) REVERT: A 1179 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7568 (tt) REVERT: A 1228 LEU cc_start: 0.8575 (mm) cc_final: 0.8359 (mt) REVERT: A 1452 LEU cc_start: 0.8516 (mm) cc_final: 0.8274 (mp) REVERT: A 1475 PHE cc_start: 0.6294 (OUTLIER) cc_final: 0.5774 (t80) outliers start: 51 outliers final: 39 residues processed: 183 average time/residue: 0.1047 time to fit residues: 27.6936 Evaluate side-chains 187 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 141 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1365 LEU Chi-restraints excluded: chain A residue 1397 GLU Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1431 VAL Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1514 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 26 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** A1468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.176516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.134554 restraints weight = 13581.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137031 restraints weight = 9069.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.138078 restraints weight = 6450.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.138374 restraints weight = 5171.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138823 restraints weight = 4916.037| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10883 Z= 0.133 Angle : 0.591 13.638 14773 Z= 0.289 Chirality : 0.041 0.148 1720 Planarity : 0.004 0.042 1831 Dihedral : 5.491 57.850 1478 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.00 % Allowed : 22.57 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.23), residues: 1318 helix: 1.62 (0.18), residues: 882 sheet: -0.42 (0.54), residues: 93 loop : -0.87 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1045 TYR 0.021 0.001 TYR A 518 PHE 0.015 0.001 PHE A 558 TRP 0.020 0.001 TRP A 82 HIS 0.010 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00297 (10883) covalent geometry : angle 0.59102 (14773) hydrogen bonds : bond 0.04112 ( 659) hydrogen bonds : angle 4.20487 ( 1953) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 PHE cc_start: 0.8551 (t80) cc_final: 0.8103 (t80) REVERT: A 67 MET cc_start: 0.5842 (mmm) cc_final: 0.5544 (mtp) REVERT: A 315 LYS cc_start: 0.7843 (ttmm) cc_final: 0.7291 (mptt) REVERT: A 378 THR cc_start: 0.8692 (OUTLIER) cc_final: 0.8289 (m) REVERT: A 416 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7704 (mmtt) REVERT: A 495 MET cc_start: 0.8429 (tpp) cc_final: 0.8035 (tmm) REVERT: A 598 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8411 (tp) REVERT: A 662 HIS cc_start: 0.7526 (OUTLIER) cc_final: 0.7037 (m90) REVERT: A 804 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8582 (tppt) REVERT: A 959 LEU cc_start: 0.8700 (mt) cc_final: 0.7987 (tt) REVERT: A 966 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7310 (mtt) REVERT: A 1078 GLU cc_start: 0.8457 (tp30) cc_final: 0.8090 (tp30) REVERT: A 1113 MET cc_start: 0.7170 (ttm) cc_final: 0.6947 (ttp) REVERT: A 1179 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7554 (tt) REVERT: A 1368 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7571 (mmtt) REVERT: A 1384 ARG cc_start: 0.7456 (tpt170) cc_final: 0.6820 (tpt90) REVERT: A 1452 LEU cc_start: 0.8563 (mm) cc_final: 0.8318 (mp) REVERT: A 1475 PHE cc_start: 0.6228 (OUTLIER) cc_final: 0.5805 (t80) outliers start: 47 outliers final: 35 residues processed: 182 average time/residue: 0.1090 time to fit residues: 28.0863 Evaluate side-chains 187 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 145 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 570 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1397 GLU Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1468 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.177488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134597 restraints weight = 13557.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137848 restraints weight = 9034.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138910 restraints weight = 5500.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138957 restraints weight = 4205.