Starting phenix.real_space_refine on Sun Dec 29 04:55:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1j_33563/12_2024/7y1j_33563.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1j_33563/12_2024/7y1j_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7y1j_33563/12_2024/7y1j_33563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1j_33563/12_2024/7y1j_33563.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1j_33563/12_2024/7y1j_33563.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1j_33563/12_2024/7y1j_33563.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.138 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3} 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: 6.29, per 1000 atoms: 0.66 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: 3.34 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.27 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: 4.53 Time building geometry restraints manager: 3.71 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: 5681 31.97 - 63.95: 103 63.95 - 95.92: 8 95.92 - 127.89: 0 127.89 - 159.86: 1 Dihedral angle restraints: 5793 sinusoidal: 2289 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 5790 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: 6.010 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: 0.140 Extract box with map and model: 0.260 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 28.120 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.060 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:16.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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= 0.247 Angle : 0.509 6.932 13146 Z= 0.273 Chirality : 0.039 0.185 1560 Planarity : 0.004 0.034 1613 Dihedral : 12.137 159.862 3523 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.015 0.001 TRP A1214 HIS 0.005 0.001 HIS A1001 PHE 0.013 0.001 PHE A 569 TYR 0.013 0.001 TYR A 228 ARG 0.003 0.000 ARG A1457 *********************** 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 : 1.096 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: 0.7158 (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: 0.8720 (mtp) outliers start: 7 outliers final: 4 residues processed: 199 average time/residue: 1.1997 time to fit residues: 257.2591 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 : 1.119 ------------------------------------------------------------------------------- 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 101 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 ASN A 271 GLN A 420 GLN A 478 GLN A 540 ASN ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1066 HIS A1319 ASN A1425 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1126 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= 0.201 Angle : 0.486 6.582 13146 Z= 0.253 Chirality : 0.039 0.165 1560 Planarity : 0.004 0.042 1613 Dihedral : 10.592 165.451 1382 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.25 % Allowed : 8.87 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.015 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 PHE 0.013 0.001 PHE A 569 TYR 0.013 0.001 TYR A 228 ARG 0.007 0.001 ARG A1413 *********************** 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 186 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.962 Fit side-chains REVERT: A 225 LYS cc_start: 0.8023 (mttm) cc_final: 0.7663 (mmtt) REVERT: A 235 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8060 (mp) REVERT: A 241 LYS cc_start: 0.7928 (pttm) cc_final: 0.7319 (tttp) REVERT: A 375 GLU cc_start: 0.7400 (tt0) cc_final: 0.7153 (tt0) REVERT: A 485 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8403 (p) REVERT: A 514 SER cc_start: 0.8623 (t) cc_final: 0.8206 (p) REVERT: A 525 SER cc_start: 0.8241 (t) cc_final: 