Starting phenix.real_space_refine on Sat Feb 7 16:48:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hux_52419/02_2026/9hux_52419.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hux_52419/02_2026/9hux_52419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hux_52419/02_2026/9hux_52419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hux_52419/02_2026/9hux_52419.map" model { file = "/net/cci-nas-00/data/ceres_data/9hux_52419/02_2026/9hux_52419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hux_52419/02_2026/9hux_52419.cif" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 P 8 5.49 5 S 80 5.16 5 C 21044 2.51 5 N 6012 2.21 5 O 6432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33576 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 8350 Classifications: {'peptide': 1075} Link IDs: {'PCIS': 2, 'PTRANS': 40, 'TRANS': 1032} Chain breaks: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 8.48, per 1000 atoms: 0.25 Number of scatterers: 33576 At special positions: 0 Unit cell: (130.532, 231.34, 138.287, 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 80 16.00 P 8 15.00 O 6432 8.00 N 6012 7.00 C 21044 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.1 seconds 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7968 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 20 sheets defined 63.7% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 500 through 510 removed outlier: 3.529A pdb=" N ASP A 504 " --> pdb=" O ASP A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 553 removed outlier: 3.841A pdb=" N LEU A 545 " --> pdb=" O SER A 541 " (cutoff:3.500A) Proline residue: A 547 - end of helix removed outlier: 3.603A pdb=" N GLY A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 628 through 646 Processing helix chain 'A' and resid 650 through 661 Processing helix chain 'A' and resid 661 through 676 Processing helix chain 'A' and resid 677 through 683 removed outlier: 3.514A pdb=" N GLU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 701 removed outlier: 3.739A pdb=" N ALA A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 720 Processing helix chain 'A' and resid 733 through 738 Processing helix chain 'A' and resid 791 through 807 removed outlier: 3.505A pdb=" N GLU A 795 " --> pdb=" O ASP A 791 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA A 802 " --> pdb=" O GLY A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 857 removed outlier: 3.928A pdb=" N VAL A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.517A pdb=" N ALA A 914 " --> pdb=" O ASP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 927 Processing helix chain 'A' and resid 927 through 944 removed outlier: 3.725A pdb=" N SER A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 995 through 1008 Processing helix chain 'A' and resid 1012 through 1016 Processing helix chain 'A' and resid 1038 through 1045 Processing helix chain 'A' and resid 1055 through 1066 Processing helix chain 'A' and resid 1092 through 1096 Processing helix chain 'A' and resid 1119 through 1129 Processing helix chain 'A' and resid 1135 through 1140 Processing helix chain 'A' and resid 1140 through 1164 removed outlier: 4.412A pdb=" N VAL A1144 " --> pdb=" O ASN A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1178 removed outlier: 4.243A pdb=" N THR A1172 " --> pdb=" O PRO A1168 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU A1173 " --> pdb=" O GLU A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1203 Processing helix chain 'A' and resid 1208 through 1222 Processing helix chain 'A' and resid 1233 through 1244 Processing helix chain 'A' and resid 1248 through 1269 Processing helix chain 'A' and resid 1275 through 1280 Processing helix chain 'A' and resid 1281 through 1286 Processing helix chain 'A' and resid 1287 through 1294 Processing helix chain 'A' and resid 1295 through 1300 removed outlier: 3.662A pdb=" N ARG A1299 " --> pdb=" O HIS A1295 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1321 Processing helix chain 'A' and resid 1324 through 1333 Processing helix chain 'A' and resid 1335 through 1351 Processing helix chain 'A' and resid 1351 through 1364 Processing helix chain 'A' and resid 1368 through 1394 Processing helix chain 'A' and resid 1399 through 1415 removed outlier: 4.743A pdb=" N ALA A1409 " --> pdb=" O ASN A1405 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS A1410 " --> pdb=" O ARG A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1421 removed outlier: 4.586A pdb=" N SER A1419 " --> pdb=" O PRO A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1424 through 1440 Processing helix chain 'A' and resid 1443 through 1452 Processing helix chain 'A' and resid 1452 through 1469 removed outlier: 3.955A pdb=" N LEU A1460 " --> pdb=" O GLN A1456 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP A1461 " --> pdb=" O TYR A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1488 Processing helix chain 'A' and resid 1488 through 1498 removed outlier: 4.161A pdb=" N LEU A1492 " --> pdb=" O GLY A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1531 Processing helix chain 'A' and resid 1538 through 1547 Processing helix chain 'A' and resid 1550 through 1567 removed outlier: 3.999A pdb=" N GLY A1567 " --> pdb=" O ILE A1563 " (cutoff:3.500A) Processing helix chain 'A' and resid 1570 through 1584 Processing helix chain 'B' and resid 501 through 510 Processing helix chain 'B' and resid 541 through 553 removed outlier: 3.841A pdb=" N LEU B 545 " --> pdb=" O SER B 541 " (cutoff:3.500A) Proline residue: B 547 - end of helix removed outlier: 3.602A pdb=" N GLY B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'B' and resid 628 through 646 Processing helix chain 'B' and resid 650 through 661 Processing helix chain 'B' and resid 661 through 676 Processing helix chain 'B' and resid 677 through 683 removed outlier: 3.514A pdb=" N GLU B 681 " --> pdb=" O ASP B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 701 removed outlier: 3.739A pdb=" N ALA B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 720 Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 791 through 807 removed outlier: 3.505A pdb=" N GLU B 795 " --> pdb=" O ASP B 791 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS B 801 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA B 802 " --> pdb=" O GLY B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 857 removed outlier: 3.928A pdb=" N VAL B 856 " --> pdb=" O GLY B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.517A pdb=" N ALA B 914 " --> pdb=" O ASP B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 927 Processing helix chain 'B' and resid 927 through 944 removed outlier: 3.725A pdb=" N SER B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'B' and resid 995 through 1008 Processing helix chain 'B' and resid 1012 through 1016 Processing helix chain 'B' and resid 1038 through 1045 Processing helix chain 'B' and resid 1055 through 1066 Processing helix chain 'B' and resid 1092 through 1096 Processing helix chain 'B' and resid 1119 through 1129 Processing helix chain 'B' and resid 1135 through 1140 Processing helix chain 'B' and resid 1140 through 1164 removed outlier: 4.412A pdb=" N VAL B1144 " --> pdb=" O ASN B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1167 through 1178 removed outlier: 4.243A pdb=" N THR B1172 " --> pdb=" O PRO B1168 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU B1173 " --> pdb=" O GLU B1169 " (cutoff:3.500A) Processing helix chain 'B' and resid 1178 through 1203 Processing helix chain 'B' and resid 1208 through 1222 Processing helix chain 'B' and resid 1233 through 1244 Processing helix chain 'B' and resid 1248 through 1269 Processing helix chain 'B' and resid 1275 through 1280 Processing helix chain 'B' and resid 1281 through 1286 Processing helix chain 'B' and resid 1287 through 1294 Processing helix chain 'B' and resid 1295 through 1300 removed outlier: 3.662A pdb=" N ARG B1299 " --> pdb=" O HIS B1295 " (cutoff:3.500A) Processing helix chain 'B' and resid 1303 through 1321 Processing helix chain 'B' and resid 1324 through 1333 Processing helix chain 'B' and resid 1335 through 1351 Processing helix chain 'B' and resid 1351 through 1364 Processing helix chain 'B' and resid 1368 through 1394 Processing helix chain 'B' and resid 1399 through 1415 removed outlier: 4.744A pdb=" N ALA B1409 " --> pdb=" O ASN B1405 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS B1410 " --> pdb=" O ARG B1406 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1421 removed outlier: 4.585A pdb=" N SER B1419 " --> pdb=" O PRO B1416 " (cutoff:3.500A) Processing helix chain 'B' and resid 1424 through 1440 Processing helix chain 'B' and resid 1443 through 1452 Processing helix chain 'B' and resid 1452 through 1469 removed outlier: 3.954A pdb=" N LEU B1460 " --> pdb=" O GLN B1456 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP B1461 " --> pdb=" O TYR B1457 " (cutoff:3.500A) Processing helix chain 'B' and resid 1472 through 1488 Processing helix chain 'B' and resid 1488 through 1498 removed outlier: 4.162A pdb=" N LEU B1492 " --> pdb=" O GLY B1488 " (cutoff:3.500A) Processing helix chain 'B' and resid 1503 through 1531 Processing helix chain 'B' and resid 1538 through 1547 Processing helix chain 'B' and resid 1550 through 1567 removed outlier: 3.999A pdb=" N GLY B1567 " --> pdb=" O ILE B1563 " (cutoff:3.500A) Processing helix chain 'B' and resid 1570 through 1584 Processing helix chain 'C' and resid 501 through 510 Processing helix chain 'C' and resid 541 through 553 removed outlier: 3.841A pdb=" N LEU C 545 " --> pdb=" O SER C 541 " (cutoff:3.500A) Proline residue: C 547 - end of helix removed outlier: 3.602A pdb=" N GLY C 553 " --> pdb=" O LEU C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 Processing helix chain 'C' and resid 616 through 624 Processing helix chain 'C' and resid 628 through 646 Processing helix chain 'C' and resid 650 through 661 Processing helix chain 'C' and resid 661 through 676 Processing helix chain 'C' and resid 677 through 683 removed outlier: 3.514A pdb=" N GLU