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.139094 restraints weight = 3929.532| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10883 Z= 0.129 Angle : 0.606 13.227 14773 Z= 0.295 Chirality : 0.041 0.187 1720 Planarity : 0.004 0.049 1831 Dihedral : 5.450 57.847 1478 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.49 % Allowed : 23.00 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.23), residues: 1318 helix: 1.70 (0.18), residues: 883 sheet: -0.39 (0.54), residues: 94 loop : -0.91 (0.32), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 655 TYR 0.022 0.001 TYR A 518 PHE 0.014 0.001 PHE A 558 TRP 0.020 0.001 TRP A 82 HIS 0.007 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00286 (10883) covalent geometry : angle 0.60571 (14773) hydrogen bonds : bond 0.04067 ( 659) hydrogen bonds : angle 4.15380 ( 1953) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.5907 (mmm) cc_final: 0.5536 (mtp) REVERT: A 315 LYS cc_start: 0.7829 (ttmm) cc_final: 0.7236 (mptt) REVERT: A 378 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8362 (m) REVERT: A 416 LYS cc_start: 0.8071 (mmtt) cc_final: 0.7720 (mmtt) REVERT: A 495 MET cc_start: 0.8395 (tpp) cc_final: 0.7971 (tmm) REVERT: A 662 HIS cc_start: 0.7333 (OUTLIER) cc_final: 0.6936 (m90) REVERT: A 695 MET cc_start: 0.8357 (mmt) cc_final: 0.8152 (mmm) REVERT: A 801 HIS cc_start: 0.6466 (t70) cc_final: 0.6224 (t-170) REVERT: A 804 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8582 (tppt) REVERT: A 959 LEU cc_start: 0.8739 (mt) cc_final: 0.7976 (tt) REVERT: A 966 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7444 (mtt) REVERT: A 1078 GLU cc_start: 0.8418 (tp30) cc_final: 0.8027 (tp30) REVERT: A 1113 MET cc_start: 0.7241 (ttm) cc_final: 0.6911 (ttt) REVERT: A 1179 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7472 (tt) REVERT: A 1368 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7515 (mmtt) REVERT: A 1384 ARG cc_start: 0.7492 (tpt170) cc_final: 0.6842 (tpt170) REVERT: A 1434 ARG cc_start: 0.8362 (mpp80) cc_final: 0.7952 (mpp80) REVERT: A 1452 LEU cc_start: 0.8559 (mm) cc_final: 0.8356 (mp) REVERT: A 1475 PHE cc_start: 0.6407 (OUTLIER) cc_final: 0.5915 (t80) outliers start: 41 outliers final: 34 residues processed: 172 average time/residue: 0.0954 time to fit residues: 23.6720 Evaluate side-chains 182 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 59 HIS Chi-restraints excluded: chain A residue 64 TYR Chi-restraints excluded: chain A residue 91 TYR Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 355 ASP Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 502 ILE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 662 HIS Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 804 LYS Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 966 MET Chi-restraints excluded: chain A residue 1013 VAL Chi-restraints excluded: chain A residue 1032 TYR Chi-restraints excluded: chain A residue 1062 PHE Chi-restraints excluded: chain A residue 1080 ASP Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1106 ILE Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1244 ASN Chi-restraints excluded: chain A residue 1269 THR Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1397 GLU Chi-restraints excluded: chain A residue 1406 HIS Chi-restraints excluded: chain A residue 1468 GLN Chi-restraints excluded: chain A residue 1475 PHE Chi-restraints excluded: chain A residue 1514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 131 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 123 optimal weight: 0.0030 chunk 132 optimal weight: 3.9990 chunk 8 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.4748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1468 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.178003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135066 restraints weight = 13644.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136530 restraints weight = 8640.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137645 restraints weight = 6347.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.138190 restraints weight = 5234.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.138611 restraints weight = 4337.540| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10883 Z= 0.125 Angle : 0.598 12.851 14773 Z= 0.291 Chirality : 0.041 0.166 1720 Planarity : 0.004 0.046 1831 Dihedral : 5.425 57.844 1478 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.75 % Allowed : 22.91 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.36 (0.24), residues: 1318 helix: 1.74 (0.18), residues: 883 sheet: -0.33 (0.54), residues: 94 loop : -0.92 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 655 TYR 0.020 0.001 TYR A 518 PHE 0.014 0.001 PHE A1154 TRP 0.024 0.001 TRP A 82 HIS 0.006 0.001 HIS A1363 Details of bonding type rmsd covalent geometry : bond 0.00278 (10883) covalent geometry : angle 0.59775 (14773) hydrogen bonds : bond 0.03984 ( 659) hydrogen bonds : angle 4.12443 ( 1953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1579.79 seconds wall clock time: 28 minutes 11.26 seconds (1691.26 seconds total)