Starting phenix.real_space_refine on Sat Feb 7 16:49:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9huy_52420/02_2026/9huy_52420.cif Found real_map, /net/cci-nas-00/data/ceres_data/9huy_52420/02_2026/9huy_52420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9huy_52420/02_2026/9huy_52420.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9huy_52420/02_2026/9huy_52420.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9huy_52420/02_2026/9huy_52420.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9huy_52420/02_2026/9huy_52420.map" } resolution = 3.54 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 Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s 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: 10.15, per 1000 atoms: 0.30 Number of scatterers: 33576 At special positions: 0 Unit cell: (130.532, 231.34, 122.778, 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: 2.89 Conformation dependent library (CDL) restraints added in 1.6 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: 208 helices and 20 sheets defined 63.9% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.637A pdb=" N SER A 506 " --> pdb=" O ILE A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 553 removed outlier: 3.754A pdb=" N LEU A 545 " --> pdb=" O SER A 541 " (cutoff:3.500A) Proline residue: A 547 - end of helix Processing helix chain 'A' and resid 590 through 610 Processing helix chain 'A' and resid 616 through 619 Processing helix chain 'A' and resid 620 through 625 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: 3.566A pdb=" N GLU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 701 removed outlier: 3.756A 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: 4.409A pdb=" N LYS A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA A 802 " --> pdb=" O GLY A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 857 removed outlier: 3.980A pdb=" N VAL A 856 " --> pdb=" O GLY A 852 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 857 " --> pdb=" O LEU A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 909 through 914 removed outlier: 3.554A 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: 3.690A 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 1163 removed outlier: 4.128A pdb=" N VAL A1144 " --> pdb=" O ASN A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1178 removed outlier: 4.324A pdb=" N THR A1172 " --> pdb=" O PRO A1168 " (cutoff:3.500A) removed outlier: 4.435A 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 1270 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: 3.852A 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 1332 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 removed outlier: 3.565A pdb=" N THR A1372 " --> pdb=" O PRO A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1399 through 1415 removed outlier: 4.844A pdb=" N ALA A1409 " --> pdb=" O ASN A1405 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS A1410 " --> pdb=" O ARG A1406 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1421 removed outlier: 4.337A pdb=" N SER A1419 " --> pdb=" O PRO A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1440 removed outlier: 3.623A pdb=" N LYS A1427 " --> pdb=" O ARG A1423 " (cutoff:3.500A) Processing helix chain 'A' and resid 1443 through 1452 Processing helix chain 'A' and resid 1452 through 1469 removed outlier: 3.908A pdb=" N LEU A1460 " --> pdb=" O GLN A1456 " (cutoff:3.500A) removed outlier: 4.202A 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: 4.099A 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: 4.208A 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 511 removed outlier: 3.637A pdb=" N SER B 506 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 553 removed outlier: 3.754A pdb=" N LEU B 545 " --> pdb=" O SER B 541 " (cutoff:3.500A) Proline residue: B 547 - end of helix Processing helix chain 'B' and resid 590 through 610 Processing helix chain 'B' and resid 616 through 619 Processing helix chain 'B' and resid 620 through 625 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: 3.566A pdb=" N GLU B 681 " --> pdb=" O ASP B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 701 removed outlier: 3.755A 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: 4.410A pdb=" N LYS B 801 " --> pdb=" O LEU B 797 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA B 802 " --> pdb=" O GLY B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 857 removed outlier: 3.980A pdb=" N VAL B 856 " --> pdb=" O GLY B 852 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B 857 " --> pdb=" O LEU B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 906 Processing helix chain 'B' and resid 909 through 914 removed outlier: 3.554A 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: 3.690A 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 1163 removed outlier: 4.128A pdb=" N VAL B1144 " --> pdb=" O ASN B1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 1167 through 1178 removed outlier: 4.324A pdb=" N THR B1172 " --> pdb=" O PRO B1168 " (cutoff:3.500A) removed outlier: 4.436A 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 1270 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: 3.852A 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 1332 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 removed outlier: 3.565A pdb=" N THR B1372 " --> pdb=" O PRO B1368 " (cutoff:3.500A) Processing helix chain 'B' and resid 1399 through 1415 removed outlier: 4.844A pdb=" N ALA B1409 " --> pdb=" O ASN B1405 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N LYS B1410 " --> pdb=" O ARG B1406 " (cutoff:3.500A) Processing helix chain 'B' and resid 1416 through 1421 removed outlier: 4.336A pdb=" N SER B1419 " --> pdb=" O PRO B1416 " (cutoff:3.500A) Processing helix chain 'B' and resid 1423 through 1440 removed outlier: 3.622A pdb=" N LYS B1427 " --> pdb=" O ARG B1423 " (cutoff:3.500A) Processing helix chain 'B' and resid 1443 through 1452 Processing helix chain 'B' and resid 1452 through 1469 removed outlier: 3.908A pdb=" N LEU B1460 " --> pdb=" O GLN B1456 " (cutoff:3.500A) removed outlier: 4.202A 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: 4.098A 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: 4.208A 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 511 removed outlier: 3.637A pdb=" N SER C 506 " --> pdb=" O ILE C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 553 removed outlier: 3.754A pdb=" N LEU C 545 " --> pdb=" O SER C 541 " (cutoff:3.500A) Proline residue: C 547 - end of helix Processing helix chain 'C' and resid 590 through 610 Processing helix chain 'C' and resid 616 through 619 Processing helix chain 'C' and resid 620 through 625 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: 3.566A pdb=" N GLU C 681 " --> pdb=" O ASP C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 701 removed outlier: 3.756A 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: 4.410A pdb=" N LYS C 801 " --> pdb=" O LEU C 797 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA C 802 " --> pdb=" O GLY C 798 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 857 removed outlier: 3.981A pdb=" N VAL C 856 " --> pdb=" O GLY C 852 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 857 " --> pdb=" O LEU C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 Processing helix chain 'C' and resid 909 through 914 removed outlier: 3.555A 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: 3.690A 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 1163 removed outlier: 4.128A pdb=" N VAL C1144 " --> pdb=" O ASN C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1178 removed outlier: 4.324A pdb=" N THR C1172 " --> pdb=" O PRO C1168 " (cutoff:3.500A) removed outlier: 4.435A 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 1270 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: 3.851A 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 1332 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 removed outlier: 3.565A pdb=" N THR C1372 " --> pdb=" O PRO C1368 " (cutoff:3.500A) Processing helix chain 'C' and resid 1399 through 1415 removed outlier: 4.844A pdb=" N ALA C1409 " --> pdb=" O ASN C1405 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS C1410 " --> pdb=" O ARG C1406 " (cutoff:3.500A) Processing helix chain 'C' and resid 1416 through 1421 removed outlier: 4.337A pdb=" N SER C1419 " --> pdb=" O PRO C1416 " (cutoff:3.500A) Processing helix chain 'C' and resid 1423 through 1440 removed outlier: 3.623A pdb=" N LYS C1427 " --> pdb=" O ARG C1423 " (cutoff:3.500A) Processing helix chain 'C' and resid 1443 through 1452 Processing helix chain 'C' and resid 1452 through 1469 removed outlier: 3.908A pdb=" N LEU C1460 " --> pdb=" O GLN C1456 " (cutoff:3.500A) removed outlier: 4.203A 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: 4.097A 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: 4.207A 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 511 removed outlier: 3.638A pdb=" N SER D 506 " --> pdb=" O ILE D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 553 removed outlier: 3.754A pdb=" N LEU D 545 " --> pdb=" O SER D 541 " (cutoff:3.500A) Proline residue: D 547 - end of helix Processing helix chain 'D' and resid 590 through 610 Processing helix chain 'D' and resid 616 through 619 Processing helix chain 'D' and resid 620 through 625 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: 3.566A pdb=" N GLU D 681 " --> pdb=" O ASP D 677 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 701 removed outlier: 3.755A 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: 4.409A pdb=" N LYS D 801 " --> pdb=" O LEU D 797 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA D 802 " --> pdb=" O GLY D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 840 through 857 removed outlier: 3.980A pdb=" N VAL D 856 " --> pdb=" O GLY D 852 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR D 857 " --> pdb=" O LEU D 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 906 Processing helix chain 'D' and resid 909 through 914 removed outlier: 3.554A 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: 3.689A 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 1163 removed outlier: 4.129A pdb=" N VAL D1144 " --> pdb=" O ASN D1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 1167 through 1178 removed outlier: 4.323A pdb=" N THR D1172 " --> pdb=" O PRO D1168 " (cutoff:3.500A) removed outlier: 4.435A 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 1270 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: 3.851A 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 1332 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 removed outlier: 3.565A pdb=" N THR D1372 " --> pdb=" O PRO D1368 " (cutoff:3.500A) Processing helix chain 'D' and resid 1399 through 1415 removed outlier: 4.844A pdb=" N ALA D1409 " --> pdb=" O ASN D1405 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS D1410 " --> pdb=" O ARG D1406 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1421 removed outlier: 4.337A pdb=" N SER D1419 " --> pdb=" O PRO D1416 " (cutoff:3.500A) Processing helix chain 'D' and resid 1423 through 1440 removed outlier: 3.622A pdb=" N LYS D1427 " --> pdb=" O ARG D1423 " (cutoff:3.500A) Processing helix chain 'D' and resid 1443 through 1452 Processing helix chain 'D' and resid 1452 through 1469 removed outlier: 3.909A pdb=" N LEU D1460 " --> pdb=" O GLN D1456 " (cutoff:3.500A) removed outlier: 4.202A 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: 4.098A 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: 4.209A 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: 7.069A pdb=" N VAL A 572 " --> pdb=" O THR A 563 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR A 563 " --> pdb=" O VAL A 572 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE A 574 " --> pdb=" O PRO A 561 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN A 576 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A 559 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 6.661A 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: 6.555A pdb=" N LYS A 743 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR A 724 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.708A 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: 6.555A pdb=" N LYS A 743 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR A 724 " --> pdb=" O ALA A 741 " (cutoff:3.500A) removed outlier: 6.708A 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 861 removed outlier: 3.538A pdb=" N ALA A 866 " --> pdb=" O ASP A 861 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1026 through 1029 removed outlier: 6.352A pdb=" N PHE A 953 " --> pdb=" O ARG A 977 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL A 979 " --> pdb=" O PHE A 953 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL A 955 " --> pdb=" O VAL A 979 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA A 981 " --> pdb=" O VAL A 955 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY A 957 " --> pdb=" O ALA A 981 " (cutoff:3.500A) removed outlier: 6.151A 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: 7.069A pdb=" N VAL B 572 " --> pdb=" O THR B 563 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR B 563 " --> pdb=" O VAL B 572 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE B 574 " --> pdb=" O PRO B 561 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN B 576 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU B 559 " --> pdb=" O GLN B 576 " (cutoff:3.500A) removed outlier: 6.661A 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: 6.555A pdb=" N LYS B 743 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR B 724 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 6.709A 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: 6.555A pdb=" N LYS B 743 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR B 724 " --> pdb=" O ALA B 741 " (cutoff:3.500A) removed outlier: 6.709A 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 861 removed outlier: 3.539A pdb=" N ALA B 866 " --> pdb=" O ASP B 861 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 1026 through 1029 removed outlier: 6.354A pdb=" N PHE B 953 " --> pdb=" O ARG B 977 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL B 979 " --> pdb=" O PHE B 953 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL B 955 " --> pdb=" O VAL B 979 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA B 981 " --> pdb=" O VAL B 955 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY B 957 " --> pdb=" O ALA B 981 " (cutoff:3.500A) removed outlier: 6.150A 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: 7.069A pdb=" N VAL C 572 " --> pdb=" O THR C 563 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR C 563 " --> pdb=" O VAL C 572 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE C 574 " --> pdb=" O PRO C 561 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN C 576 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU C 559 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 6.661A 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: 6.555A pdb=" N LYS C 743 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR C 724 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 6.709A 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: 6.555A pdb=" N LYS C 743 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR C 724 " --> pdb=" O ALA C 741 " (cutoff:3.500A) removed outlier: 6.709A 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 861 removed outlier: 3.539A pdb=" N ALA C 866 " --> pdb=" O ASP C 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1026 through 1029 removed outlier: 6.353A pdb=" N PHE C 953 " --> pdb=" O ARG C 977 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL C 979 " --> pdb=" O PHE C 953 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL C 955 " --> pdb=" O VAL C 979 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA C 981 " --> pdb=" O VAL C 955 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY C 957 " --> pdb=" O ALA C 981 " (cutoff:3.500A) removed outlier: 6.150A 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: 7.070A pdb=" N VAL D 572 " --> pdb=" O THR D 563 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR D 563 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE D 574 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN D 576 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU D 559 " --> pdb=" O GLN D 576 " (cutoff:3.500A) removed outlier: 6.660A 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: 6.555A pdb=" N LYS D 743 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR D 724 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 6.708A 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: 6.555A pdb=" N LYS D 743 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR D 724 " --> pdb=" O ALA D 741 " (cutoff:3.500A) removed outlier: 6.708A 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 861 removed outlier: 3.540A pdb=" N ALA D 866 " --> pdb=" O ASP D 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 1026 through 1029 removed outlier: 6.354A pdb=" N PHE D 953 " --> pdb=" O ARG D 977 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL D 979 " --> pdb=" O PHE D 953 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL D 955 " --> pdb=" O VAL D 979 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA D 981 " --> pdb=" O VAL D 955 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY D 957 " --> pdb=" O ALA D 981 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU D1071 " --> pdb=" O GLY D1111 " (cutoff:3.500A) 2129 hydrogen bonds defined for protein. 6111 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: 8.63 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 11589 1.34 - 1.46: 6265 1.46 - 1.58: 16186 1.58 - 1.69: 16 1.69 - 1.81: 144 Bond restraints: 34200 Sorted by residual: bond pdb=" O3 NAD C1601 " pdb=" PA NAD C1601 " ideal model delta sigma weight residual 1.653 1.602 0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" O3 NAD A1601 " pdb=" PA NAD A1601 " ideal model delta sigma weight residual 1.653 1.602 0.051 2.00e-02 2.50e+03 6.52e+00 bond pdb=" O3 NAD B1601 " pdb=" PA NAD B1601 " ideal model delta sigma weight residual 1.653 1.602 0.051 2.00e-02 2.50e+03 6.43e+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 6.35e+00 bond pdb=" C1D NAD C1601 " pdb=" O4D NAD C1601 " ideal model delta sigma weight residual 1.376 1.423 -0.047 2.00e-02 2.50e+03 5.46e+00 ... (remaining 34195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 45692 1.30 - 2.59: 533 2.59 - 3.89: 164 3.89 - 5.19: 63 5.19 - 6.48: 4 Bond angle restraints: 46456 Sorted by residual: angle pdb=" N LEU B1047 " pdb=" CA LEU B1047 " pdb=" C LEU B1047 " ideal model delta sigma weight residual 114.56 110.38 4.18 1.27e+00 6.20e-01 1.08e+01 angle pdb=" N LEU C1047 " pdb=" CA LEU C1047 " pdb=" C LEU C1047 " ideal model delta sigma weight residual 114.56 110.40 4.16 1.27e+00 6.20e-01 1.08e+01 angle pdb=" N LEU A1047 " pdb=" CA LEU A1047 " pdb=" C LEU A1047 " ideal model delta sigma weight residual 114.56 110.43 4.13 1.27e+00 6.20e-01 1.06e+01 angle pdb=" N LEU D1047 " pdb=" CA LEU D1047 " pdb=" C LEU D1047 " ideal model delta sigma weight residual 114.56 110.45 4.11 1.27e+00 6.20e-01 1.05e+01 angle pdb=" N ALA B 887 " pdb=" CA ALA B 887 " pdb=" C ALA B 887 " ideal model delta sigma weight residual 107.88 112.14 -4.26 1.41e+00 5.03e-01 9.11e+00 ... (remaining 46451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.58: 19623 14.58 - 29.15: 861 29.15 - 43.73: 212 43.73 - 58.31: 24 58.31 - 72.88: 8 Dihedral angle restraints: 20728 sinusoidal: 8364 harmonic: 12364 Sorted by residual: dihedral pdb=" CA ASP A1467 " pdb=" C ASP A1467 " pdb=" N ILE A1468 " pdb=" CA ILE A1468 " ideal model delta harmonic sigma weight residual 180.00 164.93 15.07 0 5.00e+00 4.00e-02 9.09e+00 dihedral pdb=" CA ASP C1467 " pdb=" C ASP C1467 " pdb=" N ILE C1468 " pdb=" CA ILE C1468 " ideal model delta harmonic sigma weight residual 180.00 164.94 15.06 0 5.00e+00 4.00e-02 9.08e+00 dihedral pdb=" CA ASP D1467 " pdb=" C ASP D1467 " pdb=" N ILE D1468 " pdb=" CA ILE D1468 " ideal model delta harmonic sigma weight residual 180.00 164.94 15.06 0 5.00e+00 4.00e-02 9.07e+00 ... (remaining 20725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 3478 0.027 - 0.054: 1043 0.054 - 0.081: 430 0.081 - 0.108: 262 0.108 - 0.135: 63 Chirality restraints: 5276 Sorted by residual: 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 4.58e-01 chirality pdb=" C1D NAD B1601 " pdb=" C2D NAD B1601 " pdb=" N1N NAD B1601 " pdb=" O4D NAD B1601 " both_signs ideal model delta sigma weight residual False 2.41 2.55 -0.13 2.00e-01 2.50e+01 4.54e-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 -0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 5273 not shown) Planarity restraints: 6084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A1056 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A1057 " 0.068 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 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO C1057 " -0.068 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 delta sigma weight rms_deltas residual plane pdb=" C PRO D1056 " -0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO D1057 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D1057 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D1057 " -0.022 5.00e-02 4.00e+02 ... (remaining 6081 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6279 2.77 - 3.30: 35548 3.30 - 3.83: 59151 3.83 - 4.37: 68819 4.37 - 4.90: 115440 Nonbonded interactions: 285237 Sorted by model distance: nonbonded pdb=" OG SER A 541 " pdb=" O VAL B 556 " model vdw 2.236 3.040 nonbonded pdb=" O SER C 679 " pdb=" OG1 THR C 682 " model vdw 2.238 3.040 nonbonded pdb=" O SER A 679 " pdb=" OG1 THR A 682 " model vdw 2.239 3.040 nonbonded pdb=" O SER D 679 " pdb=" OG1 THR D 682 " model vdw 2.239 3.040 nonbonded pdb=" O SER B 679 " pdb=" OG1 THR B 682 " model vdw 2.239 3.040 ... (remaining 285232 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: 0.10 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: 3.710 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: 0.420 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 35.470 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 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 0.051 34200 Z= 0.110 Angle : 0.429 6.483 46456 Z= 0.222 Chirality : 0.037 0.135 5276 Planarity : 0.003 0.039 6084 Dihedral : 8.919 72.883 12760 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: 1.74 (0.13), residues: 4284 helix: 2.03 (0.10), residues: 2540 sheet: 0.03 (0.26), residues: 432 loop : -0.12 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1417 TYR 0.005 0.001 TYR D 846 PHE 0.007 0.001 PHE D 792 TRP 0.010 0.001 TRP C 533 HIS 0.003 0.001 HIS B1149 Details of bonding type rmsd covalent geometry : bond 0.00215 (34200) covalent geometry : angle 0.42922 (46456) hydrogen bonds : bond 0.12967 ( 2053) hydrogen bonds : angle 6.05099 ( 6111) *********************** 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 754 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 754 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 750 LYS cc_start: 0.9326 (ptpp) cc_final: 0.9090 (ptpp) REVERT: A 846 TYR cc_start: 