Starting phenix.real_space_refine on Thu Jul 2 19:09:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y1j_33563/07_2026/7y1j_33563.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1j_33563/07_2026/7y1j_33563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y1j_33563/07_2026/7y1j_33563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1j_33563/07_2026/7y1j_33563.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y1j_33563/07_2026/7y1j_33563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1j_33563/07_2026/7y1j_33563.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7y1j_33563/07_2026/7y1j_33563.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y1j_33563/07_2026/7y1j_33563.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.138 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 6129 2.51 5 N 1573 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9487 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1204, 9390 Classifications: {'peptide': 1204} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 35, 'TRANS': 1168} Chain breaks: 6 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 122 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 61 Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 97 Unusual residues: {' MG': 2, 'ATP': 2, 'BJX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 1.51, per 1000 atoms: 0.16 Number of scatterers: 9487 At special positions: 0 Unit cell: (70.5324, 102.939, 133.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 6 15.00 Mg 2 11.99 O 1726 8.00 N 1573 7.00 C 6129 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: 0.72 Conformation dependent library (CDL) restraints added in 261.8 milliseconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 5 sheets defined 72.8% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 231 through 241 removed outlier: 3.525A pdb=" N ALA A 238 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N HIS A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG A 240 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 274 removed outlier: 3.521A pdb=" N LYS A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 294 through 312 removed outlier: 3.528A pdb=" N PHE A 312 " --> pdb=" O ASP A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 343 through 346 Processing helix chain 'A' and resid 347 through 395 Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 416 through 450 Proline residue: A 429 - end of helix removed outlier: 3.993A pdb=" N TRP A 432 " --> pdb=" O CYS A 428 " (cutoff:3.500A) Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 451 through 462 removed outlier: 3.929A pdb=" N VAL A 455 " --> pdb=" O SER A 451 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 497 removed outlier: 3.575A pdb=" N ILE A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 507 through 558 removed outlier: 3.653A pdb=" N THR A 518 " --> pdb=" O SER A 514 " (cutoff:3.500A) Proline residue: A 544 - end of helix Processing helix chain 'A' and resid 564 through 607 removed outlier: 4.243A pdb=" N THR A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix removed outlier: 4.677A pdb=" N SER A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 761 through 768 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 786 through 792 removed outlier: 3.730A pdb=" N LEU A 792 " --> pdb=" O PRO A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 799 removed outlier: 3.720A pdb=" N GLN A 798 " --> pdb=" O PHE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 824 removed outlier: 3.544A pdb=" N GLN A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 850 Processing helix chain 'A' and resid 853 through 858 removed outlier: 3.535A pdb=" N ASP A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 875 removed outlier: 3.927A pdb=" N THR A 873 " --> pdb=" O GLN A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 899 through 921 removed outlier: 4.070A pdb=" N LYS A 919 " --> pdb=" O GLN A 915 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 937 removed outlier: 3.535A pdb=" N LEU A 928 " --> pdb=" O ASP A 924 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET A 937 " --> pdb=" O LEU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 971 removed outlier: 3.508A pdb=" N THR A 971 " --> pdb=" O MET A 967 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 967 through 971' Processing helix chain 'A' and resid 974 through 984 Processing helix chain 'A' and resid 986 through 1016 Processing helix chain 'A' and resid 1028 through 1074 removed outlier: 3.604A pdb=" N GLU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A1070 " --> pdb=" O HIS A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 3.813A pdb=" N PHE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1102 removed outlier: 3.584A pdb=" N ILE A1088 " --> pdb=" O PRO A1084 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP A1095 " --> pdb=" O ARG A1091 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR A1096 " --> pdb=" O PHE A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1128 Processing helix chain 'A' and resid 1130 through 1176 removed outlier: 3.835A pdb=" N ALA A1134 " --> pdb=" O VAL A1130 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A1136 " --> pdb=" O LEU A1132 " (cutoff:3.500A) Proline residue: A1137 - end of helix removed outlier: 3.640A pdb=" N PHE A1149 " --> pdb=" O ILE A1145 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A1154 " --> pdb=" O ARG A1150 " (cutoff:3.500A) Proline residue: A1166 - end of helix Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1186 through 1237 Processing helix chain 'A' and resid 1240 through 1283 removed outlier: 3.885A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ASN A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A1257 " --> pdb=" O THR A1253 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1356 