Starting phenix.real_space_refine on Tue Sep 24 09:07:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvz_32863/09_2024/7wvz_32863.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvz_32863/09_2024/7wvz_32863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvz_32863/09_2024/7wvz_32863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvz_32863/09_2024/7wvz_32863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvz_32863/09_2024/7wvz_32863.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wvz_32863/09_2024/7wvz_32863.cif" } resolution = 3.38 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= 0.000 sd= 0.006 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: 5 Type Number sf(0) Gaussians S 47 5.16 5 C 15607 2.51 5 N 4654 2.21 5 O 4757 1.98 5 H 24824 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 119 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 49889 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 25011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1719, 25011 Classifications: {'peptide': 1719} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 121, 'TRANS': 1595} Chain: "B" Number of atoms: 24878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1711, 24878 Classifications: {'peptide': 1711} Link IDs: {'PCIS': 2, 'PTRANS': 120, 'TRANS': 1588} Time building chain proxies: 17.93, per 1000 atoms: 0.36 Number of scatterers: 49889 At special positions: 0 Unit cell: (187, 156.2, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 O 4757 8.00 N 4654 7.00 C 15607 6.00 H 24824 1.00 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: 9.95 Conformation dependent library (CDL) restraints added in 3.4 seconds 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6008 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 18 sheets defined 46.4% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 2 through 29 removed outlier: 3.646A pdb=" N LYS A 6 " --> pdb=" O PRO A 2 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 33 Processing helix chain 'A' and resid 51 through 61 Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.926A pdb=" N LEU A 81 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.747A pdb=" N PHE A 100 " --> pdb=" O ASP A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 110 Processing helix chain 'A' and resid 111 through 129 removed outlier: 3.525A pdb=" N TRP A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 136 removed outlier: 3.526A pdb=" N ARG A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 160 through 172 removed outlier: 3.877A pdb=" N ASP A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N HIS A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLY A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.727A pdb=" N GLY A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 197 No H-bonds generated for 'chain 'A' and resid 195 through 197' Processing helix chain 'A' and resid 198 through 213 Processing helix chain 'A' and resid 230 through 239 Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 302 through 320 Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 336 through 350 removed outlier: 3.979A pdb=" N GLY A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 376 through 392 Processing helix chain 'A' and resid 408 through 412 removed outlier: 4.035A pdb=" N SER A 411 " --> pdb=" O ASP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 491 removed outlier: 3.878A pdb=" N ALA A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 557 through 563 removed outlier: 3.855A pdb=" N GLY A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 569 Processing helix chain 'A' and resid 569 through 582 removed outlier: 3.742A pdb=" N TYR A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU A 580 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 581 " --> pdb=" O GLY A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 597 removed outlier: 4.296A pdb=" N HIS A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 601 removed outlier: 3.841A pdb=" N GLY A 601 " --> pdb=" O GLY A 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 598 through 601' Processing helix chain 'A' and resid 602 through 610 removed outlier: 3.729A pdb=" N ALA A 606 " --> pdb=" O PRO A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 619 through 640 Processing helix chain 'A' and resid 652 through 661 removed outlier: 4.095A pdb=" N ALA A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 685 Processing helix chain 'A' and resid 696 through 707 Processing helix chain 'A' and resid 729 through 743 Processing helix chain 'A' and resid 758 through 774 removed outlier: 3.843A pdb=" N ALA A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 800 Processing helix chain 'A' and resid 801 through 808 removed outlier: 3.948A pdb=" N HIS A 808 " --> pdb=" O HIS A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 825 Processing helix chain 'A' and resid 839 through 848 Processing helix chain 'A' and resid 868 through 884 removed outlier: 3.885A pdb=" N ALA A 872 " --> pdb=" O PRO A 868 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 873 " --> pdb=" O PRO A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 894 removed outlier: 4.135A pdb=" N PHE A 893 " --> pdb=" O TRP A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 925 removed outlier: 3.599A pdb=" N VAL A 924 " --> pdb=" O GLN A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 960 removed outlier: 3.695A pdb=" N GLY A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 984 removed outlier: 3.538A pdb=" N LEU A 980 " --> pdb=" O LEU A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1065 Processing helix chain 'A' and resid 1073 through 1083 Processing helix chain 'A' and resid 1090 through 1093 Processing helix chain 'A' and resid 1120 through 1122 No H-bonds generated for 'chain 'A' and resid 1120 through 1122' Processing helix chain 'A' and resid 1123 through 1138 removed outlier: 3.866A pdb=" N SER A1138 " --> pdb=" O LEU A1134 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1197 Processing helix chain 'A' and resid 1200 through 1205 removed outlier: 3.765A pdb=" N LEU A1204 " --> pdb=" O GLU A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1241 through 1255 Processing helix chain 'A' and resid 1282 through 1296 removed outlier: 4.062A pdb=" N VAL A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A1293 " --> pdb=" O THR A1289 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1310 No H-bonds generated for 'chain 'A' and resid 1308 through 1310' Processing helix chain 'A' and resid 1311 through 1317 removed outlier: 4.008A pdb=" N ALA A1315 " --> pdb=" O ALA A1311 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1344 removed outlier: 3.877A pdb=" N GLU A1342 " --> pdb=" O GLY A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1345 through 1347 No H-bonds generated for 'chain 'A' and resid 1345 through 1347' Processing helix chain 'A' and resid 1367 through 1369 No H-bonds generated for 'chain 'A' and resid 1367 through 1369' Processing helix chain 'A' and resid 1370 through 1384 removed outlier: 4.190A pdb=" N THR A1374 " --> pdb=" O GLN A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1412 Processing helix chain 'A' and resid 1438 through 1444 Processing helix chain 'A' and resid 1458 through 1472 Processing helix chain 'A' and resid 1482 through 1486 removed outlier: 4.540A pdb=" N GLU A1485 " --> pdb=" O ALA A1482 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1497 Processing helix chain 'A' and resid 1512 through 1524 Processing helix chain 'A' and resid 1544 through 1548 Processing helix chain 'A' and resid 1549 through 1574 removed outlier: 4.990A pdb=" N GLY A1563 " --> pdb=" O GLY A1559 " (cutoff:3.500A) Proline residue: A1564 - end of helix Processing helix chain 'A' and resid 1575 through 1580 removed outlier: 3.636A pdb=" N GLY A1579 " --> pdb=" O GLY A1575 " (cutoff:3.500A) Processing helix chain 'A' and resid 1590 through 1592 No H-bonds generated for 'chain 'A' and resid 1590 through 1592' Processing helix chain 'A' and resid 1598 through 1618 Processing helix chain 'A' and resid 1630 through 1634 Processing helix chain 'A' and resid 1639 through 1648 Processing helix chain 'A' and resid 1654 through 1663 Processing helix chain 'A' and resid 1664 through 1668 removed outlier: 4.209A pdb=" N ALA A1667 " --> pdb=" O PRO A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1691 Processing helix chain 'B' and