0.9481 (t80) cc_final: 0.9214 (t80) REVERT: A 970 MET cc_start: 0.9153 (mmp) cc_final: 0.8545 (mmm) REVERT: A 992 ASN cc_start: 0.9406 (t0) cc_final: 0.9080 (m-40) REVERT: A 1087 ASP cc_start: 0.8115 (m-30) cc_final: 0.7726 (m-30) REVERT: A 1136 ASP cc_start: 0.8939 (p0) cc_final: 0.8652 (t0) REVERT: A 1156 LEU cc_start: 0.9211 (tp) cc_final: 0.8985 (pp) REVERT: A 1193 GLN cc_start: 0.9344 (tt0) cc_final: 0.9060 (tt0) REVERT: A 1252 LEU cc_start: 0.9703 (mt) cc_final: 0.9456 (mp) REVERT: A 1256 MET cc_start: 0.8699 (tmm) cc_final: 0.8052 (tmm) REVERT: A 1311 MET cc_start: 0.8708 (mtp) cc_final: 0.8441 (mtp) REVERT: A 1373 ASP cc_start: 0.8844 (m-30) cc_final: 0.8594 (m-30) REVERT: A 1480 TYR cc_start: 0.8820 (t80) cc_final: 0.8405 (t80) REVERT: A 1481 PHE cc_start: 0.8352 (m-10) cc_final: 0.7871 (m-80) REVERT: A 1484 MET cc_start: 0.8677 (ttp) cc_final: 0.8477 (tpp) REVERT: A 1515 ASP cc_start: 0.8764 (m-30) cc_final: 0.8557 (m-30) REVERT: A 1579 ARG cc_start: 0.8612 (tpp-160) cc_final: 0.8323 (mmm160) REVERT: B 552 MET cc_start: 0.8751 (tpt) cc_final: 0.8308 (tpt) REVERT: B 623 MET cc_start: 0.9312 (mtt) cc_final: 0.8972 (ptp) REVERT: B 749 ILE cc_start: 0.8831 (mt) cc_final: 0.8540 (mp) REVERT: B 750 LYS cc_start: 0.9353 (ptpp) cc_final: 0.9066 (ptpp) REVERT: B 970 MET cc_start: 0.9243 (mmp) cc_final: 0.8645 (mmm) REVERT: B 992 ASN cc_start: 0.9309 (t0) cc_final: 0.9004 (m-40) REVERT: B 993 PRO cc_start: 0.4436 (Cg_exo) cc_final: 0.3922 (Cg_endo) REVERT: B 1087 ASP cc_start: 0.7924 (m-30) cc_final: 0.7607 (m-30) REVERT: B 1136 ASP cc_start: 0.8790 (p0) cc_final: 0.8430 (t0) REVERT: B 1158 ASP cc_start: 0.9253 (m-30) cc_final: 0.9016 (m-30) REVERT: B 1193 GLN cc_start: 0.9298 (tt0) cc_final: 0.9097 (tt0) REVERT: B 1247 LEU cc_start: 0.9344 (mt) cc_final: 0.9127 (mp) REVERT: B 1252 LEU cc_start: 0.9688 (mt) cc_final: 0.9411 (mp) REVERT: B 1256 MET cc_start: 0.8745 (tmm) cc_final: 0.8127 (tmm) REVERT: B 1286 PHE cc_start: 0.8455 (m-80) cc_final: 0.8244 (m-80) REVERT: B 1347 ASN cc_start: 0.9078 (t0) cc_final: 0.8849 (m-40) REVERT: B 1375 MET cc_start: 0.8680 (mtm) cc_final: 0.8370 (mtm) REVERT: B 1480 TYR cc_start: 0.8959 (t80) cc_final: 0.8517 (t80) REVERT: B 1481 PHE cc_start: 0.8431 (m-10) cc_final: 0.8037 (m-80) REVERT: B 1515 ASP cc_start: 0.8744 (m-30) cc_final: 0.8462 (m-30) REVERT: B 1579 ARG cc_start: 0.8719 (tpp-160) cc_final: 0.8485 (mmm160) REVERT: C 552 MET cc_start: 0.8704 (tpt) cc_final: 0.8360 (tpt) REVERT: C 623 MET cc_start: 0.9271 (mtt) cc_final: 0.8890 (ptp) REVERT: C 749 ILE cc_start: 0.8854 (mt) cc_final: 0.8330 (mm) REVERT: C 750 LYS cc_start: 0.9275 (ptpp) cc_final: 0.8974 (ptpp) REVERT: C 970 MET cc_start: 0.9214 (mmp) cc_final: 0.8615 (mmm) REVERT: C 992 ASN cc_start: 0.9401 (t0) cc_final: 0.9062 (m-40) REVERT: C 1087 ASP cc_start: 0.7871 (m-30) cc_final: 0.7526 (m-30) REVERT: C 1136 ASP cc_start: 0.8788 (p0) cc_final: 0.8361 (t0) REVERT: C 1156 LEU cc_start: 0.9045 (tp) cc_final: 0.8783 (pp) REVERT: C 1247 LEU cc_start: 0.9262 (mt) cc_final: 0.9027 (mp) REVERT: C 1252 LEU cc_start: 0.9678 (mt) cc_final: 0.9439 (mp) REVERT: C 1256 MET cc_start: 0.8793 (tmm) cc_final: 0.8086 (tmm) REVERT: C 1347 ASN cc_start: 0.9094 (t0) cc_final: 0.8783 (m-40) REVERT: C 1375 MET cc_start: 0.8694 (mtm) cc_final: 0.8406 (mtm) REVERT: C 1480 TYR cc_start: 0.8982 (t80) cc_final: 0.8537 (t80) REVERT: C 1481 PHE cc_start: 0.8480 (m-10) cc_final: 0.8071 (m-80) REVERT: D 552 MET cc_start: 0.8684 (tpt) cc_final: 0.8459 (tpt) REVERT: D 623 MET cc_start: 0.9293 (mtt) cc_final: 0.8936 (ptp) REVERT: D 749 ILE cc_start: 0.8834 (mt) cc_final: 0.8319 (mm) REVERT: D 750 LYS cc_start: 0.9265 (ptpp) cc_final: 0.8966 (ptpp) REVERT: D 786 SER cc_start: 0.8705 (p) cc_final: 0.8501 (t) REVERT: D 846 TYR cc_start: 0.9284 (t80) cc_final: 0.8749 (t80) REVERT: D 970 MET cc_start: 0.9336 (mmp) cc_final: 0.8783 (mmm) REVERT: D 992 ASN cc_start: 0.9414 (t0) cc_final: 0.9171 (m-40) REVERT: D 1080 ILE cc_start: 0.9294 (mp) cc_final: 0.8962 (mp) REVERT: D 1136 ASP cc_start: 0.8859 (p0) cc_final: 0.8412 (t0) REVERT: D 1247 LEU cc_start: 0.9283 (mt) cc_final: 0.8939 (mp) REVERT: D 1375 MET cc_start: 0.8357 (mtm) cc_final: 0.7663 (mmm) REVERT: D 1480 TYR cc_start: 0.8709 (t80) cc_final: 0.8353 (t80) REVERT: D 1481 PHE cc_start: 0.8440 (m-10) cc_final: 0.8191 (m-80) outliers start: 0 outliers final: 0 residues processed: 754 average time/residue: 0.2413 time to fit residues: 286.2368 Evaluate side-chains 407 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.2980 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 8.9990 chunk 424 optimal weight: 9.9990 chunk 155 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 HIS A1032 GLN A1115 ASN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 689 GLN B1032 GLN B1115 ASN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 GLN ** C1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1211 HIS ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 689 GLN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.067338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.055333 restraints weight = 189637.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.056958 restraints weight = 118743.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.058022 restraints weight = 85112.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.058828 restraints weight = 67187.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.059444 restraints weight = 55710.953| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 34200 Z= 0.193 Angle : 0.629 11.437 46456 Z= 0.325 Chirality : 0.044 0.182 5276 Planarity : 0.005 0.079 6084 Dihedral : 5.190 52.887 4980 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.96 % Allowed : 10.09 % Favored : 86.94 % 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: 1.49 (0.13), residues: 4284 helix: 1.81 (0.10), residues: 2544 sheet: 0.03 (0.25), residues: 456 loop : -0.22 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D1291 TYR 0.025 0.002 TYR A1284 PHE 0.023 0.002 PHE D 742 TRP 0.015 0.002 TRP A 609 HIS 0.014 0.002 HIS D 940 Details of bonding type rmsd covalent geometry : bond 0.00417 (34200) covalent geometry : angle 0.62907 (46456) hydrogen bonds : bond 0.04023 ( 2053) hydrogen bonds : angle 5.02974 ( 6111) *********************** 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 540 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 436 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 GLU cc_start: 0.8471 (tp30) cc_final: 0.8205 (tp30) REVERT: A 623 MET cc_start: 0.8967 (ptp) cc_final: 0.8715 (ptp) REVERT: A 846 TYR cc_start: 0.9374 (t80) cc_final: 0.9006 (t80) REVERT: A 970 MET cc_start: 0.9209 (mmp) cc_final: 0.8573 (mmm) REVERT: A 992 ASN cc_start: 0.9305 (t0) cc_final: 0.9006 (m-40) REVERT: A 1193 GLN cc_start: 0.9401 (tt0) cc_final: 0.9034 (tt0) REVERT: A 1236 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8455 (mt-10) REVERT: A 1256 MET cc_start: 0.8550 (tmm) cc_final: 0.8069 (tmm) REVERT: A 1347 ASN cc_start: 0.8431 (t0) cc_final: 0.8163 (t0) REVERT: A 1480 TYR cc_start: 0.8959 (t80) cc_final: 0.8610 (t80) REVERT: A 1481 PHE cc_start: 0.8768 (m-10) cc_final: 0.8008 (m-80) REVERT: B 749 ILE cc_start: 0.9058 (mt) cc_final: 0.8788 (mp) REVERT: B 750 LYS cc_start: 0.9305 (ptpp) cc_final: 0.8979 (pttm) REVERT: B 970 MET cc_start: 0.9228 (mmp) cc_final: 0.8588 (mmm) REVERT: B 992 ASN cc_start: 0.9269 (t0) cc_final: 0.8985 (m-40) REVERT: B 993 PRO cc_start: 0.4880 (Cg_exo) cc_final: 0.4478 (Cg_endo) REVERT: B 1158 ASP cc_start: 0.9216 (m-30) cc_final: 0.8982 (m-30) REVERT: B 1225 ASN cc_start: 0.8515 (t0) cc_final: 0.8285 (t0) REVERT: B 1227 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8645 (tm-30) REVERT: B 1256 MET cc_start: 0.8510 (tmm) cc_final: 0.7912 (tmm) REVERT: B 1347 ASN cc_start: 0.8800 (t0) cc_final: 0.8570 (m-40) REVERT: B 1375 MET cc_start: 0.8634 (mtm) cc_final: 0.8392 (mtm) REVERT: B 1480 TYR cc_start: 0.9025 (t80) cc_final: 0.8696 (t80) REVERT: B 1481 PHE cc_start: 0.8502 (m-10) cc_final: 0.8062 (m-80) REVERT: B 1515 ASP cc_start: 0.8692 (m-30) cc_final: 0.8477 (p0) REVERT: C 790 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7764 (mp0) REVERT: C 846 TYR cc_start: 0.9366 (t80) cc_final: 0.9135 (t80) REVERT: C 970 MET cc_start: 0.9201 (mmp) cc_final: 0.8581 (mmm) REVERT: C 992 ASN cc_start: 0.9297 (t0) cc_final: 0.8985 (m-40) REVERT: C 993 PRO cc_start: 0.6105 (Cg_endo) cc_final: 0.5545 (Cg_exo) REVERT: C 1214 MET cc_start: 0.8044 (mtt) cc_final: 0.7205 (mtm) REVERT: C 1227 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8723 (tm-30) REVERT: C 1256 MET cc_start: 0.8603 (tmm) cc_final: 0.8025 (tmm) REVERT: C 1347 ASN cc_start: 0.8884 (t0) cc_final: 0.8631 (m-40) REVERT: C 1480 TYR cc_start: 0.9013 (t80) cc_final: 0.8673 (t80) REVERT: C 1481 PHE cc_start: 0.8521 (m-10) cc_final: 0.8123 (m-80) REVERT: D 750 LYS cc_start: 0.9179 (ptpp) cc_final: 0.8950 (ptpp) REVERT: D 970 MET cc_start: 0.9225 (mmp) cc_final: 0.8707 (mmm) REVERT: D 992 ASN cc_start: 0.9363 (t0) cc_final: 0.9153 (m-40) REVERT: D 1197 MET cc_start: 0.8772 (mmm) cc_final: 0.8360 (mmt) REVERT: D 1214 MET cc_start: 0.8014 (mtt) cc_final: 0.7252 (mtm) REVERT: D 1480 TYR cc_start: 0.8800 (t80) cc_final: 0.8448 (t80) REVERT: D 1481 PHE cc_start: 0.8518 (m-10) cc_final: 0.8161 (m-80) REVERT: D 1493 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8591 (mm) outliers start: 104 outliers final: 60 residues processed: 509 average time/residue: 0.2311 time to fit residues: 191.1309 Evaluate side-chains 406 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 344 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 984 HIS Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1051 VAL Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1288 THR Chi-restraints excluded: chain B residue 1291 ARG Chi-restraints excluded: chain B residue 1461 ASP Chi-restraints excluded: chain B residue 1520 SER Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 638 TYR Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 719 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1145 ASP Chi-restraints excluded: chain C residue 1228 LEU Chi-restraints excluded: chain C residue 1288 THR Chi-restraints excluded: chain C residue 1461 ASP Chi-restraints excluded: chain C residue 1492 LEU Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 1051 VAL Chi-restraints excluded: chain D residue 1145 ASP Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1288 THR Chi-restraints excluded: chain D residue 1492 LEU Chi-restraints excluded: chain D residue 1493 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 427 optimal weight: 0.7980 chunk 409 optimal weight: 10.0000 chunk 292 optimal weight: 9.9990 chunk 130 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 398 optimal weight: 6.9990 chunk 264 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 39 optimal weight: 0.4980 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 HIS A1396 GLN ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1396 GLN ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1095 ASN ** D1211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1396 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.064854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.052946 restraints weight = 187901.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.054522 restraints weight = 117431.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.055578 restraints weight = 84063.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.056302 restraints weight = 66017.