removed outlier: 3.659A pdb=" N PHE A1356 " --> pdb=" O SER A1352 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1384 removed outlier: 3.511A pdb=" N ARG A1384 " --> pdb=" O THR A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1404 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1432 through 1435 removed outlier: 3.628A pdb=" N ASP A1435 " --> pdb=" O GLY A1432 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1432 through 1435' Processing helix chain 'A' and resid 1446 through 1462 removed outlier: 3.609A pdb=" N LYS A1462 " --> pdb=" O ALA A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1491 Processing helix chain 'A' and resid 1502 through 1507 removed outlier: 3.541A pdb=" N MET A1507 " --> pdb=" O SER A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1532 removed outlier: 3.593A pdb=" N HIS A1532 " --> pdb=" O ASN A1528 " (cutoff:3.500A) Processing helix chain 'A' and resid 1535 through 1542 Processing sheet with id=AA1, first strand: chain 'A' and resid 682 through 692 removed outlier: 5.085A pdb=" N SER A 685 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N PHE A 675 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE A 689 " --> pdb=" O THR A 671 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N THR A 671 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE A 691 " --> pdb=" O LYS A 669 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LYS A 669 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY A 673 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLU A 722 " --> pdb=" O GLY A 673 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N PHE A 675 " --> pdb=" O THR A 720 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR A 720 " --> pdb=" O PHE A 675 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 748 through 751 removed outlier: 6.513A pdb=" N VAL A 829 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL A 865 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU A 831 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR A 697 " --> pdb=" O LEU A 864 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU A 696 " --> pdb=" O TRP A 877 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE A 879 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N MET A 698 " --> pdb=" O ILE A 879 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N MET A 881 " --> pdb=" O MET A 698 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL A 700 " --> pdb=" O MET A 881 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 888 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1325 through 1332 removed outlier: 6.734A pdb=" N LYS A1326 " --> pdb=" O CYS A1314 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS A1314 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL A1328 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A1313 " --> pdb=" O ASP A1363 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASP A1363 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL A1315 " --> pdb=" O ILE A1361 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N ILE A1361 " --> pdb=" O VAL A1315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1386 through 1388 removed outlier: 6.618A pdb=" N SER A1386 " --> pdb=" O ILE A1467 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASP A1469 " --> pdb=" O SER A1386 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE A1388 " --> pdb=" O ASP A1469 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU A1466 " --> pdb=" O VAL A1497 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE A1499 " --> pdb=" O LEU A1466 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N MET A1468 " --> pdb=" O ILE A1499 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A1338 " --> pdb=" O THR A1498 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU A1522 " --> pdb=" O VAL A1514 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER A1516 " --> pdb=" O LEU A1520 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU A1520 " --> pdb=" O SER A1516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1397 through 1398 648 hydrogen bonds defined for protein. 1908 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: 1.53 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1499 1.31 - 1.43: 2484 1.43 - 1.56: 5599 1.56 - 1.68: 10 1.68 - 1.81: 83 Bond restraints: 9675 Sorted by residual: bond pdb=" C16 BJX A1605 " pdb=" N1 BJX A1605 " ideal model delta sigma weight residual 1.344 1.446 -0.102 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C21 BJX A1605 " pdb=" O1 BJX A1605 " ideal model delta sigma weight residual 1.347 1.397 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" O BJX A1605 " pdb=" C16 BJX A1605 " ideal model delta sigma weight residual 1.221 1.181 0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" N BJX A1605 " pdb=" C6 BJX A1605 " ideal model delta sigma weight residual 1.412 1.450 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" C17 BJX A1605 " pdb=" C18 BJX A1605 " ideal model delta sigma weight residual 1.498 1.523 -0.025 2.00e-02 2.50e+03 1.62e+00 ... (remaining 9670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 12877 1.39 - 2.77: 203 2.77 - 4.16: 45 4.16 - 5.55: 16 5.55 - 6.93: 5 Bond angle restraints: 13146 Sorted by residual: angle pdb=" N GLY A1177 " pdb=" CA GLY A1177 " pdb=" C GLY A1177 " ideal model delta sigma weight residual 115.63 110.45 5.18 1.49e+00 4.50e-01 1.21e+01 angle pdb=" CA GLY A1177 " pdb=" C GLY A1177 " pdb=" N LEU A1178 " ideal model delta sigma weight residual 118.64 115.13 3.51 1.24e+00 6.50e-01 8.01e+00 angle pdb=" CA GLY A1177 " pdb=" C GLY A1177 " pdb=" O GLY A1177 " ideal model delta sigma weight residual 118.95 121.53 -2.58 1.00e+00 1.00e+00 6.65e+00 angle pdb=" O2 BJX A1605 " pdb=" C24 BJX A1605 " pdb=" O3 BJX A1605 " ideal model delta sigma weight residual 126.98 120.05 6.93 3.00e+00 