C 681 " --> pdb=" O ASP C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 701 removed outlier: 3.740A pdb=" N ALA C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 720 Processing helix chain 'C' and resid 733 through 738 Processing helix chain 'C' and resid 791 through 807 removed outlier: 3.505A pdb=" N GLU C 795 " --> pdb=" O ASP C 791 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS C 801 " --> pdb=" O LEU C 797 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA C 802 " --> pdb=" O GLY C 798 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 857 removed outlier: 3.928A pdb=" N VAL C 856 " --> pdb=" O GLY C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 914 removed outlier: 3.517A pdb=" N ALA C 914 " --> pdb=" O ASP C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 927 Processing helix chain 'C' and resid 927 through 944 removed outlier: 3.725A pdb=" N SER C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 995 through 1008 Processing helix chain 'C' and resid 1012 through 1016 Processing helix chain 'C' and resid 1038 through 1045 Processing helix chain 'C' and resid 1055 through 1066 Processing helix chain 'C' and resid 1092 through 1096 Processing helix chain 'C' and resid 1119 through 1129 Processing helix chain 'C' and resid 1135 through 1140 Processing helix chain 'C' and resid 1140 through 1164 removed outlier: 4.412A pdb=" N VAL C1144 " --> pdb=" O ASN C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1178 removed outlier: 4.244A pdb=" N THR C1172 " --> pdb=" O PRO C1168 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU C1173 " --> pdb=" O GLU C1169 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1203 Processing helix chain 'C' and resid 1208 through 1222 Processing helix chain 'C' and resid 1233 through 1244 Processing helix chain 'C' and resid 1248 through 1269 Processing helix chain 'C' and resid 1275 through 1280 Processing helix chain 'C' and resid 1281 through 1286 Processing helix chain 'C' and resid 1287 through 1294 Processing helix chain 'C' and resid 1295 through 1300 removed outlier: 3.661A pdb=" N ARG C1299 " --> pdb=" O HIS C1295 " (cutoff:3.500A) Processing helix chain 'C' and resid 1303 through 1321 Processing helix chain 'C' and resid 1324 through 1333 Processing helix chain 'C' and resid 1335 through 1351 Processing helix chain 'C' and resid 1351 through 1364 Processing helix chain 'C' and resid 1368 through 1394 Processing helix chain 'C' and resid 1399 through 1415 removed outlier: 4.744A pdb=" N ALA C1409 " --> pdb=" O ASN C1405 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS C1410 " --> pdb=" O ARG C1406 " (cutoff:3.500A) Processing helix chain 'C' and resid 1416 through 1421 removed outlier: 4.586A pdb=" N SER C1419 " --> pdb=" O PRO C1416 " (cutoff:3.500A) Processing helix chain 'C' and resid 1424 through 1440 Processing helix chain 'C' and resid 1443 through 1452 Processing helix chain 'C' and resid 1452 through 1469 removed outlier: 3.954A pdb=" N LEU C1460 " --> pdb=" O GLN C1456 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP C1461 " --> pdb=" O TYR C1457 " (cutoff:3.500A) Processing helix chain 'C' and resid 1472 through 1488 Processing helix chain 'C' and resid 1488 through 1498 removed outlier: 4.162A pdb=" N LEU C1492 " --> pdb=" O GLY C1488 " (cutoff:3.500A) Processing helix chain 'C' and resid 1503 through 1531 Processing helix chain 'C' and resid 1538 through 1547 Processing helix chain 'C' and resid 1550 through 1567 removed outlier: 3.999A pdb=" N GLY C1567 " --> pdb=" O ILE C1563 " (cutoff:3.500A) Processing helix chain 'C' and resid 1570 through 1584 Processing helix chain 'D' and resid 501 through 510 Processing helix chain 'D' and resid 541 through 553 removed outlier: 3.842A pdb=" N LEU D 545 " --> pdb=" O SER D 541 " (cutoff:3.500A) Proline residue: D 547 - end of helix removed outlier: 3.603A pdb=" N GLY D 553 " --> pdb=" O LEU D 549 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 Processing helix chain 'D' and resid 616 through 624 Processing helix chain 'D' and resid 628 through 646 Processing helix chain 'D' and resid 650 through 661 Processing helix chain 'D' and resid 661 through 676 Processing helix chain 'D' and resid 677 through 683 removed outlier: 3.514A pdb=" N GLU D 681 " --> pdb=" O ASP D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 701 removed outlier: 3.739A pdb=" N ALA D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 720 Processing helix chain 'D' and resid 733 through 738 Processing helix chain 'D' and resid 791 through 807 removed outlier: 3.505A pdb=" N GLU D 795 " --> pdb=" O ASP D 791 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS D 801 " --> pdb=" O LEU D 797 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA D 802 " --> pdb=" O GLY D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 857 removed outlier: 3.927A pdb=" N VAL D 856 " --> pdb=" O GLY D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 906 Processing helix chain 'D' and resid 909 through 914 removed outlier: 3.517A pdb=" N ALA D 914 " --> pdb=" O ASP D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 927 Processing helix chain 'D' and resid 927 through 944 removed outlier: 3.724A pdb=" N SER D 936 " --> pdb=" O GLY D 932 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 970 Processing helix chain 'D' and resid 995 through 1008 Processing helix chain 'D' and resid 1012 through 1016 Processing helix chain 'D' and resid 1038 through 1045 Processing helix chain 'D' and resid 1055 through 1066 Processing helix chain 'D' and resid 1092 through 1096 Processing helix chain 'D' and resid 1119 through 1129 Processing helix chain 'D' and resid 1135 through 1140 Processing helix chain 'D' and resid 1140 through 1164 removed outlier: 4.411A pdb=" N VAL D1144 " --> pdb=" O ASN D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1167 through 1178 removed outlier: 4.243A pdb=" N THR D1172 " --> pdb=" O PRO D1168 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU D1173 " --> pdb=" O GLU D1169 " (cutoff:3.500A) Processing helix chain 'D' and resid 1178 through 1203 Processing helix chain 'D' and resid 1208 through 1222 Processing helix chain 'D' and resid 1233 through 1244 Processing helix chain 'D' and resid 1248 through 1269 Processing helix chain 'D' and resid 1275 through 1280 Processing helix chain 'D' and resid 1281 through 1286 Processing helix chain 'D' and resid 1287 through 1294 Processing helix chain 'D' and resid 1295 through 1300 removed outlier: 3.661A pdb=" N ARG D1299 " --> pdb=" O HIS D1295 " (cutoff:3.500A) Processing helix chain 'D' and resid 1303 through 1321 Processing helix chain 'D' and resid 1324 through 1333 Processing helix chain 'D' and resid 1335 through 1351 Processing helix chain 'D' and resid 1351 through 1364 Processing helix chain 'D' and resid 1368 through 1394 Processing helix chain 'D' and resid 1399 through 1415 removed outlier: 4.743A pdb=" N ALA D1409 " --> pdb=" O ASN D1405 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS D1410 " --> pdb=" O ARG D1406 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1421 removed outlier: 4.586A pdb=" N SER D1419 " --> pdb=" O PRO D1416 " (cutoff:3.500A) Processing helix chain 'D' and resid 1424 through 1440 Processing helix chain 'D' and resid 1443 through 1452 Processing helix chain 'D' and resid 1452 through 1469 removed outlier: 3.955A pdb=" N LEU D1460 " --> pdb=" O GLN D1456 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP D1461 " --> pdb=" O TYR D1457 " (cutoff:3.500A) Processing helix chain 'D' and resid 1472 through 1488 Processing helix chain 'D' and resid 1488 through 1498 removed outlier: 4.161A pdb=" N LEU D1492 " --> pdb=" O GLY D1488 " (cutoff:3.500A) Processing helix chain 'D' and resid 1503 through 1531 Processing helix chain 'D' and resid 1538 through 1547 Processing helix chain 'D' and resid 1550 through 1567 removed outlier: 3.999A pdb=" N GLY D1567 " --> pdb=" O ILE D1563 " (cutoff:3.500A) Processing helix chain 'D' and resid 1570 through 1584 Processing sheet with id=AA1, first strand: chain 'A' and resid 516 through 522 removed outlier: 6.951A pdb=" N VAL A 572 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR A 563 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A 574 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN A 576 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU A 559 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS A 578 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 721 through 724 removed outlier: 6.574A pdb=" N LYS A 743 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR A 724 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA A 741 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 721 through 724 removed outlier: 6.574A pdb=" N LYS A 743 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR A 724 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA A 741 " --> pdb=" O THR A 724 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 859 through 860 Processing sheet with id=AA5, first strand: chain 'A' and resid 1026 through 1029 removed outlier: 6.522A pdb=" N PHE A 953 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL A 979 " --> pdb=" O PHE A 953 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL A 955 " --> pdb=" O VAL A 979 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA A 981 " --> pdb=" O VAL A 955 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY A 957 " --> pdb=" O ALA A 981 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU A1071 " --> pdb=" O GLY A1111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 516 through 522 removed outlier: 6.951A pdb=" N VAL B 572 " --> pdb=" O THR B 563 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR B 563 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 574 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN B 576 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU B 559 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS B 578 " --> pdb=" O LEU B 557 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 721 