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.056868 restraints weight = 55267.143| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 34200 Z= 0.220 Angle : 0.627 10.970 46456 Z= 0.328 Chirality : 0.044 0.191 5276 Planarity : 0.005 0.049 6084 Dihedral : 5.041 53.327 4980 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.16 % Allowed : 10.52 % Favored : 86.32 % 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: 0.97 (0.13), residues: 4284 helix: 1.43 (0.10), residues: 2540 sheet: -0.15 (0.25), residues: 460 loop : -0.53 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 985 TYR 0.020 0.002 TYR D 846 PHE 0.017 0.002 PHE B1407 TRP 0.020 0.002 TRP A 609 HIS 0.022 0.002 HIS A 984 Details of bonding type rmsd covalent geometry : bond 0.00466 (34200) covalent geometry : angle 0.62708 (46456) hydrogen bonds : bond 0.03944 ( 2053) hydrogen bonds : angle 4.94938 ( 6111) *********************** 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 479 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 368 time to evaluate : 1.412 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 750 LYS cc_start: 0.9227 (ptpp) cc_final: 0.8952 (ptpp) REVERT: A 846 TYR cc_start: 0.9343 (t80) cc_final: 0.9023 (t80) REVERT: A 970 MET cc_start: 0.9193 (mmp) cc_final: 0.8584 (mmm) REVERT: A 992 ASN cc_start: 0.9340 (t0) cc_final: 0.9026 (m-40) REVERT: A 1156 LEU cc_start: 0.9074 (tp) cc_final: 0.8762 (pp) REVERT: A 1158 ASP cc_start: 0.9197 (m-30) cc_final: 0.8975 (m-30) REVERT: A 1197 MET cc_start: 0.9070 (mmm) cc_final: 0.8803 (mmt) REVERT: A 1227 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8911 (tm-30) REVERT: A 1236 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8464 (mt-10) REVERT: A 1256 MET cc_start: 0.8504 (tmm) cc_final: 0.8025 (tmm) REVERT: A 1347 ASN cc_start: 0.8427 (t0) cc_final: 0.8120 (t0) REVERT: A 1480 TYR cc_start: 0.9200 (t80) cc_final: 0.8805 (t80) REVERT: A 1481 PHE cc_start: 0.8698 (m-10) cc_final: 0.8176 (m-80) REVERT: B 623 MET cc_start: 0.9148 (mtm) cc_final: 0.8668 (pmm) REVERT: B 970 MET cc_start: 0.9254 (mmp) cc_final: 0.8681 (mmm) REVERT: B 992 ASN cc_start: 0.9318 (t0) cc_final: 0.9016 (m-40) REVERT: B 993 PRO cc_start: 0.4988 (Cg_exo) cc_final: 0.4576 (Cg_endo) REVERT: B 1156 LEU cc_start: 0.9000 (tp) cc_final: 0.8707 (pp) REVERT: B 1158 ASP cc_start: 0.9226 (m-30) cc_final: 0.9022 (m-30) REVERT: B 1225 ASN cc_start: 0.8538 (t0) cc_final: 0.8167 (t0) REVERT: B 1227 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8592 (tm-30) REVERT: B 1256 MET cc_start: 0.8484 (tmm) cc_final: 0.7921 (tmm) REVERT: B 1347 ASN cc_start: 0.8689 (t0) cc_final: 0.8487 (t0) REVERT: B 1375 MET cc_start: 0.8688 (mtm) cc_final: 0.8466 (mtm) REVERT: B 1480 TYR cc_start: 0.9045 (t80) cc_final: 0.8704 (t80) REVERT: B 1481 PHE cc_start: 0.8640 (m-10) cc_final: 0.8150 (m-80) REVERT: C 750 LYS cc_start: 0.9256 (ptpp) cc_final: 0.9011 (ptpp) REVERT: C 846 TYR cc_start: 0.9373 (t80) cc_final: 0.9129 (t80) REVERT: C 970 MET cc_start: 0.9267 (mmp) cc_final: 0.8621 (mmm) REVERT: C 992 ASN cc_start: 0.9314 (t0) cc_final: 0.8995 (m-40) REVERT: C 993 PRO cc_start: 0.6006 (Cg_endo) cc_final: 0.5414 (Cg_exo) REVERT: C 1225 ASN cc_start: 0.8623 (t0) cc_final: 0.8409 (t0) REVERT: C 1227 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8606 (tm-30) REVERT: C 1256 MET cc_start: 0.8535 (tmm) cc_final: 0.7896 (tmm) REVERT: C 1347 ASN cc_start: 0.8878 (t0) cc_final: 0.8609 (m-40) REVERT: C 1480 TYR cc_start: 0.9033 (t80) cc_final: 0.8667 (t80) REVERT: C 1481 PHE cc_start: 0.8611 (m-10) cc_final: 0.8137 (m-80) REVERT: D 544 GLU cc_start: 0.9083 (mp0) cc_final: 0.8881 (pm20) REVERT: D 750 LYS cc_start: 0.9277 (ptpp) cc_final: 0.9033 (ptpp) REVERT: D 970 MET cc_start: 0.9261 (mmp) cc_final: 0.8771 (mmm) REVERT: D 992 ASN cc_start: 0.9388 (t0) cc_final: 0.9148 (m-40) REVERT: D 1197 MET cc_start: 0.8854 (mmm) cc_final: 0.8497 (mmt) REVERT: D 1375 MET cc_start: 0.8590 (mtm) cc_final: 0.8294 (mtm) REVERT: D 1480 TYR cc_start: 0.8899 (t80) cc_final: 0.8533 (t80) REVERT: D 1481 PHE cc_start: 0.8658 (m-10) cc_final: 0.8227 (m-80) REVERT: D 1493 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8567 (mm) outliers start: 111 outliers final: 69 residues processed: 455 average time/residue: 0.2169 time to fit residues: 163.9427 Evaluate side-chains 403 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 333 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 805 VAL Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1288 THR Chi-restraints excluded: chain B residue 1291 ARG Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1461 ASP Chi-restraints excluded: chain B residue 1555 ARG Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 719 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1228 LEU Chi-restraints excluded: chain C residue 1288 THR Chi-restraints excluded: chain C residue 1461 ASP Chi-restraints excluded: chain C residue 1520 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 786 SER Chi-restraints excluded: chain D residue 926 MET Chi-restraints excluded: chain D residue 1141 SER Chi-restraints excluded: chain D residue 1145 ASP Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1247 LEU Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1308 ILE Chi-restraints excluded: chain D residue 1461 ASP Chi-restraints excluded: chain D residue 1493 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 44 optimal weight: 4.9990 chunk 243 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 270 optimal weight: 10.0000 chunk 363 optimal weight: 3.9990 chunk 421 optimal weight: 6.9990 chunk 367 optimal weight: 9.9990 chunk 285 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 358 optimal weight: 4.9990 chunk 238 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 HIS A 984 HIS ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 HIS ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 GLN D1032 GLN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.062149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.050345 restraints weight = 197215.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.051841 restraints weight = 122240.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.052829 restraints weight = 87542.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.053593 restraints weight = 69229.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.054110 restraints weight = 57648.351| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 34200 Z= 0.278 Angle : 0.682 8.980 46456 Z= 0.363 Chirality : 0.045 0.155 5276 Planarity : 0.005 0.065 6084 Dihedral : 5.236 55.665 4980 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.79 % Allowed : 10.95 % Favored : 85.26 % 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: 0.38 (0.13), residues: 4284 helix: 0.87 (0.10), residues: 2536 sheet: -0.16 (0.27), residues: 416 loop : -0.64 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1555 TYR 0.022 0.002 TYR B1457 PHE 0.017 0.002 PHE A1407 TRP 0.016 0.002 TRP B 609 HIS 0.007 0.002 HIS A1258 Details of bonding type rmsd covalent geometry : bond 0.00581 (34200) covalent geometry : angle 0.68184 (46456) hydrogen bonds : bond 0.04199 ( 2053) hydrogen bonds : angle 5.16952 ( 6111) *********************** 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 468 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 335 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: A 750 LYS cc_start: 0.9245 (ptpp) cc_final: 0.9003 (ptpp) REVERT: A 970 MET cc_start: 0.9132 (mmp) cc_final: 0.8517 (mmm) REVERT: A 992 ASN cc_start: 0.9311 (t0) cc_final: 0.8941 (m-40) REVERT: A 1197 MET cc_start: 0.9044 (mmm) cc_final: 0.7957 (mmt) REVERT: A 1236 GLU cc_start: 0.9001 (mm-30) cc_final: 0.8493 (mt-10) REVERT: A 1256 MET cc_start: 0.8694 (tmm) cc_final: 0.8264 (tmm) REVERT: A 1307 ILE cc_start: 0.9002 (mt) cc_final: 0.8775 (tp) REVERT: A 1330 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: A 1347 ASN cc_start: 0.8610 (t0) cc_final: 0.8313 (t0) REVERT: A 1375 MET cc_start: 0.8584 (mtm) cc_final: 0.8160 (mtp) REVERT: A 1393 TYR cc_start: 0.7726 (m-80) cc_final: 0.7511 (m-80) REVERT: A 1480 TYR cc_start: 0.9043 (t80) cc_final: 0.8824 (t80) REVERT: A 1481 PHE cc_start: 0.8710 (m-10) cc_final: 0.8108 (m-80) REVERT: A 1515 ASP cc_start: 0.8822 (m-30) cc_final: 0.8398 (p0) REVERT: B 970 MET cc_start: 0.9215 (mmp) cc_final: 0.8577 (mmm) REVERT: B 992 ASN cc_start: 0.9322 (t0) cc_final: 0.8999 (m-40) REVERT: B 993 PRO cc_start: 0.5302 (Cg_exo) cc_final: 0.4838 (Cg_endo) REVERT: B 1096 ASP cc_start: 0.8912 (p0) cc_final: 0.8494 (p0) REVERT: B 1158 ASP cc_start: 0.9297 (m-30) cc_final: 0.9090 (m-30) REVERT: B 1225 ASN cc_start: 0.8574 (t0) cc_final: 0.8366 (t0) REVERT: B 1256 MET cc_start: 0.8481 (tmm) cc_final: 0.7971 (tmm) REVERT: B 1375 MET cc_start: 0.8687 (mtm) cc_final: 0.8447 (ttm) REVERT: B 1393 TYR cc_start: 0.7931 (m-80) cc_final: 0.7727 (m-80) REVERT: B 1480 TYR cc_start: 0.9082 (t80) cc_final: 0.8750 (t80) REVERT: B 1481 PHE cc_start: 0.8729 (m-10) cc_final: 0.8299 (m-80) REVERT: C 750 LYS cc_start: 0.9260 (ptpp) cc_final: 0.8992 (ptpp) REVERT: C 790 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8327 (mp0) REVERT: C 846 TYR cc_start: 0.9427 (t80) cc_final: 0.9149 (t80) REVERT: C 926 MET cc_start: 0.7805 (tpp) cc_final: 0.7489 (tpt) REVERT: C 970 MET cc_start: 0.9261 (mmp) cc_final: 0.8624 (mmm) REVERT: C 992 ASN cc_start: 0.9313 (t0) cc_final: 0.8911 (m-40) REVERT: C 993 PRO cc_start: 0.6178 (Cg_endo) cc_final: 0.5514 (Cg_exo) REVERT: C 1197 MET cc_start: 0.8916 (tpp) cc_final: 0.8429 (mmt) REVERT: C 1256 MET cc_start: 0.8455 (tmm) cc_final: 0.8116 (tmm) REVERT: C 1347 ASN cc_start: 0.8839 (t0) cc_final: 0.8601 (t0) REVERT: C 1480 TYR cc_start: 0.9051 (t80) cc_final: 0.8754 (t80) REVERT: C 1481 PHE cc_start: 0.8542 (m-10) cc_final: 0.8149 (m-80) REVERT: C 1515 ASP cc_start: 0.9070 (m-30) cc_final: 0.8694 (p0) REVERT: D 970 MET cc_start: 0.9367 (mmp) cc_final: 0.8804 (mmm) REVERT: D 992 ASN cc_start: 0.9328 (t0) cc_final: 0.9041 (m-40) REVERT: D 1236 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8739 (mp0) REVERT: D 1375 MET cc_start: 0.8755 (mtm) cc_final: 0.8502 (mtm) REVERT: D 1480 TYR cc_start: 0.9046 (t80) cc_final: 0.8761 (t80) REVERT: D 1481 PHE cc_start: 0.8698 (m-10) cc_final: 0.8201 (m-80) REVERT: D 1493 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8611 (mm) REVERT: D 1582 ARG cc_start: 0.9038 (tmm160) cc_final: 0.8595 (ttp80) outliers start: 133 outliers final: 92 residues processed: 433 average time/residue: 0.2067 time to fit residues: 151.9862 Evaluate side-chains 399 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 304 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1145 ASP Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1311 MET Chi-restraints excluded: chain A residue 1330 GLU Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1585 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1288 THR Chi-restraints excluded: chain B residue 1291 ARG Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1461 ASP Chi-restraints excluded: chain B residue 1492 LEU Chi-restraints excluded: chain B residue 1520 SER Chi-restraints excluded: chain B residue 1585 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 719 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 791 ASP Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1141 SER Chi-restraints excluded: chain C residue 1145 ASP Chi-restraints excluded: chain C residue 1228 LEU Chi-restraints excluded: chain C residue 1247 LEU Chi-restraints excluded: chain C residue 1288 THR Chi-restraints excluded: chain C residue 1295 HIS Chi-restraints excluded: chain C residue 1461 ASP Chi-restraints excluded: chain C residue 1492 LEU Chi-restraints excluded: chain C residue 1551 SER Chi-restraints excluded: chain C residue 1585 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 786 SER Chi-restraints excluded: chain D residue 791 ASP Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 1141 SER Chi-restraints excluded: chain D residue 1145 ASP Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1247 LEU Chi-restraints excluded: chain D residue 1288 THR Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1461 ASP Chi-restraints excluded: chain D residue 1492 LEU Chi-restraints excluded: chain D residue 1493 LEU Chi-restraints excluded: chain D residue 1520 SER Chi-restraints excluded: chain D residue 1551 SER Chi-restraints excluded: chain D residue 1585 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 190 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 322 optimal weight: 7.9990 chunk 253 optimal weight: 8.9990 chunk 277 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 178 optimal weight: 3.9990 chunk 323 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 223 optimal weight: 4.9990 chunk 305 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1095 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.062432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.050666 restraints weight = 192300.