Starting phenix.real_space_refine on Mon Apr 6 02:38:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ohf_70489/04_2026/9ohf_70489.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ohf_70489/04_2026/9ohf_70489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ohf_70489/04_2026/9ohf_70489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ohf_70489/04_2026/9ohf_70489.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ohf_70489/04_2026/9ohf_70489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ohf_70489/04_2026/9ohf_70489.map" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 8603 2.51 5 N 2715 2.21 5 O 3148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14496 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 14496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2366, 14496 Classifications: {'peptide': 2366} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1049} Link IDs: {'PTRANS': 52, 'TRANS': 2313} Unresolved chain link angles: 22 Unresolved non-hydrogen bonds: 4723 Unresolved non-hydrogen angles: 6855 Unresolved non-hydrogen dihedrals: 3040 Unresolved non-hydrogen chiralities: 1383 Planarities with less than four sites: {'GLU:plan': 96, 'ARG:plan': 20, 'ASN:plan1': 85, 'ASP:plan': 94, 'PHE:plan': 69, 'HIS:plan': 14, 'TYR:plan': 66, 'GLN:plan1': 22, 'TRP:plan': 9, 'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 2477 Time building chain proxies: 3.15, per 1000 atoms: 0.22 Number of scatterers: 14496 At special positions: 0 Unit cell: (129.78, 123.6, 237.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 3148 8.00 N 2715 7.00 C 8603 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: 1.30 Conformation dependent library (CDL) restraints added in 797.5 milliseconds 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2358 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 43 sheets defined 33.3% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 21 through 37 removed outlier: 3.762A pdb=" N ILE A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ASN A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 68 through 90 removed outlier: 3.508A pdb=" N LYS A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 122 removed outlier: 3.982A pdb=" N GLN A 117 " --> pdb=" O ASN A 113 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TRP A 118 " --> pdb=" O TYR A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 155 removed outlier: 4.655A pdb=" N THR A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.985A pdb=" N GLU A 159 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 197 removed outlier: 3.604A pdb=" N GLU A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 264 through 280 Processing helix chain 'A' and resid 308 through 324 removed outlier: 3.679A pdb=" N LEU A 317 " --> pdb=" O GLU A 313 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.741A pdb=" N SER A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 393 through 420 removed outlier: 3.883A pdb=" N SER A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 423 through 439 Processing helix chain 'A' and resid 443 through 451 removed outlier: 3.714A pdb=" N GLU A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 451 " --> pdb=" O MET A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 Processing helix chain 'A' and resid 463 through 468 removed outlier: 3.697A pdb=" N ASN A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 483 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'A' and resid 500 through 502 No H-bonds generated for 'chain 'A' and resid 500 through 502' Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 523 through 539 Processing helix chain 'A' and resid 558 through 569 Processing helix chain 'A' and resid 587 through 600 Processing helix chain 'A' and resid 668 through 683 Processing helix chain 'A' and resid 706 through 709 Processing helix chain 'A' and resid 710 through 727 removed outlier: 4.808A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 733 No H-bonds generated for 'chain 'A' and resid 731 through 733' Processing helix chain 'A' and resid 764 through 775 Processing helix chain 'A' and resid 793 through 809 Processing helix chain 'A' and resid 814 through 836 Processing helix chain 'A' and resid 846 through 876 removed outlier: 3.996A pdb=" N ILE A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 935 Processing helix chain 'A' and resid 955 through 960 Processing helix chain 'A' and resid 961 through 971 removed outlier: 3.746A pdb=" N ILE A 965 " --> pdb=" O ALA A 961 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 980 removed outlier: 4.326A pdb=" N SER A 979 " --> pdb=" O LYS A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 994 Processing helix chain 'A' and resid 997 through 1001 Processing helix chain 'A' and resid 1003 through 1017 removed outlier: 4.017A pdb=" N ASP A1016 " --> pdb=" O SER A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1029 removed outlier: 3.630A pdb=" N GLY A1028 " --> pdb=" O LEU A1025 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1051 Processing helix chain 'A' and resid 1053 through 1065 Processing helix chain 'A' and resid 1072 through 1080 Processing helix chain 'A' and resid 1085 through 1089 removed outlier: 4.194A pdb=" N PHE A1089 " --> pdb=" O ALA A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1096 through 1102 Processing helix chain 'A' and resid 1116 through 1133 removed outlier: 3.900A pdb=" N VAL A1130 " --> pdb=" O HIS A1126 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU A1131 " --> pdb=" O VAL A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1240 through 1244 removed outlier: 3.603A pdb=" N GLU A1244 " --> pdb=" O ARG A1241 " (cutoff:3.500A) Processing helix chain 'A' and resid 1245 through 1258 removed outlier: 3.536A pdb=" N TYR A1258 " --> pdb=" O ILE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1311 Processing helix chain 'A' and resid 1348 through 1353 Processing helix chain 'A' and resid 1370 through 1375 Processing helix chain 'A' and resid 1432 through 1439 Processing helix chain 'A' and resid 1439 through 1451 Processing helix chain 'A' and resid 1453 through 1458 Processing