through 724 removed outlier: 6.574A pdb=" N LYS B 743 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 724 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA B 741 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 721 through 724 removed outlier: 6.574A pdb=" N LYS B 743 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 724 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ALA B 741 " --> pdb=" O THR B 724 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 859 through 860 Processing sheet with id=AB1, first strand: chain 'B' and resid 1026 through 1029 removed outlier: 6.521A pdb=" N PHE B 953 " --> pdb=" O ARG B 977 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N VAL B 979 " --> pdb=" O PHE B 953 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL B 955 " --> pdb=" O VAL B 979 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA B 981 " --> pdb=" O VAL B 955 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY B 957 " --> pdb=" O ALA B 981 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU B1071 " --> pdb=" O GLY B1111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 516 through 522 removed outlier: 6.951A pdb=" N VAL C 572 " --> pdb=" O THR C 563 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR C 563 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE C 574 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLN C 576 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU C 559 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS C 578 " --> pdb=" O LEU C 557 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 721 through 724 removed outlier: 6.573A pdb=" N LYS C 743 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR C 724 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA C 741 " --> pdb=" O THR C 724 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 721 through 724 removed outlier: 6.573A pdb=" N LYS C 743 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR C 724 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA C 741 " --> pdb=" O THR C 724 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 859 through 860 Processing sheet with id=AB6, first strand: chain 'C' and resid 1026 through 1029 removed outlier: 6.522A pdb=" N PHE C 953 " --> pdb=" O ARG C 977 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL C 979 " --> pdb=" O PHE C 953 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N VAL C 955 " --> pdb=" O VAL C 979 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ALA C 981 " --> pdb=" O VAL C 955 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY C 957 " --> pdb=" O ALA C 981 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU C1071 " --> pdb=" O GLY C1111 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 516 through 522 removed outlier: 6.952A pdb=" N VAL D 572 " --> pdb=" O THR D 563 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N THR D 563 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE D 574 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLN D 576 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU D 559 " --> pdb=" O GLN D 576 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS D 578 " --> pdb=" O LEU D 557 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 721 through 724 removed outlier: 6.574A pdb=" N LYS D 743 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR D 724 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA D 741 " --> pdb=" O THR D 724 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 721 through 724 removed outlier: 6.574A pdb=" N LYS D 743 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N THR D 724 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA D 741 " --> pdb=" O THR D 724 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 859 through 860 Processing sheet with id=AC2, first strand: chain 'D' and resid 1026 through 1029 removed outlier: 6.522A pdb=" N PHE D 953 " --> pdb=" O ARG D 977 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL D 979 " --> pdb=" O PHE D 953 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL D 955 " --> pdb=" O VAL D 979 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA D 981 " --> pdb=" O VAL D 955 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY D 957 " --> pdb=" O ALA D 981 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N LEU D1071 " --> pdb=" O GLY D1111 " (cutoff:3.500A) 2140 hydrogen bonds defined for protein. 6084 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: 7.41 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11593 1.34 - 1.46: 6946 1.46 - 1.58: 15501 1.58 - 1.69: 16 1.69 - 1.81: 144 Bond restraints: 34200 Sorted by residual: bond pdb=" O3 NAD B1601 " pdb=" PA NAD B1601 " ideal model delta sigma weight residual 1.653 1.603 0.050 2.00e-02 2.50e+03 6.30e+00 bond pdb=" O3 NAD C1601 " pdb=" PA NAD C1601 " ideal model delta sigma weight residual 1.653 1.603 0.050 2.00e-02 2.50e+03 6.26e+00 bond pdb=" O3 NAD D1601 " pdb=" PA NAD D1601 " ideal model delta sigma weight residual 1.653 1.603 0.050 2.00e-02 2.50e+03 6.21e+00 bond pdb=" O3 NAD A1601 " pdb=" PA NAD A1601 " ideal model delta sigma weight residual 1.653 1.604 0.049 2.00e-02 2.50e+03 6.04e+00 bond pdb=" C1D NAD B1601 " pdb=" O4D NAD B1601 " ideal model delta sigma weight residual 1.376 1.421 -0.045 2.00e-02 2.50e+03 5.16e+00 ... (remaining 34195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 45511 1.05 - 2.10: 651 2.10 - 3.14: 200 3.14 - 4.19: 51 4.19 - 5.24: 43 Bond angle restraints: 46456 Sorted by residual: angle pdb=" N PRO B1056 " pdb=" CA PRO B1056 " pdb=" C PRO B1056 " ideal model delta sigma weight residual 110.70 112.84 -2.14 1.22e+00 6.72e-01 3.09e+00 angle pdb=" N VAL A 811 " pdb=" CA VAL A 811 " pdb=" C VAL A 811 " ideal model delta sigma weight residual 108.88 112.65 -3.77 2.16e+00 2.14e-01 3.05e+00 angle pdb=" N PRO A1056 " pdb=" CA PRO A1056 " pdb=" C PRO A1056 " ideal model delta sigma weight residual 110.70 112.83 -2.13 1.22e+00 6.72e-01 3.04e+00 angle pdb=" N VAL B 811 " pdb=" CA VAL B 811 " pdb=" C VAL B 811 " ideal model delta sigma weight residual 108.88 112.65 -3.77 2.16e+00 2.14e-01 3.04e+00 angle pdb=" N VAL D 811 " pdb=" CA VAL D 811 " pdb=" C VAL D 811 " ideal model delta sigma weight residual 108.88 112.63 -3.75 2.16e+00 2.14e-01 3.01e+00 ... (remaining 46451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 19792 17.75 - 35.50: 740 35.50 - 53.25: 176 53.25 - 70.99: 12 70.99 - 88.74: 8 Dihedral angle restraints: 20728 sinusoidal: 8364 harmonic: 12364 Sorted by residual: dihedral pdb=" CA LYS B1081 " pdb=" CB LYS B1081 " pdb=" CG LYS B1081 " pdb=" CD LYS B1081 " ideal model delta sinusoidal sigma weight residual -180.00 -127.17 -52.83 3 1.50e+01 4.44e-03 9.15e+00 dihedral pdb=" CA LYS D1081 " pdb=" CB LYS D1081 " pdb=" CG LYS D1081 " pdb=" CD LYS D1081 " ideal model delta sinusoidal sigma weight residual -180.00 -127.19 -52.81 3 1.50e+01 4.44e-03 9.15e+00 dihedral pdb=" CA LYS A1081 " pdb=" CB LYS A1081 " pdb=" CG LYS A1081 " pdb=" CD LYS A1081 " ideal model delta sinusoidal sigma weight residual -180.00 -127.20 -52.80 3 1.50e+01 4.44e-03 9.15e+00 ... (remaining 20725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 3569 0.028 - 0.055: 981 0.055 - 0.083: 427 0.083 - 0.110: 249 0.110 - 0.138: 50 Chirality restraints: 5276 Sorted by residual: chirality pdb=" C1D NAD A1601 " pdb=" C2D NAD A1601 " pdb=" N1N NAD A1601 " pdb=" O4D NAD A1601 " both_signs ideal model delta sigma weight residual False 2.41 2.55 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" C1D NAD C1601 " pdb=" C2D NAD C1601 " pdb=" N1N NAD C1601 " pdb=" O4D NAD C1601 " both_signs ideal model delta sigma weight residual False 2.41 2.55 -0.14 2.00e-01 2.50e+01 4.68e-01 chirality pdb=" C1D NAD D1601 " pdb=" C2D NAD D1601 " pdb=" N1N NAD D1601 " pdb=" O4D NAD D1601 " both_signs ideal model delta sigma weight residual False 2.41 2.55 -0.14 2.00e-01 2.50e+01 4.61e-01 ... (remaining 5273 not shown) Planarity restraints: 6084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B1056 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO B1057 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B1057 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B1057 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1056 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A1057 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A1057 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1057 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C1056 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO C1057 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO C1057 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C1057 " 0.022 5.00e-02 4.00e+02 ... (remaining 6081 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 6722 2.78 - 3.31: 35344 3.31 - 3.84: 59526 3.84 - 4.37: 68617 4.37 - 4.90: 114994 Nonbonded interactions: 285203 Sorted by model distance: nonbonded pdb=" O ALA B1512 " pdb=" NH2 ARG C1579 " model vdw 2.244 3.120 nonbonded pdb=" CB ASP D 960 " pdb=" OD2 ASP D 983 " model vdw 2.247 3.440 nonbonded pdb=" CB ASP B 960 " pdb=" OD2 ASP B 983 " model vdw 2.248 3.440 nonbonded pdb=" CB ASP C 960 " pdb=" OD2 ASP C 983 " model vdw 2.248 3.440 nonbonded pdb=" CB ASP A 960 " pdb=" OD2 ASP A 983 " model vdw 2.248 3.440 ... (remaining 285198 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 31.030 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.002 0.050 34200 Z= 0.102 Angle : 0.393 5.241 46456 Z= 0.199 Chirality : 0.037 0.138 5276 Planarity : 0.003 0.038 6084 Dihedral : 9.810 88.742 12760 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.13), residues: 4284 helix: 1.36 (0.10), residues: 2524 sheet: -0.49 (0.27), residues: 404 loop : -0.54 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 875 TYR 0.008 0.001 TYR D 846 PHE 0.006 0.001 PHE C 953 TRP 0.009 0.001 TRP C 533 HIS 0.003 0.000 HIS D 984 Details of bonding type rmsd covalent geometry : bond 0.00198 (34200) covalent geometry : angle 0.39304 (46456) hydrogen bonds : bond 0.13017 ( 2064) hydrogen bonds : angle 6.28810 ( 