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.052179 restraints weight = 119644.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.053177 restraints weight = 85849.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.053861 restraints weight = 67752.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.054399 restraints weight = 57086.787| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34200 Z= 0.211 Angle : 0.618 11.659 46456 Z= 0.323 Chirality : 0.044 0.174 5276 Planarity : 0.005 0.055 6084 Dihedral : 5.117 56.496 4980 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.56 % Allowed : 11.83 % Favored : 84.61 % 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: 0.58 (0.13), residues: 4284 helix: 1.08 (0.10), residues: 2520 sheet: -0.19 (0.28), residues: 416 loop : -0.62 (0.17), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1555 TYR 0.018 0.002 TYR A1457 PHE 0.015 0.002 PHE C 982 TRP 0.013 0.001 TRP A 609 HIS 0.007 0.001 HIS A1149 Details of bonding type rmsd covalent geometry : bond 0.00447 (34200) covalent geometry : angle 0.61779 (46456) hydrogen bonds : bond 0.03897 ( 2053) hydrogen bonds : angle 5.00608 ( 6111) *********************** 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 459 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 334 time to evaluate : 1.377 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: A 614 GLU cc_start: 0.8456 (tp30) cc_final: 0.8200 (tp30) REVERT: A 623 MET cc_start: 0.9062 (ptp) cc_final: 0.8835 (pmm) REVERT: A 750 LYS cc_start: 0.9248 (ptpp) cc_final: 0.9020 (ptpp) REVERT: A 970 MET cc_start: 0.9289 (mmp) cc_final: 0.8670 (mmm) REVERT: A 992 ASN cc_start: 0.9295 (t0) cc_final: 0.8951 (m-40) REVERT: A 1054 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9017 (mp) REVERT: A 1197 MET cc_start: 0.9013 (mmm) cc_final: 0.7871 (mmt) REVERT: A 1236 GLU cc_start: 0.9021 (mm-30) cc_final: 0.8517 (mt-10) REVERT: A 1256 MET cc_start: 0.8678 (tmm) cc_final: 0.8244 (tmm) REVERT: A 1347 ASN cc_start: 0.8444 (t0) cc_final: 0.8156 (t0) REVERT: A 1393 TYR cc_start: 0.7580 (m-80) cc_final: 0.7339 (m-80) REVERT: A 1480 TYR cc_start: 0.9077 (t80) cc_final: 0.8783 (t80) REVERT: A 1481 PHE cc_start: 0.8690 (m-10) cc_final: 0.8046 (m-80) REVERT: B 623 MET cc_start: 0.9256 (mtm) cc_final: 0.8826 (pmm) REVERT: B 970 MET cc_start: 0.9349 (mmp) cc_final: 0.8649 (mmm) REVERT: B 992 ASN cc_start: 0.9321 (t0) cc_final: 0.9001 (m-40) REVERT: B 1096 ASP cc_start: 0.8880 (p0) cc_final: 0.8520 (p0) REVERT: B 1112 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6672 (pt0) REVERT: B 1225 ASN cc_start: 0.8554 (t0) cc_final: 0.8344 (t0) REVERT: B 1256 MET cc_start: 0.8562 (tmm) cc_final: 0.8058 (tmm) REVERT: B 1375 MET cc_start: 0.8677 (mtm) cc_final: 0.8360 (ttm) REVERT: B 1393 TYR cc_start: 0.7792 (m-80) cc_final: 0.7559 (m-80) REVERT: B 1480 TYR cc_start: 0.9035 (t80) cc_final: 0.8711 (t80) REVERT: B 1481 PHE cc_start: 0.8625 (m-10) cc_final: 0.8133 (m-80) REVERT: B 1515 ASP cc_start: 0.8867 (m-30) cc_final: 0.8529 (m-30) REVERT: C 750 LYS cc_start: 0.9256 (ptpp) cc_final: 0.9036 (ptpp) REVERT: C 790 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8442 (mp0) REVERT: C 846 TYR cc_start: 0.9377 (t80) cc_final: 0.9062 (t80) REVERT: C 926 MET cc_start: 0.7849 (tpp) cc_final: 0.7558 (tpt) REVERT: C 970 MET cc_start: 0.9361 (mmp) cc_final: 0.8631 (mmm) REVERT: C 992 ASN cc_start: 0.9313 (t0) cc_final: 0.8915 (m-40) REVERT: C 993 PRO cc_start: 0.6070 (Cg_endo) cc_final: 0.5419 (Cg_exo) REVERT: C 1112 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: C 1256 MET cc_start: 0.8503 (tmm) cc_final: 0.7988 (tmm) REVERT: C 1286 PHE cc_start: 0.7925 (m-80) cc_final: 0.7561 (m-80) REVERT: C 1347 ASN cc_start: 0.8769 (t0) cc_final: 0.8563 (t0) REVERT: C 1480 TYR cc_start: 0.9022 (t80) cc_final: 0.8718 (t80) REVERT: C 1481 PHE cc_start: 0.8588 (m-10) cc_final: 0.8080 (m-80) REVERT: D 750 LYS cc_start: 0.9262 (ptpp) cc_final: 0.9000 (ptpp) REVERT: D 961 MET cc_start: 0.8965 (tpp) cc_final: 0.8758 (tpp) REVERT: D 970 MET cc_start: 0.9334 (mmp) cc_final: 0.8836 (mmm) REVERT: D 992 ASN cc_start: 0.9332 (t0) cc_final: 0.9041 (m-40) REVERT: D 1112 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.3884 (pt0) REVERT: D 1136 ASP cc_start: 0.9073 (p0) cc_final: 0.8485 (m-30) REVERT: D 1197 MET cc_start: 0.8932 (tpp) cc_final: 0.8636 (mmt) REVERT: D 1236 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8612 (mp0) REVERT: D 1286 PHE cc_start: 0.8391 (m-80) cc_final: 0.8084 (m-80) REVERT: D 1311 MET cc_start: 0.9170 (ttm) cc_final: 0.8959 (ttm) REVERT: D 1375 MET cc_start: 0.8733 (mtm) cc_final: 0.8487 (mtm) REVERT: D 1480 TYR cc_start: 0.9033 (t80) cc_final: 0.8706 (t80) REVERT: D 1481 PHE cc_start: 0.8714 (m-10) cc_final: 0.8299 (m-80) REVERT: D 1493 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8599 (mm) REVERT: D 1569 GLN cc_start: 0.7794 (mt0) cc_final: 0.7419 (mp10) REVERT: D 1582 ARG cc_start: 0.8993 (tmm160) cc_final: 0.8560 (ttp80) outliers start: 125 outliers final: 92 residues processed: 426 average time/residue: 0.2029 time to fit residues: 148.4461 Evaluate side-chains 409 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 311 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1585 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 884 VAL Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1288 THR Chi-restraints excluded: chain B residue 1291 ARG Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1461 ASP Chi-restraints excluded: chain B residue 1520 SER Chi-restraints excluded: chain B residue 1551 SER Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 719 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 791 ASP Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 1051 VAL Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1097 GLN Chi-restraints excluded: chain C residue 1112 GLU Chi-restraints excluded: chain C residue 1228 LEU Chi-restraints excluded: chain C residue 1295 HIS Chi-restraints excluded: chain C residue 1461 ASP Chi-restraints excluded: chain C residue 1492 LEU Chi-restraints excluded: chain C residue 1585 THR Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 786 SER Chi-restraints excluded: chain D residue 791 ASP Chi-restraints excluded: chain D residue 884 VAL Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 1112 GLU Chi-restraints excluded: chain D residue 1141 SER Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1247 LEU Chi-restraints excluded: chain D residue 1288 THR Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1461 ASP Chi-restraints excluded: chain D residue 1492 LEU Chi-restraints excluded: chain D residue 1493 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 277 optimal weight: 1.9990 chunk 178 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 217 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 61 optimal weight: 0.0570 chunk 256 optimal weight: 4.9990 chunk 362 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 653 HIS ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 HIS ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.063195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.051271 restraints weight = 189376.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.052829 restraints weight = 117590.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.053885 restraints weight = 83574.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.054604 restraints weight = 65316.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.055158 restraints weight = 54753.494| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34200 Z= 0.156 Angle : 0.588 12.086 46456 Z= 0.300 Chirality : 0.043 0.189 5276 Planarity : 0.004 0.054 6084 Dihedral : 4.967 56.215 4980 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.31 % Allowed : 12.63 % Favored : 84.06 % 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: 0.83 (0.13), residues: 4284 helix: 1.31 (0.10), residues: 2520 sheet: -0.15 (0.28), residues: 400 loop : -0.55 (0.18), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1555 TYR 0.016 0.001 TYR A1518 PHE 0.011 0.002 PHE D 601 TRP 0.012 0.001 TRP A 533 HIS 0.006 0.001 HIS D1149 Details of bonding type rmsd covalent geometry : bond 0.00338 (34200) covalent geometry : angle 0.58845 (46456) hydrogen bonds : bond 0.03660 ( 2053) hydrogen bonds : angle 4.82382 ( 6111) *********************** 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 458 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 342 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 623 MET cc_start: 0.9137 (ptp) cc_final: 0.8898 (pmm) REVERT: A 970 MET cc_start: 0.9350 (mmp) cc_final: 0.8634 (mmm) REVERT: A 992 ASN cc_start: 0.9409 (t0) cc_final: 0.9099 (m-40) REVERT: A 1054 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9063 (mp) REVERT: A 1112 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.5994 (tt0) REVERT: A 1136 ASP cc_start: 0.9130 (p0) cc_final: 0.8633 (p0) REVERT: A 1197 MET cc_start: 0.9111 (mmm) cc_final: 0.8807 (mmt) REVERT: A 1236 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8550 (mt-10) REVERT: A 1256 MET cc_start: 0.8724 (tmm) cc_final: 0.8263 (tmm) REVERT: A 1347 ASN cc_start: 0.8538 (t0) cc_final: 0.8246 (t0) REVERT: A 1375 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8410 (mmm) REVERT: A 1393 TYR cc_start: 0.7642 (m-80) cc_final: 0.7385 (m-80) REVERT: A 1480 TYR cc_start: 0.9182 (t80) cc_final: 0.8793 (t80) REVERT: A 1481 PHE cc_start: 0.8747 (m-10) cc_final: 0.8068 (m-80) REVERT: A 1569 GLN cc_start: 0.7496 (mt0) cc_final: 0.7088 (mp10) REVERT: B 623 MET cc_start: 0.9368 (mtm) cc_final: 0.8794 (pmm) REVERT: B 970 MET cc_start: 0.9336 (mmp) cc_final: 0.8702 (mmm) REVERT: B 992 ASN cc_start: 0.9360 (t0) cc_final: 0.9030 (m-40) REVERT: B 1096 ASP cc_start: 0.8911 (p0) cc_final: 0.8617 (p0) REVERT: B 1112 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6603 (pm20) REVERT: B 1225 ASN cc_start: 0.8527 (t0) cc_final: 0.8298 (t0) REVERT: B 1256 MET cc_start: 0.8605 (tmm) cc_final: 0.8196 (tmm) REVERT: B 1393 TYR cc_start: 0.7753 (m-80) cc_final: 0.7486 (m-80) REVERT: B 1480 TYR cc_start: 0.9092 (t80) cc_final: 0.8712 (t80) REVERT: B 1481 PHE cc_start: 0.8680 (m-10) cc_final: 0.8205 (m-80) REVERT: B 1515 ASP cc_start: 0.8970 (m-30) cc_final: 0.8630 (m-30) REVERT: B 1569 GLN cc_start: 0.7724 (mt0) cc_final: 0.7305 (mp10) REVERT: C 750 LYS cc_start: 0.9265 (ptpp) cc_final: 0.9044 (ptpp) REVERT: C 790 