helix chain 'A' and resid 1558 through 1573 Processing helix chain 'A' and resid 1577 through 1588 removed outlier: 3.619A pdb=" N SER A1583 " --> pdb=" O ASP A1579 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1594 removed outlier: 4.252A pdb=" N PHE A1594 " --> pdb=" O ILE A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1639 through 1641 No H-bonds generated for 'chain 'A' and resid 1639 through 1641' Processing helix chain 'A' and resid 1650 through 1652 No H-bonds generated for 'chain 'A' and resid 1650 through 1652' Processing helix chain 'A' and resid 1679 through 1682 Processing helix chain 'A' and resid 1773 through 1779 removed outlier: 3.658A pdb=" N LYS A1779 " --> pdb=" O THR A1775 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1799 removed outlier: 3.811A pdb=" N LEU A1797 " --> pdb=" O SER A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1867 through 1871 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 101 removed outlier: 6.147A pdb=" N LEU A 98 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE A 130 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE A 100 " --> pdb=" O PHE A 130 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 285 removed outlier: 7.962A pdb=" N GLN A 385 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 11.341A pdb=" N LYS A 374 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 Processing sheet with id=AA5, first strand: chain 'A' and resid 627 through 632 removed outlier: 4.736A pdb=" N TYR A 621 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N SER A 605 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 578 " --> pdb=" O LYS A 647 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N THR A 649 " --> pdb=" O ILE A 578 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N TYR A 580 " --> pdb=" O THR A 649 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE A 651 " --> pdb=" O TYR A 580 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A 582 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ILE A 646 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASN A 694 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU A 648 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N LEU A 696 " --> pdb=" O LEU A 648 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N PHE A 650 " --> pdb=" O LEU A 696 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 691 " --> pdb=" O ILE A 736 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N SER A 738 " --> pdb=" O ILE A 691 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE A 693 " --> pdb=" O SER A 738 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ASN A 740 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU A 695 " --> pdb=" O ASN A 740 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE A 735 " --> pdb=" O PHE A 780 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N PHE A 780 " --> pdb=" O ILE A 735 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR A 777 " --> pdb=" O LYS A 790 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 662 through 663 Processing sheet with id=AA7, first strand: chain 'A' and resid 744 through 746 removed outlier: 3.814A pdb=" N GLU A 760 " --> pdb=" O ASP A 756 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 882 through 892 removed outlier: 10.025A pdb=" N PHE A 886 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 11.008A pdb=" N ILE A 901 " --> pdb=" O PHE A 886 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASP A 888 " --> pdb=" O ARG A 899 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ARG A 899 " --> pdb=" O ASP A 888 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 936 through 938 Processing sheet with id=AB1, first strand: chain 'A' and resid 1035 through 1036 Processing sheet with id=AB2, first strand: chain 'A' and resid 1105 through 1107 Processing sheet with id=AB3, first strand: chain 'A' and resid 1136 through 1139 removed outlier: 6.535A pdb=" N MET A1144 " --> pdb=" O VAL A1221 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N MET A1220 " --> pdb=" O ILE A1299 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ARG A1296 " --> pdb=" O ALA A1324 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N SER A1326 " --> pdb=" O ARG A1296 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE A1298 " --> pdb=" O SER A1326 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR A1323 " --> pdb=" O ILE A1345 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ASP A1347 " --> pdb=" O TYR A1323 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A1325 " --> pdb=" O ASP A1347 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TRP A1344 " --> pdb=" O PHE A1401 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A1403 " --> pdb=" O TRP A1344 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE A1412 " --> pdb=" O ILE A1408 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER A1424 " --> pdb=" O ASP A1419 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1161 through 1164 removed outlier: 7.206A pdb=" N SER A1153 " --> pdb=" O ARG A1288 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N ASN A1290 " --> pdb=" O SER A1153 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE A1155 " --> pdb=" O ASN A1290 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR A1285 " --> pdb=" O SER A1313 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N SER A1315 " --> pdb=" O THR A1285 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE A1287 " --> pdb=" O SER A1315 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TYR A1317 " --> pdb=" O ILE A1287 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE A1289 " --> pdb=" O TYR A1317 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY A1333 " --> pdb=" O LEU A1312 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ILE A1334 " --> pdb=" O ASN A1390 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER A1392 " --> pdb=" O ILE A1334 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE A1336 " --> pdb=" O SER A1392 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1200 through 1201 removed outlier: 6.724A pdb=" N GLU A1168 " --> pdb=" O PHE A1230 