0.7848 (m) REVERT: A 527 LYS cc_start: 0.7872 (ttpt) cc_final: 0.7363 (tttt) REVERT: A 672 ASN cc_start: 0.8147 (OUTLIER) cc_final: 0.7551 (t160) REVERT: A 782 ASP cc_start: 0.7355 (m-30) cc_final: 0.7146 (m-30) REVERT: A 797 ASP cc_start: 0.8064 (m-30) cc_final: 0.7770 (m-30) REVERT: A 833 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: A 853 LYS cc_start: 0.8505 (tttt) cc_final: 0.8059 (ttpt) REVERT: A 907 LYS cc_start: 0.8563 (mtpt) cc_final: 0.8340 (ttpt) REVERT: A 973 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7583 (tpt) REVERT: A 976 LYS cc_start: 0.8111 (mttt) cc_final: 0.7436 (mptt) REVERT: A 1055 TRP cc_start: 0.7258 (t60) cc_final: 0.6592 (t-100) REVERT: A 1100 ASP cc_start: 0.8050 (m-30) cc_final: 0.7780 (m-30) REVERT: A 1185 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7494 (mtt-85) REVERT: A 1277 LYS cc_start: 0.7684 (mttm) cc_final: 0.7351 (mttt) REVERT: A 1282 LEU cc_start: 0.7837 (mt) cc_final: 0.7636 (mt) REVERT: A 1307 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7059 (mt-10) REVERT: A 1312 ASP cc_start: 0.7500 (t70) cc_final: 0.6614 (t70) REVERT: A 1360 ASP cc_start: 0.7342 (t0) cc_final: 0.6928 (m-30) REVERT: A 1422 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8217 (mm-40) REVERT: A 1494 ARG cc_start: 0.7776 (mtt-85) cc_final: 0.7562 (mtt90) outliers start: 33 outliers final: 8 residues processed: 172 average time/residue: 1.1701 time to fit residues: 216.7650 Evaluate side-chains 153 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 140 time to evaluate : 1.248 ------------------------------------------------------------------------------- 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 485 SER Chi-restraints excluded: chain A residue 672 ASN 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 60 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A 540 ASN A1319 ASN A1402 ASN A1425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9675 Z= 0.186 Angle : 0.464 6.593 13146 Z= 0.243 Chirality : 0.039 0.164 1560 Planarity : 0.003 0.035 1613 Dihedral : 10.213 164.061 1382 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.76 % Allowed : 11.33 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.24), residues: 1190 helix: 2.39 (0.18), residues: 817 sheet: 0.40 (0.64), residues: 65 loop : 0.27 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1214 HIS 0.004 0.000 HIS A1001 PHE 0.021 0.001 PHE A 552 TYR 0.015 0.001 TYR A 532 ARG 0.004 0.000 ARG A1413 *********************** 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: 28 poor density : 144 time to evaluate : 1.102 Fit side-chains REVERT: A 225 LYS cc_start: 0.8018 (mttm) cc_final: 0.7687 (mmtt) REVERT: A 235 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8131 (mp) REVERT: A 241 LYS cc_start: 0.7788 (pttm) cc_final: 0.7267 (tttm) REVERT: A 485 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8410 (p) REVERT: A 514 SER cc_start: 0.8617 (t) cc_final: 0.8247 (p) REVERT: A 525 SER cc_start: 0.8280 (t) cc_final: 0.7891 (m) REVERT: A 527 LYS cc_start: 0.7886 (ttpt) cc_final: 0.7351 (tttt) REVERT: A 764 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6855 (mt-10) REVERT: A 782 ASP cc_start: 0.7379 (m-30) cc_final: 0.7169 (m-30) REVERT: A 797 ASP cc_start: 0.8067 (m-30) cc_final: 0.7776 (m-30) REVERT: A 833 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7479 (m-30) REVERT: A 853 LYS cc_start: 0.8523 (tttt) cc_final: 0.8080 (ttpt) REVERT: A 907 LYS cc_start: 0.8575 (mtpt) cc_final: 0.8332 (ttpt) REVERT: A 973 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7586 (tpt) REVERT: A 976 LYS cc_start: 0.8149 (mttt) cc_final: 0.7480 (mptt) REVERT: A 1055 TRP cc_start: 0.7241 (t60) cc_final: 0.6568 (t-100) REVERT: A 1185 ARG cc_start: 0.7856 (mtp85) cc_final: 0.7513 (mtt-85) REVERT: A 1277 LYS cc_start: 0.7672 (mttm) cc_final: 0.7416 (mttt) REVERT: A 1282 LEU cc_start: 0.7801 (mt) cc_final: 0.7588 (mt) REVERT: A 1307 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7096 (mt-10) REVERT: A 1360 ASP cc_start: 0.7426 (t0) cc_final: 0.6927 (m-30) REVERT: A 1422 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8200 (mm-40) REVERT: A 1468 MET cc_start: 0.8866 (mtm) cc_final: 0.8599 (mtp) outliers start: 28 outliers final: 12 residues processed: 158 average time/residue: 1.2738 time to fit residues: 215.9092 Evaluate side-chains 153 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 806 ILE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.0020 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A 540 ASN A1157 GLN A1319 ASN A1425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9675 Z= 0.190 Angle : 0.466 6.604 13146 Z= 0.243 Chirality : 0.038 0.164 1560 Planarity : 0.003 0.036 1613 Dihedral : 9.995 164.458 1382 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.55 % Allowed : 11.72 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.24), residues: 1190 helix: 2.40 (0.18), residues: 818 sheet: 0.31 (0.63), residues: 65 loop : 0.31 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1214 HIS 0.004 0.001 HIS A1001 PHE 0.018 0.001 PHE A 552 TYR 0.017 0.001 TYR A 532 ARG 0.007 0.000 ARG A1494 *********************** 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 174 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 1.124 Fit side-chains REVERT: A 225 LYS cc_start: 0.7987 (mttm) cc_final: 0.7646 (mmtt) REVERT: A 235 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8101 (mp) REVERT: A 240 ARG cc_start: 0.7212 (mtm-85) cc_final: 0.6990 (mtm110) REVERT: A 241 LYS cc_start: 0.7770 (pttm) cc_final: 0.7554 (pmtt) REVERT: A 485 SER cc_start: 0.8623 (OUTLIER) cc_final: 0.8412 (p) REVERT: A 514 SER cc_start: 0.8623 (t) cc_final: 0.8268 (p) REVERT: A 520 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6740 (mpm) REVERT: A 525 SER cc_start: 0.8283 (t) cc_final: 0.7886 (m) REVERT: A 527 LYS cc_start: 0.7883 (ttpt) cc_final: 0.7365 (tttt) REVERT: A 672 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7634 (t0) REVERT: A 764 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6807 (mt-10) REVERT: A 778 LYS cc_start: 0.7956 (tptt) cc_final: 0.7738 (tmtm) REVERT: A 782 ASP cc_start: 0.7344 (m-30) cc_final: 0.7142 (m-30) REVERT: A 797 ASP cc_start: 0.8064 (m-30) cc_final: 0.7778 (m-30) REVERT: A 833 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7483 (m-30) REVERT: A 853 LYS cc_start: 0.8524 (tttt) cc_final: 0.8098 (ttpt) REVERT: A 896 GLN cc_start: 0.7700 (tt0) cc_final: 0.7378 (tt0) REVERT: A 907 LYS cc_start: 0.8577 (mtpt) cc_final: 0.8312 (ttpt) REVERT: A 973 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.7579 (tpt) REVERT: A 976 LYS cc_start: 0.8154 (mttt) cc_final: 0.7473 (mptt) REVERT: A 1055 TRP cc_start: 0.7208 (t60) cc_final: 0.6543 (t-100) REVERT: A 1185 ARG cc_start: 0.7839 (mtp85) cc_final: 0.7498 (mtt-85) REVERT: A 1277 LYS cc_start: 0.7664 (mttm) cc_final: 0.7394 (mttt) REVERT: A 1282 LEU cc_start: 0.7819 (mt) cc_final: 0.7617 (mt) REVERT: A 1307 GLU cc_start: 0.7405 (mt-10) cc_final: 0.7079 (mt-10) REVERT: A 1360 ASP cc_start: 0.7372 (t0) cc_final: 0.6950 (m-30) REVERT: A 1468 MET cc_start: 0.8832 (mtm) cc_final: 0.8567 (mtp) outliers start: 36 outliers final: 12 residues processed: 156 average time/residue: 1.2674 time to fit residues: 211.8015 Evaluate side-chains 155 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 520 MET 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 1476 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.0570 chunk 65 optimal weight: 0.0010 chunk 1 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A1319 