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.8415 (mp0) REVERT: C 846 TYR cc_start: 0.9418 (t80) cc_final: 0.9080 (t80) REVERT: C 926 MET cc_start: 0.7773 (tpp) cc_final: 0.7557 (tpt) REVERT: C 970 MET cc_start: 0.9371 (mmp) cc_final: 0.8662 (mmm) REVERT: C 992 ASN cc_start: 0.9354 (t0) cc_final: 0.8948 (m-40) REVERT: C 993 PRO cc_start: 0.6058 (Cg_endo) cc_final: 0.5417 (Cg_exo) REVERT: C 1112 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6708 (pm20) REVERT: C 1256 MET cc_start: 0.8583 (tmm) cc_final: 0.8109 (tmm) REVERT: C 1286 PHE cc_start: 0.8051 (m-80) cc_final: 0.7842 (m-80) REVERT: C 1347 ASN cc_start: 0.8773 (t0) cc_final: 0.8559 (t0) REVERT: C 1480 TYR cc_start: 0.9059 (t80) cc_final: 0.8687 (t80) REVERT: C 1481 PHE cc_start: 0.8629 (m-10) cc_final: 0.8077 (m-80) REVERT: C 1515 ASP cc_start: 0.9152 (m-30) cc_final: 0.8569 (p0) REVERT: D 750 LYS cc_start: 0.9260 (ptpp) cc_final: 0.9033 (ptpp) REVERT: D 768 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8529 (p) REVERT: D 913 PHE cc_start: 0.8762 (t80) cc_final: 0.8510 (t80) REVERT: D 961 MET cc_start: 0.8975 (tpp) cc_final: 0.8766 (tpp) REVERT: D 970 MET cc_start: 0.9362 (mmp) cc_final: 0.8725 (mmm) REVERT: D 992 ASN cc_start: 0.9390 (t0) cc_final: 0.9088 (m-40) REVERT: D 1236 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8712 (mp0) REVERT: D 1286 PHE cc_start: 0.8337 (m-80) cc_final: 0.7997 (m-80) REVERT: D 1375 MET cc_start: 0.8792 (mtm) cc_final: 0.8562 (mtm) REVERT: D 1480 TYR cc_start: 0.9117 (t80) cc_final: 0.8749 (t80) REVERT: D 1481 PHE cc_start: 0.8798 (m-10) cc_final: 0.8317 (m-80) REVERT: D 1493 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8588 (mm) REVERT: D 1569 GLN cc_start: 0.7387 (mt0) cc_final: 0.7124 (mp10) REVERT: D 1582 ARG cc_start: 0.9000 (tmm160) cc_final: 0.8562 (ttp80) outliers start: 116 outliers final: 95 residues processed: 431 average time/residue: 0.2044 time to fit residues: 150.3968 Evaluate side-chains 423 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 320 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1112 GLU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1375 MET Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1097 GLN Chi-restraints excluded: chain B residue 1112 GLU Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1288 THR Chi-restraints excluded: chain B residue 1291 ARG Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1461 ASP Chi-restraints excluded: chain B residue 1492 LEU Chi-restraints excluded: chain B residue 1520 SER Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 719 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 791 ASP Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1097 GLN Chi-restraints excluded: chain C residue 1112 GLU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1228 LEU Chi-restraints excluded: chain C residue 1247 LEU Chi-restraints excluded: chain C residue 1277 VAL Chi-restraints excluded: chain C residue 1288 THR Chi-restraints excluded: chain C residue 1295 HIS Chi-restraints excluded: chain C residue 1461 ASP Chi-restraints excluded: chain C residue 1492 LEU Chi-restraints excluded: chain C residue 1551 SER Chi-restraints excluded: chain C residue 1585 THR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain D residue 768 VAL Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 786 SER Chi-restraints excluded: chain D residue 791 ASP Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 1068 VAL Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1277 VAL Chi-restraints excluded: chain D residue 1288 THR Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1461 ASP Chi-restraints excluded: chain D residue 1492 LEU Chi-restraints excluded: chain D residue 1493 LEU Chi-restraints excluded: chain D residue 1551 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 289 optimal weight: 0.2980 chunk 286 optimal weight: 3.9990 chunk 308 optimal weight: 7.9990 chunk 181 optimal weight: 0.8980 chunk 292 optimal weight: 3.9990 chunk 340 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 342 optimal weight: 6.9990 chunk 271 optimal weight: 6.9990 chunk 382 optimal weight: 0.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.062993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.051085 restraints weight = 190660.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.052622 restraints weight = 117448.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.053677 restraints weight = 83902.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.054319 restraints weight = 65656.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.054900 restraints weight = 55778.930| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4518 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= 0.168 Angle : 0.596 12.620 46456 Z= 0.304 Chirality : 0.043 0.276 5276 Planarity : 0.004 0.055 6084 Dihedral : 4.927 56.559 4980 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.36 % Allowed : 13.40 % Favored : 83.24 % 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: 0.81 (0.13), residues: 4284 helix: 1.31 (0.10), residues: 2520 sheet: -0.12 (0.28), residues: 396 loop : -0.61 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1555 TYR 0.017 0.001 TYR A1518 PHE 0.023 0.002 PHE C1350 TRP 0.012 0.001 TRP A 533 HIS 0.005 0.001 HIS D1258 Details of bonding type rmsd covalent geometry : bond 0.00365 (34200) covalent geometry : angle 0.59596 (46456) hydrogen bonds : bond 0.03624 ( 2053) hydrogen bonds : angle 4.81078 ( 6111) *********************** 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 445 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 327 time to evaluate : 1.310 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: A 623 MET cc_start: 0.9101 (ptp) cc_final: 0.8870 (pmm) REVERT: A 724 THR cc_start: 0.6958 (OUTLIER) cc_final: 0.6711 (m) REVERT: A 750 LYS cc_start: 0.9250 (ptpp) cc_final: 0.9012 (ptpp) REVERT: A 970 MET cc_start: 0.9321 (mmp) cc_final: 0.8787 (mmm) REVERT: A 992 ASN cc_start: 0.9382 (t0) cc_final: 0.9073 (m-40) REVERT: A 1054 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9048 (mp) REVERT: A 1112 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6247 (tt0) REVERT: A 1136 ASP cc_start: 0.9164 (p0) cc_final: 0.8699 (p0) REVERT: A 1197 MET cc_start: 0.9065 (mmm) cc_final: 0.8759 (mmt) REVERT: A 1236 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8597 (mt-10) REVERT: A 1256 MET cc_start: 0.8717 (tmm) cc_final: 0.8276 (tmm) REVERT: A 1347 ASN cc_start: 0.8474 (t0) cc_final: 0.8128 (t0) REVERT: A 1393 TYR cc_start: 0.7501 (m-80) cc_final: 0.7249 (m-80) REVERT: A 1480 TYR cc_start: 0.9164 (t80) cc_final: 0.8751 (t80) REVERT: A 1481 PHE cc_start: 0.8697 (m-10) cc_final: 0.8009 (m-80) REVERT: A 1515 ASP cc_start: 0.8859 (m-30) cc_final: 0.8544 (m-30) REVERT: A 1569 GLN cc_start: 0.7247 (mt0) cc_final: 0.6792 (mp10) REVERT: B 970 MET cc_start: 0.9358 (mmp) cc_final: 0.8589 (mmm) REVERT: B 992 ASN cc_start: 0.9367 (t0) cc_final: 0.9010 (m-40) REVERT: B 1225 ASN cc_start: 0.8508 (t0) cc_final: 0.8290 (t0) REVERT: B 1256 MET cc_start: 0.8597 (tmm) cc_final: 0.8153 (tmm) REVERT: B 1393 TYR cc_start: 0.7721 (m-80) cc_final: 0.7411 (m-80) REVERT: B 1480 TYR cc_start: 0.9079 (t80) cc_final: 0.8697 (t80) REVERT: B 1481 PHE cc_start: 0.8631 (m-10) cc_final: 0.8144 (m-80) REVERT: B 1515 ASP cc_start: 0.8926 (m-30) cc_final: 0.8595 (m-30) REVERT: C 750 LYS cc_start: 0.9245 (ptpp) cc_final: 0.9037 (ptpp) REVERT: C 790 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8480 (mp0) REVERT: C 846 TYR cc_start: 0.9387 (t80) cc_final: 0.9054 (t80) REVERT: C 970 MET cc_start: 0.9364 (mmp) cc_final: 0.8637 (mmm) REVERT: C 992 ASN cc_start: 0.9322 (t0) cc_final: 0.8919 (m-40) REVERT: C 993 PRO cc_start: 0.6136 (Cg_endo) cc_final: 0.5509 (Cg_exo) REVERT: C 1112 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6769 (pm20) REVERT: C 1256 MET cc_start: 0.8587 (tmm) cc_final: 0.8109 (tmm) REVERT: C 1286 PHE cc_start: 0.8072 (m-80) cc_final: 0.7814 (m-80) REVERT: C 1480 TYR cc_start: 0.9070 (t80) cc_final: 0.8686 (t80) REVERT: C 1481 PHE cc_start: 0.8588 (m-10) cc_final: 0.8099 (m-80) REVERT: C 1515 ASP cc_start: 0.9126 (m-30) cc_final: 0.8556 (p0) REVERT: C 1569 GLN cc_start: 0.7821 (mt0) cc_final: 0.7312 (mp10) REVERT: D 750 LYS cc_start: 0.9242 (ptpp) cc_final: 0.9026 (ptpp) REVERT: D 913 PHE cc_start: 0.8759 (t80) cc_final: 0.8545 (t80) REVERT: D 926 MET cc_start: 0.7629 (tpp) cc_final: 0.7136 (tpt) REVERT: D 970 MET cc_start: 0.9323 (mmp) cc_final: 0.8813 (mmm) REVERT: D 992 ASN cc_start: 0.9346 (t0) cc_final: 0.9046 (m-40) REVERT: D 1112 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6501 (pm20) REVERT: D 1236 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8683 (mp0) REVERT: D 1286 PHE cc_start: 0.8334 (m-80) cc_final: 0.8012 (m-80) REVERT: D 1375 MET cc_start: 0.8750 (mtm) cc_final: 0.8531 (mtm) REVERT: D 1480 TYR cc_start: 0.9097 (t80) cc_final: 0.8705 (t80) REVERT: D 1481 PHE cc_start: 0.8690 (m-10) cc_final: 0.8206 (m-80) REVERT: D 1569 GLN cc_start: 0.7276 (mt0) cc_final: 0.7050 (mp10) REVERT: D 1582 ARG cc_start: 0.9004 (tmm160) cc_final: 0.8587 (ttp80) outliers start: 118 outliers final: 97 residues processed: 418 average time/residue: 0.2019 time to fit residues: 143.8635 Evaluate side-chains 422 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 319 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1112 GLU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 750 LYS Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 885 VAL Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1097 GLN Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1288 THR Chi-restraints excluded: chain B residue 1291 ARG Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1461 ASP Chi-restraints excluded: chain B residue 1492 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 719 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 790 GLU Chi-restraints excluded: chain C residue 791 ASP Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1112 GLU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1228 LEU Chi-restraints excluded: chain C residue 1277 VAL Chi-restraints excluded: chain C residue 1288 THR Chi-restraints excluded: chain C residue 1295 HIS Chi-restraints excluded: chain C residue 1461 ASP Chi-restraints excluded: chain C residue 1492 LEU Chi-restraints excluded: chain C residue 1585 THR Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 786 SER Chi-restraints excluded: chain D residue 791 ASP Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 1112 GLU Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1277 VAL Chi-restraints excluded: chain D residue 1288 THR Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1461 ASP Chi-restraints excluded: chain D residue 1492 LEU Chi-restraints excluded: chain D residue 1520 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 227 optimal weight: 5.9990 chunk 252 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 418 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 83 optimal weight: 0.8980 chunk 352 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 393 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.063808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.051955 restraints weight = 189052.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.053483 restraints weight = 117167.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.054486 restraints weight = 83984.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.055244 restraints weight = 66679.