1.11e-01 5.34e+00 angle pdb=" C1 BJX A1605 " pdb=" N BJX A1605 " pdb=" C6 BJX A1605 " ideal model delta sigma weight residual 117.04 110.14 6.90 3.00e+00 1.11e-01 5.29e+00 ... (remaining 13141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.97: 5653 31.97 - 63.95: 64 63.95 - 95.92: 3 95.92 - 127.89: 0 127.89 - 159.86: 1 Dihedral angle restraints: 5721 sinusoidal: 2217 harmonic: 3504 Sorted by residual: dihedral pdb=" O BJX A1605 " pdb=" C16 BJX A1605 " pdb=" C17 BJX A1605 " pdb=" C18 BJX A1605 " ideal model delta sinusoidal sigma weight residual 10.31 -149.55 159.86 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" CA LEU A 448 " pdb=" C LEU A 448 " pdb=" N LEU A 449 " pdb=" CA LEU A 449 " ideal model delta harmonic sigma weight residual -180.00 -164.06 -15.94 0 5.00e+00 4.00e-02 1.02e+01 dihedral pdb=" N GLN A 870 " pdb=" CA GLN A 870 " pdb=" CB GLN A 870 " pdb=" CG GLN A 870 " ideal model delta sinusoidal sigma weight residual 60.00 0.10 59.90 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 5718 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1133 0.037 - 0.074: 312 0.074 - 0.111: 94 0.111 - 0.148: 19 0.148 - 0.185: 2 Chirality restraints: 1560 Sorted by residual: chirality pdb=" C5 BJX A1605 " pdb=" C7 BJX A1605 " pdb=" C8 BJX A1605 " pdb=" N1 BJX A1605 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA CYS A 428 " pdb=" N CYS A 428 " pdb=" C CYS A 428 " pdb=" CB CYS A 428 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA ILE A1361 " pdb=" N ILE A1361 " pdb=" C ILE A1361 " pdb=" CB ILE A1361 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 ... (remaining 1557 not shown) Planarity restraints: 1613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A1103 " 0.023 5.00e-02 4.00e+02 3.44e-02 1.89e+00 pdb=" N PRO A1104 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A1104 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1104 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A1526 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO A1527 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A1527 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A1527 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A1143 " 0.007 2.00e-02 2.50e+03 1.36e-02 1.84e+00 pdb=" C TYR A1143 " -0.023 2.00e-02 2.50e+03 pdb=" O TYR A1143 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE A1144 " 0.008 2.00e-02 2.50e+03 ... (remaining 1610 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 62 2.56 - 3.14: 7773 3.14 - 3.73: 15412 3.73 - 4.31: 21524 4.31 - 4.90: 36631 Nonbonded interactions: 81402 Sorted by model distance: nonbonded pdb=" OG SER A1349 " pdb="MG MG A1603 " model vdw 1.971 2.170 nonbonded pdb=" OG SER A 708 " pdb="MG MG A1604 " model vdw 1.972 2.170 nonbonded pdb=" OE1 GLN A 753 " pdb="MG MG A1604 " model vdw 1.978 2.170 nonbonded pdb=" O1G ATP A1601 " pdb="MG MG A1604 " model vdw 2.166 2.170 nonbonded pdb=" O2B ATP A1601 " pdb="MG MG A1604 " model vdw 2.168 2.170 ... (remaining 81397 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 8.040 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.004 0.102 9675 Z= 0.171 Angle : 0.509 6.932 13146 Z= 0.273 Chirality : 0.039 0.185 1560 Planarity : 0.004 0.034 1613 Dihedral : 10.871 159.862 3451 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.69 % Allowed : 3.35 % Favored : 95.96 % 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: 2.20 (0.24), residues: 1190 helix: 2.04 (0.18), residues: 808 sheet: 0.57 (0.65), residues: 65 loop : 0.23 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1457 TYR 0.013 0.001 TYR A 228 PHE 0.013 0.001 PHE A 569 TRP 0.015 0.001 TRP A1214 HIS 0.005 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 9675) covalent geometry : angle 0.50918 / 0.27 (13146) hydrogen bonds : bond 0.10953 / 7.07 ( 648) hydrogen bonds : angle 5.17416 / 3.88 ( 1908) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 193 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 225 LYS cc_start: 0.7879 (mttm) cc_final: 0.7640 (mmtt) REVERT: A 235 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7990 (mp) REVERT: A 375 GLU cc_start: 0.7437 (tt0) cc_final: 0.7150 (tt0) REVERT: A 472 THR cc_start: 0.8678 (m) cc_final: 0.8477 (p) REVERT: A 514 SER cc_start: 0.8568 (t) cc_final: 0.8222 (p) REVERT: A 525 SER cc_start: 0.8045 (t) cc_final: 0.7718 (m) REVERT: A 527 LYS cc_start: 0.7871 (ttpt) cc_final: 0.7371 (tttt) REVERT: A 607 LEU cc_start: 0.8151 (mp) cc_final: 0.7497 (pp) REVERT: A 782 ASP cc_start: 0.7396 (m-30) cc_final: 0.7102 (m-30) REVERT: A 797 ASP cc_start: 0.8117 (m-30) cc_final: 0.7755 (m-30) REVERT: A 853 LYS cc_start: 0.8435 (tttt) cc_final: 0.7970 (tttm) REVERT: A 976 LYS cc_start: 0.8079 (mttt) cc_final: 0.7622 (mmpt) REVERT: A 1004 ILE cc_start: 0.8367 (mt) cc_final: 0.8162 (mm) REVERT: A 1055 TRP cc_start: 0.7288 (t60) cc_final: 0.6644 (t-100) REVERT: A 1100 ASP cc_start: 0.7924 (m-30) cc_final: 0.7665 (m-30) REVERT: A 1185 ARG cc_start: 0.7894 (mtp85) cc_final: 0.7587 (mtt-85) REVERT: A 1282 LEU cc_start: 0.7993 (mt) cc_final: 0.7774 (mt) REVERT: A 1307 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7039 (mt-10) REVERT: A 1312 ASP cc_start: 0.7486 (t70) cc_final: 0.6581 (t70) REVERT: A 1360 ASP cc_start: 0.7650 (t0) cc_final: 0.7113 (m-30) REVERT: A 1422 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8125 (mm-40) REVERT: A 1468 MET cc_start: 0.8954 (mtm) cc_final: 0.8719 (mtp) outliers start: 7 outliers final: 4 residues processed: 199 average time/residue: 0.4486 time to fit residues: 96.0606 Evaluate side-chains 148 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 1281 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 221 ASN A 271 GLN A 420 GLN A 478 GLN A 540 ASN A1066 HIS A1319 ASN A1425 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.140565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.107682 restraints