Starting phenix.real_space_refine on Tue Feb 13 14:30:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txb_41679/02_2024/8txb_41679.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txb_41679/02_2024/8txb_41679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txb_41679/02_2024/8txb_41679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txb_41679/02_2024/8txb_41679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txb_41679/02_2024/8txb_41679.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txb_41679/02_2024/8txb_41679.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.023 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 332 5.16 5 C 34572 2.51 5 N 8936 2.21 5 O 10908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 401": "OD1" <-> "OD2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 611": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 726": "OD1" <-> "OD2" Residue "A PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1017": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1130": "OE1" <-> "OE2" Residue "A ASP 1184": "OD1" <-> "OD2" Residue "A TYR 1235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1239": "OE1" <-> "OE2" Residue "A GLU 1282": "OE1" <-> "OE2" Residue "A GLU 1440": "OE1" <-> "OE2" Residue "A ASP 1492": "OD1" <-> "OD2" Residue "A GLU 1628": "OE1" <-> "OE2" Residue "A ASP 1690": "OD1" <-> "OD2" Residue "A GLU 1728": "OE1" <-> "OE2" Residue "A ASP 1760": "OD1" <-> "OD2" Residue "A ASP 1786": "OD1" <-> "OD2" Residue "A GLU 1826": "OE1" <-> "OE2" Residue "A ASP 1831": "OD1" <-> "OD2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 326": "OD1" <-> "OD2" Residue "B ASP 401": "OD1" <-> "OD2" Residue "B TYR 581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 911": "OE1" <-> "OE2" Residue "B GLU 1009": "OE1" <-> "OE2" Residue "B TYR 1029": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1239": "OE1" <-> "OE2" Residue "B ASP 1267": "OD1" <-> "OD2" Residue "B GLU 1282": "OE1" <-> "OE2" Residue "B TYR 1291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1492": "OD1" <-> "OD2" Residue "B TYR 1553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1604": "OE1" <-> "OE2" Residue "B GLU 1728": "OE1" <-> "OE2" Residue "B ASP 1760": "OD1" <-> "OD2" Residue "B TYR 1780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1782": "OD1" <-> "OD2" Residue "B GLU 1826": "OE1" <-> "OE2" Residue "C TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "C TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 807": "OD1" <-> "OD2" Residue "C TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1130": "OE1" <-> "OE2" Residue "C ASP 1224": "OD1" <-> "OD2" Residue "C GLU 1282": "OE1" <-> "OE2" Residue "C PHE 1308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1345": "OD1" <-> "OD2" Residue "C GLU 1393": "OE1" <-> "OE2" Residue "C ASP 1534": "OD1" <-> "OD2" Residue "C GLU 1628": "OE1" <-> "OE2" Residue "C GLU 1728": "OE1" <-> "OE2" Residue "C TYR 1780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1782": "OD1" <-> "OD2" Residue "C GLU 1787": "OE1" <-> "OE2" Residue "C PHE 1801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1826": "OE1" <-> "OE2" Residue "D TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D GLU 530": "OE1" <-> "OE2" Residue "D TYR 738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 911": "OE1" <-> "OE2" Residue "D TYR 1195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1239": "OE1" <-> "OE2" Residue "D GLU 1282": "OE1" <-> "OE2" Residue "D PHE 1308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1394": "OD1" <-> "OD2" Residue "D ASP 1430": "OD1" <-> "OD2" Residue "D GLU 1440": "OE1" <-> "OE2" Residue "D ASP 1492": "OD1" <-> "OD2" Residue "D PHE 1537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1558": "OD1" <-> "OD2" Residue "D GLU 1628": "OE1" <-> "OE2" Residue "D TYR 1670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1676": "OE1" <-> "OE2" Residue "D TYR 1780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1786": "OD1" <-> "OD2" Residue "D ASP 1804": "OD1" <-> "OD2" Residue "D GLU 1826": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 54748 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1894, 13687 Classifications: {'peptide': 1894} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 5, 'PTRANS': 194, 'TRANS': 1694} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 13687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1894, 13687 Classifications: {'peptide': 1894} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 5, 'PTRANS': 194, 'TRANS': 1694} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 13687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1894, 13687 Classifications: {'peptide': 1894} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 5, 'PTRANS': 194, 'TRANS': 1694} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 13687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1894, 13687 Classifications: {'peptide': 1894} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 5, 'PTRANS': 194, 'TRANS': 1694} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 20.79, per 1000 atoms: 0.38 Number of scatterers: 54748 At special positions: 0 Unit cell: (135.582, 134.433, 776.724, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 332 16.00 O 10908 8.00 N 8936 7.00 C 34572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=116, symmetry=0 Simple disulfide: pdb=" SG CYS A 534 " - pdb=" SG CYS A 594 " distance=2.03 Simple disulfide: pdb=" SG CYS A 790 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 905 " - pdb=" SG CYS A 947 " distance=2.03 Simple disulfide: pdb=" SG CYS A1052 " - pdb=" SG CYS A1110 " distance=2.04 Simple disulfide: pdb=" SG CYS A1182 " - pdb=" SG CYS A1213 " distance=2.03 Simple disulfide: pdb=" SG CYS A1216 " - pdb=" SG CYS A1228 " distance=2.03 Simple disulfide: pdb=" SG CYS A1231 " - pdb=" SG CYS A1244 " distance=2.03 Simple disulfide: pdb=" SG CYS A1247 " - pdb=" SG CYS A1284 " distance=2.03 Simple disulfide: pdb=" SG CYS A1287 " - pdb=" SG CYS A1301 " distance=2.03 Simple disulfide: pdb=" SG CYS A1304 " - pdb=" SG CYS A1317 " distance=2.03 Simple disulfide: pdb=" SG CYS A1320 " - pdb=" SG CYS A1358 " distance=2.03 Simple disulfide: pdb=" SG CYS A1361 " - pdb=" SG CYS A1389 " distance=2.04 Simple disulfide: pdb=" SG CYS A1392 " - pdb=" SG CYS A1405 " distance=2.03 Simple disulfide: pdb=" SG CYS A1408 " - pdb=" SG CYS A1445 " distance=2.03 Simple disulfide: pdb=" SG CYS A1448 " - pdb=" SG CYS A1462 " distance=2.04 Simple disulfide: pdb=" SG CYS A1465 " - pdb=" SG CYS A1479 " distance=2.03 Simple disulfide: pdb=" SG CYS A1482 " - pdb=" SG CYS A1546 " distance=2.03 Simple disulfide: pdb=" SG CYS A1566 " - pdb=" SG CYS A1593 " distance=2.03 Simple disulfide: pdb=" SG CYS A1596 " - pdb=" SG CYS A1610 " distance=2.03 Simple disulfide: pdb=" SG CYS A1613 " - pdb=" SG CYS A1627 " distance=2.03 Simple disulfide: pdb=" SG CYS A1666 " - pdb=" SG CYS A1680 " distance=2.03 Simple disulfide: pdb=" SG CYS A1683 " - pdb=" SG CYS A1697 " distance=2.03 Simple disulfide: pdb=" SG CYS A1700 " - pdb=" SG CYS A1714 " distance=2.03 Simple disulfide: pdb=" SG CYS A1717 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS A1733 " - pdb=" SG CYS A1747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1750 " - pdb=" SG CYS A1765 " distance=2.03 Simple disulfide: pdb=" SG CYS A1768 " - pdb=" SG CYS A1794 " distance=2.03 Simple disulfide: pdb=" SG CYS A1797 " - pdb=" SG CYS A1811 " distance=2.03 Simple disulfide: pdb=" SG CYS A1814 " - pdb=" SG CYS A1837 " distance=2.03 Simple disulfide: pdb=" SG CYS B 534 " - pdb=" SG CYS B 594 " distance=2.03 Simple disulfide: pdb=" SG CYS B 790 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 905 " - pdb=" SG CYS B 947 " distance=2.04 Simple disulfide: pdb=" SG CYS B1052 " - pdb=" SG CYS B1110 " distance=2.04 Simple disulfide: pdb=" SG CYS B1182 " - pdb=" SG CYS B1213 " distance=2.03 Simple disulfide: pdb=" SG CYS B1216 " - pdb=" SG CYS B1228 " distance=2.03 Simple disulfide: pdb=" SG CYS B1231 " - pdb=" SG CYS B1244 " distance=2.03 Simple disulfide: pdb=" SG CYS B1247 " - pdb=" SG CYS B1284 " distance=2.03 Simple disulfide: pdb=" SG CYS B1287 " - pdb=" SG CYS B1301 " distance=2.03 Simple disulfide: pdb=" SG CYS B1304 " - pdb=" SG CYS B1317 " distance=2.03 Simple disulfide: pdb=" SG CYS B1320 " - pdb=" SG CYS B1358 " distance=2.03 Simple disulfide: pdb=" SG CYS B1361 " - pdb=" SG CYS B1389 " distance=2.03 Simple disulfide: pdb=" SG CYS B1392 " - pdb=" SG CYS B1405 " distance=2.03 Simple disulfide: pdb=" SG CYS B1408 " - pdb=" SG CYS B1445 " distance=2.03 Simple disulfide: pdb=" SG CYS B1448 " - pdb=" SG CYS B1462 " distance=2.04 Simple disulfide: pdb=" SG CYS B1465 " - pdb=" SG CYS B1479 " distance=2.03 Simple disulfide: pdb=" SG CYS B1482 " - pdb=" SG CYS B1546 " distance=2.03 Simple disulfide: pdb=" SG CYS B1566 " - pdb=" SG CYS B1593 " distance=2.03 Simple disulfide: pdb=" SG CYS B1596 " - pdb=" SG CYS B1610 " distance=2.03 Simple disulfide: pdb=" SG CYS B1613 " - pdb=" SG CYS B1627 " distance=2.03 Simple disulfide: pdb=" SG CYS B1666 " - pdb=" SG CYS B1680 " distance=2.03 Simple disulfide: pdb=" SG CYS B1683 " - pdb=" SG CYS B1697 " distance=2.03 Simple disulfide: pdb=" SG CYS B1700 " - pdb=" SG CYS B1714 " distance=2.03 Simple disulfide: pdb=" SG CYS B1717 " - pdb=" SG CYS B1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B1733 " - pdb=" SG CYS B1747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1750 " - pdb=" SG CYS B1765 " distance=2.03 Simple disulfide: pdb=" SG CYS B1768 " - pdb=" SG CYS B1794 " distance=2.03 Simple disulfide: pdb=" SG CYS B1797 " - pdb=" SG CYS B1811 " distance=2.04 Simple disulfide: pdb=" SG CYS B1814 " - pdb=" SG CYS B1837 " distance=2.03 Simple disulfide: pdb=" SG CYS C 534 " - pdb=" SG CYS C 594 " distance=2.03 Simple disulfide: pdb=" SG CYS C 790 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 905 " - pdb=" SG CYS C 947 " distance=2.04 Simple disulfide: pdb=" SG CYS C1052 " - pdb=" SG CYS C1110 " distance=2.04 Simple disulfide: pdb=" SG CYS C1182 " - pdb=" SG CYS C1213 " distance=2.03 Simple disulfide: pdb=" SG CYS C1216 " - pdb=" SG CYS C1228 " distance=2.03 Simple disulfide: pdb=" SG CYS C1231 " - pdb=" SG CYS C1244 " distance=2.03 Simple disulfide: pdb=" SG CYS C1247 " - pdb=" SG CYS C1284 " distance=2.03 Simple disulfide: pdb=" SG CYS C1287 " - pdb=" SG CYS C1301 " distance=2.03 Simple disulfide: pdb=" SG CYS C1304 " - pdb=" SG CYS C1317 " distance=2.03 Simple disulfide: pdb=" SG CYS C1320 " - pdb=" SG CYS C1358 " distance=2.03 Simple disulfide: pdb=" SG CYS C1361 " - pdb=" SG CYS C1389 " distance=2.04 Simple disulfide: pdb=" SG CYS C1392 " - pdb=" SG CYS C1405 " distance=2.03 Simple disulfide: pdb=" SG CYS C1408 " - pdb=" SG CYS C1445 " distance=2.03 Simple disulfide: pdb=" SG CYS C1448 " - pdb=" SG CYS C1462 " distance=2.04 Simple disulfide: pdb=" SG CYS C1465 " - pdb=" SG CYS C1479 " distance=2.03 Simple disulfide: pdb=" SG CYS C1482 " - pdb=" SG CYS C1546 " distance=2.03 Simple disulfide: pdb=" SG CYS C1566 " - pdb=" SG CYS C1593 " distance=2.03 Simple disulfide: pdb=" SG CYS C1596 " - pdb=" SG CYS C1610 " distance=2.03 Simple disulfide: pdb=" SG CYS C1613 " - pdb=" SG CYS C1627 " distance=2.03 Simple disulfide: pdb=" SG CYS C1666 " - pdb=" SG CYS C1680 " distance=2.03 Simple disulfide: pdb=" SG CYS C1683 " - pdb=" SG CYS C1697 " distance=2.03 Simple disulfide: pdb=" SG CYS C1700 " - pdb=" SG CYS C1714 " distance=2.03 Simple disulfide: pdb=" SG CYS C1717 " - pdb=" SG CYS C1730 " distance=2.03 Simple disulfide: pdb=" SG CYS C1733 " - pdb=" SG CYS C1747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1750 " - pdb=" SG CYS C1765 " distance=2.03 Simple disulfide: pdb=" SG CYS C1768 " - pdb=" SG CYS C1794 " distance=2.03 Simple disulfide: pdb=" SG CYS C1797 " - pdb=" SG CYS C1811 " distance=2.03 Simple disulfide: pdb=" SG CYS C1814 " - pdb=" SG CYS C1837 " distance=2.03 Simple disulfide: pdb=" SG CYS D 534 " - pdb=" SG CYS D 594 " distance=2.03 Simple disulfide: pdb=" SG CYS D 790 " - pdb=" SG CYS D 817 " distance=2.03 Simple disulfide: pdb=" SG CYS D 905 " - pdb=" SG CYS D 947 " distance=2.04 Simple disulfide: pdb=" SG CYS D1052 " - pdb=" SG CYS D1110 " distance=2.04 Simple disulfide: pdb=" SG CYS D1182 " - pdb=" SG CYS D1213 " distance=2.03 Simple disulfide: pdb=" SG CYS D1216 " - pdb=" SG CYS D1228 " distance=2.03 Simple disulfide: pdb=" SG CYS D1231 " - pdb=" SG CYS D1244 " distance=2.03 Simple disulfide: pdb=" SG CYS D1247 " - pdb=" SG CYS D1284 " distance=2.03 Simple disulfide: pdb=" SG CYS D1287 " - pdb=" SG CYS D1301 " distance=2.03 Simple disulfide: pdb=" SG CYS D1304 " - pdb=" SG CYS D1317 " distance=2.03 Simple disulfide: pdb=" SG CYS D1320 " - pdb=" SG CYS D1358 " distance=2.03 Simple disulfide: pdb=" SG CYS D1361 " - pdb=" SG CYS D1389 " distance=2.04 Simple disulfide: pdb=" SG CYS D1392 " - pdb=" SG CYS D1405 " distance=2.03 Simple disulfide: pdb=" SG CYS D1408 " - pdb=" SG CYS D1445 " distance=2.03 Simple disulfide: pdb=" SG CYS D1448 " - pdb=" SG CYS D1462 " distance=2.04 Simple disulfide: pdb=" SG CYS D1465 " - pdb=" SG CYS D1479 " distance=2.03 Simple disulfide: pdb=" SG CYS D1482 " - pdb=" SG