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.055746 restraints weight = 55543.116| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34200 Z= 0.133 Angle : 0.606 17.907 46456 Z= 0.299 Chirality : 0.043 0.214 5276 Planarity : 0.004 0.054 6084 Dihedral : 4.841 57.271 4980 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.11 % Allowed : 14.08 % Favored : 82.81 % 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: 0.92 (0.13), residues: 4284 helix: 1.47 (0.10), residues: 2488 sheet: -0.38 (0.26), residues: 444 loop : -0.56 (0.18), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1555 TYR 0.018 0.001 TYR D1518 PHE 0.012 0.001 PHE B 792 TRP 0.014 0.001 TRP A 533 HIS 0.005 0.001 HIS D1149 Details of bonding type rmsd covalent geometry : bond 0.00294 (34200) covalent geometry : angle 0.60561 (46456) hydrogen bonds : bond 0.03512 ( 2053) hydrogen bonds : angle 4.70067 ( 6111) *********************** 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 446 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 337 time to evaluate : 1.378 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 750 LYS cc_start: 0.9224 (ptpp) cc_final: 0.9018 (ptpp) REVERT: A 970 MET cc_start: 0.9295 (mmp) cc_final: 0.8762 (mmm) REVERT: A 992 ASN cc_start: 0.9394 (t0) cc_final: 0.9106 (m-40) REVERT: A 1054 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.9019 (mp) REVERT: A 1112 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6709 (pm20) REVERT: A 1178 MET cc_start: 0.8843 (tpp) cc_final: 0.8494 (mtt) REVERT: A 1197 MET cc_start: 0.8995 (mmm) cc_final: 0.8711 (mmt) REVERT: A 1236 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8599 (mt-10) REVERT: A 1256 MET cc_start: 0.8589 (tmm) cc_final: 0.8114 (tmm) REVERT: A 1347 ASN cc_start: 0.8419 (t0) cc_final: 0.8086 (t0) REVERT: A 1393 TYR cc_start: 0.7420 (m-80) cc_final: 0.7178 (m-80) REVERT: A 1480 TYR cc_start: 0.9079 (t80) cc_final: 0.8658 (t80) REVERT: A 1481 PHE cc_start: 0.8700 (m-10) cc_final: 0.8034 (m-80) REVERT: A 1515 ASP cc_start: 0.8882 (m-30) cc_final: 0.8593 (m-30) REVERT: A 1569 GLN cc_start: 0.7181 (mt0) cc_final: 0.6761 (mp10) REVERT: B 970 MET cc_start: 0.9338 (mmp) cc_final: 0.8700 (mmm) REVERT: B 992 ASN cc_start: 0.9360 (t0) cc_final: 0.9014 (m-40) REVERT: B 1156 LEU cc_start: 0.8983 (tp) cc_final: 0.8661 (pp) REVERT: B 1256 MET cc_start: 0.8566 (tmm) cc_final: 0.8102 (tmm) REVERT: B 1306 GLU cc_start: 0.8690 (tp30) cc_final: 0.8428 (tp30) REVERT: B 1393 TYR cc_start: 0.7584 (m-80) cc_final: 0.7265 (m-80) REVERT: B 1480 TYR cc_start: 0.9038 (t80) cc_final: 0.8620 (t80) REVERT: B 1481 PHE cc_start: 0.8549 (m-10) cc_final: 0.8058 (m-80) REVERT: B 1515 ASP cc_start: 0.8862 (m-30) cc_final: 0.8535 (m-30) REVERT: C 846 TYR cc_start: 0.9334 (t80) cc_final: 0.9015 (t80) REVERT: C 961 MET cc_start: 0.9109 (tpp) cc_final: 0.8594 (tpp) REVERT: C 970 MET cc_start: 0.9335 (mmp) cc_final: 0.8614 (mmm) REVERT: C 992 ASN cc_start: 0.9307 (t0) cc_final: 0.8913 (m-40) REVERT: C 993 PRO cc_start: 0.6084 (Cg_endo) cc_final: 0.5498 (Cg_exo) REVERT: C 1112 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6707 (pm20) REVERT: C 1236 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8547 (mp0) REVERT: C 1256 MET cc_start: 0.8485 (tmm) cc_final: 0.7991 (tmm) REVERT: C 1306 GLU cc_start: 0.8749 (tp30) cc_final: 0.8513 (tp30) REVERT: C 1480 TYR cc_start: 0.8992 (t80) cc_final: 0.8581 (t80) REVERT: C 1481 PHE cc_start: 0.8506 (m-10) cc_final: 0.7980 (m-80) REVERT: C 1484 MET cc_start: 0.9080 (tpp) cc_final: 0.8830 (tpt) REVERT: C 1569 GLN cc_start: 0.7684 (mt0) cc_final: 0.7100 (mp10) REVERT: D 913 PHE cc_start: 0.8695 (t80) cc_final: 0.8474 (t80) REVERT: D 970 MET cc_start: 0.9342 (mmp) cc_final: 0.8711 (mmm) REVERT: D 992 ASN cc_start: 0.9372 (t0) cc_final: 0.9044 (m-40) REVERT: D 1112 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6549 (pm20) REVERT: D 1236 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8688 (mp0) REVERT: D 1286 PHE cc_start: 0.8308 (m-80) cc_final: 0.8013 (m-80) REVERT: D 1375 MET cc_start: 0.8702 (mtm) cc_final: 0.8422 (ttm) REVERT: D 1480 TYR cc_start: 0.9069 (t80) cc_final: 0.8656 (t80) REVERT: D 1481 PHE cc_start: 0.8618 (m-10) cc_final: 0.8095 (m-80) REVERT: D 1484 MET cc_start: 0.9045 (tpp) cc_final: 0.8743 (tpt) REVERT: D 1582 ARG cc_start: 0.8819 (tmm160) cc_final: 0.8459 (ttp80) outliers start: 109 outliers final: 92 residues processed: 422 average time/residue: 0.2094 time to fit residues: 150.2978 Evaluate side-chains 412 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 316 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1112 GLU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 686 ARG Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1097 GLN Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1277 VAL Chi-restraints excluded: chain B residue 1288 THR Chi-restraints excluded: chain B residue 1291 ARG Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1461 ASP Chi-restraints excluded: chain B residue 1492 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 719 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1097 GLN Chi-restraints excluded: chain C residue 1112 GLU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1228 LEU Chi-restraints excluded: chain C residue 1277 VAL Chi-restraints excluded: chain C residue 1288 THR Chi-restraints excluded: chain C residue 1295 HIS Chi-restraints excluded: chain C residue 1461 ASP Chi-restraints excluded: chain C residue 1492 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 786 SER Chi-restraints excluded: chain D residue 791 ASP Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 1112 GLU Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1277 VAL Chi-restraints excluded: chain D residue 1288 THR Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1460 LEU Chi-restraints excluded: chain D residue 1461 ASP Chi-restraints excluded: chain D residue 1492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 161 optimal weight: 2.9990 chunk 199 optimal weight: 0.8980 chunk 334 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 397 optimal weight: 1.9990 chunk 383 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 113 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 651 GLN ** B1134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1149 HIS ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.063523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.051573 restraints weight = 189956.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.053132 restraints weight = 117840.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.054195 restraints weight = 83936.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.054902 restraints weight = 65628.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.055453 restraints weight = 55206.595| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34200 Z= 0.150 Angle : 0.622 15.395 46456 Z= 0.308 Chirality : 0.044 0.285 5276 Planarity : 0.004 0.054 6084 Dihedral : 4.834 58.358 4980 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.96 % Allowed : 14.68 % Favored : 82.35 % 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: 0.82 (0.13), residues: 4284 helix: 1.34 (0.10), residues: 2536 sheet: -0.40 (0.26), residues: 436 loop : -0.58 (0.18), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1498 TYR 0.021 0.001 TYR D1518 PHE 0.028 0.002 PHE C1350 TRP 0.023 0.001 TRP A 533 HIS 0.005 0.001 HIS B1258 Details of bonding type rmsd covalent geometry : bond 0.00330 (34200) covalent geometry : angle 0.62171 (46456) hydrogen bonds : bond 0.03527 ( 2053) hydrogen bonds : angle 4.73258 ( 6111) *********************** 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 429 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 325 time to evaluate : 1.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 614 GLU cc_start: 0.8498 (tp30) cc_final: 0.8280 (tp30) REVERT: A 750 LYS cc_start: 0.9238 (ptpp) cc_final: 0.9034 (ptpp) REVERT: A 970 MET cc_start: 0.9318 (mmp) cc_final: 0.8776 (mmm) REVERT: A 992 ASN cc_start: 0.9408 (t0) cc_final: 0.9112 (m-40) REVERT: A 1054 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9016 (mp) REVERT: A 1112 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6355 (tt0) REVERT: A 1197 MET cc_start: 0.9065 (mmm) cc_final: 0.8776 (mmt) REVERT: A 1256 MET cc_start: 0.8630 (tmm) cc_final: 0.8158 (tmm) REVERT: A 1347 ASN cc_start: 0.8491 (t0) cc_final: 0.8164 (t0) REVERT: A 1393 TYR cc_start: 0.7498 (m-80) cc_final: 0.7234 (m-80) REVERT: A 1480 TYR cc_start: 0.9122 (t80) cc_final: 0.8679 (t80) REVERT: A 1481 PHE cc_start: 0.8772 (m-10) cc_final: 0.8086 (m-80) REVERT: A 1515 ASP cc_start: 0.8910 (m-30) cc_final: 0.8638 (m-30) REVERT: A 1569 GLN cc_start: 0.7180 (mt0) cc_final: 0.6831 (mp10) REVERT: B 961 MET cc_start: 0.9085 (tpp) cc_final: 0.8544 (tpp) REVERT: B 970 MET cc_start: 0.9394 (mmp) cc_final: 0.8738 (mmm) REVERT: B 992 ASN cc_start: 0.9377 (t0) cc_final: 0.9019 (m-40) REVERT: B 1156 LEU cc_start: 0.9013 (tp) cc_final: 0.8671 (pp) REVERT: B 1227 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8782 (tm-30) REVERT: B 1256 MET cc_start: 0.8634 (tmm) cc_final: 0.8206 (tmm) REVERT: B 1306 GLU cc_start: 0.8750 (tp30) cc_final: 0.8510 (tp30) REVERT: B 1393 TYR cc_start: 0.7641 (m-80) cc_final: 0.7280 (m-80) REVERT: B 1480 TYR cc_start: 0.9097 (t80) cc_final: 0.8661 (t80) REVERT: B 1481 PHE cc_start: 0.8621 (m-10) cc_final: 0.8105 (m-80) REVERT: B 1515 ASP cc_start: 0.8857 (m-30) cc_final: 0.8533 (m-30) REVERT: C 623 MET cc_start: 0.9055 (pmm) cc_final: 0.8685 (pmm) REVERT: C 846 TYR cc_start: 0.9355 (t80) cc_final: 0.9039 (t80) REVERT: C 970 MET cc_start: 0.9383 (mmp) cc_final: 0.8617 (mmm) REVERT: C 992 ASN cc_start: 0.9320 (t0) cc_final: 0.8909 (m-40) REVERT: C 993 PRO cc_start: 0.6298 (Cg_endo) cc_final: 0.5800 (Cg_exo) REVERT: C 1112 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6535 (pm20) REVERT: C 1227 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8783 (tm-30) REVERT: C 1236 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8499 (mp0) REVERT: C 1256 MET cc_start: 0.8517 (tmm) cc_final: 0.7982 (tmm) REVERT: C 1480 TYR cc_start: 0.9085 (t80) cc_final: 0.8669 (t80) REVERT: C 1481 PHE cc_start: 0.8572 (m-10) cc_final: 0.8020 (m-80) REVERT: C 1569 GLN cc_start: 0.7638 (mt0) cc_final: 0.7082 (mp10) REVERT: D 913 PHE cc_start: 0.8753 (t80) cc_final: 0.8526 (t80) REVERT: D 961 MET cc_start: 0.9035 (tpp) cc_final: 0.8518 (tpp) REVERT: D 970 MET cc_start: 0.9378 (mmp) cc_final: 0.8815 (mmm) REVERT: D 992 ASN cc_start: 0.9351 (t0) cc_final: 0.9014 (m-40) REVERT: D 1136 ASP cc_start: 0.9098 (p0) cc_final: 0.8652 (m-30) REVERT: D 1236 GLU cc_start: 0.8992 (mt-10) cc_final: 0.8702 (mp0) REVERT: D 1286 PHE cc_start: 0.8362 (m-80) cc_final: 0.8038 (m-80) REVERT: D 1480 TYR cc_start: 0.9095 (t80) cc_final: 0.8663 (t80) REVERT: D 1481 PHE cc_start: 0.8645 (m-10) cc_final: 0.8161 (m-80) outliers start: 104 outliers final: 96 residues processed: 408 average time/residue: 0.2060 time to fit residues: 142.6413 Evaluate side-chains 407 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 308 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 638 TYR Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 790 GLU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1112 GLU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 686 ARG Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1175 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1277 VAL Chi-restraints excluded: chain B residue 1288 THR Chi-restraints excluded: chain B residue 1291 ARG Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1461 ASP Chi-restraints excluded: chain B residue 1492 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 719 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1097 GLN Chi-restraints excluded: chain C residue 1112 GLU Chi-restraints excluded: chain C residue 1175 LEU Chi-restraints excluded: chain C residue 1228 LEU Chi-restraints excluded: chain C residue 1277 VAL Chi-restraints excluded: chain C residue 1288 THR Chi-restraints excluded: chain C residue 1295 HIS Chi-restraints excluded: chain C residue 1461 ASP Chi-restraints excluded: chain C residue 1492 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 613 VAL Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 686 ARG Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 786 SER Chi-restraints excluded: chain D residue 791 ASP Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 1068 VAL Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1277 VAL Chi-restraints excluded: chain D residue 1288 THR Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1460 LEU Chi-restraints excluded: chain D residue 1461 ASP Chi-restraints excluded: chain D residue 1492 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: 0.9990 chunk 381 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 272 optimal weight: 20.0000 chunk 229 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 651 GLN A1095 ASN C 651 GLN ** C1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1396 GLN D1095 ASN ** D1115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.061082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.049502 restraints weight = 197416.