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N TRP A1232 " --> pdb=" O GLU A1168 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1175 through 1180 removed outlier: 5.898A pdb=" N GLY A1177 " --> pdb=" O PHE A1188 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N PHE A1188 " --> pdb=" O GLY A1177 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP A1185 " --> pdb=" O PHE A1267 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1356 through 1358 Processing sheet with id=AB8, first strand: chain 'A' and resid 1459 through 1466 Processing sheet with id=AB9, first strand: chain 'A' and resid 1514 through 1521 removed outlier: 5.815A pdb=" N ASP A1515 " --> pdb=" O TYR A1530 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N TYR A1530 " --> pdb=" O ASP A1515 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ASN A1525 " --> pdb=" O LEU A1544 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU A1544 " --> pdb=" O ASN A1525 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY A1529 " --> pdb=" O LEU A1540 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N LYS A1537 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N LEU A1557 " --> pdb=" O LYS A1537 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N SER A1539 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL A1555 " --> pdb=" O SER A1539 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER A1541 " --> pdb=" O ASN A1553 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A1550 " --> pdb=" O ILE A1605 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASP A1607 " --> pdb=" O ILE A1550 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LEU A1552 " --> pdb=" O ASP A1607 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ASN A1609 " --> pdb=" O LEU A1552 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER A1554 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE A1611 " --> pdb=" O SER A1554 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N HIS A1556 " --> pdb=" O ILE A1611 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER A1613 " --> pdb=" O HIS A1556 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N PHE A1610 " --> pdb=" O CYS A1625 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN A1620 " --> pdb=" O ILE A1636 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ILE A1636 " --> pdb=" O GLN A1620 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N GLU A1622 " --> pdb=" O TYR A1634 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN A1630 " --> pdb=" O ASP A1626 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET A1655 " --> pdb=" O VAL A1692 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL A1691 " --> pdb=" O ILE A1718 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1673 through 1677 Processing sheet with id=AC2, first strand: chain 'A' and resid 1814 through 1818 Processing sheet with id=AC3, first strand: chain 'A' and resid 1834 through 1838 Processing sheet with id=AC4, first strand: chain 'A' and resid 1855 through 1859 Processing sheet with id=AC5, first strand: chain 'A' and resid 1877 through 1881 removed outlier: 4.693A pdb=" N TYR A1887 " --> pdb=" O GLN A1895 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1897 through 1899 Processing sheet with id=AC7, first strand: chain 'A' and resid 1927 through 1931 Processing sheet with id=AC8, first strand: chain 'A' and resid 1948 through 1951 Processing sheet with id=AC9, first strand: chain 'A' and resid 1969 through 1972 Processing sheet with id=AD1, first strand: chain 'A' and resid 1989 through 1992 Processing sheet with id=AD2, first strand: chain 'A' and resid 2009 through 2012 Processing sheet with id=AD3, first strand: chain 'A' and resid 2028 through 2032 Processing sheet with id=AD4, first strand: chain 'A' and resid 2059 through 2061 removed outlier: 3.591A pdb=" N THR A2074 " --> pdb=" O ASP A2070 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 2100 through 2104 Processing sheet with id=AD6, first strand: chain 'A' and resid 2120 through 2124 Processing sheet with id=AD7, first strand: chain 'A' and resid 2140 through 2144 Processing sheet with id=AD8, first strand: chain 'A' and resid 2160 through 2164 Processing sheet with id=AD9, first strand: chain 'A' and resid 2190 through 2191 Processing sheet with id=AE1, first strand: chain 'A' and resid 2210 through 2211 Processing sheet with id=AE2, first strand: chain 'A' and resid 2235 through 2238 Processing sheet with id=AE3, first strand: chain 'A' and resid 2254 through 2258 Processing sheet with id=AE4, first strand: chain 'A' and resid 2275 through 2277 Processing sheet with id=AE5, first strand: chain 'A' and resid 2296 through 2298 removed outlier: 3.787A pdb=" N PHE A2296 " --> pdb=" O LYS A2303 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 2324 through 2325 Processing sheet with id=AE7, first strand: chain 'A' and resid 2346 through 2348 removed outlier: 3.522A pdb=" N VAL A2346 " --> pdb=" O TYR A2353 " (cutoff:3.500A) 794 hydrogen bonds defined for protein. 2133 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.54 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5338 1.33 - 1.45: 1701 1.45 - 1.57: 7586 1.57 - 1.69: 0 1.69 - 1.80: 54 Bond restraints: 14679 Sorted by residual: bond pdb=" CB LYS A 48 " pdb=" CG LYS A 48 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.74e+00 bond pdb=" CB THR A1800 " pdb=" CG2 THR A1800 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.68e+00 bond pdb=" CG1 ILE A 628 " pdb=" CD1 ILE A 628 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.66e+00 bond pdb=" CB ASN A 596 " pdb=" CG ASN A 596 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.58e+00 bond pdb=" CB ILE A 778 " pdb=" CG2 ILE A 778 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.14e+00 ... (remaining 14674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 18666 1.91 - 3.82: 636 3.82 - 5.73: 67 5.73 - 7.64: 14 7.64 - 9.55: 5 Bond angle restraints: 19388 Sorted by residual: angle pdb=" N GLU A1197 " pdb=" CA GLU A1197 " pdb=" C GLU A1197 " ideal model delta sigma weight residual 109.81 117.83 -8.02 2.21e+00 2.05e-01 1.32e+01 angle pdb=" N