weight = 10402.608| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.54 r_work: 0.2946 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9675 Z= 0.140 Angle : 0.485 6.544 13146 Z= 0.252 Chirality : 0.039 0.166 1560 Planarity : 0.004 0.043 1613 Dihedral : 7.480 161.765 1310 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.25 % Allowed : 8.97 % Favored : 87.78 % 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: 2.57 (0.24), residues: 1190 helix: 2.32 (0.18), residues: 814 sheet: 0.44 (0.65), residues: 65 loop : 0.38 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1413 TYR 0.013 0.001 TYR A 228 PHE 0.013 0.001 PHE A 569 TRP 0.014 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 ( 9675) covalent geometry : angle 0.48496 / 0.25 (13146) hydrogen bonds : bond 0.05008 / 3.11 ( 648) hydrogen bonds : angle 4.13511 / 3.10 ( 1908) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 151 time to evaluate : 0.299 Fit side-chains REVERT: A 225 LYS cc_start: 0.8621 (mttm) cc_final: 0.8123 (mmtt) REVERT: A 235 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8432 (mp) REVERT: A 241 LYS cc_start: 0.8207 (pttm) cc_final: 0.7355 (tttp) REVERT: A 375 GLU cc_start: 0.8276 (tt0) cc_final: 0.8067 (tt0) REVERT: A 514 SER cc_start: 0.8970 (t) cc_final: 0.8626 (p) REVERT: A 525 SER cc_start: 0.8607 (t) cc_final: 0.8208 (m) REVERT: A 527 LYS cc_start: 0.8322 (ttpt) cc_final: 0.7802 (tttt) REVERT: A 672 ASN cc_start: 0.8570 (t0) cc_final: 0.7927 (t160) REVERT: A 782 ASP cc_start: 0.8022 (m-30) cc_final: 0.7765 (m-30) REVERT: A 797 ASP cc_start: 0.8563 (m-30) cc_final: 0.8289 (m-30) REVERT: A 833 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7981 (m-30) REVERT: A 853 LYS cc_start: 0.8862 (tttt) cc_final: 0.8268 (ttpt) REVERT: A 907 LYS cc_start: 0.8631 (mtpt) cc_final: 0.8384 (ttpt) REVERT: A 973 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7595 (tpt) REVERT: A 976 LYS cc_start: 0.8404 (mttt) cc_final: 0.7618 (mptt) REVERT: A 1055 TRP cc_start: 0.7949 (t60) cc_final: 0.7195 (t-100) REVERT: A 1100 ASP cc_start: 0.8316 (m-30) cc_final: 0.8053 (m-30) REVERT: A 1169 CYS cc_start: 0.8603 (m) cc_final: 0.8239 (t) REVERT: A 1185 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8196 (mtt-85) REVERT: A 1277 LYS cc_start: 0.7966 (mttm) cc_final: 0.7577 (mttt) REVERT: A 1282 LEU cc_start: 0.7778 (mt) cc_final: 0.7573 (mt) REVERT: A 1307 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 1312 ASP cc_start: 0.7876 (t70) cc_final: 0.6952 (t70) REVERT: A 1360 ASP cc_start: 0.7817 (t0) cc_final: 0.7286 (m-30) REVERT: A 1422 GLN cc_start: 0.8574 (mm-40) cc_final: 0.8341 (mm-40) REVERT: A 1463 SER cc_start: 0.7984 (t) cc_final: 0.7739 (p) outliers start: 33 outliers final: 8 residues processed: 171 average time/residue: 0.4647 time to fit residues: 85.6129 Evaluate side-chains 151 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1318 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 86 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN A 540 ASN A1319 ASN A1402 ASN A1425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.137716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.106537 restraints weight = 10320.977| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.53 r_work: 0.2895 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9675 Z= 0.182 Angle : 0.512 6.584 13146 Z= 0.264 Chirality : 0.041 0.170 1560 Planarity : 0.004 0.043 1613 Dihedral : 7.543 161.386 1310 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.05 % Allowed : 11.43 % Favored : 85.52 % 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: 2.42 (0.24), residues: 1190 helix: 2.22 (0.18), residues: 816 sheet: 0.32 (0.64), residues: 65 loop : 0.28 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1494 TYR 0.019 0.001 TYR A 532 PHE 0.021 0.002 PHE A 552 TRP 0.015 0.001 TRP A1214 HIS 0.006 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 9675) covalent geometry : angle 0.51243 / 0.26 (13146) hydrogen bonds : bond 0.05208 / 3.22 ( 648) hydrogen bonds : angle 4.10727 / 3.09 ( 1908) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.379 Fit side-chains REVERT: A 225 LYS cc_start: 0.8602 (mttm) cc_final: 0.8135 (mmtt) REVERT: A 235 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8463 (mp) REVERT: A 241 LYS cc_start: 0.8162 (pttm) cc_final: 0.7322 (tttm) REVERT: A 514 SER cc_start: 0.8973 (t) cc_final: 0.8618 (p) REVERT: A 525 SER cc_start: 0.8643 (t) cc_final: 0.8208 (m) REVERT: A 527 LYS cc_start: 0.8335 (ttpt) cc_final: 0.7818 (tttt) REVERT: A 672 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8137 (t0) REVERT: A 782 ASP cc_start: 0.7965 (m-30) cc_final: 0.7700 (m-30) REVERT: A 797 ASP cc_start: 0.8620 (m-30) cc_final: 0.8352 (m-30) REVERT: A 833 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: A 853 LYS cc_start: 0.8911 (tttt) cc_final: 0.8324 (ttpt) REVERT: A 907 LYS cc_start: 0.8657 (mtpt) cc_final: 0.8376 (ttpt) REVERT: A 973 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7612 (tpt) REVERT: A 976 LYS cc_start: 0.8484 (mttt) cc_final: 0.7688 (mptt) REVERT: A 1055 TRP cc_start: 0.7956 (t60) cc_final: 0.7189 (t-100) REVERT: A 1100 ASP cc_start: 0.8401 (m-30) cc_final: 0.8128 (m-30) REVERT: A 1169 CYS cc_start: 0.8612 (m) cc_final: 0.8269 (t) REVERT: A 1185 ARG cc_start: 0.8590 (mtp85) cc_final: 0.8224 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7683 (mt-10) REVERT: A 1360 ASP cc_start: 0.7967 (t0) cc_final: 0.7327 (m-30) REVERT: A 1422 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8323 (mm-40) REVERT: A 1468 MET cc_start: 0.9159 (mtm) cc_final: 0.8945 (mtp) REVERT: A 1480 GLU cc_start: 0.7057 (tt0) cc_final: 0.6056 (mt-10) outliers start: 31 outliers final: 14 residues processed: 155 average time/residue: 0.4970 time to fit residues: 82.6309 Evaluate side-chains 155 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 