6084) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 438 time to evaluate : 1.259 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: A 552 MET cc_start: 0.9122 (tpt) cc_final: 0.8195 (tpp) REVERT: A 601 PHE cc_start: 0.9276 (t80) cc_final: 0.8790 (t80) REVERT: A 1115 ASN cc_start: 0.9532 (t160) cc_final: 0.9157 (m110) REVERT: A 1327 ARG cc_start: 0.8722 (mtp-110) cc_final: 0.8084 (mtm110) REVERT: A 1484 MET cc_start: 0.9089 (ttp) cc_final: 0.8725 (ptt) REVERT: A 1493 LEU cc_start: 0.9660 (mt) cc_final: 0.9399 (pp) REVERT: A 1515 ASP cc_start: 0.9194 (m-30) cc_final: 0.8721 (t0) REVERT: A 1582 ARG cc_start: 0.8996 (tmm160) cc_final: 0.8320 (ptm160) REVERT: B 552 MET cc_start: 0.9105 (tpt) cc_final: 0.8821 (tpt) REVERT: B 601 PHE cc_start: 0.9256 (t80) cc_final: 0.8889 (t80) REVERT: B 1115 ASN cc_start: 0.9542 (t160) cc_final: 0.9191 (m110) REVERT: B 1312 LEU cc_start: 0.9470 (mt) cc_final: 0.9244 (mt) REVERT: B 1327 ARG cc_start: 0.8721 (mtp-110) cc_final: 0.8411 (mtm110) REVERT: B 1484 MET cc_start: 0.9070 (ttp) cc_final: 0.8739 (ptt) REVERT: B 1493 LEU cc_start: 0.9651 (mt) cc_final: 0.9336 (pp) REVERT: B 1515 ASP cc_start: 0.9182 (m-30) cc_final: 0.8748 (t70) REVERT: C 552 MET cc_start: 0.9081 (tpt) cc_final: 0.8650 (tpt) REVERT: C 554 VAL cc_start: 0.8911 (m) cc_final: 0.8710 (p) REVERT: C 1115 ASN cc_start: 0.9506 (t160) cc_final: 0.9077 (m110) REVERT: C 1327 ARG cc_start: 0.8740 (mtp-110) cc_final: 0.8161 (mtm110) REVERT: C 1493 LEU cc_start: 0.9652 (mt) cc_final: 0.9391 (pp) REVERT: C 1515 ASP cc_start: 0.9145 (m-30) cc_final: 0.8712 (t0) REVERT: C 1582 ARG cc_start: 0.9017 (tmm160) cc_final: 0.8649 (ptm-80) REVERT: D 552 MET cc_start: 0.9117 (tpt) cc_final: 0.8223 (tpp) REVERT: D 601 PHE cc_start: 0.9252 (t80) cc_final: 0.8772 (t80) REVERT: D 1115 ASN cc_start: 0.9538 (t160) cc_final: 0.9183 (m110) REVERT: D 1327 ARG cc_start: 0.8745 (mtp-110) cc_final: 0.8515 (mtm110) REVERT: D 1484 MET cc_start: 0.9116 (ttp) cc_final: 0.8743 (ptt) REVERT: D 1493 LEU cc_start: 0.9648 (mt) cc_final: 0.9401 (pp) REVERT: D 1515 ASP cc_start: 0.9179 (m-30) cc_final: 0.8683 (t0) REVERT: D 1516 ASP cc_start: 0.9290 (t0) cc_final: 0.9059 (t0) REVERT: D 1582 ARG cc_start: 0.8997 (tmm160) cc_final: 0.8624 (ptm-80) outliers start: 4 outliers final: 4 residues processed: 442 average time/residue: 0.2241 time to fit residues: 156.4944 Evaluate side-chains 242 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 238 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain D residue 1051 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 GLN A 803 GLN A 807 ASN A1115 ASN A1193 GLN A1225 ASN B 631 GLN B 803 GLN B 807 ASN B1115 ASN B1193 GLN B1225 ASN C 631 GLN C 803 GLN C 807 ASN C1115 ASN C1193 GLN C1225 ASN D 631 GLN D 803 GLN D 807 ASN D1115 ASN D1193 GLN D1225 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.044698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.034000 restraints weight = 278293.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.035064 restraints weight = 186576.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.035823 restraints weight = 140483.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.036386 restraints weight = 114050.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.036793 restraints weight = 97486.299| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 34200 Z= 0.173 Angle : 0.547 7.817 46456 Z= 0.290 Chirality : 0.042 0.187 5276 Planarity : 0.005 0.041 6084 Dihedral : 4.761 48.556 4984 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.45 % Allowed : 9.32 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.13), residues: 4284 helix: 1.74 (0.10), residues: 2568 sheet: -0.77 (0.26), residues: 428 loop : -0.17 (0.19), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 643 TYR 0.017 0.001 TYR A1448 PHE 0.014 0.001 PHE C1481 TRP 0.009 0.001 TRP A 609 HIS 0.004 0.001 HIS C1149 Details of bonding type rmsd covalent geometry : bond 0.00359 (34200) covalent geometry : angle 0.54674 (46456) hydrogen bonds : bond 0.03992 ( 2064) hydrogen bonds : angle 5.17042 ( 6084) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 252 time to evaluate : 1.277 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 714 PHE cc_start: 0.9576 (OUTLIER) cc_final: 0.9328 (t80) REVERT: A 791 ASP cc_start: 0.9126 (t0) cc_final: 0.8865 (t0) REVERT: A 1178 MET cc_start: 0.9240 (mmp) cc_final: 0.8967 (tpp) REVERT: A 1225 ASN cc_start: 0.9472 (m110) cc_final: 0.9183 (p0) REVERT: A 1228 LEU cc_start: 0.9562 (mp) cc_final: 0.9332 (mp) REVERT: A 1256 MET cc_start: 0.9259 (ptm) cc_final: 0.8967 (ppp) REVERT: A 1327 ARG cc_start: 0.8801 (mtp-110) cc_final: 0.8455 (mtm110) REVERT: A 1393 TYR cc_start: 0.8784 (m-80) cc_final: 0.8355 (m-80) REVERT: A 1515 ASP cc_start: 0.9148 (m-30) cc_final: 0.8844 (t0) REVERT: A 1579 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8043 (tpt-90) REVERT: A 1582 ARG cc_start: 0.9015 (tmm160) cc_final: 0.8482 (ptm-80) REVERT: A 1584 MET cc_start: 0.7919 (mtp) cc_final: 0.7624 (mtt) REVERT: B 552 MET cc_start: 0.9180 (tpt) cc_final: 0.8218 (tpp) REVERT: B 574 ILE cc_start: 0.8848 (mm) cc_final: 0.8645 (tp) REVERT: B 791 ASP cc_start: 0.9160 (t0) cc_final: 0.8898 (t0) REVERT: B 1225 ASN cc_start: 0.9450 (m110) cc_final: 0.9149 (p0) REVERT: B 1228 LEU cc_start: 0.9581 (mp) cc_final: 0.9333 (mp) REVERT: B 1256 MET cc_start: 0.9257 (ptm) cc_final: 0.8987 (ppp) REVERT: B 1393 TYR cc_start: 0.8824 (m-80) cc_final: 0.8388 (m-80) REVERT: B 1515 ASP cc_start: 0.9141 (m-30) cc_final: 0.8841 (t0) REVERT: B 1582 ARG cc_start: 0.9006 (tmm160) cc_final: 0.8472 (ptm160) REVERT: B 1584 MET cc_start: 0.8003 (mtp) cc_final: 0.7711 (mtt) REVERT: C 552 MET cc_start: 0.9138 (tpt) cc_final: 0.8316 (tpp) REVERT: C 791 ASP cc_start: 0.9194 (t0) cc_final: 0.8954 (t0) REVERT: C 1093 ARG cc_start: 0.9228 (mmp80) cc_final: 0.9015 (mmp80) REVERT: C 1225 ASN cc_start: 0.9470 (m110) cc_final: 0.9166 (p0) REVERT: C 1228 LEU cc_start: 0.9583 (mp) cc_final: 0.9326 (mp) REVERT: C 1256 MET cc_start: 0.9229 (ptm) cc_final: 0.8939 (ppp) REVERT: C 1327 ARG cc_start: 0.8800 (mtp-110) cc_final: 0.8385 (mtm110) REVERT: C 1393 TYR cc_start: 0.8759 (m-80) cc_final: 0.8354 (m-80) REVERT: C 1515 ASP cc_start: 0.9173 (m-30) cc_final: 0.8711 (t0) REVERT: D 791 ASP cc_start: 0.9149 (t0) cc_final: 0.8888 (t0) REVERT: D 1225 ASN cc_start: 0.9450 (m110) cc_final: 0.9159 (p0) REVERT: D 1228 LEU cc_start: 0.9571 (mp) cc_final: 0.9336 (mp) REVERT: D 1256 MET cc_start: 0.9267 (ptm) cc_final: 0.8978 (ppp) REVERT: D 1327 ARG cc_start: 0.8777 (mtp-110) cc_final: 0.8474 (mtm110) REVERT: D 1393 TYR cc_start: 0.8796 (m-80) cc_final: 0.8362 (m-80) REVERT: D 1515 ASP cc_start: 0.9156 (m-30) cc_final: 0.8632 (t0) outliers start: 51 outliers final: 21 residues processed: 284 average time/residue: 0.2322 time to fit residues: 103.9511 Evaluate side-chains 228 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 801 LYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1151 VAL Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1579 ARG Chi-restraints excluded: chain B residue 714 PHE Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 801 LYS Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1141 SER Chi-restraints excluded: chain C residue 1151 VAL Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain D residue 714 PHE Chi-restraints excluded: chain D residue 801 LYS Chi-restraints excluded: chain D residue 1051 VAL Chi-restraints excluded: chain D residue 1141 SER Chi-restraints excluded: chain D residue 1158 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 427 optimal weight: 5.9990 chunk 409 optimal weight: 6.9990 chunk 292 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 398 optimal weight: 0.9990 chunk 264 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 268 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 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 576 GLN A1449 HIS A1456 GLN B 576 GLN B1449 HIS B1456 GLN C 576 GLN C1449 HIS C1456 GLN D 576 GLN D1449 HIS D1456 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.042058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.031920 restraints weight = 292414.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.032940 restraints weight = 194672.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.033651 restraints weight = 146006.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.034174 restraints weight = 118344.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.034555 restraints weight = 101143.184| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 34200 Z= 0.273 Angle : 0.640 8.454 46456 Z= 0.342 Chirality : 0.043 0.140 5276 Planarity : 0.005 0.044 6084 Dihedral : 4.874 44.410 4984 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.60 % Allowed : 10.26 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.13), residues: 4284 helix: 1.38 (0.10), residues: 2604 sheet: -0.67 (0.25), residues: 440 loop : -0.43 (0.19), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 997 TYR 0.021 0.002 TYR B1448 PHE 0.028 0.002 PHE C1481 TRP 0.014 0.002 TRP D 609 HIS 0.005 0.001 HIS C1258 Details of bonding type rmsd covalent geometry : bond 0.00549 (34200) covalent geometry : angle 0.63964 (46456) hydrogen bonds : bond 0.03965 ( 2064) hydrogen bonds : angle 5.17146 ( 6084) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 193 time to evaluate : 1.217 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: A 791 ASP cc_start: 0.9241 (t0) cc_final: 0.8972 (t0) REVERT: A 1225 ASN cc_start: 0.9490 (m110) cc_final: 0.9152 (p0) REVERT: A 1228 LEU cc_start: 0.9701 (mp) cc_final: 0.9393 (mp) REVERT: A 1256 MET cc_start: 0.9253 (ptm) cc_final: 0.8978 (ppp) REVERT: A 1327 ARG cc_start: 0.8935 (mtp-110) cc_final: 0.8283 (mtm110) REVERT: A 1393 TYR cc_start: 0.8912 (m-80) cc_final: 0.8504 (m-80) REVERT: A 1515 ASP cc_start: 0.9100 (m-30) cc_final: 0.8784 (t0) REVERT: A 1579 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7974 (tpt-90) REVERT: B 552 MET cc_start: 0.9228 (tpt) cc_final: 0.8950 (tpp) REVERT: B 791 ASP cc_start: 0.9238 (t0) cc_final: 