CYS D1546 " distance=2.04 Simple disulfide: pdb=" SG CYS D1566 " - pdb=" SG CYS D1593 " distance=2.03 Simple disulfide: pdb=" SG CYS D1596 " - pdb=" SG CYS D1610 " distance=2.03 Simple disulfide: pdb=" SG CYS D1613 " - pdb=" SG CYS D1627 " distance=2.03 Simple disulfide: pdb=" SG CYS D1666 " - pdb=" SG CYS D1680 " distance=2.03 Simple disulfide: pdb=" SG CYS D1683 " - pdb=" SG CYS D1697 " distance=2.03 Simple disulfide: pdb=" SG CYS D1700 " - pdb=" SG CYS D1714 " distance=2.03 Simple disulfide: pdb=" SG CYS D1717 " - pdb=" SG CYS D1730 " distance=2.03 Simple disulfide: pdb=" SG CYS D1733 " - pdb=" SG CYS D1747 " distance=2.03 Simple disulfide: pdb=" SG CYS D1750 " - pdb=" SG CYS D1765 " distance=2.03 Simple disulfide: pdb=" SG CYS D1768 " - pdb=" SG CYS D1794 " distance=2.03 Simple disulfide: pdb=" SG CYS D1797 " - pdb=" SG CYS D1811 " distance=2.03 Simple disulfide: pdb=" SG CYS D1814 " - pdb=" SG CYS D1837 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 15.29 Conformation dependent library (CDL) restraints added in 7.8 seconds 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13944 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 163 sheets defined 4.4% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.40 Creating SS restraints... Processing helix chain 'A' and resid 547 through 557 removed outlier: 3.518A pdb=" N TRP A 551 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 683 removed outlier: 3.859A pdb=" N LEU A 680 " --> pdb=" O GLY A 676 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N SER A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 827 removed outlier: 3.776A pdb=" N THR A 825 " --> pdb=" O ALA A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1075 removed outlier: 3.521A pdb=" N TYR A1074 " --> pdb=" O THR A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1284 Processing helix chain 'A' and resid 1339 through 1345 removed outlier: 3.530A pdb=" N THR A1343 " --> pdb=" O THR A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1492 through 1498 Processing helix chain 'A' and resid 1844 through 1848 Processing helix chain 'A' and resid 1959 through 1979 removed outlier: 3.755A pdb=" N GLU A1971 " --> pdb=" O ALA A1967 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 557 removed outlier: 3.594A pdb=" N TRP B 551 " --> pdb=" O ASP B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 673 through 682 removed outlier: 4.231A pdb=" N ALA B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B 680 " --> pdb=" O GLY B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 827 removed outlier: 4.037A pdb=" N THR B 825 " --> pdb=" O ALA B 822 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR B 826 " --> pdb=" O GLY B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1075 removed outlier: 3.527A pdb=" N TYR B1074 " --> pdb=" O THR B1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 1280 through 1284 Processing helix chain 'B' and resid 1339 through 1344 removed outlier: 3.511A pdb=" N THR B1343 " --> pdb=" O THR B1339 " (cutoff:3.500A) Processing helix chain 'B' and resid 1492 through 1498 Processing helix chain 'B' and resid 1844 through 1848 Processing helix chain 'B' and resid 1959 through 1982 removed outlier: 3.501A pdb=" N GLU B1963 " --> pdb=" O LEU B1959 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA B1965 " --> pdb=" O GLU B1961 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU B1966 " --> pdb=" O ASP B1962 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLU B1971 " --> pdb=" O ALA B1967 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU B1980 " --> pdb=" O ASP B1976 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N MET B1981 " --> pdb=" O VAL B1977 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B1982 " --> pdb=" O ASP B1978 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 269 Processing helix chain 'C' and resid 547 through 557 removed outlier: 3.618A pdb=" N TRP C 551 " --> pdb=" O ASP C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 683 removed outlier: 3.765A pdb=" N ALA C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 827 removed outlier: 4.032A pdb=" N THR C 825 " --> pdb=" O ALA C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1075 Processing helix chain 'C' and resid 1280 through 1284 removed outlier: 3.706A pdb=" N SER C1283 " --> pdb=" O GLY C1280 " (cutoff:3.500A) Processing helix chain 'C' and resid 1339 through 1344 Processing helix chain 'C' and resid 1492 through 1498 Processing helix chain 'C' and resid 1507 through 1511 removed outlier: 3.907A pdb=" N LEU C1511 " --> pdb=" O PHE C1508 " (cutoff:3.500A) Processing helix chain 'C' and resid 1844 through 1848 Processing helix chain 'C' and resid 1957 through 1982 removed outlier: 4.132A pdb=" N GLU C1961 " --> pdb=" O LEU C1957 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ASP C1962 " --> pdb=" O SER C1958 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C1965 " --> pdb=" O GLU C1961 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU C1971 " --> pdb=" O ALA C1967 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU C1980 " --> pdb=" O ASP C1976 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET C1981 " --> pdb=" O VAL C1977 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN C1982 " --> pdb=" O ASP C1978 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 557 removed outlier: 3.861A pdb=" N TRP D 551 " --> pdb=" O ASP D 547 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 683 removed outlier: 3.560A pdb=" N TRP D 677 " --> pdb=" O THR D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 822 through 827 removed outlier: 3.931A pdb=" N THR D 825 " --> pdb=" O ALA D 822 " (cutoff:3.500A) Processing helix chain 'D' and resid 1070 through 1075 Processing helix chain 'D' and resid 1280 through 1284 Processing helix chain 'D' and resid 1339 through 1344 Processing helix chain 'D' and resid 1492 through 1498 Processing helix chain 'D' and resid 1844 through 1848 Processing helix chain 'D' and resid 1959 through 1982 removed outlier: 3.552A pdb=" N GLU D1971 " --> pdb=" O ALA D1967 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN D1982 " --> pdb=" O ASP D1978 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 3.519A pdb=" N THR A 67 " --> pdb=" O ASP A 50 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 4.114A pdb=" N ALA A 68 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 70 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 106 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 97 removed outlier: 6.334A pdb=" N LYS A 125 " --> pdb=" O PRO A 148 