898 LYS Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1318 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 62 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN A 540 ASN A1157 GLN A1319 ASN A1425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.140015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.109709 restraints weight = 10458.838| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.49 r_work: 0.2920 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9675 Z= 0.125 Angle : 0.457 6.608 13146 Z= 0.238 Chirality : 0.038 0.162 1560 Planarity : 0.003 0.036 1613 Dihedral : 7.421 158.333 1310 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.15 % Allowed : 11.63 % Favored : 85.22 % 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: 2.60 (0.24), residues: 1190 helix: 2.39 (0.18), residues: 817 sheet: 0.25 (0.64), residues: 65 loop : 0.27 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1494 TYR 0.013 0.001 TYR A 532 PHE 0.018 0.001 PHE A 552 TRP 0.015 0.001 TRP A1214 HIS 0.003 0.000 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 9675) covalent geometry : angle 0.45717 / 0.24 (13146) hydrogen bonds : bond 0.04634 / 2.86 ( 648) hydrogen bonds : angle 3.93938 / 2.96 ( 1908) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.233 Fit side-chains REVERT: A 225 LYS cc_start: 0.8565 (mttm) cc_final: 0.8124 (mmtt) REVERT: A 235 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8487 (mp) REVERT: A 241 LYS cc_start: 0.8108 (pttm) cc_final: 0.7331 (tttm) REVERT: A 514 SER cc_start: 0.9017 (t) cc_final: 0.8741 (p) REVERT: A 525 SER cc_start: 0.8664 (t) cc_final: 0.8235 (m) REVERT: A 527 LYS cc_start: 0.8325 (ttpt) cc_final: 0.7823 (tttt) REVERT: A 764 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7675 (mt-10) REVERT: A 778 LYS cc_start: 0.8468 (tptt) cc_final: 0.8159 (tmtm) REVERT: A 782 ASP cc_start: 0.8061 (m-30) cc_final: 0.7792 (m-30) REVERT: A 797 ASP cc_start: 0.8618 (m-30) cc_final: 0.8369 (m-30) REVERT: A 853 LYS cc_start: 0.8956 (tttt) cc_final: 0.8496 (ttpt) REVERT: A 896 GLN cc_start: 0.7889 (tt0) cc_final: 0.7434 (tt0) REVERT: A 907 LYS cc_start: 0.8658 (mtpt) cc_final: 0.8376 (ttpt) REVERT: A 973 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7586 (tpt) REVERT: A 976 LYS cc_start: 0.8512 (mttt) cc_final: 0.7734 (mptt) REVERT: A 1055 TRP cc_start: 0.7932 (t60) cc_final: 0.7188 (t-100) REVERT: A 1169 CYS cc_start: 0.8487 (m) cc_final: 0.8217 (t) REVERT: A 1185 ARG cc_start: 0.8537 (mtp85) cc_final: 0.8204 (mtt-85) REVERT: A 1277 LYS cc_start: 0.8033 (mttm) cc_final: 0.7736 (mttt) REVERT: A 1307 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7640 (mt-10) REVERT: A 1360 ASP cc_start: 0.7910 (t0) cc_final: 0.7345 (m-30) REVERT: A 1420 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7759 (mt) REVERT: A 1422 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8326 (mm-40) REVERT: A 1463 SER cc_start: 0.8127 (t) cc_final: 0.7708 (p) REVERT: A 1468 MET cc_start: 0.9112 (mtm) cc_final: 0.8911 (mtp) outliers start: 32 outliers final: 13 residues processed: 164 average time/residue: 0.4835 time to fit residues: 85.0309 Evaluate side-chains 156 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 806 ILE Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1318 GLU Chi-restraints excluded: chain A residue 1420 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 61 optimal weight: 0.0670 chunk 85 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN A1157 GLN A1279 ASN A1319 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.140113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.109769 restraints weight = 10398.974| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.47 r_work: 0.2912 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9675 Z= 0.151 Angle : 0.480 6.606 13146 Z= 0.249 Chirality : 0.039 0.166 1560 Planarity : 0.004 0.042 1613 Dihedral : 7.465 160.059 1310 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.96 % Allowed : 12.51 % Favored : 84.53 % 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: 2.52 (0.24), residues: 1190 helix: 2.32 (0.18), residues: 818 sheet: 0.24 (0.64), residues: 65 loop : 0.29 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1494 TYR 0.018 0.001 TYR A 532 PHE 0.017 0.001 PHE A 552 TRP 0.014 0.001 TRP A1214 HIS 0.005 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 9675) covalent geometry : angle 0.48004 / 0.25 (13146) hydrogen bonds : bond 0.04840 / 2.99 ( 648) hydrogen bonds : angle 3.96743 / 2.98 ( 1908) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 0.301 Fit side-chains REVERT: A 225 LYS cc_start: 0.8600 (mttm) cc_final: 0.8191 (mmtt) REVERT: A 235 ILE cc_start: 0.9106 (OUTLIER) cc_final: 0.8513 (mp) REVERT: A 241 LYS cc_start: 0.8160 (pttm) cc_final: 0.7429 (tttm) REVERT: A 514 SER cc_start: 0.9014 (t) cc_final: 0.8683 (p) REVERT: A 525 SER cc_start: 0.8706 (t) cc_final: 0.8272 (m) REVERT: A 527 LYS cc_start: 0.8367 (ttpt) cc_final: 0.7889 (tttt) REVERT: A 672 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8203 (t0) REVERT: A 764 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7711 (mt-10) REVERT: A 778 LYS cc_start: 0.8509 (tptt) cc_final: 0.8214 (tmtm) REVERT: A 782 ASP cc_start: 0.8042 (m-30) cc_final: 0.7818 (m-30) REVERT: A 797 ASP cc_start: 0.8650 (m-30) cc_final: 0.8393 (m-30) REVERT: A 833 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: A 853 LYS cc_start: 0.9005 (tttt) cc_final: 0.8550 (ttpt) REVERT: A 896 GLN cc_start: 0.7979 (tt0) cc_final: 0.7548 (tt0) REVERT: A 907 LYS cc_start: 0.8661 (mtpt) cc_final: 0.8386 (ttpt) REVERT: A 973 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7691 (tpt) REVERT: A 976 LYS cc_start: 0.8551 (mttt) cc_final: 0.7788 (mptt) REVERT: A 1055 TRP cc_start: 0.7994 (t60) cc_final: 0.7260 (t-100) REVERT: A 1169 CYS cc_start: 0.8531 (m) cc_final: 0.8272 (t) REVERT: A 