0.8977 (t0) REVERT: B 1178 MET cc_start: 0.9274 (tpp) cc_final: 0.8779 (tpp) REVERT: B 1225 ASN cc_start: 0.9481 (m110) cc_final: 0.9139 (p0) REVERT: B 1228 LEU cc_start: 0.9672 (mp) cc_final: 0.9353 (mp) REVERT: B 1256 MET cc_start: 0.9268 (ptm) cc_final: 0.8679 (ppp) REVERT: B 1393 TYR cc_start: 0.8886 (m-80) cc_final: 0.8500 (m-80) REVERT: B 1515 ASP cc_start: 0.9061 (m-30) cc_final: 0.8795 (t0) REVERT: B 1579 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8298 (tpt-90) REVERT: C 623 MET cc_start: 0.9324 (ptp) cc_final: 0.9008 (mpp) REVERT: C 791 ASP cc_start: 0.9232 (t0) cc_final: 0.8985 (t0) REVERT: C 1178 MET cc_start: 0.9269 (tpp) cc_final: 0.8768 (tpp) REVERT: C 1225 ASN cc_start: 0.9494 (m110) cc_final: 0.9146 (p0) REVERT: C 1228 LEU cc_start: 0.9691 (mp) cc_final: 0.9369 (mp) REVERT: C 1256 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8640 (ppp) REVERT: C 1327 ARG cc_start: 0.8938 (mtp-110) cc_final: 0.8270 (mtm110) REVERT: C 1393 TYR cc_start: 0.8923 (m-80) cc_final: 0.8586 (m-80) REVERT: C 1484 MET cc_start: 0.8418 (ppp) cc_final: 0.8186 (ppp) REVERT: C 1582 ARG cc_start: 0.8834 (tmm160) cc_final: 0.7878 (mmt180) REVERT: D 552 MET cc_start: 0.9264 (tpp) cc_final: 0.8931 (tpp) REVERT: D 791 ASP cc_start: 0.9247 (t0) cc_final: 0.8983 (t0) REVERT: D 1178 MET cc_start: 0.9259 (tpp) cc_final: 0.8735 (tpp) REVERT: D 1225 ASN cc_start: 0.9480 (m110) cc_final: 0.9138 (p0) REVERT: D 1228 LEU cc_start: 0.9694 (mp) cc_final: 0.9388 (mp) REVERT: D 1256 MET cc_start: 0.9288 (ptm) cc_final: 0.9003 (ppp) REVERT: D 1327 ARG cc_start: 0.8891 (mtp-110) cc_final: 0.8422 (mtm110) REVERT: D 1393 TYR cc_start: 0.8891 (m-80) cc_final: 0.8577 (m-80) outliers start: 56 outliers final: 34 residues processed: 237 average time/residue: 0.2084 time to fit residues: 80.1713 Evaluate side-chains 211 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 801 LYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1579 ARG Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1053 GLU Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1579 ARG Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 801 LYS Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1141 SER Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1256 MET Chi-restraints excluded: chain C residue 1460 LEU Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 714 PHE Chi-restraints excluded: chain D residue 801 LYS Chi-restraints excluded: chain D residue 1051 VAL Chi-restraints excluded: chain D residue 1053 GLU Chi-restraints excluded: chain D residue 1141 SER Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1460 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 44 optimal weight: 0.9990 chunk 243 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 270 optimal weight: 10.0000 chunk 363 optimal weight: 1.9990 chunk 421 optimal weight: 5.9990 chunk 367 optimal weight: 3.9990 chunk 285 optimal weight: 10.0000 chunk 327 optimal weight: 0.5980 chunk 358 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1449 HIS A1456 GLN B1449 HIS B1456 GLN C1449 HIS C1456 GLN D1449 HIS D1456 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.043111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.032719 restraints weight = 282766.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.033773 restraints weight = 188511.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.034528 restraints weight = 141375.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.035051 restraints weight = 114553.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.035445 restraints weight = 98130.583| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34200 Z= 0.143 Angle : 0.504 6.341 46456 Z= 0.272 Chirality : 0.041 0.211 5276 Planarity : 0.004 0.044 6084 Dihedral : 4.592 42.694 4984 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.97 % Allowed : 11.43 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.13), residues: 4284 helix: 1.68 (0.10), residues: 2600 sheet: -0.13 (0.28), residues: 344 loop : -0.56 (0.18), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1586 TYR 0.019 0.001 TYR A 846 PHE 0.012 0.001 PHE C1350 TRP 0.012 0.001 TRP A 609 HIS 0.003 0.001 HIS D1258 Details of bonding type rmsd covalent geometry : bond 0.00302 (34200) covalent geometry : angle 0.50450 (46456) hydrogen bonds : bond 0.03504 ( 2064) hydrogen bonds : angle 4.82544 ( 6084) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 192 time to evaluate : 1.284 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: A 552 MET cc_start: 0.9162 (tpp) cc_final: 0.8677 (tpp) REVERT: A 1178 MET cc_start: 0.9326 (tpp) cc_final: 0.8533 (tpp) REVERT: A 1225 ASN cc_start: 0.9496 (m110) cc_final: 0.9151 (p0) REVERT: A 1228 LEU cc_start: 0.9711 (mp) cc_final: 0.9360 (mp) REVERT: A 1256 MET cc_start: 0.9385 (ptm) cc_final: 0.8828 (ppp) REVERT: A 1327 ARG cc_start: 0.8919 (mtp-110) cc_final: 0.8455 (mtm110) REVERT: A 1393 TYR cc_start: 0.8874 (m-80) cc_final: 0.8651 (m-80) REVERT: A 1515 ASP cc_start: 0.9080 (m-30) cc_final: 0.8741 (t0) REVERT: B 1178 MET cc_start: 0.9296 (tpp) cc_final: 0.8707 (tpp) REVERT: B 1225 ASN cc_start: 0.9477 (m110) cc_final: 0.9212 (p0) REVERT: B 1256 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.8831 (ppp) REVERT: B 1515 ASP cc_start: 0.9065 (m-30) cc_final: 0.8758 (t0) REVERT: C 623 MET cc_start: 0.9093 (ptp) cc_final: 0.8851 (mpp) REVERT: C 926 MET cc_start: 0.6427 (OUTLIER) cc_final: 0.6221 (ptt) REVERT: C 1178 MET cc_start: 0.9288 (tpp) cc_final: 0.8683 (tpp) REVERT: C 1225 ASN cc_start: 0.9488 (m110) cc_final: 0.9216 (p0) REVERT: C 1256 MET cc_start: 0.9360 (ptm) cc_final: 0.8802 (ppp) REVERT: C 1327 ARG cc_start: 0.8932 (mtp-110) cc_final: 0.8228 (mtm110) REVERT: C 1393 TYR cc_start: 0.8900 (m-80) cc_final: 0.8630 (m-80) REVERT: C 1515 ASP cc_start: 0.8918 (m-30) cc_final: 0.8517 (t0) REVERT: D 1178 MET cc_start: 0.9293 (tpp) cc_final: 0.8704 (tpp) REVERT: D 1225 ASN cc_start: 0.9488 (m110) cc_final: 0.9139 (p0) REVERT: D 1228 LEU cc_start: 0.9711 (mp) cc_final: 0.9353 (mp) REVERT: D 1256 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.8982 (ppp) REVERT: D 1327 ARG cc_start: 0.8903 (mtp-110) cc_final: 0.8471 (mtm110) REVERT: D 1393 TYR cc_start: 0.8886 (m-80) cc_final: 0.8607 (m-80) REVERT: D 1515 ASP cc_start: 0.8916 (m-30) cc_final: 0.8546 (t0) REVERT: D 1516 ASP cc_start: 0.9112 (OUTLIER) cc_final: 0.8868 (m-30) outliers start: 69 outliers final: 36 residues processed: 251 average time/residue: 0.2106 time to fit residues: 86.6437 Evaluate side-chains 216 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 176 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 801 LYS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1579 ARG Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1053 GLU Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1256 MET Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1579 ARG Chi-restraints excluded: chain C residue 548 MET Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 801 LYS Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 926 MET Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1460 LEU Chi-restraints excluded: chain C residue 1516 ASP Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 801 LYS Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 1051 VAL Chi-restraints excluded: chain D residue 1053 GLU Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1256 MET Chi-restraints excluded: chain D residue 1460 LEU Chi-restraints excluded: chain D residue 1516 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 190 optimal weight: 0.6980 chunk 229 optimal weight: 2.9990 chunk 322 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 chunk 277 optimal weight: 7.9990 chunk 200 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 223 optimal weight: 0.0070 chunk 305 optimal weight: 3.9990 overall best weight: 2.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1449 HIS A1456 GLN B1449 HIS B1456 GLN C1449 HIS C1456 GLN D1449 HIS D1456 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.042217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.032152 restraints weight = 287637.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.033182 restraints weight = 191865.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.033882 restraints weight = 143551.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.034408 restraints weight = 116718.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.034786 restraints weight = 99475.763| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 34200 Z= 0.184 Angle : 0.537 9.913 46456 Z= 0.289 Chirality : 0.041 0.407 5276 Planarity : 0.004 0.044 6084 Dihedral : 4.600 41.148 4984 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.14 % Allowed : 11.92 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.13), residues: 4284 helix: 1.60 (0.10), residues: 2600 sheet: -0.18 (0.28), residues: 352 loop : -0.51 (0.18), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 997 TYR 0.018 0.001 TYR D 846 PHE 0.009 0.001 PHE C1350 TRP 0.011 0.001 TRP A 609 HIS 0.003 0.001 HIS C 538 Details of bonding type rmsd covalent geometry : bond 0.00379 (34200) covalent geometry : angle 0.53684 (46456) hydrogen bonds : bond 0.03478 ( 2064) hydrogen bonds : angle 4.87278 ( 6084) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 177 time to evaluate : 1.196 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: A 1178 MET cc_start: 0.9314 (tpp) cc_final: 0.8512 (tpp) REVERT: A 1225 ASN cc_start: 0.9499 (m110) cc_final: 0.9230 (p0) REVERT: A 1327 ARG cc_start: 0.8938 (mtp-110) cc_final: 0.8475 (mtm110) REVERT: A 1515 ASP cc_start: 0.9110 (m-30) cc_final: 0.8805 (t70) REVERT: B 552 MET cc_start: 0.9091 (tpp) cc_final: 0.8603 (tpp) REVERT: B 1178 MET cc_start: 0.9338 (tpp) cc_final: 0.8722 (tpp) REVERT: B 1225 ASN cc_start: 0.9486 (m110) cc_final: 0.9199 (p0) REVERT: B 1256 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8938 (ppp) REVERT: B 1393 TYR cc_start: 0.8862 (m-80) cc_final: 0.8516 (m-80) REVERT: B 1515 ASP cc_start: 0.9088 (m-30) cc_final: 0.8782 (t0) REVERT: C 