resid 11 through 24 Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 51 through 61 Processing helix chain 'B' and resid 78 through 82 removed outlier: 3.881A pdb=" N LEU B 81 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 111 through 129 removed outlier: 3.647A pdb=" N TRP B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 160 through 172 removed outlier: 4.284A pdb=" N HIS B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N LEU B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 removed outlier: 4.292A pdb=" N SER B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 198 through 214 Processing helix chain 'B' and resid 230 through 239 Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 302 through 320 Processing helix chain 'B' and resid 322 through 326 removed outlier: 3.633A pdb=" N VAL B 326 " --> pdb=" O ALA B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 Processing helix chain 'B' and resid 350 through 354 Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 373 through 375 No H-bonds generated for 'chain 'B' and resid 373 through 375' Processing helix chain 'B' and resid 376 through 392 Processing helix chain 'B' and resid 408 through 412 removed outlier: 4.453A pdb=" N SER B 411 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 490 removed outlier: 3.813A pdb=" N ALA B 488 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 506 removed outlier: 3.822A pdb=" N THR B 504 " --> pdb=" O HIS B 500 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 532 Processing helix chain 'B' and resid 557 through 562 Processing helix chain 'B' and resid 564 through 569 Processing helix chain 'B' and resid 569 through 582 removed outlier: 4.334A pdb=" N GLY B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU B 578 " --> pdb=" O THR B 574 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 579 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU B 580 " --> pdb=" O ARG B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 597 removed outlier: 4.390A pdb=" N HIS B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 601 removed outlier: 4.103A pdb=" N GLY B 601 " --> pdb=" O GLY B 598 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 598 through 601' Processing helix chain 'B' and resid 602 through 610 removed outlier: 3.501A pdb=" N ALA B 606 " --> pdb=" O PRO B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 617 removed outlier: 3.593A pdb=" N ALA B 616 " --> pdb=" O GLY B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 640 Processing helix chain 'B' and resid 652 through 661 removed outlier: 4.194A pdb=" N ALA B 656 " --> pdb=" O ALA B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 685 Processing helix chain 'B' and resid 696 through 707 removed outlier: 3.935A pdb=" N SER B 705 " --> pdb=" O ARG B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 711 Processing helix chain 'B' and resid 729 through 743 Processing helix chain 'B' and resid 758 through 774 removed outlier: 3.534A pdb=" N GLU B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 800 Processing helix chain 'B' and resid 801 through 807 Processing helix chain 'B' and resid 808 through 810 No H-bonds generated for 'chain 'B' and resid 808 through 810' Processing helix chain 'B' and resid 814 through 825 removed outlier: 3.528A pdb=" N GLY B 818 " --> pdb=" O ARG B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 848 Processing helix chain 'B' and resid 868 through 884 Processing helix chain 'B' and resid 888 through 893 removed outlier: 4.139A pdb=" N GLN B 891 " --> pdb=" O ASP B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 960 removed outlier: 4.216A pdb=" N ALA B 957 " --> pdb=" O PRO B 953 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY B 958 " --> pdb=" O GLY B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 984 Processing helix chain 'B' and resid 1061 through 1069 Proline residue: B1066 - end of helix Processing helix chain 'B' and resid 1073 through 1083 Processing helix chain 'B' and resid 1090 through 1093 Processing helix chain 'B' and resid 1122 through 1138 removed outlier: 4.353A pdb=" N ALA B1126 " --> pdb=" O SER B1122 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B1138 " --> pdb=" O LEU B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1193 through 1197 Processing helix chain 'B' and resid 1229 through 1233 removed outlier: 3.915A pdb=" N THR B1232 " --> pdb=" O GLY B1229 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLY B1233 " --> pdb=" O GLY B1230 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1229 through 1233' Processing helix chain 'B' and resid 1241 through 1255 Processing helix chain 'B' and resid 1282 through 1296 removed outlier: 4.000A pdb=" N VAL B1286 " --> pdb=" O ASP B1282 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B1293 " --> pdb=" O THR B1289 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1310 No H-bonds generated for 'chain 'B' and resid 1308 through 1310' Processing helix chain 'B' and resid 1311 through 1317 Processing helix chain 'B' and resid 1320 through 1344 removed outlier: 3.712A pdb=" N GLU B1342 " --> pdb=" O GLY B1338 " (cutoff:3.500A) Processing helix chain 'B' and resid 1345 through 1347 No H-bonds generated for 'chain 'B' and resid 1345 through 1347' Processing helix chain 'B' and resid 1367 through 1370 Processing helix chain 'B' and resid 1371 through 1384 Processing helix chain 'B' and resid 1402 through 1412 Processing helix chain 'B' and resid 1438 through 1444 removed outlier: 3.506A pdb=" N GLU B1442 " --> pdb=" O ALA B1438 " (cutoff:3.500A) Processing helix chain 'B' and resid 1458 through 1472 Processing helix chain 'B' and resid 1489 through 1497 Processing helix chain 'B' and resid 1512 through 1522 Processing helix chain 'B' and resid 1549 through 1574 removed outlier: 5.022A pdb=" N GLY B1563 " --> pdb=" O GLY B1559 " (cutoff:3.500A) Proline residue: B1564 - end of helix Processing helix chain 'B' and resid 1575 through 1580 removed outlier: 4.137A pdb=" N GLY B1579 " --> pdb=" O GLY B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1590 through 1592 No H-bonds generated for 'chain 'B' and resid 1590 through 1592' Processing helix chain 'B' and resid 1598 through 1618 Processing helix chain 'B' and resid 1630 through 1634 Processing helix chain 'B' and resid 1639 through 1648 Processing helix chain 'B' and resid 1654 through 1663 Processing helix chain 'B' and resid 1664 through 1669 removed outlier: 3.804A pdb=" N ALA B1667 " --> pdb=" O PRO B1664 " (cutoff:3.500A) Processing helix chain 'B' and resid 1683 through 1690 Processing sheet with id=AA1, first strand: chain 'A' and resid 414 through 416 removed outlier: 3.671A pdb=" N ALA A 328 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASN A 443 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE A 291 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS A 445 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR A 289 " --> pdb=" O HIS A 445 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE A 447 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A 284 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU A 268 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE A 41 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N MET A 266 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N CYS A 43 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA A 264 " --> pdb=" O CYS A 43 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N VAL A 191 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL A 142 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL A 193 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A 144 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N VAL B 191 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 142 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL B 193 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ALA B 144 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA B 264 " --> pdb=" O CYS B 43 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS B 43 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N MET B 266 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 41 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU B 268 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA B 284 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE B 447 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N THR B 289 " --> pdb=" O HIS