TYR A 603 " pdb=" CA TYR A 603 " pdb=" C TYR A 603 " ideal model delta sigma weight residual 110.50 105.54 4.96 1.41e+00 5.03e-01 1.24e+01 angle pdb=" N PRO A1847 " pdb=" CA PRO A1847 " pdb=" C PRO A1847 " ideal model delta sigma weight residual 110.70 114.93 -4.23 1.22e+00 6.72e-01 1.20e+01 angle pdb=" N MET A 283 " pdb=" CA MET A 283 " pdb=" C MET A 283 " ideal model delta sigma weight residual 110.28 115.19 -4.91 1.48e+00 4.57e-01 1.10e+01 angle pdb=" N PHE A1638 " pdb=" CA PHE A1638 " pdb=" CB PHE A1638 " ideal model delta sigma weight residual 111.37 117.26 -5.89 1.82e+00 3.02e-01 1.05e+01 ... (remaining 19383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 6800 17.53 - 35.06: 385 35.06 - 52.60: 59 52.60 - 70.13: 28 70.13 - 87.66: 12 Dihedral angle restraints: 7284 sinusoidal: 2493 harmonic: 4791 Sorted by residual: dihedral pdb=" CA ASP A1607 " pdb=" C ASP A1607 " pdb=" N ALA A1608 " pdb=" CA ALA A1608 " ideal model delta harmonic sigma weight residual 180.00 155.26 24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA ASN A 422 " pdb=" C ASN A 422 " pdb=" N ASP A 423 " pdb=" CA ASP A 423 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA ILE A 612 " pdb=" C ILE A 612 " pdb=" N GLU A 613 " pdb=" CA GLU A 613 " ideal model delta harmonic sigma weight residual -180.00 -155.64 -24.36 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 7281 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 938 0.050 - 0.100: 451 0.100 - 0.149: 121 0.149 - 0.199: 14 0.199 - 0.249: 1 Chirality restraints: 1525 Sorted by residual: chirality pdb=" CA ARG A 499 " pdb=" N ARG A 499 " pdb=" C ARG A 499 " pdb=" CB ARG A 499 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA TYR A 634 " pdb=" N TYR A 634 " pdb=" C TYR A 634 " pdb=" CB TYR A 634 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.21e-01 chirality pdb=" CB ILE A 612 " pdb=" CA ILE A 612 " pdb=" CG1 ILE A 612 " pdb=" CG2 ILE A 612 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.37e-01 ... (remaining 1522 not shown) Planarity restraints: 2919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 453 " -0.001 2.00e-02 2.50e+03 1.95e-02 7.58e+00 pdb=" CG TYR A 453 " 0.003 2.00e-02 2.50e+03 pdb=" CD1 TYR A 453 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR A 453 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 453 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TYR A 453 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 453 " -0.029 2.00e-02 2.50e+03 pdb=" OH TYR A 453 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 406 " 0.200 9.50e-02 1.11e+02 9.03e-02 6.60e+00 pdb=" NE ARG A 406 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 406 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 406 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 406 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1740 " -0.021 2.00e-02 2.50e+03 1.55e-02 4.79e+00 pdb=" CG TYR A1740 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A1740 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A1740 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A1740 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A1740 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A1740 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR A1740 " -0.018 2.00e-02 2.50e+03 ... (remaining 2916 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3307 2.77 - 3.30: 14231 3.30 - 3.83: 22234 3.83 - 4.37: 26036 4.37 - 4.90: 44116 Nonbonded interactions: 109924 Sorted by model distance: nonbonded pdb=" OE1 GLN A 385 " pdb=" NE2 GLN A 510 " model vdw 2.237 3.120 nonbonded pdb=" ND2 ASN A 596 " pdb=" OE2 GLU A 743 " model vdw 2.249 3.120 nonbonded pdb=" OE1 GLU A 155 " pdb=" OH TYR A 538 " model vdw 2.260 3.040 nonbonded pdb=" OE1 GLN A 183 " pdb=" NH1 ARG A 262 " model vdw 2.261 3.120 nonbonded pdb=" NZ LYS A 143 " pdb=" OE2 GLU A 147 " model vdw 2.303 3.120 ... (remaining 109919 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: 5.370 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.490 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 : 0.010 0.075 14679 Z= 0.426 Angle : 0.821 9.550 19388 Z= 0.471 Chirality : 0.058 0.249 1525 Planarity : 0.005 0.090 2919 Dihedral : 11.890 87.660 4926 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.08 % Favored : 94.88 % Rotamer: Outliers : 0.27 % Allowed : 1.50 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.16), residues: 2364 helix: -1.81 (0.16), residues: 682 sheet: -0.71 (0.22), residues: 501 loop : -0.58 (0.18), residues: 1181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.003 ARG A 406 TYR 0.029 0.004 TYR A 453 PHE 0.034 0.003 PHE A1638 TRP 0.022 0.003 TRP A 102 HIS 0.009 0.002 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00981 (14679) covalent geometry : angle 0.82090 (19388) hydrogen bonds : bond 0.24546 ( 794) hydrogen bonds : angle 9.14860 ( 2133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 128 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 MET cc_start: 0.8945 (ptm) cc_final: 0.8731 (ptm) REVERT: A 77 GLU cc_start: 0.8647 (tt0) cc_final: 0.8220 (tm-30) REVERT: A 310 ASP cc_start: 0.8940 (t0) cc_final: 0.8580 (t0) REVERT: A 321 MET cc_start: 0.8746 (mmt) cc_final: 0.8051 (mmt) REVERT: A 489 MET cc_start: 0.8742 (mtp) cc_final: 0.8481 (mtp) REVERT: A 811 SER cc_start: 0.8415 (m) cc_final: 0.8210 (p) REVERT: A 854 TYR cc_start: 0.8473 (t80) cc_final: 0.7983 (t80) REVERT: A 1794 GLU cc_start: 0.8770 (tt0) cc_final: 0.8478 (tt0) REVERT: A 1831 MET cc_start: 0.8150 (ttm) cc_final: 0.7772 (ttm) REVERT: A 1840 ASP cc_start: 0.8655 (t0) cc_final: 0.7733 (t0) REVERT: A 1876 ILE cc_start: 0.8687 (mt) cc_final: 0.8271 (mm) REVERT: A 1889 ASN cc_start: 0.7198 (m110) cc_final: 0.6669 (m-40) REVERT: A 1890 GLN cc_start: 0.8767 (tp40) cc_final: 0.8495 (tp40) REVERT: A 1907 TYR cc_start: 0.8366 (t80) cc_final: 0.8158 (t80) outliers start: 3 outliers final: 1 residues processed: 131 average time/residue: 0.1200 time to fit residues: 24.0110 Evaluate side-chains 79 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 50.0000 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.0470 chunk 235 optimal weight: 6.