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A 127 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR A 146 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU A 129 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER A 144 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 131 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 158 through 162 Processing sheet with id=AA5, first strand: chain 'A' and resid 207 through 210 removed outlier: 7.371A pdb=" N MET A 189 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 238 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR A 252 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A 240 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA7, first strand: chain 'A' and resid 308 through 310 Processing sheet with id=AA8, first strand: chain 'A' and resid 385 through 391 Processing sheet with id=AA9, first strand: chain 'A' and resid 421 through 423 Processing sheet with id=AB1, first strand: chain 'A' and resid 498 through 502 removed outlier: 3.741A pdb=" N VAL A 510 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR A 581 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TRP A 514 " --> pdb=" O PHE A 577 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 561 through 565 removed outlier: 3.963A pdb=" N GLU A 530 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 591 " --> pdb=" O PHE A 537 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 625 through 627 removed outlier: 3.585A pdb=" N TRP A 639 " --> pdb=" O PHE A 702 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 687 through 691 removed outlier: 3.718A pdb=" N ILE A 719 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 718 " --> pdb=" O GLY A 732 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY A 732 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 751 through 758 removed outlier: 4.007A pdb=" N ALA A 769 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE A 821 " --> pdb=" O ALA A 769 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 786 through 790 removed outlier: 3.559A pdb=" N LYS A 786 " --> pdb=" O ILE A 808 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 830 through 840 removed outlier: 6.794A pdb=" N ASP A 840 " --> pdb=" O THR A 844 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N THR A 844 " --> pdb=" O ASP A 840 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 865 through 870 Processing sheet with id=AB9, first strand: chain 'A' and resid 876 through 877 removed outlier: 6.771A pdb=" N VAL A 876 " --> pdb=" O ALA A1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 934 through 936 removed outlier: 3.573A pdb=" N HIS A 993 " --> pdb=" O LEU A 965 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1007 through 1013 removed outlier: 5.599A pdb=" N VAL A1008 " --> pdb=" O LEU A1035 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU A1035 " --> pdb=" O VAL A1008 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER A1010 " --> pdb=" O THR A1033 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1101 removed outlier: 4.186A pdb=" N GLN A1049 " --> pdb=" O TYR A1131 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL A1128 " --> pdb=" O ASN A1139 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN A1139 " --> pdb=" O VAL A1128 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU A1130 " --> pdb=" O GLY A1137 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 1094 through 1101 removed outlier: 4.186A pdb=" N GLN A1049 " --> pdb=" O TYR A1131 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A1126 " --> pdb=" O THR A1148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1121 through 1122 removed outlier: 3.509A pdb=" N PHE A1153 " --> pdb=" O PHE A1122 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1187 through 1191 Processing sheet with id=AC7, first strand: chain 'A' and resid 1256 through 1257 Processing sheet with id=AC8, first strand: chain 'A' and resid 1291 through 1292 Processing sheet with id=AC9, first strand: chain 'A' and resid 1324 through 1325 Processing sheet with id=AD1, first strand: chain 'A' and resid 1396 through 1397 Processing sheet with id=AD2, first strand: chain 'A' and resid 1412 through 1413 Processing sheet with id=AD3, first strand: chain 'A' and resid 1421 through 1423 removed outlier: 3.896A pdb=" N GLY A1423 " --> pdb=" O VAL A1434 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A1434 " --> pdb=" O GLY A1423 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1469 through 1470 Processing sheet with id=AD5, first strand: chain 'A' and resid 1486 through 1487 Processing sheet with id=AD6, first strand: chain 'A' and resid 1553 through 1554 Processing sheet with id=AD7, first strand: chain 'A' and resid 1570 through 1571 removed outlier: 3.610A pdb=" N TYR A1594 " --> pdb=" O PHE A1571 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 1600 through 1601 Processing sheet with id=AD9, first strand: chain 'A' and resid 1670 through 1671 Processing sheet with id=AE1, first strand: chain 'A' and resid 1687 through 1688 Processing sheet with id=AE2, first strand: chain 'A' and resid 1704 through 1705 Processing sheet with id=AE3, first strand: chain 'A' and resid 1721 through 1722 Processing sheet with id=AE4, first strand: chain 'A' and resid 1737 through 1738 Processing sheet with id=AE5, first strand: chain 'A' and resid 1754 through 1756 Processing sheet with id=AE6, first strand: chain 'A' and resid 1817 through 1819 Processing sheet with id=AE7, first strand: chain 'A' and resid 1827 through 1828 Processing sheet with id=AE8, first strand: chain 'B' and resid 46 through 47 Processing sheet with id=AE9, first strand: chain 'B' and resid 50 through 51 removed outlier: 3.780A pdb=" N THR B 67 " --> pdb=" O ASP B 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.689A pdb=" N THR B 96 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE B 81 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA B 143 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 157 through 162 Processing sheet with id=AF3, first strand: chain 'B' and resid 207 through 210 removed outlier: 7.339A pdb=" N MET B 189 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU B 238 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR B 252 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE B 240 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 286 through 289 Processing sheet with id=AF5, first strand: chain 'B' and resid 308 through 310 removed outlier: 4.332A pdb=" N ALA B 372 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 385 