1185 ARG cc_start: 0.8631 (mtp85) cc_final: 0.8305 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7716 (mt-10) REVERT: A 1360 ASP cc_start: 0.8013 (t0) cc_final: 0.7491 (m-30) REVERT: A 1425 ASN cc_start: 0.8071 (m110) cc_final: 0.7451 (p0) outliers start: 30 outliers final: 14 residues processed: 153 average time/residue: 0.4753 time to fit residues: 78.0584 Evaluate side-chains 154 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1318 GLU Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1476 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN A1319 ASN A1422 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.140090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.109902 restraints weight = 10319.848| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.48 r_work: 0.2948 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9675 Z= 0.140 Angle : 0.473 6.627 13146 Z= 0.245 Chirality : 0.039 0.163 1560 Planarity : 0.004 0.044 1613 Dihedral : 7.447 159.693 1310 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.66 % Allowed : 13.00 % Favored : 84.33 % 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: 2.57 (0.24), residues: 1190 helix: 2.36 (0.18), residues: 818 sheet: 0.49 (0.66), residues: 59 loop : 0.24 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1494 TYR 0.018 0.001 TYR A 532 PHE 0.018 0.001 PHE A1445 TRP 0.014 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 9675) covalent geometry : angle 0.47311 / 0.25 (13146) hydrogen bonds : bond 0.04723 / 2.92 ( 648) hydrogen bonds : angle 3.91719 / 2.94 ( 1908) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.333 Fit side-chains REVERT: A 225 LYS cc_start: 0.8577 (mttm) cc_final: 0.8167 (mmtt) REVERT: A 235 ILE cc_start: 0.9097 (OUTLIER) cc_final: 0.8499 (mp) REVERT: A 241 LYS cc_start: 0.8117 (pttm) cc_final: 0.7327 (tttm) REVERT: A 514 SER cc_start: 0.9052 (t) cc_final: 0.8739 (p) REVERT: A 525 SER cc_start: 0.8687 (t) cc_final: 0.8255 (m) REVERT: A 527 LYS cc_start: 0.8351 (ttpt) cc_final: 0.7854 (tttt) REVERT: A 764 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: A 778 LYS cc_start: 0.8488 (tptt) cc_final: 0.8190 (tmtm) REVERT: A 782 ASP cc_start: 0.8018 (m-30) cc_final: 0.7790 (m-30) REVERT: A 797 ASP cc_start: 0.8641 (m-30) cc_final: 0.8391 (m-30) REVERT: A 833 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8045 (m-30) REVERT: A 853 LYS cc_start: 0.9002 (tttt) cc_final: 0.8541 (ttpt) REVERT: A 896 GLN cc_start: 0.8033 (tt0) cc_final: 0.7580 (tt0) REVERT: A 907 LYS cc_start: 0.8699 (mtpt) cc_final: 0.8442 (ttpt) REVERT: A 973 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7683 (tpt) REVERT: A 976 LYS cc_start: 0.8544 (mttt) cc_final: 0.7768 (mptt) REVERT: A 1055 TRP cc_start: 0.7969 (t60) cc_final: 0.7220 (t-100) REVERT: A 1169 CYS cc_start: 0.8503 (m) cc_final: 0.8249 (t) REVERT: A 1185 ARG cc_start: 0.8580 (mtp85) cc_final: 0.8238 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 1360 ASP cc_start: 0.7992 (t0) cc_final: 0.7549 (m-30) REVERT: A 1420 ILE cc_start: 0.8043 (mt) cc_final: 0.7773 (mt) REVERT: A 1425 ASN cc_start: 0.8052 (m110) cc_final: 0.7496 (p0) outliers start: 27 outliers final: 12 residues processed: 154 average time/residue: 0.4672 time to fit residues: 77.4799 Evaluate side-chains 154 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 870 GLN Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1318 GLU Chi-restraints excluded: chain A residue 1460 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 0.0170 chunk 68 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN A1319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.142576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.109595 restraints weight = 10254.276| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.58 r_work: 0.2933 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9675 Z= 0.124 Angle : 0.459 6.634 13146 Z= 0.239 Chirality : 0.038 0.161 1560 Planarity : 0.003 0.043 1613 Dihedral : 7.348 158.609 1309 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.27 % Allowed : 13.99 % Favored : 83.74 % 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: 2.71 (0.24), residues: 1190 helix: 2.46 (0.18), residues: 818 sheet: 0.62 (0.66), residues: 59 loop : 0.29 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1494 TYR 0.018 0.001 TYR A 532 PHE 0.019 0.001 PHE A1445 TRP 0.014 0.001 TRP A1214 HIS 0.003 0.000 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 ( 9675) covalent geometry : angle 0.45888 / 0.24 (13146) hydrogen bonds : bond 0.04526 / 2.80 ( 648) hydrogen bonds : angle 3.84469 / 2.89 ( 1908) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.230 Fit side-chains REVERT: A 225 LYS cc_start: 0.8482 (mttm) cc_final: 0.8052 (mmtt) REVERT: A 235 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8464 (mp) REVERT: A 241 LYS cc_start: 0.7960 (pttm) cc_final: 0.7222 (tttm) REVERT: A 514 SER cc_start: 0.8986 (t) cc_final: 0.8684 (p) REVERT: A 525 SER cc_start: 0.8687 (t) cc_final: 0.8235 (m) REVERT: A 527 LYS cc_start: 0.8299 (ttpt) cc_final: 0.7766 (tttt) REVERT: A 764 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: A 778 LYS cc_start: 0.8427 (tptt) cc_final: 0.8074 (tmtm) REVERT: A 782 ASP cc_start: 0.7964 (m-30) cc_final: 0.7704 (m-30) REVERT: A 789 ASP cc_start: 0.8459 (p0) cc_final: 0.8182 (m-30) REVERT: A 797 ASP cc_start: 0.8606 (m-30) cc_final: 0.8355 (m-30) REVERT: A 827 ASN cc_start: 0.8297 (t0) cc_final: 0.7827 (t0) REVERT: A 833 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: A 853 LYS cc_start: 0.8929 (tttt) cc_final: 0.8430 (ttpt) REVERT: A 907 LYS cc_start: 0.8686 (mtpt) cc_final: 0.8449 (ttpt) REVERT: A 973 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7500 (tpt) REVERT: A 976 LYS cc_start: 0.8448 (mttt) cc_final: 0.7653 (mptt) REVERT: A 1055 TRP cc_start: 0.7861 (t60) cc_final: 0.7080 (t-100) REVERT: A 