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 HIS A 334 HIS A 653 HIS A 706 ASN A 741 GLN A 757 HIS A 924 HIS A1778 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.096560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.067529 restraints weight = 45592.889| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 3.68 r_work: 0.3021 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14679 Z= 0.207 Angle : 0.542 6.230 19388 Z= 0.308 Chirality : 0.047 0.151 1525 Planarity : 0.003 0.038 2919 Dihedral : 4.637 44.612 2465 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.88 % Allowed : 5.84 % Favored : 93.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2364 helix: 0.58 (0.19), residues: 701 sheet: -0.58 (0.22), residues: 523 loop : 0.20 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.016 0.002 TYR A1645 PHE 0.016 0.002 PHE A 964 TRP 0.018 0.002 TRP A 102 HIS 0.004 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00472 (14679) covalent geometry : angle 0.54245 (19388) hydrogen bonds : bond 0.04246 ( 794) hydrogen bonds : angle 5.63950 ( 2133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.559 Fit side-chains REVERT: A 77 GLU cc_start: 0.8828 (tt0) cc_final: 0.8486 (tm-30) REVERT: A 310 ASP cc_start: 0.8658 (t0) cc_final: 0.8347 (t0) REVERT: A 321 MET cc_start: 0.8796 (mmt) cc_final: 0.8121 (mmt) REVERT: A 337 MET cc_start: 0.9149 (mtp) cc_final: 0.8861 (mtp) REVERT: A 445 ARG cc_start: 0.8510 (ptm160) cc_final: 0.8025 (mtp85) REVERT: A 447 MET cc_start: 0.9173 (tpp) cc_final: 0.8760 (tpp) REVERT: A 449 GLU cc_start: 0.8734 (mp0) cc_final: 0.8420 (mp0) REVERT: A 489 MET cc_start: 0.8860 (mtp) cc_final: 0.8527 (mtp) REVERT: A 765 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8690 (tp30) REVERT: A 854 TYR cc_start: 0.8393 (t80) cc_final: 0.7946 (t80) REVERT: A 1794 GLU cc_start: 0.8931 (tt0) cc_final: 0.8534 (tm-30) REVERT: A 1831 MET cc_start: 0.8237 (ttm) cc_final: 0.7854 (ttm) REVERT: A 1840 ASP cc_start: 0.8732 (t0) cc_final: 0.7783 (t0) REVERT: A 1876 ILE cc_start: 0.8748 (mt) cc_final: 0.8391 (mm) REVERT: A 1889 ASN cc_start: 0.7388 (m110) cc_final: 0.6973 (m110) outliers start: 10 outliers final: 3 residues processed: 93 average time/residue: 0.1088 time to fit residues: 16.0803 Evaluate side-chains 76 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 1697 ILE Chi-restraints excluded: chain A residue 1819 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 38 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 132 optimal weight: 30.0000 chunk 176 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 741 GLN A 802 GLN A1762 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.096381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.067451 restraints weight = 45795.315| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.69 r_work: 0.3045 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14679 Z= 0.144 Angle : 0.452 5.690 19388 Z= 0.256 Chirality : 0.044 0.142 1525 Planarity : 0.003 0.033 2919 Dihedral : 4.210 58.485 2465 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.62 % Allowed : 6.90 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.18), residues: 2364 helix: 1.48 (0.20), residues: 707 sheet: -0.38 (0.23), residues: 495 loop : 0.39 (0.19), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 455 TYR 0.014 0.001 TYR A1645 PHE 0.014 0.001 PHE A1866 TRP 0.012 0.001 TRP A 102 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00324 (14679) covalent geometry : angle 0.45225 (19388) hydrogen bonds : bond 0.03356 ( 794) hydrogen bonds : angle 4.79926 ( 2133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3751 (tpt) cc_final: 0.3312 (tpt) REVERT: A 77 GLU cc_start: 0.8812 (tt0) cc_final: 0.8464 (tm-30) REVERT: A 310 ASP cc_start: 0.8599 (t0) cc_final: 0.8283 (t0) REVERT: A 321 MET cc_start: 0.8828 (mmt) cc_final: 0.8238 (mmt) REVERT: A 447 MET cc_start: 0.9229 (tpp) cc_final: 0.8223 (mpp) REVERT: A 449 GLU cc_start: 0.8776 (mp0) cc_final: 0.8416 (mp0) REVERT: A 489 MET cc_start: 0.8796 (mtp) cc_final: 0.8508 (mtp) REVERT: A 765 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8645 (tp30) REVERT: A 854 TYR cc_start: 0.8505 (t80) cc_final: 0.8108 (t80) REVERT: A 1661 TYR cc_start: 0.8567 (OUTLIER) cc_final: 0.8241 (t80) REVERT: A 1794 GLU cc_start: 0.8947 (tt0) cc_final: 0.8649 (tm-30) REVERT: A 1840 ASP cc_start: 0.8734 (t0) cc_final: 0.7807 (t0) REVERT: A 1876 ILE cc_start: 0.8772 (mt) cc_final: 0.8460 (mm) REVERT: A 1889 ASN cc_start: 0.7383 (m110) cc_final: 0.6989 (m110) outliers start: 7 outliers final: 3 residues processed: 91 average time/residue: 0.0929 time to fit residues: 14.1140 Evaluate side-chains 80 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 985 MET Chi-restraints excluded: chain A residue 1661 TYR Chi-restraints excluded: chain A residue 1778 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 90 optimal weight: 4.9990 chunk 221 optimal weight: 50.0000 chunk 15 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 127 optimal weight: 50.0000 chunk 133 optimal weight: 20.0000 chunk 28 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 122 optimal weight: 50.0000 chunk 232 optimal weight: 50.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 GLN A1653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.096524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.067425 restraints weight = 45769.287| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.75 r_work: 0.3052 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14679 Z= 0.128 Angle : 0.424 6.725 19388 Z= 0.239 Chirality : 0.043 0.170 1525 Planarity : 0.002 0.031 2919 Dihedral : 3.735 17.748 2463 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.88 % Allowed : 7.35 % Favored : 91.