B 445 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N HIS B 445 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE B 291 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ASN B 443 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA B 328 " --> pdb=" O ARG B 431 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU B 361 " --> pdb=" O ARG B 415 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA3, first strand: chain 'A' and resid 393 through 394 Processing sheet with id=AA4, first strand: chain 'A' and resid 467 through 473 Processing sheet with id=AA5, first strand: chain 'A' and resid 792 through 793 removed outlier: 3.625A pdb=" N GLN A 792 " --> pdb=" O SER A 787 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR A 647 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA A 646 " --> pdb=" O THR A 550 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 714 through 720 removed outlier: 6.607A pdb=" N VAL A 725 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N VAL A 718 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N THR A 723 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TRP A 692 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA A 749 " --> pdb=" O TRP A 692 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 935 through 936 removed outlier: 3.515A pdb=" N VAL A1026 " --> pdb=" O VAL A1048 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLY A1032 " --> pdb=" O GLU A1042 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU A1042 " --> pdb=" O GLY A1032 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLY A1045 " --> pdb=" O ILE A 997 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ILE A 997 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR A 993 " --> pdb=" O VAL A1049 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ASP A1149 " --> pdb=" O GLY A 996 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG A 998 " --> pdb=" O SER A1147 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER A1147 " --> pdb=" O ARG A 998 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A1148 " --> pdb=" O LEU A1191 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU A1191 " --> pdb=" O VAL A1148 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU A1185 " --> pdb=" O SER A1154 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N LEU A1185 " --> pdb=" O SER A1179 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER A1179 " --> pdb=" O LEU A1185 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N ALA A1187 " --> pdb=" O VAL A1177 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL A1177 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLN A1189 " --> pdb=" O ALA A1175 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ALA A1175 " --> pdb=" O GLN A1189 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ALA A1172 " --> pdb=" O GLY A1168 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N GLY A1168 " --> pdb=" O ALA A1172 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A1161 " --> pdb=" O VAL A1109 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A1098 " --> pdb=" O LEU A1072 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 967 through 969 removed outlier: 3.734A pdb=" N GLN A 962 " --> pdb=" O VAL A 969 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1274 through 1276 removed outlier: 8.708A pdb=" N GLU A1274 " --> pdb=" O ALA A1259 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA A1261 " --> pdb=" O GLU A1274 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL A1276 " --> pdb=" O ALA A1261 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA A1263 " --> pdb=" O VAL A1276 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLY A1264 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER A1234 " --> pdb=" O GLY A1302 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LEU A1304 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU A1236 " --> pdb=" O LEU A1304 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N HIS A1306 " --> pdb=" O LEU A1236 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N PHE A1238 " --> pdb=" O HIS A1306 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA A1301 " --> pdb=" O ARG A1349 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N VAL A1351 " --> pdb=" O ALA A1301 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A1303 " --> pdb=" O VAL A1351 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N CYS A1353 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A1305 " --> pdb=" O CYS A1353 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ALA A1355 " --> pdb=" O VAL A1305 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ILE A1350 " --> pdb=" O ALA A1390 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL A1392 " --> pdb=" O ILE A1350 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU A1352 " --> pdb=" O VAL A1392 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU A1394 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N SER A1354 " --> pdb=" O LEU A1394 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS A1389 " --> pdb=" O GLY A1417 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU A1419 " --> pdb=" O CYS A1389 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N GLN A1391 " --> pdb=" O LEU A1419 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL A1421 " --> pdb=" O GLN A1391 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP A1393 " --> pdb=" O VAL A1421 " (cutoff:3.500A) removed outlier: 14.947A pdb=" N ALA A1416 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 10.654A pdb=" N LEU A1431 " --> pdb=" O ALA A1416 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ARG A1418 " --> pdb=" O ALA A1429 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU A1676 " --> pdb=" O VAL A1214 " (cutoff:3.500A) removed outlier: 10.603A pdb=" N ALA A1677 " --> pdb=" O VAL A1622 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA A1624 " --> pdb=" O ALA A1677 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU A1679 " --> pdb=" O ALA A1624 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ALA A1626 " --> pdb=" O LEU A1679 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ARG A1531 " --> pdb=" O PHE A1582 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N VAL A1584 " --> pdb=" O ARG A1531 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL A1533 " --> pdb=" O VAL A1584 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N SER A1586 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N LEU A1535 " --> pdb=" O SER A1586 " (cutoff:3.500A) removed outlier: 9.634A pdb=" N SER A1588 " --> pdb=" O LEU A1535 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N THR A1451 " --> pdb=" O LEU A1530 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A1532 " --> pdb=" O THR A1451 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AB2, first strand: chain 'B' and resid 393 through 394 Processing sheet with id=AB3, first strand: chain 'B' and resid 467 through 473 Processing sheet with id=AB4, first strand: chain 'B' and resid 785 through 787 removed outlier: 6.553A pdb=" N THR B 647 " --> pdb=" O LEU B 786 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR B 550 " --> pdb=" O ALA B 646 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LEU B 648 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B 552 " --> pdb=" O LEU B 648 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N HIS B 650 " --> pdb=" O LEU B 552 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N PHE B 554 " --> pdb=" O HIS B 650 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 713 through 720 removed outlier: 6.461A pdb=" N VAL B 725 " --> pdb=" O ALA B 716 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL B 718 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N THR B 723 " --> pdb=" O VAL B 718 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER B 690 " --> pdb=" O PRO B 750 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 935 through 937 removed outlier: 4.703A pdb=" N SER B 946 " --> pdb=" O LEU B 937 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N GLY B1032 " --> pdb=" O GLU B1042 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N GLU B1042 " --> pdb=" O GLY B1032 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY B1045 " --> pdb=" O ILE B 997 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE B 997 " --> pdb=" O GLY B1045 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B1149 " --> pdb=" O GLY B 996 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ARG B 998 " --> pdb=" O SER B1147 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N SER B1147 " --> pdb=" O ARG B 998 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B1148 " --> pdb=" O LEU B1191 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B1191 " --> pdb=" O VAL B1148 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N LEU B1185 " --> pdb=" O SER B1154 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU B1185 " --> pdb=" O SER B1179 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N SER B1179 " --> pdb=" O LEU B1185 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ALA B1187 " --> pdb=" O VAL B1177 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B1177 " --> pdb=" O ALA B1187 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLN B1189 " --> pdb=" O ALA B1175 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALA B1175 " --> pdb=" O GLN B1189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL B1161 " --> pdb=" O VAL B1109 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL B1098 " --> pdb=" O LEU B1072 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 967 through 969 removed outlier: 3.735A pdb=" N GLN B 962 " --> pdb=" O VAL B 969 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1274 through 1276 removed outlier: 9.287A pdb=" N GLU B1274 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA B1261 " --> pdb=" O GLU B1274 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL B1276 " --> pdb=" O ALA B1261 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA B1263 " --> pdb=" O VAL B1276 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY B1264 " --> pdb=" O SER B1239 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER B1234 " --> pdb=" O VAL B1300 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B1302 " --> pdb=" O SER B1234 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA B1301 " --> pdb=" O ARG B1349 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL B1351 " --> pdb=" O ALA B1301 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B1303 " --> pdb=" O VAL B1351 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N CYS B1353 " --> pdb=" O LEU B1303 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B1305 " --> pdb=" O CYS B1353 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ALA B1355 " --> pdb=" O VAL B1305 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N CYS B1389 " --> pdb=" O GLY B1417 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU B1419 " --> pdb=" O CYS B1389 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN B1391 " --> pdb=" O LEU B1419 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL B1421 " --> pdb=" O GLN B1391 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP B1393 " --> pdb=" O VAL B1421 " (cutoff:3.500A) removed outlier: 14.867A pdb=" N ALA B1416 " --> pdb=" O LEU B1431 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N LEU B1431 " --> pdb=" O ALA B1416 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ARG B1418 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B1676 " --> pdb=" O VAL B1214 " (cutoff:3.500A) removed outlier: 10.829A pdb=" N ALA B1677 " --> pdb=" O VAL B1622 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA B1624 " --> pdb=" O ALA B1677 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU B1679 " --> pdb=" O ALA B1624 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ALA B1626 " --> pdb=" O LEU B1679 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ARG B1681 " --> pdb=" O ALA B1626 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE B1583 " --> pdb=" O VAL B1623 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ALA B1625 " --> pdb=" O PHE B1583 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU B1585 " --> pdb=" O ALA B1625 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N TRP B1627 " --> pdb=" O LEU B1585 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR B1587 " --> pdb=" O TRP B1627 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N THR B1451 " --> pdb=" O LEU B1530 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY B1532 " --> pdb=" O THR B1451 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR B1452 " --> pdb=" O VAL B1478 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ALA B1480 " --> pdb=" O TYR B1452 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N VAL B1454 " --> pdb=" O ALA B1480 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1274 through 1276 removed outlier: 9.287A pdb=" N GLU B1274 " --> pdb=" O ALA B1259 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ALA B1261 " --> pdb=" O GLU B1274 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N VAL B1276 " --> pdb=" O ALA B1261 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA B1263 " --> pdb=" O VAL B1276 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY B1264 " --> pdb=" O SER B1239 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER B1234 " --> pdb=" O VAL B1300 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B1302 " --> pdb=" O SER B1234 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ALA B1301 " --> pdb=" O ARG B1349 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL B1351 " --> pdb=" O ALA B1301 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LEU B1303 " --> pdb=" O VAL B1351 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N CYS B1353 " --> pdb=" O LEU B1303 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL B1305 " --> pdb=" O CYS B1353 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N ALA B1355 " --> pdb=" O VAL B1305 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N CYS B1389 " --> pdb=" O GLY B1417 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N LEU B1419 " --> pdb=" O CYS B1389 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN B1391 " --> pdb=" O LEU B1419 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL B1421 " --> pdb=" O GLN B1391 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASP B1393 " --> pdb=" O VAL B1421 " (cutoff:3.500A) removed outlier: 14.867A pdb=" N ALA B1416 " --> pdb=" O LEU B1431 " (cutoff:3.500A) removed outlier: 10.590A pdb=" N LEU B1431 " --> pdb=" O ALA B1416 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ARG B1418 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B1676 " --> pdb=" O VAL B1214 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ARG B1681 " --> pdb=" O TYR B1651 " (cutoff:3.500A) 1296 hydrogen bonds defined for protein. 3633 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: 23.04 Time building geometry restraints manager: 12.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.93 - 1.11: 24800 1.11 - 1.29: 4371 1.29 - 1.47: 8785 1.47 - 1.64: 12396 1.64 - 1.82: 70 Bond restraints: 50422 Sorted by residual: bond pdb=" NH2 ARG A1430 " pdb="HH22 ARG A1430 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N VAL A1109 " pdb=" H VAL A1109 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ALA A 652 " pdb=" H ALA A 652 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" CD1 TRP B 992 " pdb=" HD1 TRP B 992 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" N ASP A 537 " pdb=" H ASP A 537 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 50417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.14: 90927 7.14 - 14.28: 353 14.28 - 21.43: 0 21.43 - 28.57: 1 28.57 - 35.71: 2 Bond angle restraints: 91283 Sorted by residual: angle pdb=" N ASP A1271 " pdb=" CA ASP A1271 " pdb=" HA ASP A1271 " ideal model delta sigma weight residual 110.00 74.29 35.71 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CB ASP A1271 " pdb=" CA ASP A1271 " pdb=" HA ASP A1271 " ideal model delta sigma weight residual 109.00 80.05 28.95 3.00e+00 1.11e-01 9.31e+01 angle pdb=" C ASP A1271 " pdb=" CA ASP A1271 " pdb=" HA ASP A1271 " ideal model delta sigma weight residual 109.00 80.81 28.19 3.00e+00 1.11e-01 8.83e+01 angle pdb=" N ASP A1271 " pdb=" CA ASP A1271 " pdb=" C ASP A1271 " ideal model delta sigma weight residual 112.87 123.01 -10.14 1.20e+00 6.94e-01 7.13e+01 angle pdb=" CA ASP A1271 " pdb=" CB ASP A1271 " pdb=" CG ASP A1271 " ideal model delta sigma weight residual 112.60 120.15 -7.55 1.00e+00 1.00e+00 5.70e+01 ... (remaining 91278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 21505 17.81 - 35.63: 1326 35.63 - 53.44: 631 53.44 - 71.26: 221 71.26 - 89.07: 30 Dihedral angle restraints: 23713 sinusoidal: 13187 harmonic: 10526 