ASN A1422 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9675 Z= 0.169 Angle : 0.454 6.608 13146 Z= 0.238 Chirality : 0.038 0.161 1560 Planarity : 0.003 0.042 1613 Dihedral : 9.762 164.124 1382 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.46 % Allowed : 13.50 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.24), residues: 1190 helix: 2.49 (0.18), residues: 818 sheet: 0.33 (0.64), residues: 65 loop : 0.32 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1214 HIS 0.003 0.000 HIS A1001 PHE 0.017 0.001 PHE A1445 TYR 0.015 0.001 TYR A 532 ARG 0.008 0.000 ARG A1494 *********************** 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 163 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.118 Fit side-chains REVERT: A 225 LYS cc_start: 0.7949 (mttm) cc_final: 0.7641 (mmtt) REVERT: A 235 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8121 (mp) REVERT: A 241 LYS cc_start: 0.7746 (pttm) cc_final: 0.7264 (tttm) REVERT: A 485 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8410 (p) REVERT: A 514 SER cc_start: 0.8613 (t) cc_final: 0.8279 (p) REVERT: A 520 MET cc_start: 0.6961 (OUTLIER) cc_final: 0.6725 (mpm) REVERT: A 525 SER cc_start: 0.8330 (t) cc_final: 0.7886 (m) REVERT: A 527 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7356 (tttt) REVERT: A 764 GLU cc_start: 0.7086 (mt-10) cc_final: 0.6780 (mt-10) REVERT: A 778 LYS cc_start: 0.7947 (tptt) cc_final: 0.7692 (tmtm) REVERT: A 782 ASP cc_start: 0.7357 (m-30) cc_final: 0.7154 (m-30) REVERT: A 797 ASP cc_start: 0.8089 (m-30) cc_final: 0.7808 (m-30) REVERT: A 853 LYS cc_start: 0.8505 (tttt) cc_final: 0.8123 (ttpt) REVERT: A 896 GLN cc_start: 0.7831 (tt0) cc_final: 0.7485 (tt0) REVERT: A 907 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8341 (ttpt) REVERT: A 973 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7488 (tpt) REVERT: A 976 LYS cc_start: 0.8142 (mttt) cc_final: 0.7705 (mmpt) REVERT: A 1055 TRP cc_start: 0.7207 (t60) cc_final: 0.6532 (t-100) REVERT: A 1185 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7430 (mtt-85) REVERT: A 1277 LYS cc_start: 0.7638 (mttm) cc_final: 0.7353 (mttt) REVERT: A 1282 LEU cc_start: 0.7781 (mt) cc_final: 0.7559 (mt) REVERT: A 1360 ASP cc_start: 0.7410 (t0) cc_final: 0.7031 (m-30) REVERT: A 1420 ILE cc_start: 0.8058 (mt) cc_final: 0.7826 (mt) REVERT: A 1425 ASN cc_start: 0.8002 (m110) cc_final: 0.7415 (p0) REVERT: A 1463 SER cc_start: 0.7918 (p) cc_final: 0.7596 (t) REVERT: A 1468 MET cc_start: 0.8830 (mtm) cc_final: 0.8573 (mtp) outliers start: 25 outliers final: 9 residues processed: 154 average time/residue: 1.2687 time to fit residues: 209.4303 Evaluate side-chains 144 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 520 MET Chi-restraints excluded: chain A residue 771 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 0.2980 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A1101 GLN A1157 GLN A1279 ASN A1319 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9675 Z= 0.267 Angle : 0.508 6.610 13146 Z= 0.263 Chirality : 0.040 0.168 1560 Planarity : 0.004 0.039 1613 Dihedral : 9.792 166.455 1378 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.66 % Allowed : 13.30 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.24), residues: 1190 helix: 2.27 (0.18), residues: 818 sheet: 0.52 (0.65), residues: 59 loop : 0.23 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1214 HIS 0.006 0.001 HIS A1001 PHE 0.020 0.002 PHE A 569 TYR 0.023 0.001 TYR A 532 ARG 0.010 0.001 ARG A1494 *********************** 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 162 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.110 Fit side-chains REVERT: A 225 LYS cc_start: 0.8061 (mttm) cc_final: 0.7730 (mmtt) REVERT: A 235 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8074 (mp) REVERT: A 241 LYS cc_start: 0.7782 (pttm) cc_final: 0.7360 (tttm) REVERT: A 485 SER cc_start: 0.8618 (OUTLIER) cc_final: 0.8394 (p) REVERT: A 514 SER cc_start: 0.8615 (t) cc_final: 0.8159 (p) REVERT: A 520 MET cc_start: 0.7024 (OUTLIER) cc_final: 0.6790 (mpm) REVERT: A 525 SER cc_start: 0.8306 (t) cc_final: 0.7901 (m) REVERT: A 527 LYS cc_start: 0.7924 (ttpt) cc_final: 0.7380 (tttt) REVERT: A 764 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6879 (mt-10) REVERT: A 778 LYS cc_start: 0.7957 (tptt) cc_final: 0.7710 (tmtm) REVERT: A 782 ASP cc_start: 0.7351 (m-30) cc_final: 0.7119 (m-30) REVERT: A 797 ASP cc_start: 0.8048 (m-30) cc_final: 0.7736 (m-30) REVERT: A 827 ASN cc_start: 0.7963 (t0) cc_final: 0.7388 (t0) REVERT: A 833 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7556 (m-30) REVERT: A 853 LYS cc_start: 0.8531 (tttt) cc_final: 0.8145 (ttpt) REVERT: A 896 GLN cc_start: 0.7774 (tt0) cc_final: 0.7394 (tt0) REVERT: A 907 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8353 (ttpt) REVERT: A 973 MET cc_start: 0.8248 (OUTLIER) cc_final: 0.7565 (tpt) REVERT: A 976 LYS cc_start: 0.8166 (mttt) cc_final: 0.7735 (mmpt) REVERT: A 1055 TRP cc_start: 0.7239 (t60) cc_final: 0.6575 (t-100) REVERT: A 1091 ARG cc_start: 0.7360 (OUTLIER) cc_final: 0.6911 (mpt180) REVERT: A 1185 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7486 (mtt-85) REVERT: A 1360 ASP cc_start: 0.7561 (t0) cc_final: 0.7081 (m-30) REVERT: A 1420 ILE cc_start: 0.8027 (mt) cc_final: 0.7772 (mt) REVERT: A 1425 ASN cc_start: 0.8002 (m110) cc_final: 0.7504 (p0) REVERT: A 1468 MET cc_start: 0.8848 (mtm) cc_final: 0.8598 (mtp) outliers start: 27 outliers final: 12 residues processed: 151 average time/residue: 1.2334 time to fit residues: 200.3136 Evaluate side-chains 150 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 520 MET Chi-restraints excluded: chain A residue 602 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 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 1091 ARG Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1511 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 65 optimal weight: 0.0170 chunk 97 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 115 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A1319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9675 Z= 0.165 Angle : 0.456 6.639 13146 Z= 0.239 Chirality : 0.038 0.161 1560 Planarity : 0.003 0.037 1613 Dihedral : 9.452 163.893 1378 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.66 % Allowed : 13.50 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.24), residues: 1190 helix: 2.46 (0.18), residues: 818 sheet: 0.61 (0.66), residues: 59 loop : 0.27 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1214 HIS 0.003 0.000 HIS A1001 PHE 0.020 0.001 PHE A1445 TYR 0.015 0.001 TYR A 532 ARG 0.009 0.000 ARG A1494 *********************** 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 162 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.076 Fit side-chains REVERT: A 225 LYS cc_start: 0.7959 (mttm) cc_final: 0.7653 (mmtt) REVERT: A 235 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8067 (mp) REVERT: A 241 LYS cc_start: 0.7673 (pttm) cc_final: 0.7242 (tttm) REVERT: A 514 SER cc_start: 0.8618 (t) cc_final: 0.8274 (p) REVERT: A 525 SER cc_start: 0.8352 (t) cc_final: 0.7907 (m) REVERT: A 527 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7355 (tttt) REVERT: A 607 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7151 (pp) REVERT: A 764 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6789 (mt-10) REVERT: A 778 LYS cc_start: 0.7959 (tptt) cc_final: 0.7706 (tmtm) REVERT: A 782 ASP cc_start: 0.7350 (m-30) cc_final: 0.7125 (m-30) REVERT: A 797 ASP cc_start: 0.8048 (m-30) cc_final: 0.7751 (m-30) REVERT: A 827 ASN cc_start: 0.7884 (t0) cc_final: 0.7377 (t0) REVERT: A 833 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7521 (m-30) REVERT: A 853 LYS cc_start: 0.8522 (tttt) cc_final: 0.8174 (ttpt) REVERT: A 896 GLN cc_start: 0.7857 (tt0) cc_final: 0.7460 (tt0) REVERT: A 907 LYS cc_start: 0.8614 (mtpt) cc_final: 0.8372 (ttpt) REVERT: A 973 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7539 (tpt) REVERT: A 976 LYS cc_start: 0.8147 (mttt) cc_final: 0.7718 (mmpt) REVERT: A 1055 TRP cc_start: 0.7172 (t60) cc_final: 0.6513 (t-100) REVERT: A 1091 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6776 (mpt180) REVERT: A 1185 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7404 (mtt-85) REVERT: A 1277 LYS cc_start: 0.7617 (mttm) cc_final: 0.7309 (mttt) REVERT: A 1318 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6732 (tp30) REVERT: A 1319 ASN cc_start: 0.7326 (m-40) cc_final: 0.6833 (m110) REVERT: A 1360 ASP cc_start: 0.7393 (t0) cc_final: 0.7048 (m-30) REVERT: A 1420 ILE cc_start: 0.7936 (mt) cc_final: 0.7634 (mt) REVERT: A 1425 ASN cc_start: 0.7990 (m110) cc_final: 0.7514 (p0) REVERT: A 1463 SER cc_start: 0.7817 (p) cc_final: 0.7567 (t) REVERT: A 1468 MET cc_start: 0.8815 (mtm) cc_final: 0.8558 (mtp) outliers start: 27 outliers final: 8 residues processed: 152 average time/residue: 1.2362 time to fit residues: 201.9299 Evaluate side-chains 145 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 607 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 973 MET Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 0.0670 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A 719 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9675 Z= 0.191 Angle : 0.474 6.629 13146 Z= 0.246 Chirality : 0.039 0.162 1560 Planarity : 0.003 0.037 1613 Dihedral : 9.441 164.951 1378 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.36 % Allowed : 14.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.24), residues: 1190 helix: 2.46 (0.18), residues: 818 sheet: 0.36 (0.60), residues: 69 loop : 0.33 (0.35), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1214 HIS 0.004 0.000 HIS A1001 PHE 0.019 0.001 PHE A1445 TYR 0.019 0.001 TYR A 532 ARG 0.008 0.000 ARG A1494 *********************** 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 159 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.312 Fit side-chains REVERT: A 225 LYS cc_start: 0.7967 (mttm) cc_final: 0.7662 (mmtt) REVERT: A 235 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8073 (mp) REVERT: A 241 LYS cc_start: 0.7678 (pttm) cc_final: 0.7241 (tttm) REVERT: A 514 SER cc_start: 0.8621 (t) cc_final: 0.8259 (p) REVERT: A 525 SER cc_start: 0.8364 (t) cc_final: 0.7906 (m) REVERT: A 527 LYS cc_start: 0.7921 (ttpt) cc_final: 0.7386 (tttt) REVERT: A 607 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7168 (pp) REVERT: A 764 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6799 (mt-10) REVERT: A 778 LYS cc_start: 0.7972 (tptt) cc_final: 0.7732 (tmtm) REVERT: A 797 ASP cc_start: 0.8060 (m-30) cc_final: 0.7763 (m-30) REVERT: A 827 ASN cc_start: 0.7898 (t0) cc_final: 0.7402 (t0) REVERT: A 833 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7509 (m-30) REVERT: A 853 LYS cc_start: 0.8530 (tttt) cc_final: 0.8181 (ttpt) REVERT: A 893 LYS cc_start: 0.8506 (mptt) cc_final: 0.8169 (mmtm) REVERT: A 907 LYS cc_start: 0.8613 (mtpt) cc_final: 0.8382 (ttpt) REVERT: A 973 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7522 (tpt) REVERT: A 976 LYS cc_start: 0.8148 (mttt) cc_final: 0.7709 (mmpt) REVERT: A 1055 TRP cc_start: 0.7204 (t60) cc_final: 0.6533 (t-100) REVERT: A 1091 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6899 (mpt180) REVERT: A 1185 ARG cc_start: 0.7798 (mtp85) cc_final: 0.7442 (mtt-85) REVERT: A 1318 