1169 CYS cc_start: 0.8363 (m) cc_final: 0.8131 (t) REVERT: A 1185 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8142 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7548 (mt-10) REVERT: A 1360 ASP cc_start: 0.7942 (t0) cc_final: 0.7353 (m-30) REVERT: A 1420 ILE cc_start: 0.7903 (mt) cc_final: 0.7618 (mt) REVERT: A 1425 ASN cc_start: 0.7974 (m110) cc_final: 0.7439 (p0) outliers start: 23 outliers final: 11 residues processed: 155 average time/residue: 0.4631 time to fit residues: 77.0663 Evaluate side-chains 151 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 609 ASP Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1460 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 10 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 115 optimal weight: 0.2980 chunk 35 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN A 719 GLN A 896 GLN A1101 GLN A1157 GLN A1319 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.142613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.109815 restraints weight = 10237.620| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.56 r_work: 0.2915 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9675 Z= 0.124 Angle : 0.465 6.646 13146 Z= 0.241 Chirality : 0.038 0.162 1560 Planarity : 0.004 0.054 1613 Dihedral : 7.050 158.418 1306 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.46 % Allowed : 13.79 % Favored : 83.74 % 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: 2.75 (0.24), residues: 1190 helix: 2.47 (0.18), residues: 818 sheet: 0.40 (0.64), residues: 65 loop : 0.42 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1494 TYR 0.020 0.001 TYR A 532 PHE 0.019 0.001 PHE A1445 TRP 0.014 0.001 TRP A1214 HIS 0.004 0.000 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 9675) covalent geometry : angle 0.46452 / 0.24 (13146) hydrogen bonds : bond 0.04512 / 2.80 ( 648) hydrogen bonds : angle 3.84090 / 2.89 ( 1908) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8477 (mttm) cc_final: 0.8058 (mmtt) REVERT: A 235 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8442 (mp) REVERT: A 241 LYS cc_start: 0.8030 (pttm) cc_final: 0.7224 (tttm) REVERT: A 514 SER cc_start: 0.8992 (t) cc_final: 0.8700 (p) REVERT: A 525 SER cc_start: 0.8680 (t) cc_final: 0.8229 (m) REVERT: A 527 LYS cc_start: 0.8300 (ttpt) cc_final: 0.7780 (tttt) REVERT: A 672 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.8056 (t0) REVERT: A 764 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7599 (mt-10) REVERT: A 778 LYS cc_start: 0.8412 (tptt) cc_final: 0.8061 (tmtm) REVERT: A 782 ASP cc_start: 0.7936 (m-30) cc_final: 0.7675 (m-30) REVERT: A 797 ASP cc_start: 0.8596 (m-30) cc_final: 0.8337 (m-30) REVERT: A 827 ASN cc_start: 0.8290 (t0) cc_final: 0.7812 (t0) REVERT: A 833 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7991 (m-30) REVERT: A 853 LYS cc_start: 0.8924 (tttt) cc_final: 0.8421 (ttpt) REVERT: A 893 LYS cc_start: 0.8496 (mptt) cc_final: 0.8124 (mmtm) REVERT: A 896 GLN cc_start: 0.7824 (tt0) cc_final: 0.7518 (tt0) REVERT: A 973 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7470 (tpt) REVERT: A 976 LYS cc_start: 0.8418 (mttt) cc_final: 0.7807 (mmpt) REVERT: A 1055 TRP cc_start: 0.7851 (t60) cc_final: 0.7061 (t-100) REVERT: A 1169 CYS cc_start: 0.8365 (m) cc_final: 0.8132 (t) REVERT: A 1185 ARG cc_start: 0.8477 (mtp85) cc_final: 0.8117 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7530 (mt-10) REVERT: A 1318 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7290 (tp30) REVERT: A 1319 ASN cc_start: 0.7547 (m-40) cc_final: 0.6890 (m110) REVERT: A 1360 ASP cc_start: 0.7924 (t0) cc_final: 0.7477 (m-30) REVERT: A 1420 ILE cc_start: 0.7910 (mt) cc_final: 0.7600 (mt) REVERT: A 1425 ASN cc_start: 0.7924 (m110) cc_final: 0.7433 (p0) REVERT: A 1463 SER cc_start: 0.8124 (t) cc_final: 0.7747 (p) outliers start: 25 outliers final: 11 residues processed: 152 average time/residue: 0.4741 time to fit residues: 77.4800 Evaluate side-chains 152 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1318 GLU Chi-restraints excluded: chain A residue 1460 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.139059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.108752 restraints weight = 10306.472| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.46 r_work: 0.2890 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9675 Z= 0.185 Angle : 0.519 6.629 13146 Z= 0.267 Chirality : 0.040 0.169 1560 Planarity : 0.004 0.047 1613 Dihedral : 7.205 159.630 1306 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.27 % Allowed : 14.19 % Favored : 83.55 % 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: 2.49 (0.24), residues: 1190 helix: 2.25 (0.18), residues: 819 sheet: 0.40 (0.64), residues: 65 loop : 0.36 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1494 TYR 0.031 0.002 TYR A 532 PHE 0.020 0.002 PHE A 569 TRP 0.013 0.001 TRP A1214 HIS 0.006 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 ( 9675) covalent geometry : angle 0.51902 / 0.27 (13146) hydrogen bonds : bond 0.05085 / 3.15 ( 648) hydrogen bonds : angle 4.00472 / 3.01 ( 1908) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8632 (mttm) cc_final: 0.8189 (mmtt) REVERT: A 235 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8451 (mp) REVERT: A 514 SER cc_start: 0.8988 (t) cc_final: 0.8668 (p) REVERT: A 525 SER cc_start: 0.8715 (t) cc_final: 0.8274 (m) REVERT: A 527 LYS cc_start: 0.8387 (ttpt) cc_final: 0.7890 (tttt) REVERT: A 607 LEU cc_start: 0.8275 (mm) cc_final: 0.7626 (pp) REVERT: A 672 ASN cc_start: 0.8669 (OUTLIER) cc_final: 0.8217 (t0) REVERT: A 764 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: A 778 LYS cc_start: 0.8502 (tptt) cc_final: 0.8197 (tmtm) REVERT: A 782 ASP cc_start: 0.7995 (m-30) cc_final: 0.7733 (m-30) REVERT: A 797 ASP cc_start: 0.8622 (m-30) cc_final: 0.8360 (m-30) REVERT: A 827 ASN cc_start: 0.8404 (t0) cc_final: 0.7907 (t0) REVERT: A 833 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.8076 (m-30) REVERT: A 853 LYS cc_start: 0.9012 (tttt) cc_final: 0.8562 (ttpt) REVERT: A 896 GLN cc_start: 0.7821 (tt0) cc_final: 0.7530 (tt0) REVERT: A 973 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7639 (tpt) REVERT: A 976 LYS cc_start: 0.8524 (mttt) cc_final: 0.7915 (mmpt) REVERT: A 1055 TRP cc_start: 0.7980 (t60) cc_final: 0.7238 (t-100) REVERT: A 1169 CYS cc_start: 0.8542 (m) cc_final: 0.8263 (t) REVERT: A 1185 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8268 (mtt-85) REVERT: A 1282 LEU cc_start: 0.7985 (mt) cc_final: 0.7773 (mt) REVERT: A 1307 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7679 (mt-10) REVERT: A 1318 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7318 (tp30) REVERT: A 1319 ASN cc_start: 0.7509 (m-40) cc_final: 0.6894 (m110) REVERT: A 1360 ASP cc_start: 0.8125 (t0) cc_final: 0.7580 (m-30) REVERT: A 1420 ILE cc_start: 0.7977 (mt) cc_final: 0.7661 (mt) REVERT: A 1425 ASN cc_start: 0.7951 (m110) cc_final: 0.7489 (p0) outliers start: 23 outliers final: 11 residues processed: 149 average time/residue: 0.4672 time to fit residues: 74.8890 Evaluate side-chains 148 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 672 ASN Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1318 GLU Chi-restraints excluded: chain A residue 1460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 63 optimal weight: 0.2980 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 113 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.138774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.108414 restraints weight = 10325.363| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.45 r_work: 0.2924 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9675 Z= 0.130 Angle : 0.477 6.670 13146 Z= 0.247 Chirality : 0.039 0.162 1560 Planarity : 0.003 0.042 1613 Dihedral : 7.102 158.329 1306 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.77 % Allowed : 14.98 % Favored : 83.25 % 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: 2.65 (0.24), residues: 1190 helix: 2.39 (0.18), residues: 817 sheet: 0.46 (0.64), residues: 65 loop : 0.38 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1494 TYR 0.021 0.001 TYR A 532 PHE 0.018 0.001 PHE A1445 TRP 0.015 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 9675) covalent geometry : angle 0.47731 / 0.25 (13146) hydrogen bonds : bond 0.04627 / 2.87 ( 648) hydrogen bonds : angle 3.89732 / 2.93 ( 1908) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8593 (mttm) cc_final: 0.8196 (mmtt) REVERT: A 235 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8475 (mp) REVERT: A 514 SER cc_start: 0.9081 (t) cc_final: 0.8766 (p) REVERT: A 525 SER cc_start: 0.8706 (t) cc_final: 0.8250 (m) REVERT: A 527 LYS cc_start: 0.8378 (ttpt) cc_final: 0.7896 (tttt) REVERT: A 607 LEU cc_start: 0.8213 (mm) cc_final: 0.7546 (pp) REVERT: A 764 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7696 (mt-10) REVERT: A 778 LYS cc_start: 0.8526 (tptt) cc_final: 0.8197 (tmtm) REVERT: A 782 ASP cc_start: 0.8024 (m-30) cc_final: 0.7771 (m-30) REVERT: A 797 ASP cc_start: 0.8620 (m-30) cc_final: 0.8369 (m-30) REVERT: A 827 ASN cc_start: 0.8343 (t0) cc_final: 0.7933 (t0) REVERT: A 833 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8054 (m-30) REVERT: A 853 LYS cc_start: 0.9040 (tttt) cc_final: 0.8567 (ttpt) REVERT: A 896 GLN cc_start: 0.7795 (tt0) cc_final: 0.7555 (tt0) REVERT: A 973 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7646 (tpt) REVERT: A 976 LYS cc_start: 0.8529 (mttt) cc_final: 0.7754 (mptt) REVERT: A 987 PHE cc_start: 0.8392 (m-10) cc_final: 0.8144 (m-10) REVERT: A 1055 TRP cc_start: 0.7989 (t60) cc_final: 0.7243 (t-100) REVERT: A 1169 CYS cc_start: 0.8502 (m) cc_final: 0.8267 (t) REVERT: A 1185 ARG cc_start: 0.8552 (mtp85) cc_final: 0.8218 (mtt-85) REVERT: A 1307 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 1318 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7308 (tp30) REVERT: A 1319 ASN cc_start: 0.7576 (m-40) cc_final: 0.7037 (m110) REVERT: A 1360 ASP cc_start: 0.8045 (t0) cc_final: 0.7586 (m-30) REVERT: A 1420 ILE cc_start: 0.7987 (mt) cc_final: 0.7641 (mt) REVERT: A 1425 ASN cc_start: 0.7965 (m110) cc_final: 0.7525 (p0) outliers start: 18 outliers final: 10 residues processed: 144 average time/residue: 0.4493 time to fit residues: 69.5940 Evaluate side-chains 148 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 833 ASP Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1318 GLU Chi-restraints excluded: chain A residue 1460 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 9 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 106 optimal weight: 0.0050 chunk 100 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.142449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.109474 restraints weight = 10179.174| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.57 r_work: 0.2906 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9675 Z= 0.130 Angle : 0.475 6.651 13146 Z= 0.246 Chirality : 0.039 0.162 1560 Planarity : 0.003 0.042 1613 Dihedral : 7.085 158.713 1306 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.67 % Allowed : 15.17 % Favored : 83.15 % 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: 2.71 (0.24), residues: 1190 helix: 2.43 (0.18), residues: 817 sheet: 0.49 (0.64), residues: 65 loop : 0.41 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1494 TYR 0.024 0.001 TYR A 532 PHE 0.018 0.001 PHE A1445 TRP 0.014 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 ( 9675) covalent geometry : angle 0.47503 / 0.25 (13146) hydrogen bonds : bond 0.04584 / 2.84 ( 648) hydrogen bonds : angle 3.87616 / 2.91 ( 1908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2785.44 seconds wall clock time: 48 minutes 16.71 seconds (2896.71 seconds total)