through 390 Processing sheet with id=AF7, first strand: chain 'B' and resid 403 through 404 removed outlier: 3.606A pdb=" N ASN B 453 " --> pdb=" O ILE B 403 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 419 through 423 Processing sheet with id=AF9, first strand: chain 'B' and resid 495 through 502 removed outlier: 3.854A pdb=" N VAL B 510 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR B 581 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TRP B 514 " --> pdb=" O PHE B 577 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 561 through 565 removed outlier: 4.055A pdb=" N GLU B 530 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 591 " --> pdb=" O PHE B 537 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 561 through 565 removed outlier: 4.055A pdb=" N GLU B 530 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 591 " --> pdb=" O PHE B 537 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY B 590 " --> pdb=" O PHE B 611 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 611 " --> pdb=" O GLY B 590 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 620 through 627 Processing sheet with id=AG4, first strand: chain 'B' and resid 687 through 691 removed outlier: 3.875A pdb=" N ILE B 719 " --> pdb=" O LEU B 659 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 751 through 758 removed outlier: 4.067A pdb=" N ALA B 769 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE B 821 " --> pdb=" O ALA B 769 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AG7, first strand: chain 'B' and resid 830 through 840 removed outlier: 3.722A pdb=" N GLY B 830 " --> pdb=" O VAL B 854 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 854 " --> pdb=" O GLY B 830 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP B 840 " --> pdb=" O THR B 844 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N THR B 844 " --> pdb=" O ASP B 840 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 865 through 870 Processing sheet with id=AG9, first strand: chain 'B' and resid 876 through 877 removed outlier: 6.758A pdb=" N VAL B 876 " --> pdb=" O ALA B1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'B' and resid 934 through 936 removed outlier: 3.675A pdb=" N HIS B 993 " --> pdb=" O LEU B 965 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 1007 through 1013 removed outlier: 6.560A pdb=" N THR B1033 " --> pdb=" O GLU B1009 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N THR B1011 " --> pdb=" O THR B1031 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR B1031 " --> pdb=" O THR B1011 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE B1013 " --> pdb=" O TYR B1029 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR B1029 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'B' and resid 1094 through 1101 removed outlier: 4.094A pdb=" N GLN B1049 " --> pdb=" O TYR B1131 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N VAL B1128 " --> pdb=" O ASN B1139 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASN B1139 " --> pdb=" O VAL B1128 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU B1130 " --> pdb=" O GLY B1137 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 1094 through 1101 removed outlier: 4.094A pdb=" N GLN B1049 " --> pdb=" O TYR B1131 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 1121 through 1122 Processing sheet with id=AH6, first strand: chain 'B' and resid 1188 through 1191 Processing sheet with id=AH7, first strand: chain 'B' and resid 1235 through 1236 Processing sheet with id=AH8, first strand: chain 'B' and resid 1256 through 1257 Processing sheet with id=AH9, first strand: chain 'B' and resid 1291 through 1292 Processing sheet with id=AI1, first strand: chain 'B' and resid 1396 through 1397 Processing sheet with id=AI2, first strand: chain 'B' and resid 1412 through 1413 Processing sheet with id=AI3, first strand: chain 'B' and resid 1421 through 1423 removed outlier: 4.093A pdb=" N GLY B1423 " --> pdb=" O VAL B1434 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL B1434 " --> pdb=" O GLY B1423 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'B' and resid 1469 through 1470 Processing sheet with id=AI5, first strand: chain 'B' and resid 1486 through 1487 Processing sheet with id=AI6, first strand: chain 'B' and resid 1553 through 1554 Processing sheet with id=AI7, first strand: chain 'B' and resid 1570 through 1571 removed outlier: 3.640A pdb=" N TYR B1594 " --> pdb=" O PHE B1571 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'B' and resid 1600 through 1601 Processing sheet with id=AI9, first strand: chain 'B' and resid 1670 through 1671 Processing sheet with id=AJ1, first strand: chain 'B' and resid 1687 through 1688 Processing sheet with id=AJ2, first strand: chain 'B' and resid 1704 through 1705 Processing sheet with id=AJ3, first strand: chain 'B' and resid 1721 through 1722 removed outlier: 3.774A pdb=" N TYR B1722 " --> pdb=" O THR B1731 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N THR B1731 " --> pdb=" O TYR B1722 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'B' and resid 1754 through 1756 Processing sheet with id=AJ5, first strand: chain 'B' and resid 1817 through 1819 Processing sheet with id=AJ6, first strand: chain 'B' and resid 1827 through 1828 Processing sheet with id=AJ7, first strand: chain 'C' and resid 46 through 47 Processing sheet with id=AJ8, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AJ9, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.635A pdb=" N THR C 96 " --> pdb=" O PHE C 81 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'C' and resid 157 through 162 Processing sheet with id=AK2, first strand: chain 'C' and resid 207 through 210 removed outlier: 7.023A pdb=" N MET C 189 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU C 238 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR C 252 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE C 240 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'C' and resid 270 through 271 Processing sheet with id=AK4, first strand: chain 'C' and resid 286 through 289 Processing sheet with id=AK5, first strand: chain 'C' and resid 308 through 311 removed outlier: 4.286A pdb=" N ALA C 372 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'C' and resid 385 through 391 Processing sheet with id=AK7, first strand: chain 'C' and resid 419 through 423 Processing sheet with id=AK8, first strand: chain 'C' and resid 495 through 502 Processing sheet with id=AK9, first strand: chain 'C' and resid 561 through 565 removed outlier: 3.804A pdb=" N GLU C 530 " --> pdb=" O ILE C 565 