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6738 (tp30) REVERT: A 1319 ASN cc_start: 0.7304 (m-40) cc_final: 0.6740 (m110) REVERT: A 1360 ASP cc_start: 0.7396 (t0) cc_final: 0.7066 (m-30) REVERT: A 1420 ILE cc_start: 0.7929 (mt) cc_final: 0.7616 (mt) REVERT: A 1425 ASN cc_start: 0.7922 (m110) cc_final: 0.7470 (p0) REVERT: A 1463 SER cc_start: 0.7786 (p) cc_final: 0.7542 (t) REVERT: A 1468 MET cc_start: 0.8835 (mtm) cc_final: 0.8584 (mtp) outliers start: 24 outliers final: 12 residues processed: 146 average time/residue: 1.2000 time to fit residues: 188.3687 Evaluate side-chains 151 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 607 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 987 PHE Chi-restraints excluded: chain A residue 1005 VAL Chi-restraints excluded: chain A residue 1073 ILE Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain A residue 1281 PHE Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1318 GLU Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1511 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 97 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A 896 GLN A1157 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9675 Z= 0.239 Angle : 0.499 6.646 13146 Z= 0.259 Chirality : 0.040 0.166 1560 Planarity : 0.004 0.037 1613 Dihedral : 9.581 165.802 1378 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.46 % Allowed : 14.19 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.24), residues: 1190 helix: 2.34 (0.18), residues: 818 sheet: 0.63 (0.65), residues: 59 loop : 0.30 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 980 HIS 0.005 0.001 HIS A1001 PHE 0.019 0.001 PHE A1445 TYR 0.023 0.001 TYR A 532 ARG 0.008 0.000 ARG A1494 *********************** 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 157 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 132 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8002 (mttm) cc_final: 0.7667 (mmtt) REVERT: A 235 ILE cc_start: 0.8588 (OUTLIER) cc_final: 0.8062 (mp) REVERT: A 514 SER cc_start: 0.8649 (t) cc_final: 0.8225 (p) REVERT: A 525 SER cc_start: 0.8287 (t) cc_final: 0.7870 (m) REVERT: A 527 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7400 (tttt) REVERT: A 607 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7179 (pp) REVERT: A 764 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6847 (mt-10) REVERT: A 797 ASP cc_start: 0.8073 (m-30) cc_final: 0.7773 (m-30) REVERT: A 827 ASN cc_start: 0.7970 (t0) cc_final: 0.7406 (t0) REVERT: A 833 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: A 853 LYS cc_start: 0.8539 (tttt) cc_final: 0.8196 (ttpt) REVERT: A 896 GLN cc_start: 0.7661 (tt0) cc_final: 0.7398 (tt0) REVERT: A 973 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7589 (tpt) REVERT: A 976 LYS cc_start: 0.8159 (mttt) cc_final: 0.7714 (mmpt) REVERT: A 1055 TRP cc_start: 0.7231 (t60) cc_final: 0.6558 (t-100) REVERT: A 1185 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7468 (mtt-85) REVERT: A 1316 ARG cc_start: 0.7725 (ptp90) cc_final: 0.7106 (ptt90) REVERT: A 1319 ASN cc_start: 0.7361 (m-40) cc_final: 0.6742 (m110) REVERT: A 1420 ILE cc_start: 0.7940 (mt) cc_final: 0.7617 (mt) REVERT: A 1425 ASN cc_start: 0.7896 (m110) cc_final: 0.7489 (p0) REVERT: A 1468 MET cc_start: 0.8863 (mtm) cc_final: 0.8607 (mtp) REVERT: A 1480 GLU cc_start: 0.6979 (tt0) cc_final: 0.6690 (tt0) REVERT: A 1494 ARG cc_start: 0.7740 (mtt-85) cc_final: 0.7465 (mtt90) outliers start: 25 outliers final: 12 residues processed: 143 average time/residue: 1.2708 time to fit residues: 195.5672 Evaluate side-chains 144 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 1.130 ------------------------------------------------------------------------------- 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 607 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 1281 PHE Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1511 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 0.0020 chunk 9 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1798 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= 0.253 Angle : 0.513 6.631 13146 Z= 0.265 Chirality : 0.040 0.168 1560 Planarity : 0.004 0.037 1613 Dihedral : 9.667 165.883 1378 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.97 % Allowed : 14.