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.18), residues: 2364 helix: 1.87 (0.20), residues: 707 sheet: -0.32 (0.23), residues: 498 loop : 0.50 (0.20), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 406 TYR 0.023 0.001 TYR A 478 PHE 0.013 0.001 PHE A1866 TRP 0.011 0.001 TRP A 102 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00290 (14679) covalent geometry : angle 0.42429 (19388) hydrogen bonds : bond 0.03021 ( 794) hydrogen bonds : angle 4.48238 ( 2133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3864 (tpt) cc_final: 0.3246 (tpt) REVERT: A 77 GLU cc_start: 0.8815 (tt0) cc_final: 0.8463 (tm-30) REVERT: A 83 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8384 (t) REVERT: A 310 ASP cc_start: 0.8595 (t0) cc_final: 0.8230 (t0) REVERT: A 321 MET cc_start: 0.8792 (mmt) cc_final: 0.8270 (mmt) REVERT: A 436 MET cc_start: 0.9438 (mmm) cc_final: 0.9207 (mmp) REVERT: A 445 ARG cc_start: 0.8515 (ptm160) cc_final: 0.7871 (mtm180) REVERT: A 447 MET cc_start: 0.9227 (tpp) cc_final: 0.8051 (mpp) REVERT: A 448 MET cc_start: 0.9033 (mtm) cc_final: 0.7980 (ptp) REVERT: A 449 GLU cc_start: 0.8802 (mp0) cc_final: 0.7872 (mp0) REVERT: A 489 MET cc_start: 0.8824 (mtp) cc_final: 0.8485 (mtp) REVERT: A 765 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8651 (tp30) REVERT: A 854 TYR cc_start: 0.8538 (t80) cc_final: 0.8146 (t80) REVERT: A 1020 ASP cc_start: 0.8906 (m-30) cc_final: 0.8595 (p0) REVERT: A 1661 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8231 (t80) REVERT: A 1794 GLU cc_start: 0.8908 (tt0) cc_final: 0.8583 (tm-30) REVERT: A 1840 ASP cc_start: 0.8712 (t0) cc_final: 0.7804 (t0) outliers start: 10 outliers final: 4 residues processed: 91 average time/residue: 0.0919 time to fit residues: 14.2064 Evaluate side-chains 84 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 968 LEU Chi-restraints excluded: chain A residue 1661 TYR Chi-restraints excluded: chain A residue 1778 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 197 optimal weight: 40.0000 chunk 187 optimal weight: 5.9990 chunk 126 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 109 optimal weight: 0.3980 chunk 157 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 229 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1639 ASN ** A1889 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.095609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.067328 restraints weight = 44937.384| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.67 r_work: 0.3019 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 14679 Z= 0.196 Angle : 0.469 6.554 19388 Z= 0.260 Chirality : 0.045 0.152 1525 Planarity : 0.003 0.030 2919 Dihedral : 3.816 19.109 2463 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.24 % Allowed : 8.14 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.18), residues: 2364 helix: 1.80 (0.20), residues: 714 sheet: -0.28 (0.23), residues: 486 loop : 0.42 (0.20), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 406 TYR 0.034 0.002 TYR A 478 PHE 0.014 0.001 PHE A 186 TRP 0.014 0.002 TRP A 102 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00451 (14679) covalent geometry : angle 0.46920 (19388) hydrogen bonds : bond 0.03287 ( 794) hydrogen bonds : angle 4.54658 ( 2133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3792 (tpt) cc_final: 0.3198 (tpt) REVERT: A 77 GLU cc_start: 0.8793 (tt0) cc_final: 0.8457 (tm-30) REVERT: A 176 MET cc_start: 0.7766 (tpp) cc_final: 0.7515 (tpp) REVERT: A 310 ASP cc_start: 0.8634 (t0) cc_final: 0.8244 (t0) REVERT: A 321 MET cc_start: 0.8805 (mmt) cc_final: 0.8242 (mmt) REVERT: A 447 MET cc_start: 0.9265 (tpp) cc_final: 0.8107 (mpp) REVERT: A 449 GLU cc_start: 0.8864 (mp0) cc_final: 0.8457 (mp0) REVERT: A 489 MET cc_start: 0.8858 (mtp) cc_final: 0.8535 (mtp) REVERT: A 765 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8664 (tp30) REVERT: A 854 TYR cc_start: 0.8560 (t80) cc_final: 0.8102 (t80) REVERT: A 1794 GLU cc_start: 0.8883 (tt0) cc_final: 0.8531 (tm-30) REVERT: A 1840 ASP cc_start: 0.8712 (t0) cc_final: 0.7776 (t0) REVERT: A 1876 ILE cc_start: 0.8793 (mt) cc_final: 0.8519 (mm) outliers start: 14 outliers final: 5 residues processed: 90 average time/residue: 0.0890 time to fit residues: 13.8582 Evaluate side-chains 80 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1778 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 202 optimal weight: 50.0000 chunk 80 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 195 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 115 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 149 optimal weight: 40.0000 chunk 78 optimal weight: 0.0070 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A1639 ASN A1660 ASN A1889 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.096280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.067589 restraints weight = 45080.586| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 3.64 r_work: 0.3027 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14679 Z= 0.156 Angle : 0.431 6.153 19388 Z= 0.241 Chirality : 0.043 0.146 1525 Planarity : 0.003 0.031 2919 Dihedral : 3.676 18.251 2463 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.97 % Allowed : 8.94 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.18), residues: 2364 helix: 1.97 (0.20), residues: 714 sheet: -0.34 (0.23), residues: 493 loop : 0.43 (0.20), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 406 TYR 0.034 0.001 TYR A 478 PHE 0.012 0.001 PHE A 186 TRP 0.013 0.001 TRP A 102 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00356 (14679) covalent geometry : angle 0.43111 (19388) hydrogen bonds : bond 0.03010 ( 794) hydrogen bonds : angle 4.36579 ( 2133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3791 (tpt) cc_final: 0.3585 (tpt) REVERT: A 77 GLU cc_start: 0.8827 (tt0) cc_final: 0.8454 (tm-30) REVERT: A 277 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8751 (tp) REVERT: A 310 ASP cc_start: 0.8582 (t0) cc_final: 0.8196 (t0) REVERT: A 321 MET cc_start: 0.8806 (mmt) cc_final: 0.8266 (mmt) REVERT: A 445 ARG cc_start: 0.8610 (ptm160) cc_final: 0.8309 (ptp-170) REVERT: A 447 MET cc_start: 0.9241 (tpp) cc_final: 0.8011 (mpp) REVERT: A 448 MET cc_start: 0.9073 (mtm) cc_final: 0.8132 (ptp) REVERT: A 449 GLU cc_start: 0.8779 (mp0) cc_final: 0.7952 (mp0) REVERT: A 489 MET cc_start: 0.8848 (mtp) cc_final: 0.8561 (mtp) REVERT: A 765 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8614 (tp30) REVERT: A 854 TYR cc_start: 0.8552 (t80) cc_final: 0.8104 (t80) REVERT: A 1794 GLU cc_start: 0.8876 (tt0) cc_final: 0.8521 (tm-30) REVERT: A 1840 ASP cc_start: 0.8758 (t0) cc_final: 0.7810 (t0) REVERT: A 1876 ILE cc_start: 0.8817 (mt) cc_final: 0.8512 (mm) outliers start: 11 outliers final: 5 residues processed: 90 average time/residue: 0.0971 time to fit residues: 14.7749 Evaluate side-chains 84 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 968 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 100 optimal weight: 5.9990 chunk 70 optimal weight: 0.0470 chunk 73 optimal weight: 0.9980 chunk 153 optimal weight: 0.0070 chunk 209 optimal weight: 1.9990 chunk 127 optimal weight: 50.0000 chunk 64 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 129 optimal weight: 40.0000 chunk 47 optimal weight: 0.5980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.096750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.068027 restraints weight = 44631.400| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.63 r_work: 0.3042 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14679 Z= 0.123 Angle : 0.410 6.801 19388 Z= 0.230 Chirality : 0.042 0.141 1525 Planarity : 0.002 0.032 2919 Dihedral : 3.508 17.492 2463 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.97 % Allowed : 9.29 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.18), residues: 2364 helix: 2.07 (0.20), residues: 715 sheet: -0.24 (0.23), residues: 488 loop : 0.42 (0.20), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 406 TYR 0.030 0.001 TYR A 478 PHE 0.012 0.001 PHE A 186 TRP 0.010 0.001 TRP A 102 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00279 (14679) covalent geometry : angle 0.41041 (19388) hydrogen bonds : bond 0.02835 ( 794) hydrogen bonds : angle 4.23142 ( 2133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3784 (tpt) cc_final: 0.3554 (tpt) REVERT: A 77 GLU cc_start: 0.8804 (tt0) cc_final: 0.8421 (tm-30) REVERT: A 310 ASP cc_start: 0.8576 (t0) cc_final: 0.8164 (t0) REVERT: A 321 MET cc_start: 0.8795 (mmt) cc_final: 0.8284 (mmt) REVERT: A 445 ARG cc_start: 0.8591 (ptm160) cc_final: 0.8366 (ptp-170) REVERT: A 447 MET cc_start: 0.9226 (tpp) cc_final: 0.7952 (mpp) REVERT: A 448 MET cc_start: 0.8990 (mtm) cc_final: 0.8327 (ptp) REVERT: A 449 GLU cc_start: 0.8775 (mp0) cc_final: 0.7992 (mp0) REVERT: A 489 MET cc_start: 0.8878 (mtp) cc_final: 0.8602 (mtp) REVERT: A 765 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8584 (tp30) REVERT: A 854 TYR cc_start: 0.8563 (t80) cc_final: 0.8129 (t80) REVERT: A 1794 GLU cc_start: 0.8867 (tt0) cc_final: 0.8513 (tm-30) REVERT: A 1840 ASP cc_start: 0.8726 (t0) cc_final: 0.7717 (t0) REVERT: A 1876 ILE cc_start: 0.8802 (mt) cc_final: 0.8506 (mm) outliers start: 11 outliers final: 6 residues processed: 92 average time/residue: 0.0944 time to fit residues: 14.5046 Evaluate side-chains 84 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1021 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 204 optimal weight: 40.0000 chunk 231 optimal weight: 50.0000 chunk 149 optimal weight: 40.0000 chunk 174 optimal weight: 0.0270 chunk 175 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 145 optimal weight: 0.0570 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1639 ASN A1689 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.096297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.067467 restraints weight = 44620.944| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.62 r_work: 0.3035 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14679 Z= 0.150 Angle : 0.431 8.161 19388 Z= 0.239 Chirality : 0.043 0.158 1525 Planarity : 0.002 0.032 2919 Dihedral : 3.530 17.647 2463 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.97 % Allowed : 9.38 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.18), residues: 2364 helix: 2.05 (0.20), residues: 715 sheet: -0.28 (0.23), residues: 497 loop : 0.43 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 406 TYR 0.030 0.001 TYR A 478 PHE 0.012 0.001 PHE A 186 TRP 0.012 0.001 TRP A 102 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00344 (14679) covalent geometry : angle 0.43116 (19388) hydrogen bonds : bond 0.02917 ( 794) hydrogen bonds : angle 4.24858 ( 2133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3673 (tpt) cc_final: 0.3392 (tpt) REVERT: A 77 GLU cc_start: 0.8805 (tt0) cc_final: 0.8430 (tm-30) REVERT: A 310 ASP cc_start: 0.8598 (t0) cc_final: 0.8183 (t0) REVERT: A 321 MET cc_start: 0.8796 (mmt) cc_final: 0.8265 (mmt) REVERT: A 445 ARG cc_start: 0.8620 (ptm160) cc_final: 0.8308 (ptp-170) REVERT: A 447 MET cc_start: 0.9229 (tpp) cc_final: 0.7949 (mpp) REVERT: A 448 MET cc_start: 0.8989 (mtm) cc_final: 0.8361 (ptp) REVERT: A 449 GLU cc_start: 0.8788 (mp0) cc_final: 0.7999 (mp0) REVERT: A 489 MET cc_start: 0.8893 (mtp) cc_final: 0.8604 (mtp) REVERT: A 700 MET cc_start: 0.9081 (tpp) cc_final: 0.8767 (tpp) REVERT: A 765 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8595 (tp30) REVERT: A 854 TYR cc_start: 0.8579 (t80) cc_final: 0.8138 (t80) REVERT: A 1661 TYR cc_start: 0.8633 (OUTLIER) cc_final: 0.8342 (t80) REVERT: A 1794 GLU cc_start: 0.8852 (tt0) cc_final: 0.8490 (tm-30) REVERT: A 1840 ASP cc_start: 0.8724 (t0) cc_final: 0.7689 (t0) REVERT: A 1876 ILE cc_start: 0.8812 (mt) cc_final: 0.8520 (mm) outliers start: 11 outliers final: 8 residues processed: 90 average time/residue: 0.0995 time to fit residues: 14.6833 Evaluate side-chains 87 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1661 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 108 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 183 optimal weight: 0.4980 chunk 182 optimal weight: 0.6980 chunk 179 optimal weight: 0.0770 chunk 150 optimal weight: 40.0000 chunk 22 optimal weight: 0.5980 chunk 207 optimal weight: 50.0000 chunk 122 optimal weight: 10.0000 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A1639 ASN A1870 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.097274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.068511 restraints weight = 44955.733| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.65 r_work: 0.3060 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14679 Z= 0.103 Angle : 0.398 6.263 19388 Z= 0.223 Chirality : 0.042 