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR C 599 " --> pdb=" O ILE C 596 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'C' and resid 620 through 622 removed outlier: 3.554A pdb=" N ILE C 644 " --> pdb=" O THR C 621 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'C' and resid 620 through 622 removed outlier: 3.554A pdb=" N ILE C 644 " --> pdb=" O THR C 621 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'C' and resid 687 through 691 Processing sheet with id=AL4, first strand: chain 'C' and resid 751 through 758 removed outlier: 3.909A pdb=" N ALA C 769 " --> pdb=" O ILE C 821 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE C 821 " --> pdb=" O ALA C 769 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'C' and resid 787 through 790 Processing sheet with id=AL6, first strand: chain 'C' and resid 830 through 840 removed outlier: 3.623A pdb=" N GLY C 830 " --> pdb=" O VAL C 854 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP C 840 " --> pdb=" O THR C 844 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR C 844 " --> pdb=" O ASP C 840 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'C' and resid 864 through 870 Processing sheet with id=AL8, first strand: chain 'C' and resid 876 through 877 removed outlier: 6.661A pdb=" N VAL C 876 " --> pdb=" O ALA C1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL8 Processing sheet with id=AL9, first strand: chain 'C' and resid 934 through 938 removed outlier: 3.777A pdb=" N GLN C 901 " --> pdb=" O MET C 938 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'C' and resid 1007 through 1013 removed outlier: 6.560A pdb=" N THR C1033 " --> pdb=" O GLU C1009 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N THR C1011 " --> pdb=" O THR C1031 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR C1031 " --> pdb=" O THR C1011 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ILE C1013 " --> pdb=" O TYR C1029 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR C1029 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'C' and resid 1094 through 1101 removed outlier: 3.923A pdb=" N VAL C1048 " --> pdb=" O MET C1101 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN C1049 " --> pdb=" O TYR C1131 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'C' and resid 1121 through 1122 removed outlier: 3.504A pdb=" N PHE C1153 " --> pdb=" O PHE C1122 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain 'C' and resid 1188 through 1191 Processing sheet with id=AM5, first strand: chain 'C' and resid 1256 through 1257 Processing sheet with id=AM6, first strand: chain 'C' and resid 1291 through 1292 Processing sheet with id=AM7, first strand: chain 'C' and resid 1325 through 1326 Processing sheet with id=AM8, first strand: chain 'C' and resid 1396 through 1397 Processing sheet with id=AM9, first strand: chain 'C' and resid 1412 through 1413 Processing sheet with id=AN1, first strand: chain 'C' and resid 1421 through 1423 removed outlier: 4.151A pdb=" N GLY C1423 " --> pdb=" O VAL C1434 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL C1434 " --> pdb=" O GLY C1423 " (cutoff:3.500A) Processing sheet with id=AN2, first strand: chain 'C' and resid 1469 through 1470 Processing sheet with id=AN3, first strand: chain 'C' and resid 1553 through 1554 Processing sheet with id=AN4, first strand: chain 'C' and resid 1670 through 1671 Processing sheet with id=AN5, first strand: chain 'C' and resid 1687 through 1688 Processing sheet with id=AN6, first strand: chain 'C' and resid 1704 through 1705 Processing sheet with id=AN7, first strand: chain 'C' and resid 1721 through 1722 removed outlier: 3.502A pdb=" N THR C1731 " --> pdb=" O TYR C1722 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'C' and resid 1754 through 1755 Processing sheet with id=AN9, first strand: chain 'C' and resid 1817 through 1819 Processing sheet with id=AO1, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AO2, first strand: chain 'D' and resid 96 through 97 removed outlier: 3.539A pdb=" N THR D 96 " --> pdb=" O PHE D 81 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA D 143 " --> pdb=" O LEU D 131 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'D' and resid 157 through 162 Processing sheet with id=AO4, first strand: chain 'D' and resid 207 through 210 removed outlier: 6.865A pdb=" N MET D 189 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU D 238 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR D 252 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ILE D 240 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'D' and resid 270 through 271 Processing sheet with id=AO6, first strand: chain 'D' and resid 286 through 289 Processing sheet with id=AO7, first strand: chain 'D' and resid 308 through 311 removed outlier: 4.320A pdb=" N ALA D 372 " --> pdb=" O LEU D 363 " (cutoff:3.500A) Processing sheet with id=AO8, first strand: chain 'D' and resid 385 through 391 Processing sheet with id=AO9, first strand: chain 'D' and resid 419 through 420 Processing sheet with id=AP1, first strand: chain 'D' and resid 495 through 502 Processing sheet with id=AP2, first strand: chain 'D' and resid 561 through 564 removed outlier: 3.729A pdb=" N LYS D 591 " --> pdb=" O PHE D 537 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR D 599 " --> pdb=" O ILE D 596 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'D' and resid 620 through 627 removed outlier: 3.555A pdb=" N TRP D 639 " --> pdb=" O PHE D 702 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR D 641 " --> pdb=" O CYS D 700 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'D' and resid 687 through 690 removed outlier: 8.077A pdb=" N LEU D 716 " --> pdb=" O PHE D 733 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE D 733 " --> pdb=" O LEU D 716 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU D 718 " --> pdb=" O VAL D 731 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL D 731 " --> pdb=" O LEU D 718 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'D' and resid 751 through 758 Processing sheet with id=AP6, first strand: chain 'D' and resid 786 through 790 Processing sheet with id=AP7, first strand: chain 'D' and resid 830 through 840 removed outlier: 6.719A pdb=" N ASP D 840 " --> pdb=" O THR D 844 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR D 844 " --> pdb=" O ASP D 840 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'D' and resid 864 through 870 Processing sheet with id=AP9, first strand: chain 'D' and resid 876 through 877 removed outlier: 6.636A pdb=" N VAL D 876 " --> pdb=" O ALA D1002 " (cutoff:3.500A) No H-bonds