Sorted by residual: dihedral pdb=" N ASP A1271 " pdb=" C ASP A1271 " pdb=" CA ASP A1271 " pdb=" CB ASP A1271 " ideal model delta harmonic sigma weight residual 122.80 140.21 -17.41 0 2.50e+00 1.60e-01 4.85e+01 dihedral pdb=" C ASP A1271 " pdb=" N ASP A1271 " pdb=" CA ASP A1271 " pdb=" CB ASP A1271 " ideal model delta harmonic sigma weight residual -122.60 -138.51 15.91 0 2.50e+00 1.60e-01 4.05e+01 dihedral pdb=" CA LEU B1413 " pdb=" C LEU B1413 " pdb=" N PRO B1414 " pdb=" CA PRO B1414 " ideal model delta harmonic sigma weight residual 180.00 150.51 29.49 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 23710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 3479 0.144 - 0.288: 437 0.288 - 0.433: 18 0.433 - 0.577: 0 0.577 - 0.721: 1 Chirality restraints: 3935 Sorted by residual: chirality pdb=" CA ASP A1271 " pdb=" N ASP A1271 " pdb=" C ASP A1271 " pdb=" CB ASP A1271 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA ASP B1222 " pdb=" N ASP B1222 " pdb=" C ASP B1222 " pdb=" CB ASP B1222 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.66e+00 chirality pdb=" CA LEU B1663 " pdb=" N LEU B1663 " pdb=" C LEU B1663 " pdb=" CB LEU B1663 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.88e+00 ... (remaining 3932 not shown) Planarity restraints: 7914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1337 " -0.259 9.50e-02 1.11e+02 1.34e-01 2.45e+02 pdb=" NE ARG A1337 " -0.083 2.00e-02 2.50e+03 pdb=" CZ ARG A1337 " -0.079 2.00e-02 2.50e+03 pdb=" NH1 ARG A1337 " -0.067 2.00e-02 2.50e+03 pdb=" NH2 ARG A1337 " -0.067 2.00e-02 2.50e+03 pdb="HH11 ARG A1337 " 0.197 2.00e-02 2.50e+03 pdb="HH12 ARG A1337 " -0.048 2.00e-02 2.50e+03 pdb="HH21 ARG A1337 " 0.177 2.00e-02 2.50e+03 pdb="HH22 ARG A1337 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1527 " 0.127 9.50e-02 1.11e+02 1.11e-01 2.41e+02 pdb=" NE ARG A1527 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A1527 " -0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG A1527 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A1527 " -0.050 2.00e-02 2.50e+03 pdb="HH11 ARG A1527 " -0.019 2.00e-02 2.50e+03 pdb="HH12 ARG A1527 " 0.170 2.00e-02 2.50e+03 pdb="HH21 ARG A1527 " 0.175 2.00e-02 2.50e+03 pdb="HH22 ARG A1527 " -0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1337 " -0.274 9.50e-02 1.11e+02 1.35e-01 2.29e+02 pdb=" NE ARG B1337 " -0.088 2.00e-02 2.50e+03 pdb=" CZ ARG B1337 " -0.071 2.00e-02 2.50e+03 pdb=" NH1 ARG B1337 " -0.063 2.00e-02 2.50e+03 pdb=" NH2 ARG B1337 " -0.043 2.00e-02 2.50e+03 pdb="HH11 ARG B1337 " 0.195 2.00e-02 2.50e+03 pdb="HH12 ARG B1337 " -0.050 2.00e-02 2.50e+03 pdb="HH21 ARG B1337 " 0.167 2.00e-02 2.50e+03 pdb="HH22 ARG B1337 " -0.034 2.00e-02 2.50e+03 ... (remaining 7911 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 3357 2.18 - 2.78: 88565 2.78 - 3.39: 143068 3.39 - 3.99: 189278 3.99 - 4.60: 278102 Nonbonded interactions: 702370 Sorted by model distance: nonbonded pdb=" OD2 ASP A 834 " pdb=" HG SER A 861 " model vdw 1.572 2.450 nonbonded pdb=" HG SER A1512 " pdb=" OD1 ASP A1515 " model vdw 1.596 2.450 nonbonded pdb=" OE1 GLU B 654 " pdb=" HG SER B 787 " model vdw 1.596 2.450 nonbonded pdb=" HG SER A 665 " pdb=" OD2 ASP A 668 " model vdw 1.602 2.450 nonbonded pdb=" HG1 THR A 322 " pdb=" OD1 ASP A 324 " model vdw 1.604 2.450 ... (remaining 702365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 9 through 1719) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.750 Extract box with map and model: 1.600 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 89.940 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.150 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: 0.020 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 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 : 0.012 0.046 25598 Z= 0.794 Angle : 1.766 10.136 34943 Z= 1.185 Chirality : 0.094 0.721 3935 Planarity : 0.017 0.147 4731 Dihedral : 12.985 89.072 9227 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.35 % Favored : 95.50 % Rotamer: Outliers : 1.38 % Allowed : 2.88 % Favored : 95.74 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 1.63 % 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: -0.87 (0.13), residues: 3426 helix: -0.65 (0.12), residues: 1355 sheet: 0.83 (0.24), residues: 463 loop : -0.83 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.135 0.021 TRP A 122 HIS 0.020 0.004 HIS B1505 PHE 0.059 0.013 PHE B1290 TYR 0.132 0.026 TYR B 659 ARG 0.015 0.001 ARG A1613 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 477 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3129 (mtm) cc_final: 0.2540 (mtt) REVERT: A 98 TYR cc_start: 0.7882 (t80) cc_final: 0.7028 (m-80) REVERT: A 165 ASP cc_start: 0.7518 (m-30) cc_final: 0.7310 (t0) REVERT: A 235 ASP cc_start: 0.7615 (t0) cc_final: 0.6683 (m-30) REVERT: A 609 ARG cc_start: 0.6154 (OUTLIER) cc_final: 0.5904 (tpt170) REVERT: A 850 PHE cc_start: 0.7090 (OUTLIER) cc_final: 0.5723 (t80) REVERT: A 1029 PHE cc_start: 0.7944 (m-80) cc_final: 0.7628 (m-10) REVERT: A 1538 GLN cc_start: 0.8032 (mt0) cc_final: 0.7659 (mm110) REVERT: A 1692 HIS cc_start: 0.6877 (m-70) cc_final: 0.6448 (m-70) REVERT: A 1719 MET cc_start: 0.2437 (ttm) cc_final: 0.1727 (tpt) REVERT: B 54 ASP cc_start: 0.7826 (m-30) cc_final: 0.7589 (m-30) REVERT: B 155 MET cc_start: 0.7242 (mtm) cc_final: 0.6991 (mtp) REVERT: B 365 SER cc_start: 0.8861 (t) cc_final: 0.8640 (p) REVERT: B 484 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6855 (mt-10) REVERT: B 833 LEU cc_start: 0.7290 (mt) cc_final: 0.6566 (mt) REVERT: B 883 ASP cc_start: 0.8249 (t70) cc_final: 0.7600 (t70) REVERT: B 888 ASP cc_start: 0.8114 (t0) cc_final: 0.7798 (t0) REVERT: B 1515 ASP cc_start: 0.5497 (m-30) cc_final: 0.5273 (m-30) REVERT: B 1552 ARG cc_start: 0.6603 (ttt180) cc_final: 0.6176 (ttt90) REVERT: B 1692 HIS cc_start: 0.5451 (OUTLIER) cc_final: 0.5232 (m-70) REVERT: B 1702 THR cc_start: 0.8531 (m) cc_final: 0.8145 (p) outliers start: 34 outliers final: 8 residues processed: 506 average time/residue: 0.9489 time to fit residues: 680.2175 Evaluate side-chains 265 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 254 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 609 ARG Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 1304 LEU Chi-restraints excluded: chain B residue 1692 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 288 optimal weight: 6.9990 chunk 259 optimal weight: 1.9990 chunk 143 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 310 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 739 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 HIS B 945 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25598 Z= 0.248 Angle : 0.699 9.146 34943 Z= 0.367 Chirality : 0.044 0.395 3935 Planarity : 0.007 0.078 4731 Dihedral : 6.635 59.263 3784 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.94 % Rotamer: Outliers : 1.42 % Allowed : 6.37 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.20 (0.14), residues: 3426 helix: 0.35 (0.14), residues: 1373 sheet: 0.51 (0.22), residues: 516 loop : -0.71 (0.15), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 740 HIS 0.011 0.002 HIS A 739 PHE 0.022 0.002 PHE A1290 TYR 0.014 0.001 TYR A 151 ARG 0.006 0.001 ARG A1460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 279 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3186 (mtm) cc_final: 0.2900 (mtt) REVERT: A 98 TYR cc_start: 0.7699 (t80) cc_final: 0.6881 (m-80) REVERT: A 162 GLN cc_start: 0.7522 (mp10) cc_final: 0.7175 (mp10) REVERT: A 850 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6264 (t80) REVERT: A 883 ASP cc_start: 0.7866 (t70) cc_final: 0.7407 (t70) REVERT: A 1029 PHE cc_start: 0.7682 (m-80) cc_final: 0.7397 (m-10) REVERT: A 1284 ASP cc_start: 0.6381 (m-30) cc_final: 0.6054 (m-30) REVERT: A 1331 ARG cc_start: 0.8103 (mtp85) cc_final: 0.7797 (mtp85) REVERT: A 1339 PHE cc_start: 0.6355 (m-80) cc_final: 0.5946 (m-80) REVERT: A 1538 GLN cc_start: 0.8202 (mt0) cc_final: 0.7767 (tp40) REVERT: A 1692 HIS cc_start: 0.6957 (m-70) cc_final: 0.6579 (m-70) REVERT: B 155 MET cc_start: 0.7253 (mtm) cc_final: 0.7007 (mtp) REVERT: B 387 MET cc_start: 0.8340 (mmm) cc_final: 0.8102 (mmm) REVERT: B 888 ASP cc_start: 0.8260 (t0) cc_final: 0.7996 (t0) REVERT: B 941 ASP cc_start: 0.6592 (OUTLIER) cc_final: 0.6303 (m-30) REVERT: B 967 THR cc_start: 0.8186 (OUTLIER) cc_final: 0.7958 (p) REVERT: B 1189 GLN cc_start: 0.7379 (mp10) cc_final: 0.6979 (mt0) REVERT: B 1333 LEU cc_start: 