0.139 1525 Planarity : 0.002 0.032 2919 Dihedral : 3.379 15.852 2463 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.97 % Allowed : 9.38 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.18), residues: 2364 helix: 2.17 (0.20), residues: 716 sheet: -0.20 (0.24), residues: 491 loop : 0.46 (0.20), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.029 0.001 TYR A 478 PHE 0.010 0.001 PHE A 186 TRP 0.009 0.001 TRP A 102 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00230 (14679) covalent geometry : angle 0.39768 (19388) hydrogen bonds : bond 0.02660 ( 794) hydrogen bonds : angle 4.08709 ( 2133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8796 (tt0) cc_final: 0.8522 (mt-10) REVERT: A 310 ASP cc_start: 0.8557 (t0) cc_final: 0.8128 (t0) REVERT: A 321 MET cc_start: 0.8783 (mmt) cc_final: 0.8291 (mmt) REVERT: A 445 ARG cc_start: 0.8613 (ptm160) cc_final: 0.8318 (ptp-170) REVERT: A 447 MET cc_start: 0.9273 (tpp) cc_final: 0.8025 (mpp) REVERT: A 448 MET cc_start: 0.8933 (mtm) cc_final: 0.8253 (ptp) REVERT: A 449 GLU cc_start: 0.8756 (mp0) cc_final: 0.7967 (mp0) REVERT: A 489 MET cc_start: 0.8898 (mtp) cc_final: 0.8618 (mtp) REVERT: A 516 MET cc_start: 0.8462 (ttp) cc_final: 0.8240 (ttp) REVERT: A 700 MET cc_start: 0.9070 (tpp) cc_final: 0.8802 (tpp) REVERT: A 765 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8566 (tp30) REVERT: A 854 TYR cc_start: 0.8564 (t80) cc_final: 0.8134 (t80) REVERT: A 1661 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8348 (t80) REVERT: A 1794 GLU cc_start: 0.8807 (tt0) cc_final: 0.8479 (tm-30) REVERT: A 1840 ASP cc_start: 0.8711 (t0) cc_final: 0.7688 (t0) REVERT: A 1876 ILE cc_start: 0.8808 (mt) cc_final: 0.8533 (mm) outliers start: 11 outliers final: 8 residues processed: 91 average time/residue: 0.0953 time to fit residues: 14.5830 Evaluate side-chains 89 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1661 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 82 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.3980 chunk 140 optimal weight: 50.0000 chunk 185 optimal weight: 2.9990 chunk 198 optimal weight: 30.0000 chunk 99 optimal weight: 4.9990 chunk 129 optimal weight: 0.0870 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.095680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067145 restraints weight = 45733.405| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.73 r_work: 0.3009 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14679 Z= 0.191 Angle : 0.459 8.058 19388 Z= 0.253 Chirality : 0.044 0.165 1525 Planarity : 0.003 0.033 2919 Dihedral : 3.558 18.773 2463 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.80 % Allowed : 9.56 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.18), residues: 2364 helix: 2.07 (0.20), residues: 713 sheet: -0.36 (0.23), residues: 533 loop : 0.46 (0.20), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 455 TYR 0.035 0.002 TYR A 478 PHE 0.013 0.001 PHE A 186 TRP 0.014 0.001 TRP A 102 HIS 0.004 0.001 HIS A 334 Details of bonding type rmsd covalent geometry : bond 0.00441 (14679) covalent geometry : angle 0.45854 (19388) hydrogen bonds : bond 0.03064 ( 794) hydrogen bonds : angle 4.29251 ( 2133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4728 Ramachandran restraints generated. 2364 Oldfield, 0 Emsley, 2364 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3505 (tpt) cc_final: 0.3227 (tpt) REVERT: A 77 GLU cc_start: 0.8824 (tt0) cc_final: 0.8451 (tm-30) REVERT: A 310 ASP cc_start: 0.8599 (t0) cc_final: 0.8179 (t0) REVERT: A 321 MET cc_start: 0.8797 (mmt) cc_final: 0.8223 (mmt) REVERT: A 445 ARG cc_start: 0.8635 (ptm160) cc_final: 0.8358 (ptp-170) REVERT: A 447 MET cc_start: 0.9287 (tpp) cc_final: 0.8032 (mpp) REVERT: A 448 MET cc_start: 0.8996 (mtm) cc_final: 0.8282 (ptp) REVERT: A 449 GLU cc_start: 0.8828 (mp0) cc_final: 0.7989 (mp0) REVERT: A 489 MET cc_start: 0.8943 (mtp) cc_final: 0.8636 (mtp) REVERT: A 516 MET cc_start: 0.8589 (ttp) cc_final: 0.8349 (ttp) REVERT: A 700 MET cc_start: 0.9142 (tpp) cc_final: 0.8755 (tpp) REVERT: A 765 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8591 (tp30) REVERT: A 854 TYR cc_start: 0.8555 (t80) cc_final: 0.8057 (t80) REVERT: A 1794 GLU cc_start: 0.8861 (tt0) cc_final: 0.8471 (tm-30) REVERT: A 1840 ASP cc_start: 0.8735 (t0) cc_final: 0.7682 (t0) REVERT: A 1876 ILE cc_start: 0.8812 (mt) cc_final: 0.8524 (mm) outliers start: 9 outliers final: 7 residues processed: 86 average time/residue: 0.0970 time to fit residues: 13.8883 Evaluate side-chains 85 residues out of total 2137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 578 ILE Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 1021 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 153 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 225 optimal weight: 20.0000 chunk 20 optimal weight: 0.0970 chunk 97 optimal weight: 0.0670 chunk 103 optimal weight: 9.9990 chunk 222 optimal weight: 8.9990 chunk 208 optimal weight: 50.0000 chunk 56 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1639 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.096837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.068330 restraints weight = 44723.792| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.62 r_work: 0.3050 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14679 Z= 0.115 Angle : 0.412 7.330 19388 Z= 0.230 Chirality : 0.042 0.143 1525 Planarity : 0.002 0.034 2919 Dihedral : 3.417 17.590 2463 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.71 % Allowed : 10.09 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.18), residues: 2364 helix: 2.18 (0.20), residues: 715 sheet: -0.28 (0.23), residues: 526 loop : 0.49 (0.20), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 406 TYR 0.028 0.001 TYR A 478 PHE 0.010 0.001 PHE A 186 TRP 0.010 0.001 TRP A 102 HIS 0.003 0.001 HIS A 492 Details of bonding type rmsd covalent geometry : bond 0.00261 (14679) covalent geometry : angle 0.41163 (19388) hydrogen bonds : bond 0.02724 ( 794) hydrogen bonds : angle 4.12910 ( 2133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4471.97 seconds wall clock time: 76 minutes 55.43 seconds (4615.43 seconds total)