1178 MET cc_start: 0.9340 (tpp) cc_final: 0.8738 (tpp) REVERT: C 1197 MET cc_start: 0.8314 (tpt) cc_final: 0.8108 (mmt) REVERT: C 1225 ASN cc_start: 0.9497 (m110) cc_final: 0.9206 (p0) REVERT: C 1327 ARG cc_start: 0.8950 (mtp-110) cc_final: 0.8475 (mtm110) REVERT: C 1515 ASP cc_start: 0.8957 (m-30) cc_final: 0.8565 (t0) REVERT: D 1178 MET cc_start: 0.9331 (tpp) cc_final: 0.8726 (tpp) REVERT: D 1225 ASN cc_start: 0.9502 (m110) cc_final: 0.9231 (p0) REVERT: D 1256 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.8843 (ppp) REVERT: D 1327 ARG cc_start: 0.8924 (mtp-110) cc_final: 0.8469 (mtm110) REVERT: D 1515 ASP cc_start: 0.8938 (m-30) cc_final: 0.8516 (t0) outliers start: 75 outliers final: 52 residues processed: 242 average time/residue: 0.2037 time to fit residues: 81.9243 Evaluate side-chains 219 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 165 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 801 LYS Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1579 ARG Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 810 ILE Chi-restraints excluded: chain B residue 846 TYR Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1053 GLU Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1256 MET Chi-restraints excluded: chain B residue 1263 LEU Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1579 ARG Chi-restraints excluded: chain C residue 548 MET Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 801 LYS Chi-restraints excluded: chain C residue 810 ILE Chi-restraints excluded: chain C residue 846 TYR Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1141 SER Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1295 HIS Chi-restraints excluded: chain C residue 1460 LEU Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 801 LYS Chi-restraints excluded: chain D residue 810 ILE Chi-restraints excluded: chain D residue 846 TYR Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 1051 VAL Chi-restraints excluded: chain D residue 1053 GLU Chi-restraints excluded: chain D residue 1141 SER Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1256 MET Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1460 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 277 optimal weight: 9.9990 chunk 178 optimal weight: 10.0000 chunk 268 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 217 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 256 optimal weight: 0.9990 chunk 362 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 155 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 659 ASN A1449 HIS A1456 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1449 HIS B1456 GLN C1449 HIS C1456 GLN D 659 ASN D1449 HIS D1456 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.042984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.032700 restraints weight = 283028.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.033777 restraints weight = 187023.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.034533 restraints weight = 139469.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.035056 restraints weight = 112570.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.035449 restraints weight = 96205.577| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34200 Z= 0.120 Angle : 0.516 11.893 46456 Z= 0.272 Chirality : 0.042 0.396 5276 Planarity : 0.004 0.045 6084 Dihedral : 4.476 40.859 4984 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.94 % Allowed : 13.00 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.13), residues: 4284 helix: 1.69 (0.10), residues: 2620 sheet: 0.13 (0.28), residues: 352 loop : -0.54 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 997 TYR 0.017 0.001 TYR B 846 PHE 0.011 0.001 PHE C1350 TRP 0.011 0.001 TRP A 533 HIS 0.004 0.001 HIS A1258 Details of bonding type rmsd covalent geometry : bond 0.00258 (34200) covalent geometry : angle 0.51616 (46456) hydrogen bonds : bond 0.03328 ( 2064) hydrogen bonds : angle 4.70048 ( 6084) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 192 time to evaluate : 1.311 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: A 1178 MET cc_start: 0.9336 (tpp) cc_final: 0.8474 (tpp) REVERT: A 1225 ASN cc_start: 0.9499 (m110) cc_final: 0.9224 (p0) REVERT: A 1327 ARG cc_start: 0.8917 (mtp-110) cc_final: 0.8463 (mtm110) REVERT: A 1393 TYR cc_start: 0.8792 (m-80) cc_final: 0.8553 (m-80) REVERT: A 1515 ASP cc_start: 0.9090 (m-30) cc_final: 0.8800 (t70) REVERT: A 1579 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7904 (tpt-90) REVERT: B 1178 MET cc_start: 0.9359 (tpp) cc_final: 0.8670 (tpp) REVERT: B 1225 ASN cc_start: 0.9494 (m110) cc_final: 0.9221 (p0) REVERT: B 1256 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8880 (ppp) REVERT: B 1393 TYR cc_start: 0.8837 (m-80) cc_final: 0.8363 (m-80) REVERT: B 1515 ASP cc_start: 0.9081 (m-30) cc_final: 0.8849 (t70) REVERT: C 665 THR cc_start: 0.9539 (m) cc_final: 0.9331 (p) REVERT: C 1178 MET cc_start: 0.9369 (tpp) cc_final: 0.8695 (tpp) REVERT: C 1225 ASN cc_start: 0.9507 (m110) cc_final: 0.9229 (p0) REVERT: C 1256 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8910 (ppp) REVERT: C 1327 ARG cc_start: 0.8922 (mtp-110) cc_final: 0.8454 (mtm110) REVERT: C 1393 TYR cc_start: 0.8706 (m-80) cc_final: 0.8305 (m-80) REVERT: C 1515 ASP cc_start: 0.8981 (m-30) cc_final: 0.8607 (t0) REVERT: C 1516 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8893 (m-30) REVERT: D 552 MET cc_start: 0.9188 (tpp) cc_final: 0.8603 (tpp) REVERT: D 1093 ARG cc_start: 0.9336 (mmp80) cc_final: 0.9125 (mmm160) REVERT: D 1178 MET cc_start: 0.9364 (tpp) cc_final: 0.8680 (tpp) REVERT: D 1225 ASN cc_start: 0.9498 (m110) cc_final: 0.9225 (p0) REVERT: D 1327 ARG cc_start: 0.8892 (mtp-110) cc_final: 0.8437 (mtm110) REVERT: D 1516 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8864 (m-30) outliers start: 68 outliers final: 39 residues processed: 251 average time/residue: 0.2168 time to fit residues: 88.4866 Evaluate side-chains 224 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 801 LYS Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1579 ARG Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1053 GLU Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1256 MET Chi-restraints excluded: chain B residue 1263 LEU Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1579 ARG Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1141 SER Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1256 MET Chi-restraints excluded: chain C residue 1295 HIS Chi-restraints excluded: chain C residue 1460 LEU Chi-restraints excluded: chain C residue 1516 ASP Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 801 LYS Chi-restraints excluded: chain D residue 1051 VAL Chi-restraints excluded: chain D residue 1053 GLU Chi-restraints excluded: chain D residue 1141 SER Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1256 MET Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1460 LEU Chi-restraints excluded: chain D residue 1516 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 289 optimal weight: 0.0980 chunk 286 optimal weight: 2.9990 chunk 308 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 292 optimal weight: 6.9990 chunk 340 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 254 optimal weight: 9.9990 chunk 342 optimal weight: 0.5980 chunk 271 optimal weight: 0.2980 chunk 382 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1449 HIS A1456 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1449 HIS B1456 GLN C1449 HIS C1456 GLN D1449 HIS D1456 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.042544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.032309 restraints weight = 286512.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.033371 restraints weight = 189247.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.034121 restraints weight = 141110.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.034661 restraints weight = 113864.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.035040 restraints weight = 96912.233| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34200 Z= 0.145 Angle : 0.538 12.436 46456 Z= 0.283 Chirality : 0.042 0.422 5276 Planarity : 0.004 0.045 6084 Dihedral : 4.473 41.152 4984 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.80 % Allowed : 13.63 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.13), residues: 4284 helix: 1.80 (0.10), residues: 2592 sheet: 0.07 (0.28), residues: 356 loop : -0.55 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 997 TYR 0.018 0.001 TYR A 846 PHE 0.009 0.001 PHE A1350 TRP 0.012 0.001 TRP B 609 HIS 0.005 0.001 HIS D 923 Details of bonding type rmsd covalent geometry : bond 0.00305 (34200) covalent geometry : angle 0.53767 (46456) hydrogen bonds : bond 0.03308 ( 2064) hydrogen bonds : angle 4.77157 ( 6084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 180 time to evaluate : 1.349 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: A 1178 MET cc_start: 0.9367 (tpp) cc_final: 0.8406 (tpp) REVERT: A 1225 ASN cc_start: 0.9504 (m110) cc_final: 0.9222 (p0) REVERT: A 1327 ARG cc_start: 0.8940 (mtp-110) cc_final: 0.8494 (mtm110) REVERT: A 1515 ASP cc_start: 0.9093 (m-30) cc_final: 0.8803 (t70) REVERT: A 1579 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8102 (tpt-90) REVERT: A 1582 ARG cc_start: 0.8912 (tmm160) cc_final: 0.8630 (ttp80) REVERT: B 1178 MET cc_start: 0.9355 (tpp) cc_final: 0.8656 (tpp) REVERT: B 1225 ASN cc_start: 0.9500 (m110) cc_final: 0.9214 (p0) REVERT: B 1256 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8925 (ppp) REVERT: B 1393 TYR cc_start: 0.8885 (m-80) cc_final: 0.8378 (m-80) REVERT: B 1515 ASP cc_start: 0.9085 (m-30) cc_final: 0.8836 (t70) REVERT: B 1579 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8158 (tpt-90) REVERT: B 1582 ARG cc_start: 0.8970 (tmm160) cc_final: 0.8678 (ttp80) REVERT: C 665 THR cc_start: 0.9534 (m) cc_final: 0.9326 (p) REVERT: C 1178 MET cc_start: 0.9377 (tpp) cc_final: 0.8690 (tpp) REVERT: C 1197 MET cc_start: 0.8465 (mmm) cc_final: 0.7998 (mmm) REVERT: C 1225 ASN cc_start: 0.9513 (m110) cc_final: 0.9222 (p0) REVERT: C 1256 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8862 (ppp) REVERT: C 1327 ARG cc_start: 0.8929 (mtp-110) cc_final: 0.8458 (mtm110) REVERT: C 1393 TYR cc_start: 0.8791 (m-80) cc_final: 0.8505 (m-80) REVERT: D 1093 ARG cc_start: 0.9350 (mmp80) cc_final: 0.9134 (mmm160) REVERT: D 1178 MET cc_start: 0.9330 (tpp) cc_final: 0.8627 (tpp) REVERT: D 1225 ASN cc_start: 0.9505 (m110) cc_final: 0.9222 (p0) REVERT: D 1256 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8843 (ppp) REVERT: D 1327 ARG cc_start: 0.8914 (mtp-110) cc_final: 0.8510 (mtm110) REVERT: D 1393 TYR cc_start: 0.8823 (m-80) cc_final: 0.8543 (m-80) outliers start: 63 outliers final: 49 residues processed: 234 average time/residue: 0.2291 time to fit residues: 85.4413 Evaluate side-chains 230 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1579 ARG Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 686 ARG Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 714 PHE Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1053 GLU Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1256 MET Chi-restraints excluded: chain B residue 1263 LEU Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1579 ARG Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 686 ARG Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 846 TYR Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1141 SER Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1256 MET Chi-restraints excluded: chain C residue 1295 HIS Chi-restraints excluded: chain C residue 1460 LEU Chi-restraints excluded: chain C residue 1584 MET Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 686 ARG Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 721 THR Chi-restraints excluded: chain D residue 801 LYS Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 1051 VAL Chi-restraints excluded: chain D residue 1053 GLU Chi-restraints excluded: chain D residue 1141 SER Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1256 MET Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1460 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 227 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 chunk 418 optimal weight: 0.3980 chunk 53 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 352 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 393 optimal weight: 1.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1449 HIS A1456 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1449 HIS B1456 GLN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1449 HIS C1456 GLN D1449 HIS D1456 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.042401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.032232 restraints weight = 286669.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.033283 restraints weight = 190068.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.034033 restraints weight = 141850.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.034565 restraints weight = 114428.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.034937 restraints weight = 97484.389| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34200 Z= 0.155 Angle : 0.553 13.259 46456 Z= 0.290 Chirality : 0.043 0.432 5276 Planarity : 0.004 0.045 6084 Dihedral : 4.499 41.616 4984 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.82 % Allowed : 13.91 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.13), residues: 4284 helix: 1.79 (0.10), residues: 2592 sheet: 0.03 (0.28), residues: 356 loop : -0.54 (0.18), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 997 TYR 0.017 0.001 TYR B 846 PHE 0.008 0.001 PHE D1526 TRP 0.012 0.001 TRP A1389 HIS 0.005 0.001 HIS A 923 Details of bonding type rmsd covalent geometry : bond 0.00324 (34200) covalent geometry : angle 0.55291 (46456) hydrogen bonds : bond 0.03320 ( 2064) hydrogen bonds : angle 4.80630 ( 6084) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 175 time to evaluate : 1.351 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: A 1178 MET cc_start: 0.9368 (tpp) cc_final: 0.8409 (tpp) REVERT: A 1225 ASN cc_start: 0.9503 (m110) cc_final: 0.9216 (p0) REVERT: A 1256 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8854 (ppp) REVERT: A 1327 ARG cc_start: 0.8963 (mtp-110) cc_final: 0.8515 (mtm110) REVERT: A 1393 TYR cc_start: 0.8852 (m-80) cc_final: 0.8381 (m-80) REVERT: A 1515 ASP cc_start: 0.9077 (m-30) cc_final: 0.8814 (t70) REVERT: B 1178 MET cc_start: 0.9349 (tpp) cc_final: 0.8622 (tpp) REVERT: B 1225 ASN cc_start: 0.9507 (m110) cc_final: 0.9212 (p0) REVERT: B 1256 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8933 (ppp) REVERT: B 1393 TYR cc_start: 0.8914 (m-80) cc_final: 0.8273 (m-80) REVERT: B 1461 ASP cc_start: 0.9231 (p0) cc_final: 0.8777 (t0) REVERT: B 1515 ASP cc_start: 0.9078 (m-30) cc_final: 0.8830 (t70) REVERT: B 1579 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8160 (tpt-90) REVERT: B 1582 ARG cc_start: 0.8981 (tmm160) cc_final: 0.8647 (ttp80) REVERT: C 552 MET cc_start: 0.9234 (tpt) cc_final: 0.8715 (tpp) REVERT: C 665 THR cc_start: 0.9541 (m) cc_final: 0.9329 (p) REVERT: C 1178 MET cc_start: 0.9354 (tpp) cc_final: 0.8609 (tpp) REVERT: C 1225 ASN cc_start: 0.9512 (m110) cc_final: 0.9218 (p0) REVERT: C 1256 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8959 (ppp) REVERT: C 1327 ARG cc_start: 0.8950 (mtp-110) cc_final: 0.8445 (mtm110) REVERT: C 1393 TYR cc_start: 0.8779 (m-80) cc_final: 0.8500 (m-80) REVERT: D 1093 ARG cc_start: 0.9355 (mmp80) cc_final: 0.9140 (mmm160) REVERT: D 1178 MET cc_start: 0.9338 (tpp) cc_final: 0.8603 (tpp) REVERT: D 1225 ASN cc_start: 0.9504 (m110) cc_final: 0.9215 (p0) REVERT: D 1256 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8846 (ppp) REVERT: D 1327 ARG cc_start: 0.8933 (mtp-110) cc_final: 0.8525 (mtm110) REVERT: D 1393 TYR cc_start: 0.8919 (m-80) cc_final: 0.8491 (m-80) REVERT: D 1515 ASP cc_start: 0.8941 (m-30) cc_final: 0.8622 (t0) outliers start: 64 outliers final: 50 residues processed: 231 average time/residue: 0.2349 time to fit residues: 87.1970 Evaluate side-chains 233 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1256 MET Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1579 ARG Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 686 ARG Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 846 TYR Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1053 GLU Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1256 MET Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1579 ARG Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 686 ARG Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 846 TYR Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1141 SER Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1256 MET Chi-restraints excluded: chain C residue 1295 HIS Chi-restraints excluded: chain C residue 1460 LEU Chi-restraints excluded: chain C residue 1584 MET Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 686 ARG Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 801 LYS Chi-restraints excluded: chain D residue 846 TYR Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 1051 VAL Chi-restraints excluded: chain D residue 1053 GLU Chi-restraints excluded: chain D residue 1141 SER Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1256 MET Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1460 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 161 optimal weight: 10.0000 chunk 199 optimal weight: 4.9990 chunk 334 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 397 optimal weight: 2.9990 chunk 383 optimal weight: 1.9990 chunk 324 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 HIS A1449 HIS A1456 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1449 HIS B1456 GLN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 663 HIS C1449 HIS C1456 GLN D1449 HIS D1456 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.041271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.031344 restraints weight = 293966.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.032353 restraints weight = 194516.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.033077 restraints weight = 145270.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.033569 restraints weight = 117345.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.033938 restraints weight = 100237.884| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 34200 Z= 0.222 Angle : 0.623 13.256 46456 Z= 0.329 Chirality : 0.043 0.439 5276 Planarity : 0.004 0.045 6084 Dihedral : 4.709 42.128 4984 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.71 % Allowed : 14.11 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.13), residues: 4284 helix: 1.61 (0.10), residues: 2592 sheet: -0.27 (0.27), residues: 376 loop : -0.49 (0.19), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1579 TYR 0.018 0.002 TYR D 846 PHE 0.010 0.001 PHE D1286 TRP 0.018 0.002 TRP C 609 HIS 0.005 0.001 HIS A1258 Details of bonding type rmsd covalent geometry : bond 0.00454 (34200) covalent geometry : angle 0.62328 (46456) hydrogen bonds : bond 0.03579 ( 2064) hydrogen bonds : angle 5.05285 ( 6084) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 1.319 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 552 MET cc_start: 0.9166 (tpp) cc_final: 0.8909 (tpp) REVERT: A 1178 MET cc_start: 0.9384 (tpp) cc_final: 0.8463 (tpp) REVERT: A 1327 ARG cc_start: 0.9006 (mtp-110) cc_final: 0.8511 (mtm110) REVERT: A 1393 TYR cc_start: 0.8902 (m-80) cc_final: 0.8549 (m-80) REVERT: A 1461 ASP cc_start: 0.9269 (p0) cc_final: 0.8794 (t0) REVERT: A 1515 ASP cc_start: 0.9050 (m-30) cc_final: 0.8823 (t70) REVERT: B 552 MET cc_start: 0.9160 (tpp) cc_final: 0.8876 (tpp) REVERT: B 1178 MET cc_start: 0.9342 (tpp) cc_final: 0.8592 (tpp) REVERT: B 1256 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8906 (ppp) REVERT: B 1375 MET cc_start: 0.9202 (ptp) cc_final: 0.8739 (mpp) REVERT: B 1393 TYR cc_start: 0.8984 (m-80) cc_final: 0.8325 (m-80) REVERT: B 1461 ASP cc_start: 0.9264 (p0) cc_final: 0.8771 (t0) REVERT: B 1579 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7888 (tpt-90) REVERT: B 1582 ARG