0.7067 (OUTLIER) cc_final: 0.6837 (tt) REVERT: B 1393 ASP cc_start: 0.8141 (t70) cc_final: 0.7751 (t0) REVERT: B 1433 ARG cc_start: 0.8420 (ptm-80) cc_final: 0.8062 (ptt90) REVERT: B 1552 ARG cc_start: 0.6622 (ttt180) cc_final: 0.6150 (mtp85) REVERT: B 1632 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7216 (pm20) REVERT: B 1692 HIS cc_start: 0.5487 (OUTLIER) cc_final: 0.5190 (m-70) REVERT: B 1702 THR cc_start: 0.8474 (m) cc_final: 0.8054 (p) outliers start: 35 outliers final: 14 residues processed: 307 average time/residue: 0.9987 time to fit residues: 442.0823 Evaluate side-chains 238 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 218 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1386 GLU Chi-restraints excluded: chain A residue 1586 SER Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 941 ASP Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 LYS Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain B residue 1333 LEU Chi-restraints excluded: chain B residue 1632 GLU Chi-restraints excluded: chain B residue 1692 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 172 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 211 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 311 optimal weight: 6.9990 chunk 336 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 308 optimal weight: 3.9990 chunk 106 optimal weight: 0.3980 chunk 249 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25598 Z= 0.189 Angle : 0.601 10.270 34943 Z= 0.308 Chirality : 0.043 0.388 3935 Planarity : 0.006 0.066 4731 Dihedral : 5.663 55.114 3773 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 1.01 % Allowed : 7.62 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.07 (0.14), residues: 3426 helix: 0.78 (0.14), residues: 1385 sheet: 0.40 (0.22), residues: 508 loop : -0.68 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 740 HIS 0.011 0.001 HIS A 739 PHE 0.023 0.002 PHE A1290 TYR 0.012 0.001 TYR A 151 ARG 0.008 0.000 ARG A1552 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 250 time to evaluate : 2.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7748 (t80) cc_final: 0.6868 (m-80) REVERT: A 850 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6505 (t80) REVERT: A 883 ASP cc_start: 0.7903 (t70) cc_final: 0.7370 (t70) REVERT: A 1029 PHE cc_start: 0.7641 (m-80) cc_final: 0.7334 (m-10) REVERT: A 1167 HIS cc_start: 0.7810 (m-70) cc_final: 0.7236 (t-90) REVERT: A 1284 ASP cc_start: 0.6495 (m-30) cc_final: 0.6204 (m-30) REVERT: A 1339 PHE cc_start: 0.6544 (m-80) cc_final: 0.6152 (m-80) REVERT: A 1538 GLN cc_start: 0.8247 (mt0) cc_final: 0.7818 (tp40) REVERT: A 1719 MET cc_start: 0.1746 (ttm) cc_final: 0.1331 (tpt) REVERT: B 155 MET cc_start: 0.7112 (mtm) cc_final: 0.6839 (mtp) REVERT: B 888 ASP cc_start: 0.8205 (t0) cc_final: 0.7934 (t0) REVERT: B 967 THR cc_start: 0.8195 (OUTLIER) cc_final: 0.7870 (p) REVERT: B 1189 GLN cc_start: 0.7319 (mp10) cc_final: 0.6876 (mt0) REVERT: B 1206 GLU cc_start: 0.6129 (OUTLIER) cc_final: 0.5833 (tt0) REVERT: B 1393 ASP cc_start: 0.8238 (t70) cc_final: 0.7861 (t0) REVERT: B 1433 ARG cc_start: 0.8507 (ptm-80) cc_final: 0.8163 (ptt90) REVERT: B 1515 ASP cc_start: 0.5936 (m-30) cc_final: 0.5680 (m-30) REVERT: B 1632 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7412 (pm20) REVERT: B 1692 HIS cc_start: 0.5455 (OUTLIER) cc_final: 0.5212 (m-70) REVERT: B 1702 THR cc_start: 0.8488 (m) cc_final: 0.8029 (p) outliers start: 25 outliers final: 14 residues processed: 267 average time/residue: 0.8897 time to fit residues: 345.6512 Evaluate side-chains 232 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 213 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1379 SER Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 LYS Chi-restraints excluded: chain B residue 1206 GLU Chi-restraints excluded: chain B residue 1632 GLU Chi-restraints excluded: chain B residue 1692 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 307 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 208 optimal weight: 3.9990 chunk 312 optimal weight: 4.9990 chunk 330 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 295 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 482 GLN B1167 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 25598 Z= 0.409 Angle : 0.670 10.376 34943 Z= 0.347 Chirality : 0.046 0.398 3935 Planarity : 0.007 0.067 4731 Dihedral : 5.649 55.137 3773 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.58 % Allowed : 8.56 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: -0.34 (0.14), residues: 3426 helix: 0.59 (0.14), residues: 1371 sheet: -0.00 (0.21), residues: 533 loop : -1.01 (0.15), residues: 1522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 740 HIS 0.011 0.002 HIS A 739 PHE 0.023 0.002 PHE B 947 TYR 0.016 0.002 TYR A 151 ARG 0.010 0.001 ARG A 899 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 221 time to evaluate : 2.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7786 (t80) cc_final: 0.6985 (m-80) REVERT: A 708 GLN cc_start: 0.3765 (OUTLIER) cc_final: 0.3557 (tt0) REVERT: A 850 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.5772 (t80) REVERT: A 883 ASP cc_start: 0.7851 (t70) cc_final: 0.7432 (t70) REVERT: A 977 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7689 (tm-30) REVERT: A 1029 PHE cc_start: 0.7790 (m-80) cc_final: 0.7499 (m-10) REVERT: A 1167 HIS cc_start: 0.8034 (m-70) cc_final: 0.7679 (m-70) REVERT: A 1339 PHE cc_start: 0.6336 (m-80) cc_final: 0.5974 (m-80) REVERT: A 1538 GLN cc_start: 0.8353 (mt0) cc_final: 0.7904 (tp40) REVERT: B 155 MET cc_start: 0.7186 (mtm) cc_final: 0.6888 (mtp) REVERT: B 610 GLU cc_start: 0.5568 (OUTLIER) cc_final: 0.5282 (tt0) REVERT: B 782 GLU cc_start: 0.7121 (mp0) cc_final: 0.6597 (tt0) REVERT: B 1189 GLN cc_start: 0.7417 (mp10) cc_final: 0.7114 (mp10) REVERT: B 1518 ARG cc_start: 0.6062 (ttm110) cc_final: 0.5840 (ttp-110) REVERT: B 1632 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7512 (pm20) REVERT: B 1692 HIS cc_start: 0.5686 (OUTLIER) cc_final: 0.5136 (m-70) REVERT: B 1702 THR cc_start: 0.8499 (m) cc_final: 0.7976 (p) outliers start: 39 outliers final: 21 residues processed: 247 average time/residue: 0.8616 time to fit residues: 315.6537 Evaluate side-chains 227 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 201 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1379 SER Chi-restraints excluded: chain A residue 1386 GLU Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1586 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 LYS Chi-restraints excluded: chain B residue 1632 GLU Chi-restraints excluded: chain B residue 1692 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 275 optimal weight: 0.9990 chunk 187 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 282 optimal weight: 8.9990 chunk 228 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 391 ASN B1461 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25598 Z= 0.273 Angle : 0.585 9.619 34943 Z= 0.299 Chirality : 0.043 0.392 3935 Planarity : 0.006 0.069 4731 Dihedral : 5.307 51.020 3771 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.42 % Allowed : 8.96 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: -0.19 (0.14), residues: 3426 helix: 0.82 (0.14), residues: 1379 sheet: -0.02 (0.21), residues: 541 loop : -1.02 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 692 HIS 0.007 0.001 HIS A1505 PHE 0.020 0.002 PHE A1290 TYR 0.011 0.001 TYR A 151 ARG 0.007 0.000 ARG A1460 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 206 time to evaluate : 2.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7786 (t80) cc_final: 0.6994 (m-80) REVERT: A 424 ARG cc_start: 0.8340 (mmp80) cc_final: 0.7903 (mtm110) REVERT: A 850 PHE cc_start: 0.6929 (OUTLIER) cc_final: 0.5775 (t80) REVERT: A 883 ASP cc_start: 0.8062 (t70) cc_final: 0.7582 (t70) REVERT: A 899 ARG cc_start: 0.7360 (mtt-85) cc_final: 0.7001 (mtt-85) REVERT: A 977 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7582 (tm-30) REVERT: A 1029 PHE cc_start: 0.7757 (m-80) cc_final: 0.7487 (m-10) REVERT: A 1167 HIS cc_start: 0.7984 (m-70) cc_final: 0.7633 (m-70) REVERT: A 1339 PHE cc_start: 0.6784 (m-80) cc_final: 0.6496 (m-80) REVERT: A 1433 ARG cc_start: 0.7528 (ptp90) cc_final: 0.7195 (ptt90) REVERT: A 1505 HIS cc_start: 0.5734 (m170) cc_final: 0.5485 (m170) REVERT: A 1538 GLN cc_start: 0.8358 (mt0) cc_final: 0.7949 (tp40) REVERT: B 155 MET cc_start: 0.7154 (mtm) cc_final: 0.6866 (mtp) REVERT: B 1189 GLN cc_start: 0.7399 (mp10) cc_final: 0.7094 (mp10) REVERT: B 1393 ASP cc_start: 0.8296 (t70) cc_final: 0.7830 (t0) REVERT: B 1515 ASP cc_start: 0.5937 (m-30) cc_final: 0.5582 (m-30) REVERT: B 1632 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7551 (pm20) REVERT: B 1692 HIS cc_start: 0.5776 (OUTLIER) cc_final: 0.5227 (m-70) REVERT: B 1702 THR cc_start: 0.8462 (m) cc_final: 0.7941 (p) outliers start: 35 outliers final: 23 residues processed: 232 average time/residue: 0.8406 time to fit residues: 292.0903 Evaluate side-chains 217 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 191 time to evaluate : 2.