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.24), residues: 1190 helix: 2.28 (0.18), residues: 817 sheet: 0.54 (0.65), residues: 59 loop : 0.30 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1214 HIS 0.005 0.001 HIS A1001 PHE 0.019 0.002 PHE A1445 TYR 0.025 0.001 TYR A 532 ARG 0.007 0.000 ARG A1494 ********************** 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 148 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 225 LYS cc_start: 0.8055 (mttm) cc_final: 0.7728 (mmtt) REVERT: A 235 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8048 (mp) REVERT: A 514 SER cc_start: 0.8594 (t) cc_final: 0.8127 (p) REVERT: A 525 SER cc_start: 0.8305 (t) cc_final: 0.7900 (m) REVERT: A 527 LYS cc_start: 0.7914 (ttpt) cc_final: 0.7379 (tttt) REVERT: A 607 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7238 (pp) REVERT: A 764 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6858 (mt-10) REVERT: A 797 ASP cc_start: 0.8073 (m-30) cc_final: 0.7780 (m-30) REVERT: A 827 ASN cc_start: 0.7982 (t0) cc_final: 0.7400 (t0) REVERT: A 833 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7574 (m-30) REVERT: A 853 LYS cc_start: 0.8552 (tttt) cc_final: 0.8192 (ttpt) REVERT: A 973 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7565 (tpt) REVERT: A 976 LYS cc_start: 0.8163 (mttt) cc_final: 0.7695 (mmpt) REVERT: A 1055 TRP cc_start: 0.7245 (t60) cc_final: 0.6567 (t-100) REVERT: A 1185 ARG cc_start: 0.7849 (mtp85) cc_final: 0.7477 (mtt-85) REVERT: A 1420 ILE cc_start: 0.7941 (mt) cc_final: 0.7615 (mt) REVERT: A 1425 ASN cc_start: 0.7888 (m110) cc_final: 0.7503 (p0) REVERT: A 1468 MET cc_start: 0.8854 (mtm) cc_final: 0.8588 (mtp) outliers start: 20 outliers final: 12 residues processed: 138 average time/residue: 1.2467 time to fit residues: 185.3078 Evaluate side-chains 146 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 607 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 1281 PHE Chi-restraints excluded: chain A residue 1293 MET Chi-restraints excluded: chain A residue 1298 VAL Chi-restraints excluded: chain A residue 1460 VAL Chi-restraints excluded: chain A residue 1511 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 chunk 5 optimal weight: 0.3980 chunk 68 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A1311 HIS A1319 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.141203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.108178 restraints weight = 10225.503| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.57 r_work: 0.2959 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1906 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= 0.170 Angle : 0.467 6.670 13146 Z= 0.244 Chirality : 0.038 0.160 1560 Planarity : 0.003 0.037 1613 Dihedral : 9.369 163.809 1378 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.67 % Allowed : 15.37 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.71 (0.24), residues: 1190 helix: 2.45 (0.18), residues: 817 sheet: 0.84 (0.63), residues: 59 loop : 0.26 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1214 HIS 0.003 0.000 HIS A1001 PHE 0.017 0.001 PHE A1445 TYR 0.020 0.001 TYR A 532 ARG 0.008 0.000 ARG A1494 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3638.09 seconds wall clock time: 66 minutes 20.11 seconds (3980.11 seconds total)