cc_start: 0.9043 (tmm160) cc_final: 0.8730 (ttp80) REVERT: B 1584 MET cc_start: 0.8337 (pmm) cc_final: 0.8130 (pmm) REVERT: C 552 MET cc_start: 0.9315 (tpt) cc_final: 0.9051 (tpp) REVERT: C 665 THR cc_start: 0.9532 (m) cc_final: 0.9324 (p) REVERT: C 1178 MET cc_start: 0.9377 (tpp) cc_final: 0.8612 (tpp) REVERT: C 1327 ARG cc_start: 0.8992 (mtp-110) cc_final: 0.8490 (mtm110) REVERT: C 1375 MET cc_start: 0.9196 (ptp) cc_final: 0.8739 (mpp) REVERT: C 1393 TYR cc_start: 0.8846 (m-80) cc_final: 0.8536 (m-80) REVERT: D 1178 MET cc_start: 0.9353 (tpp) cc_final: 0.8603 (tpp) REVERT: D 1256 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8817 (ppp) REVERT: D 1327 ARG cc_start: 0.8998 (mtp-110) cc_final: 0.8498 (mtm110) REVERT: D 1393 TYR cc_start: 0.8934 (m-80) cc_final: 0.8538 (m-80) REVERT: D 1515 ASP cc_start: 0.8902 (m-30) cc_final: 0.8624 (t0) outliers start: 60 outliers final: 52 residues processed: 224 average time/residue: 0.2265 time to fit residues: 82.5332 Evaluate side-chains 219 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 164 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 801 LYS Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1579 ARG Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 686 ARG Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 846 TYR Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1053 GLU Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1256 MET Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1579 ARG Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 686 ARG Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 846 TYR Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1141 SER Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1256 MET Chi-restraints excluded: chain C residue 1295 HIS Chi-restraints excluded: chain C residue 1460 LEU Chi-restraints excluded: chain C residue 1584 MET Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 686 ARG Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 801 LYS Chi-restraints excluded: chain D residue 846 TYR Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 1051 VAL Chi-restraints excluded: chain D residue 1053 GLU Chi-restraints excluded: chain D residue 1141 SER Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1256 MET Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 167 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 381 optimal weight: 10.0000 chunk 251 optimal weight: 0.0970 chunk 154 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 229 optimal weight: 3.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1449 HIS A1456 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1449 HIS B1456 GLN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1449 HIS C1456 GLN D1449 HIS D1456 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.041862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.031799 restraints weight = 291401.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.032840 restraints weight = 191493.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.033588 restraints weight = 142485.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.034118 restraints weight = 114680.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.034484 restraints weight = 97431.916| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34200 Z= 0.164 Angle : 0.591 14.070 46456 Z= 0.305 Chirality : 0.043 0.461 5276 Planarity : 0.004 0.058 6084 Dihedral : 4.630 42.701 4984 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.65 % Allowed : 14.60 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.13), residues: 4284 helix: 1.71 (0.10), residues: 2612 sheet: -0.22 (0.27), residues: 376 loop : -0.57 (0.18), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 997 TYR 0.017 0.001 TYR D 846 PHE 0.009 0.001 PHE D1526 TRP 0.017 0.001 TRP A1013 HIS 0.003 0.001 HIS A1258 Details of bonding type rmsd covalent geometry : bond 0.00343 (34200) covalent geometry : angle 0.59096 (46456) hydrogen bonds : bond 0.03417 ( 2064) hydrogen bonds : angle 4.90404 ( 6084) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8568 Ramachandran restraints generated. 4284 Oldfield, 0 Emsley, 4284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 170 time to evaluate : 1.127 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 1178 MET cc_start: 0.9374 (tpp) cc_final: 0.8440 (tpp) REVERT: A 1327 ARG cc_start: 0.8992 (mtp-110) cc_final: 0.8489 (mtm110) REVERT: A 1393 TYR cc_start: 0.8936 (m-80) cc_final: 0.8538 (m-80) REVERT: A 1461 ASP cc_start: 0.9292 (p0) cc_final: 0.8802 (t0) REVERT: A 1515 ASP cc_start: 0.9021 (m-30) cc_final: 0.8801 (t70) REVERT: A 1579 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7917 (tpt-90) REVERT: A 1582 ARG cc_start: 0.9024 (tmm160) cc_final: 0.8712 (ttp80) REVERT: B 1178 MET cc_start: 0.9388 (tpp) cc_final: 0.8595 (tpp) REVERT: B 1256 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8904 (ppp) REVERT: B 1393 TYR cc_start: 0.8758 (m-80) cc_final: 0.8288 (m-80) REVERT: B 1461 ASP cc_start: 0.9328 (p0) cc_final: 0.8853 (t0) REVERT: C 552 MET cc_start: 0.9316 (tpt) cc_final: 0.9031 (tpp) REVERT: C 665 THR cc_start: 0.9531 (m) cc_final: 0.9319 (p) REVERT: C 1178 MET cc_start: 0.9354 (tpp) cc_final: 0.8958 (tpp) REVERT: C 1256 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8899 (ppp) REVERT: C 1327 ARG cc_start: 0.8981 (mtp-110) cc_final: 0.8464 (mtm110) REVERT: C 1393 TYR cc_start: 0.8850 (m-80) cc_final: 0.8315 (m-80) REVERT: C 1461 ASP cc_start: 0.9251 (p0) cc_final: 0.8847 (t0) REVERT: C 1515 ASP cc_start: 0.8947 (m-30) cc_final: 0.8605 (t0) REVERT: C 1582 ARG cc_start: 0.8918 (tmm160) cc_final: 0.8076 (mmt-90) REVERT: D 1178 MET cc_start: 0.9390 (tpp) cc_final: 0.8605 (tpp) REVERT: D 1256 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8873 (ppp) REVERT: D 1327 ARG cc_start: 0.8988 (mtp-110) cc_final: 0.8472 (mtm110) REVERT: D 1375 MET cc_start: 0.9213 (ptp) cc_final: 0.8743 (mpp) REVERT: D 1393 TYR cc_start: 0.8963 (m-80) cc_final: 0.8724 (m-80) outliers start: 58 outliers final: 49 residues processed: 223 average time/residue: 0.2281 time to fit residues: 82.1283 Evaluate side-chains 219 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 166 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 686 ARG Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1053 GLU Chi-restraints excluded: chain A residue 1141 SER Chi-restraints excluded: chain A residue 1158 ASP Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1460 LEU Chi-restraints excluded: chain A residue 1579 ARG Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 686 ARG Chi-restraints excluded: chain B residue 705 LEU Chi-restraints excluded: chain B residue 846 TYR Chi-restraints excluded: chain B residue 868 VAL Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1053 GLU Chi-restraints excluded: chain B residue 1141 SER Chi-restraints excluded: chain B residue 1158 ASP Chi-restraints excluded: chain B residue 1256 MET Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1579 ARG Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 686 ARG Chi-restraints excluded: chain C residue 705 LEU Chi-restraints excluded: chain C residue 846 TYR Chi-restraints excluded: chain C residue 868 VAL Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1141 SER Chi-restraints excluded: chain C residue 1158 ASP Chi-restraints excluded: chain C residue 1256 MET Chi-restraints excluded: chain C residue 1295 HIS Chi-restraints excluded: chain C residue 1460 LEU Chi-restraints excluded: chain C residue 1584 MET Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 686 ARG Chi-restraints excluded: chain D residue 705 LEU Chi-restraints excluded: chain D residue 801 LYS Chi-restraints excluded: chain D residue 846 TYR Chi-restraints excluded: chain D residue 868 VAL Chi-restraints excluded: chain D residue 1051 VAL Chi-restraints excluded: chain D residue 1053 GLU Chi-restraints excluded: chain D residue 1141 SER Chi-restraints excluded: chain D residue 1158 ASP Chi-restraints excluded: chain D residue 1256 MET Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1460 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 69 optimal weight: 6.9990 chunk 262 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 398 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 chunk 296 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 408 optimal weight: 7.9990 chunk 371 optimal weight: 20.0000 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1449 HIS A1456 GLN ** B 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1449 HIS B1456 GLN ** C 659 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1449 HIS C1456 GLN D1449 HIS D1456 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.042050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.031997 restraints weight = 287889.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.033052 restraints weight = 189244.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.033805 restraints weight = 140597.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.034333 restraints weight = 112936.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.034679 restraints weight = 95946.755| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 34200 Z= 0.147 Angle : 0.589 12.810 46456 Z= 0.303 Chirality : 0.043 0.467 5276 Planarity : 0.004 0.064 6084 Dihedral : 4.578 43.643 4984 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.65 % Allowed : 14.57 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.13), residues: 4284 helix: 1.80 (0.10), residues: 2588 sheet: -0.17 (0.27), residues: 376 loop : -0.52 (0.18), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 997 TYR 0.017 0.001 TYR B 846 PHE 0.008 0.001 PHE D1526 TRP 0.011 0.001 TRP B 533 HIS 0.004 0.001 HIS C1258 Details of bonding type rmsd covalent geometry : bond 0.00311 (34200) covalent geometry : angle 0.58889 (46456) hydrogen bonds : bond 0.03360 ( 2064) hydrogen bonds : angle 4.84882 ( 6084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4768.19 seconds wall clock time: 84 minutes 12.54 seconds (5052.54 seconds total)