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1379 SER Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 LYS Chi-restraints excluded: chain B residue 1547 GLU Chi-restraints excluded: chain B residue 1632 GLU Chi-restraints excluded: chain B residue 1692 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 111 optimal weight: 20.0000 chunk 297 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 330 optimal weight: 5.9990 chunk 274 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 173 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1167 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25598 Z= 0.305 Angle : 0.588 9.491 34943 Z= 0.300 Chirality : 0.043 0.396 3935 Planarity : 0.006 0.070 4731 Dihedral : 5.184 51.422 3771 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.46 % Allowed : 9.57 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: -0.24 (0.14), residues: 3426 helix: 0.88 (0.14), residues: 1382 sheet: -0.25 (0.20), residues: 549 loop : -1.06 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 692 HIS 0.007 0.001 HIS B 205 PHE 0.019 0.002 PHE A1290 TYR 0.011 0.001 TYR A 151 ARG 0.008 0.000 ARG A1460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 195 time to evaluate : 2.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7795 (t80) cc_final: 0.7000 (m-80) REVERT: A 424 ARG cc_start: 0.8287 (mmp80) cc_final: 0.7902 (mtm110) REVERT: A 850 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.5789 (t80) REVERT: A 883 ASP cc_start: 0.8084 (t70) cc_final: 0.7664 (t70) REVERT: A 977 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7655 (tm-30) REVERT: A 1009 THR cc_start: 0.8333 (m) cc_final: 0.8072 (p) REVERT: A 1029 PHE cc_start: 0.7867 (m-80) cc_final: 0.7621 (m-10) REVERT: A 1167 HIS cc_start: 0.7999 (m-70) cc_final: 0.7672 (m-70) REVERT: A 1433 ARG cc_start: 0.7548 (ptp90) cc_final: 0.7211 (ptt90) REVERT: A 1538 GLN cc_start: 0.8398 (mt0) cc_final: 0.7962 (tp40) REVERT: B 155 MET cc_start: 0.7154 (mtm) cc_final: 0.6872 (mtp) REVERT: B 610 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.5183 (tt0) REVERT: B 1189 GLN cc_start: 0.7427 (mp10) cc_final: 0.7106 (mp10) REVERT: B 1515 ASP cc_start: 0.5713 (m-30) cc_final: 0.5494 (m-30) REVERT: B 1632 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: B 1692 HIS cc_start: 0.5567 (OUTLIER) cc_final: 0.4968 (m-70) REVERT: B 1702 THR cc_start: 0.8443 (m) cc_final: 0.7911 (p) outliers start: 36 outliers final: 25 residues processed: 221 average time/residue: 0.8423 time to fit residues: 276.4043 Evaluate side-chains 213 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 2.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1144 THR Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1379 SER Chi-restraints excluded: chain A residue 1386 GLU Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 LYS Chi-restraints excluded: chain B residue 1547 GLU Chi-restraints excluded: chain B residue 1632 GLU Chi-restraints excluded: chain B residue 1692 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 319 optimal weight: 20.0000 chunk 37 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 241 optimal weight: 20.0000 chunk 187 optimal weight: 2.9990 chunk 278 optimal weight: 4.9990 chunk 184 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 206 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN ** B 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25598 Z= 0.248 Angle : 0.558 9.052 34943 Z= 0.283 Chirality : 0.042 0.392 3935 Planarity : 0.006 0.068 4731 Dihedral : 5.027 48.892 3769 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.22 % Allowed : 9.73 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: -0.14 (0.14), residues: 3426 helix: 1.04 (0.14), residues: 1377 sheet: -0.30 (0.20), residues: 549 loop : -1.05 (0.15), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 740 HIS 0.006 0.001 HIS B 205 PHE 0.017 0.002 PHE A1290 TYR 0.011 0.001 TYR B 659 ARG 0.009 0.000 ARG A 899 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7801 (t80) cc_final: 0.7013 (m-80) REVERT: A 424 ARG cc_start: 0.8294 (mmp80) cc_final: 0.7901 (mtm110) REVERT: A 850 PHE cc_start: 0.6919 (OUTLIER) cc_final: 0.5699 (t80) REVERT: A 883 ASP cc_start: 0.8148 (t70) cc_final: 0.7690 (t70) REVERT: A 977 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7653 (tm-30) REVERT: A 1009 THR cc_start: 0.8321 (m) cc_final: 0.8056 (p) REVERT: A 1167 HIS cc_start: 0.7977 (m-70) cc_final: 0.7730 (m-70) REVERT: A 1339 PHE cc_start: 0.6900 (m-80) cc_final: 0.6533 (m-80) REVERT: A 1433 ARG cc_start: 0.7532 (ptp90) cc_final: 0.7219 (ptt90) REVERT: A 1505 HIS cc_start: 0.5671 (m170) cc_final: 0.5422 (m170) REVERT: A 1538 GLN cc_start: 0.8383 (mt0) cc_final: 0.7967 (tp40) REVERT: B 155 MET cc_start: 0.7141 (mtm) cc_final: 0.6852 (mtp) REVERT: B 164 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8506 (tt) REVERT: B 782 GLU cc_start: 0.6946 (mp0) cc_final: 0.6552 (tt0) REVERT: B 1189 GLN cc_start: 0.7428 (mp10) cc_final: 0.7108 (mp10) REVERT: B 1515 ASP cc_start: 0.5731 (m-30) cc_final: 0.5478 (m-30) REVERT: B 1632 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7649 (pm20) REVERT: B 1692 HIS cc_start: 0.5769 (OUTLIER) cc_final: 0.5151 (m-70) REVERT: B 1702 THR cc_start: 0.8411 (m) cc_final: 0.7876 (p) outliers start: 30 outliers final: 23 residues processed: 207 average time/residue: 0.8530 time to fit residues: 264.3612 Evaluate side-chains 212 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 LYS Chi-restraints excluded: chain B residue 1547 GLU Chi-restraints excluded: chain B residue 1632 GLU Chi-restraints excluded: chain B residue 1692 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 203 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 259 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.4445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 25598 Z= 0.290 Angle : 0.571 9.265 34943 Z= 0.290 Chirality : 0.043 0.392 3935 Planarity : 0.006 0.072 4731 Dihedral : 4.970 50.499 3769 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.42 % Allowed : 9.98 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: -0.19 (0.14), residues: 3426 helix: 1.07 (0.14), residues: 1377 sheet: -0.40 (0.21), residues: 548 loop : -1.12 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 692 HIS 0.007 0.001 HIS B 205 PHE 0.016 0.002 PHE A1290 TYR 0.011 0.001 TYR A 151 ARG 0.011 0.000 ARG A1331 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 192 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7804 (t80) cc_final: 0.7019 (m-80) REVERT: A 424 ARG cc_start: 0.8300 (mmp80) cc_final: 0.7884 (mtm-85) REVERT: A 437 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7608 (mt) REVERT: A 883 ASP cc_start: 0.8050 (t70) cc_final: 0.7641 (t70) REVERT: A 977 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7685 (tm-30) REVERT: A 1009 THR cc_start: 0.8312 (m) cc_final: 0.8053 (p) REVERT: A 1167 HIS cc_start: 0.8007 (m-70) cc_final: 0.7783 (m-70) REVERT: A 1339 PHE cc_start: 0.6842 (m-80) cc_final: 0.6349 (m-80) REVERT: A 1433 ARG cc_start: 0.7552 (ptp90) cc_final: 0.7222 (ptt90) REVERT: A 1505 HIS cc_start: 0.5711 (m170) cc_final: 0.5507 (m170) REVERT: A 1538 GLN cc_start: 0.8333 (mt0) cc_final: 0.7936 (tp40) REVERT: B 155 MET cc_start: 0.7158 (mtm) cc_final: 0.6862 (mtp) REVERT: B 164 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8515 (tt) REVERT: B 610 GLU cc_start: 0.5535 (OUTLIER) cc_final: 0.5234 (tt0) REVERT: B 782 GLU cc_start: 0.6951 (mp0) cc_final: 0.6575 (tt0) REVERT: B 1189 GLN cc_start: 0.7449 (mp10) cc_final: 0.7136 (mp10) REVERT: B 1515 ASP cc_start: 0.5727 (m-30) cc_final: 0.5468 (m-30) REVERT: B 1632 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: B 1692 HIS cc_start: 0.5553 (OUTLIER) cc_final: 0.4921 (m-70) REVERT: B 1702 THR cc_start: 0.8394 (m) cc_final: 0.7857 (p) outliers start: 35 