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.051012 restraints weight = 120309.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.052047 restraints weight = 85251.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.052762 restraints weight = 66470.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.053294 restraints weight = 55560.455| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 34200 Z= 0.271 Angle : 0.704 13.496 46456 Z= 0.365 Chirality : 0.046 0.242 5276 Planarity : 0.005 0.054 6084 Dihedral : 5.121 59.425 4980 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.99 % Allowed : 14.51 % Favored : 82.50 % 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: 0.33 (0.13), residues: 4284 helix: 0.86 (0.10), residues: 2516 sheet: -0.34 (0.27), residues: 412 loop : -0.65 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1498 TYR 0.024 0.002 TYR D1457 PHE 0.020 0.002 PHE A1286 TRP 0.016 0.002 TRP A 533 HIS 0.009 0.002 HIS C1149 Details of bonding type rmsd covalent geometry : bond 0.00570 (34200) covalent geometry : angle 0.70413 (46456) hydrogen bonds : bond 0.04018 ( 2053) hydrogen bonds : angle 5.06334 ( 6111) ********************** 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 419 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 314 time to evaluate : 1.360 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: A 961 MET cc_start: 0.8868 (tpp) cc_final: 0.8632 (tpp) REVERT: A 970 MET cc_start: 0.9353 (mmp) cc_final: 0.8753 (mmm) REVERT: A 992 ASN cc_start: 0.9432 (t0) cc_final: 0.9069 (m-40) REVERT: A 1112 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: A 1178 MET cc_start: 0.8947 (tpp) cc_final: 0.8743 (mtt) REVERT: A 1197 MET cc_start: 0.9185 (mmm) cc_final: 0.8851 (mmt) REVERT: A 1256 MET cc_start: 0.8773 (tmm) cc_final: 0.8379 (tmm) REVERT: A 1347 ASN cc_start: 0.8681 (t0) cc_final: 0.8403 (t0) REVERT: A 1375 MET cc_start: 0.8619 (tpp) cc_final: 0.8187 (tpp) REVERT: A 1480 TYR cc_start: 0.9175 (t80) cc_final: 0.8773 (t80) REVERT: A 1481 PHE cc_start: 0.8864 (m-10) cc_final: 0.8186 (m-80) REVERT: A 1515 ASP cc_start: 0.8839 (m-30) cc_final: 0.8511 (m-30) REVERT: A 1569 GLN cc_start: 0.7132 (mt0) cc_final: 0.6771 (mp10) REVERT: B 623 MET cc_start: 0.9066 (pmm) cc_final: 0.8670 (pmm) REVERT: B 961 MET cc_start: 0.9064 (tpp) cc_final: 0.8656 (tpp) REVERT: B 970 MET cc_start: 0.9365 (mmp) cc_final: 0.8653 (mmm) REVERT: B 992 ASN cc_start: 0.9368 (t0) cc_final: 0.8968 (m-40) REVERT: B 1227 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8495 (tm-30) REVERT: B 1256 MET cc_start: 0.8670 (tmm) cc_final: 0.8204 (tmm) REVERT: B 1306 GLU cc_start: 0.8807 (tp30) cc_final: 0.8570 (tp30) REVERT: B 1480 TYR cc_start: 0.9204 (t80) cc_final: 0.8762 (t80) REVERT: B 1481 PHE cc_start: 0.8830 (m-10) cc_final: 0.8269 (m-80) REVERT: B 1515 ASP cc_start: 0.8915 (m-30) cc_final: 0.8595 (m-30) REVERT: C 623 MET cc_start: 0.9072 (pmm) cc_final: 0.8731 (pmm) REVERT: C 846 TYR cc_start: 0.9450 (t80) cc_final: 0.9176 (t80) REVERT: C 970 MET cc_start: 0.9385 (mmp) cc_final: 0.8661 (mmm) REVERT: C 992 ASN cc_start: 0.9351 (t0) cc_final: 0.8914 (m-40) REVERT: C 1112 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6352 (tt0) REVERT: C 1136 ASP cc_start: 0.9181 (p0) cc_final: 0.8680 (p0) REVERT: C 1227 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8374 (tm-30) REVERT: C 1256 MET cc_start: 0.8590 (tmm) cc_final: 0.8089 (tmm) REVERT: C 1480 TYR cc_start: 0.9194 (t80) cc_final: 0.8843 (t80) REVERT: C 1481 PHE cc_start: 0.8759 (m-10) cc_final: 0.8271 (m-80) REVERT: C 1515 ASP cc_start: 0.9036 (m-30) cc_final: 0.8499 (p0) REVERT: C 1569 GLN cc_start: 0.7302 (mt0) cc_final: 0.6925 (mp10) REVERT: D 623 MET cc_start: 0.9076 (pmm) cc_final: 0.8788 (pmm) REVERT: D 643 ARG cc_start: 0.9245 (mmm-85) cc_final: 0.8980 (tpp-160) REVERT: D 913 PHE cc_start: 0.8886 (t80) cc_final: 0.8665 (t80) REVERT: D 961 MET cc_start: 0.9086 (tpp) cc_final: 0.8688 (tpp) REVERT: D 970 MET cc_start: 0.9429 (mmp) cc_final: 0.8875 (mmm) REVERT: D 992 ASN cc_start: 0.9282 (t0) cc_final: 0.8977 (m-40) REVERT: D 1112 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6499 (pm20) REVERT: D 1236 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8653 (mp0) REVERT: D 1286 PHE cc_start: 0.8522 (m-80) cc_final: 0.8111 (m-80) REVERT: D 1375 MET cc_start: 0.8783 (mtm) cc_final: 0.8494 (mtm) REVERT: D 1480 TYR cc_start: 0.9185 (t80) cc_final: 0.8784 (t80) REVERT: D 1481 PHE cc_start: 0.8772 (m-10) cc_final: 0.8277 (m-80) outliers start: 105 outliers final: 95 residues processed: 397 average time/residue: 0.1991 time to fit residues: 134.5538 Evaluate side-chains 407 residues out of total 3508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 309 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 719 GLU Chi-restraints excluded: chain A residue 728 VAL Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 885 VAL Chi-restraints excluded: chain A residue 896 ASP Chi-restraints excluded: chain A residue 948 THR Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1017 ASP Chi-restraints excluded: chain A residue 1051 VAL Chi-restraints excluded: chain A residue 1059 LEU Chi-restraints excluded: chain A residue 1112 GLU Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1277 VAL Chi-restraints excluded: chain A residue 1288 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1461 ASP Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 642 LEU Chi-restraints excluded: chain B residue 686 ARG Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 719 GLU Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 748 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 786 SER Chi-restraints excluded: chain B residue 791 ASP Chi-restraints excluded: chain B residue 806 LYS Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 948 THR Chi-restraints excluded: chain B residue 1059 LEU Chi-restraints excluded: chain B residue 1228 LEU Chi-restraints excluded: chain B residue 1277 VAL Chi-restraints excluded: chain B residue 1288 THR Chi-restraints excluded: chain B residue 1291 ARG Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1460 LEU Chi-restraints excluded: chain B residue 1461 ASP Chi-restraints excluded: chain B residue 1492 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 642 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 719 GLU Chi-restraints excluded: chain C residue 728 VAL Chi-restraints excluded: chain C residue 748 VAL Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain C residue 750 LYS Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 786 SER Chi-restraints excluded: chain C residue 885 VAL Chi-restraints excluded: chain C residue 896 ASP Chi-restraints excluded: chain C residue 948 THR Chi-restraints excluded: chain C residue 1059 LEU Chi-restraints excluded: chain C residue 1097 GLN Chi-restraints excluded: chain C residue 1112 GLU Chi-restraints excluded: chain C residue 1228 LEU Chi-restraints excluded: chain C residue 1277 VAL Chi-restraints excluded: chain C residue 1288 THR Chi-restraints excluded: chain C residue 1295 HIS Chi-restraints excluded: chain C residue 1461 ASP Chi-restraints excluded: chain C residue 1492 LEU Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 642 LEU Chi-restraints excluded: chain D residue 686 ARG Chi-restraints excluded: chain D residue 703 VAL Chi-restraints excluded: chain D residue 719 GLU Chi-restraints excluded: chain D residue 728 VAL Chi-restraints excluded: chain D residue 748 VAL Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain D residue 750 LYS Chi-restraints excluded: chain D residue 773 LEU Chi-restraints excluded: chain D residue 783 LEU Chi-restraints excluded: chain D residue 786 SER Chi-restraints excluded: chain D residue 791 ASP Chi-restraints excluded: chain D residue 885 VAL Chi-restraints excluded: chain D residue 896 ASP Chi-restraints excluded: chain D residue 1097 GLN Chi-restraints excluded: chain D residue 1112 GLU Chi-restraints excluded: chain D residue 1228 LEU Chi-restraints excluded: chain D residue 1277 VAL Chi-restraints excluded: chain D residue 1288 THR Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1460 LEU Chi-restraints excluded: chain D residue 1461 ASP Chi-restraints excluded: chain D residue 1492 LEU Chi-restraints excluded: chain D residue 1520 SER Chi-restraints excluded: chain D residue 1585 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 428 random chunks: chunk 69 optimal weight: 2.9990 chunk 262 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 398 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 31 optimal weight: 0.4980 chunk 296 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 408 optimal weight: 0.6980 chunk 371 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1032 GLN C1115 ASN D1095 ASN D1115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.063208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.051685 restraints weight = 190372.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.053209 restraints weight = 117656.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.054277 restraints weight = 83415.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.055034 restraints weight = 64920.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.055537 restraints weight = 53873.549| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34200 Z= 0.133 Angle : 0.648 16.293 46456 Z= 0.317 Chirality : 0.044 0.261 5276 Planarity : 0.004 0.054 6084 Dihedral : 4.920 59.597 4980 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.57 % Allowed : 15.31 % Favored : 82.13 % 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: 0.73 (0.13), residues: 4284 helix: 1.18 (0.10), residues: 2536 sheet: -0.09 (0.27), residues: 388 loop : -0.53 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1498 TYR 0.016 0.001 TYR D1518 PHE 0.020 0.001 PHE C1350 TRP 0.019 0.001 TRP A 533 HIS 0.005 0.001 HIS B1258 Details of bonding type rmsd covalent geometry : bond 0.00294 (34200) covalent geometry : angle 0.64794 (46456) hydrogen bonds : bond 0.03604 ( 2053) hydrogen bonds : angle 4.77560 ( 6111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6103.77 seconds wall clock time: 106 minutes 49.28 seconds (6409.28 seconds total)