outliers final: 27 residues processed: 220 average time/residue: 0.8305 time to fit residues: 274.9556 Evaluate side-chains 212 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 180 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 437 LEU Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1386 GLU Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 668 ASP Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 LYS Chi-restraints excluded: chain B residue 1547 GLU Chi-restraints excluded: chain B residue 1632 GLU Chi-restraints excluded: chain B residue 1692 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 299 optimal weight: 0.8980 chunk 315 optimal weight: 10.0000 chunk 288 optimal weight: 6.9990 chunk 307 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 241 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 277 optimal weight: 0.9980 chunk 290 optimal weight: 7.9990 chunk 306 optimal weight: 0.5980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25598 Z= 0.224 Angle : 0.542 8.683 34943 Z= 0.274 Chirality : 0.042 0.390 3935 Planarity : 0.006 0.066 4731 Dihedral : 4.816 47.292 3768 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.30 % Allowed : 10.14 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: -0.08 (0.14), residues: 3426 helix: 1.20 (0.14), residues: 1377 sheet: -0.39 (0.21), residues: 548 loop : -1.08 (0.15), residues: 1501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1468 HIS 0.005 0.001 HIS B 205 PHE 0.018 0.001 PHE A1290 TYR 0.010 0.001 TYR B 659 ARG 0.005 0.000 ARG A1460 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 187 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7797 (t80) cc_final: 0.7016 (m-80) REVERT: A 424 ARG cc_start: 0.8304 (mmp80) cc_final: 0.7932 (mtm-85) REVERT: A 850 PHE cc_start: 0.6833 (OUTLIER) cc_final: 0.5290 (t80) REVERT: A 883 ASP cc_start: 0.8170 (t70) cc_final: 0.7784 (t70) REVERT: A 977 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 1009 THR cc_start: 0.8303 (m) cc_final: 0.8034 (p) REVERT: A 1167 HIS cc_start: 0.8006 (m-70) cc_final: 0.7775 (m-70) REVERT: A 1179 SER cc_start: 0.8898 (t) cc_final: 0.8332 (p) REVERT: A 1433 ARG cc_start: 0.7555 (ptp90) cc_final: 0.7238 (ptt90) REVERT: A 1505 HIS cc_start: 0.5676 (m170) cc_final: 0.5441 (m170) REVERT: A 1538 GLN cc_start: 0.8380 (mt0) cc_final: 0.7956 (tp40) REVERT: B 155 MET cc_start: 0.7133 (mtm) cc_final: 0.6861 (mtp) REVERT: B 164 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8549 (tt) REVERT: B 782 GLU cc_start: 0.6923 (mp0) cc_final: 0.6572 (tt0) REVERT: B 1189 GLN cc_start: 0.7438 (mp10) cc_final: 0.7109 (mp10) REVERT: B 1280 THR cc_start: 0.6773 (m) cc_final: 0.6405 (p) REVERT: B 1478 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.7414 (m) REVERT: B 1515 ASP cc_start: 0.5698 (m-30) cc_final: 0.5438 (m-30) REVERT: B 1632 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7720 (pm20) REVERT: B 1692 HIS cc_start: 0.5572 (OUTLIER) cc_final: 0.5329 (m-70) REVERT: B 1702 THR cc_start: 0.8368 (m) cc_final: 0.7840 (p) outliers start: 32 outliers final: 26 residues processed: 212 average time/residue: 0.8640 time to fit residues: 276.3270 Evaluate side-chains 210 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 179 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1379 SER Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 665 SER Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 LYS Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain B residue 1547 GLU Chi-restraints excluded: chain B residue 1632 GLU Chi-restraints excluded: chain B residue 1692 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 201 optimal weight: 2.9990 chunk 324 optimal weight: 0.6980 chunk 198 optimal weight: 0.7980 chunk 154 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 chunk 340 optimal weight: 3.9990 chunk 313 optimal weight: 2.9990 chunk 271 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 743 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1692 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25598 Z= 0.218 Angle : 0.536 8.557 34943 Z= 0.270 Chirality : 0.042 0.390 3935 Planarity : 0.006 0.079 4731 Dihedral : 4.765 48.161 3768 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.26 % Allowed : 10.30 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: -0.01 (0.14), residues: 3426 helix: 1.30 (0.14), residues: 1375 sheet: -0.44 (0.20), residues: 552 loop : -1.05 (0.15), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 692 HIS 0.005 0.001 HIS B 205 PHE 0.017 0.001 PHE A1290 TYR 0.009 0.001 TYR B 659 ARG 0.012 0.000 ARG A1331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6852 Ramachandran restraints generated. 3426 Oldfield, 0 Emsley, 3426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.7798 (t80) cc_final: 0.7017 (m-80) REVERT: A 424 ARG cc_start: 0.8312 (mmp80) cc_final: 0.7948 (mtm-85) REVERT: A 850 PHE cc_start: 0.6806 (OUTLIER) cc_final: 0.5310 (t80) REVERT: A 883 ASP cc_start: 0.8159 (t70) cc_final: 0.7763 (t70) REVERT: A 977 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7672 (tm-30) REVERT: A 1009 THR cc_start: 0.8290 (m) cc_final: 0.8015 (p) REVERT: A 1167 HIS cc_start: 0.7973 (m-70) cc_final: 0.7759 (m-70) REVERT: A 1179 SER cc_start: 0.9002 (t) cc_final: 0.8441 (p) REVERT: A 1339 PHE cc_start: 0.6784 (m-80) cc_final: 0.6338 (m-80) REVERT: A 1433 ARG cc_start: 0.7557 (ptp90) cc_final: 0.7231 (ptt90) REVERT: A 1505 HIS cc_start: 0.5748 (m170) cc_final: 0.5517 (m170) REVERT: A 1538 GLN cc_start: 0.8362 (mt0) cc_final: 0.7957 (tp40) REVERT: B 155 MET cc_start: 0.7120 (mtm) cc_final: 0.6846 (mtp) REVERT: B 610 GLU cc_start: 0.5660 (OUTLIER) cc_final: 0.5415 (tt0) REVERT: B 782 GLU cc_start: 0.6899 (mp0) cc_final: 0.6578 (tt0) REVERT: B 1189 GLN cc_start: 0.7444 (mp10) cc_final: 0.7102 (mp10) REVERT: B 1280 THR cc_start: 0.6838 (m) cc_final: 0.6483 (p) REVERT: B 1478 VAL cc_start: 0.7640 (OUTLIER) cc_final: 0.7397 (m) REVERT: B 1515 ASP cc_start: 0.5598 (m-30) cc_final: 0.5321 (m-30) REVERT: B 1632 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7802 (pm20) REVERT: B 1692 HIS cc_start: 0.5364 (OUTLIER) cc_final: 0.4552 (m90) REVERT: B 1702 THR cc_start: 0.8364 (m) cc_final: 0.7833 (p) outliers start: 31 outliers final: 23 residues processed: 214 average time/residue: 0.8741 time to fit residues: 283.5720 Evaluate side-chains 207 residues out of total 2466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 947 PHE Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1106 VAL Chi-restraints excluded: chain A residue 1138 SER Chi-restraints excluded: chain A residue 1307 ASP Chi-restraints excluded: chain A residue 1459 THR Chi-restraints excluded: chain B residue 162 GLN Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 610 GLU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 697 GLU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1030 VAL Chi-restraints excluded: chain B residue 1031 LYS Chi-restraints excluded: chain B residue 1478 VAL Chi-restraints excluded: chain B residue 1547 GLU Chi-restraints excluded: chain B residue 1632 GLU Chi-restraints excluded: chain B residue 1692 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 215 optimal weight: 0.9980 chunk 289 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 271 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 279 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 GLN ** B 743 HIS ** 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 = 0.3848 r_free = 0.3848 target = 0.161994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126670 restraints weight = 91935.712| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.28 r_work: 0.3182 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 25598 Z= 0.163 Angle : 0.513 8.138 34943 Z= 0.256 Chirality : 0.041 0.386 3935 Planarity : 0.005 0.066 4731 Dihedral : 4.594 45.126 3768 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.05 % Allowed : 10.62 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % 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: 0.14 (0.14), residues: 3426 helix: 1.46 (0.14), residues: 1375 sheet: -0.41 (0.20), residues: 552 loop : -0.97 (0.16), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 692 HIS 0.004 0.001 HIS A1505 PHE 0.017 0.001 PHE A1290 TYR 0.009 0.001 TYR B 659 ARG 0.007 0.000 ARG A1460 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8478.33 seconds wall clock time: 145 minutes 5.28 seconds (8705.28 seconds total)