generated for sheet with id=AP9 Processing sheet with id=AQ1, first strand: chain 'D' and resid 934 through 936 removed outlier: 3.792A pdb=" N VAL D 934 " --> pdb=" O CYS D 905 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS D 993 " --> pdb=" O LEU D 965 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'D' and resid 1007 through 1013 removed outlier: 6.575A pdb=" N THR D1033 " --> pdb=" O GLU D1009 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR D1011 " --> pdb=" O THR D1031 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR D1031 " --> pdb=" O THR D1011 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE D1013 " --> pdb=" O TYR D1029 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TYR D1029 " --> pdb=" O ILE D1013 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'D' and resid 1094 through 1101 removed outlier: 3.680A pdb=" N VAL D1048 " --> pdb=" O MET D1101 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLN D1049 " --> pdb=" O TYR D1131 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL D1128 " --> pdb=" O ASN D1139 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ASN D1139 " --> pdb=" O VAL D1128 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N GLU D1130 " --> pdb=" O GLY D1137 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'D' and resid 1121 through 1122 removed outlier: 3.665A pdb=" N PHE D1153 " --> pdb=" O PHE D1122 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain 'D' and resid 1187 through 1191 Processing sheet with id=AQ6, first strand: chain 'D' and resid 1291 through 1292 removed outlier: 3.513A pdb=" N LEU D1302 " --> pdb=" O PHE D1292 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'D' and resid 1308 through 1309 Processing sheet with id=AQ8, first strand: chain 'D' and resid 1396 through 1397 Processing sheet with id=AQ9, first strand: chain 'D' and resid 1412 through 1413 Processing sheet with id=AR1, first strand: chain 'D' and resid 1421 through 1423 removed outlier: 3.777A pdb=" N GLY D1423 " --> pdb=" O VAL D1434 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N VAL D1434 " --> pdb=" O GLY D1423 " (cutoff:3.500A) Processing sheet with id=AR2, first strand: chain 'D' and resid 1469 through 1470 removed outlier: 3.573A pdb=" N PHE D1470 " --> pdb=" O GLN D1480 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'D' and resid 1553 through 1554 Processing sheet with id=AR4, first strand: chain 'D' and resid 1570 through 1571 Processing sheet with id=AR5, first strand: chain 'D' and resid 1645 through 1647 removed outlier: 3.624A pdb=" N ILE D1652 " --> pdb=" O ASN D1647 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'D' and resid 1687 through 1688 Processing sheet with id=AR7, first strand: chain 'D' and resid 1704 through 1705 Processing sheet with id=AR8, first strand: chain 'D' and resid 1721 through 1722 removed outlier: 3.582A pdb=" N THR D1731 " --> pdb=" O TYR D1722 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'D' and resid 1754 through 1756 Processing sheet with id=AS1, first strand: chain 'D' and resid 1827 through 1828 removed outlier: 3.562A pdb=" N LYS D1838 " --> pdb=" O CYS D1828 " (cutoff:3.500A) 1099 hydrogen bonds defined for protein. 2655 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: 24.92 Time building geometry restraints manager: 17.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.53 - 0.92: 5 0.92 - 1.31: 8953 1.31 - 1.69: 46889 1.69 - 2.08: 418 2.08 - 2.47: 3 Bond restraints: 56268 Sorted by residual: bond pdb=" CG PRO B 396 " pdb=" CD PRO B 396 " ideal model delta sigma weight residual 1.503 0.532 0.971 3.40e-02 8.65e+02 8.16e+02 bond pdb=" CG PRO C 396 " pdb=" CD PRO C 396 " ideal model delta sigma weight residual 1.503 0.601 0.902 3.40e-02 8.65e+02 7.04e+02 bond pdb=" CG PRO D1769 " pdb=" CD PRO D1769 " ideal model delta sigma weight residual 1.503 0.793 0.710 3.40e-02 8.65e+02 4.36e+02 bond pdb=" CG PRO B1769 " pdb=" CD PRO B1769 " ideal model delta sigma weight residual 1.503 0.816 0.687 3.40e-02 8.65e+02 4.09e+02 bond pdb=" CB PRO A 396 " pdb=" CG PRO A 396 " ideal model delta sigma weight residual 1.492 2.466 -0.974 5.00e-02 4.00e+02 3.80e+02 ... (remaining 56263 not shown) Histogram of bond angle deviations from ideal: 0.04 - 30.60: 1 30.60 - 61.15: 2 61.15 - 91.71: 27 91.71 - 122.27: 66576 122.27 - 152.82: 10966 Bond angle restraints: 77572 Sorted by residual: angle pdb=" CB PRO A 396 " pdb=" CG PRO A 396 " pdb=" CD PRO A 396 " ideal model delta sigma weight residual 106.10 0.04 106.06 3.20e+00 9.77e-02 1.10e+03 angle pdb=" N PRO D1769 " pdb=" CD PRO D1769 " pdb=" CG PRO D1769 " ideal model delta sigma weight residual 103.20 62.81 40.39 1.50e+00 4.44e-01 7.25e+02 angle pdb=" CB PRO B1769 " pdb=" CG PRO B1769 " pdb=" CD PRO B1769 " ideal model delta sigma weight residual 106.10 36.95 69.15 3.20e+00 9.77e-02 4.67e+02 angle pdb=" CA PRO D1769 " pdb=" CB PRO D1769 " pdb=" CG PRO D1769 " ideal model delta sigma weight residual 104.50 64.99 39.51 1.90e+00 2.77e-01 4.32e+02 angle pdb=" N PRO B1769 " pdb=" CD PRO B1769 " pdb=" CG PRO B1769 " ideal model delta sigma weight residual 103.20 74.66 28.54 1.50e+00 4.44e-01 3.62e+02 ... (remaining 77567 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.29: 32024 24.29 - 48.58: 1599 48.58 - 72.87: 184 72.87 - 97.16: 43 97.16 - 121.45: 2 Dihedral angle restraints: 33852 sinusoidal: 12056 harmonic: 21796 Sorted by residual: dihedral pdb=" CA THR B 393 " pdb=" C THR B 393 " pdb=" N ALA B 394 " pdb=" CA ALA B 394 " ideal model delta harmonic sigma weight residual -180.00 -127.58 -52.42 0 5.00e+00 4.00e-02 1.10e+02 dihedral pdb=" CB CYS C1361 " pdb=" SG CYS C1361 " pdb=" SG CYS C1389 " pdb=" CB CYS C1389 " ideal model delta sinusoidal sigma weight residual 93.00 -177.50 -89.50 1 1.00e+01 1.00e-02 9.52e+01 dihedral pdb=" CA ASP A 395 " pdb=" C ASP A 395 " pdb=" N PRO A 396 " pdb=" CA PRO A 396 " ideal model delta harmonic sigma weight residual 180.00 132.41 47.59 0 5.00e+00 4.00e-02 9.06e+01 ... (remaining 33849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 9142 0.136 - 0.273: 63 0.273 - 0.409: 6 0.409 - 0.545: 0 0.545 - 0.682: 1 Chirality restraints: 9212 Sorted by residual: chirality pdb=" CA PRO B 396 " pdb=" N PRO B 396 " pdb=" C PRO B 396 " pdb=" CB PRO B 396 " both_signs ideal model delta sigma weight residual False 2.72 2.04 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA PRO A1062 " pdb=" N PRO A1062 " pdb=" C PRO A1062 " pdb=" CB PRO A1062 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.35 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA PRO B1062 " pdb=" N PRO B1062 " pdb=" C PRO B1062 " pdb=" CB PRO B1062 " both_signs ideal model delta sigma weight residual False 2.72 2.36 0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 9209 not shown) Planarity restraints: 10148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B1061 " -0.193 5.00e-02 4.00e+02 2.50e-01 1.00e+02 pdb=" N PRO B1062 " 0.424 5.00e-02 4.00e+02 pdb=" CA PRO B1062 " -0.176 5.00e-02 4.00e+02 pdb=" CD PRO B1062 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A1061 " 0.192 5.00e-02 4.00e+02 2.50e-01 9.99e+01 pdb=" N PRO A1062 " -0.423 5.00e-02 4.00e+02 pdb=" CA PRO A1062 " 0.174 5.00e-02 4.00e+02 pdb=" CD PRO A1062 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C1061 " -0.192 5.00e-02 4.00e+02 2.50e-01 9.97e+01 pdb=" N PRO C1062 " 0.423 5.00e-02 4.00e+02 pdb=" CA PRO C1062 " -0.174 5.00e-02 4.00e+02 pdb=" CD PRO C1062 " -0.057 5.00e-02 4.00e+02 ... (remaining 10145 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1093 2.66 - 3.22: 53902 3.22 - 3.78: 81792 3.78 - 4.34: 106581 4.34 - 4.90: 173731 Nonbonded interactions: 417099 Sorted by model distance: nonbonded pdb=" OD1 ASP C 401 " pdb=" N THR C 402 " model vdw 2.101 2.520 nonbonded pdb=" OD1 ASP B 401 " pdb=" N THR B 402 " model vdw 2.107 2.520 nonbonded pdb=" O THR A 828 " pdb=" OH TYR A 832 " model vdw 2.109 2.440 nonbonded pdb=" O THR B 828 " pdb=" OH TYR B 832 " model vdw 2.114 2.440 nonbonded pdb=" O THR D 828 " pdb=" OH TYR D 832 " model vdw 2.116 2.440 ... (remaining 417094 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.350 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: 0.070 Extract box with map and model: 8.540 Check model and map are aligned: 0.750 Set scattering table: 0.500 Process input model: 115.460 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.230 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:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.974 56268 Z= 0.738 Angle : 1.128 106.059 77572 Z= 0.587 Chirality : 0.046 0.682 9212 Planarity : 0.010 0.250 10148 Dihedral : 13.615 121.454 19560 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 1.05 % Allowed : 7.18 % Favored : 91.77 % Rotamer: Outliers : 0.57 % Allowed : 16.35 % Favored : 83.08 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.09), residues: 7536 helix: -2.06 (0.29), residues: 272 sheet: -1.49 (0.11), residues: 1916 loop : -2.56 (0.08), residues: 5348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 312 HIS 0.012 0.001 HIS C1272 PHE 0.021 0.002 PHE C 702 TYR 0.025 0.001 TYR D1670 ARG 0.009 0.001 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 340 time to evaluate : 4.369 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: A 966 MET cc_start: 0.8887 (mmm) cc_final: 0.6996 (mtm) REVERT: A 1220 THR cc_start: 0.8531 (p) cc_final: 0.8295 (t) REVERT: A 1728 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7927 (tm-30) REVERT: B 537 PHE cc_start: 0.8141 (m-80) cc_final: 0.7880 (m-80) REVERT: B 612 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7652 (tp-100) REVERT: B 1208 TYR cc_start: 0.6606 (m-80) cc_final: 0.6364 (m-10) REVERT: B 1456 THR cc_start: 0.8997 (m) cc_final: 0.8718 (p) REVERT: B 1459 MET cc_start: 0.8252 (pmm) cc_final: 0.7807 (pmm) REVERT: B 1515 THR cc_start: 0.6977 (m) cc_final: 0.6712 (p) REVERT: B 1719 MET cc_start: 0.8924 (tpp) cc_final: 0.8683 (tpt) REVERT: B 1960 MET cc_start: 0.7363 (tpp) cc_final: 0.7002 (tmm) REVERT: C 519 GLN cc_start: 0.7364 (mm-40) cc_final: 0.7140 (mp10) REVERT: C 966 MET cc_start: 0.7929 (tpp) cc_final: 0.6919 (mtt) REVERT: C 1441 LEU cc_start: 0.9154 (pt) cc_final: 0.8860 (pp) REVERT: C 1801 PHE cc_start: 0.8096 (m-10) cc_final: 0.7759 (m-10) REVERT: D 209 ILE cc_start: 0.9417 (pt) cc_final: 0.8877 (mt) REVERT: D 437 MET cc_start: 0.7806 (tpp) cc_final: 0.7088 (tpp) REVERT: D 1258 LEU cc_start: 0.9375 (tt) cc_final: 0.8851 (mt) REVERT: D 1613 CYS cc_start: 0.2349 (OUTLIER) cc_final: 0.1122 (p) REVERT: D 1844 SER cc_start: 0.8649 (m) cc_final: 0.7724 (p) outliers start: 34 outliers final: 10 residues processed: 370 average time/residue: 0.4625 time to fit residues: 305.3655 Evaluate side-chains 230 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 218 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 519 GLN Chi-restraints excluded: chain A residue 612 GLN Chi-restraints excluded: chain A residue 1610 CYS Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 612 GLN Chi-restraints excluded: chain B residue 1167 ASN Chi-restraints excluded: chain B residue 1178 PHE Chi-restraints excluded: chain B residue 1677 THR Chi-restraints excluded: chain C residue 162 GLN Chi-restraints excluded: chain D residue 1558 ASP Chi-restraints excluded: chain D residue 1613 CYS Chi-restraints excluded: chain D residue 1769 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 638 optimal weight: 5.9990 chunk 573 optimal weight: 0.0470 chunk 317 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 386 optimal weight: 7.9990 chunk 306 optimal weight: 2.9990 chunk 592 optimal weight: 30.0000 chunk 229 optimal weight: 8.9990 chunk 360 optimal weight: 9.9990 chunk 441 optimal weight: 4.9990 chunk 686 optimal weight: 7.9990 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1602 ASN ** A1810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1212 GLN ** B1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 685 ASN D 797 GLN D1487 ASN D1563 GLN D1672 GLN D1823 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 56268 Z= 0.230 Angle : 0.680 15.445 77572 Z= 0.343 Chirality : 0.043 0.214 9212 Planarity : 0.006 0.098 10148 Dihedral : 5.591 57.451 8079 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.78 % Favored : 91.40 % Rotamer: Outliers : 2.81 % Allowed : 15.37 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.09), residues: 7536 helix: -1.33 (0.30), residues: 284 sheet: -1.02 (0.11), residues: 1852 loop : -2.15 (0.08), residues: 5400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1614 HIS 0.007 0.001 HIS C1272 PHE 0.024 0.001 PHE B 611 TYR 0.016 0.001 TYR A1017 ARG 0.007 0.000 ARG B 517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 229 time to evaluate : 4.555 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: A 642 ASN cc_start: 0.6857 (p0) cc_final: 0.6591 (p0) REVERT: A 1101 MET cc_start: 0.8509 (ttp) cc_final: 0.8153 (tpp) REVERT: A 1189 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8962 (tt) REVERT: A 1220 THR cc_start: 0.8450 (p) cc_final: 0.8249 (t) REVERT: B 47 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9187 (mt) REVERT: B 290 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8824 (mp10) REVERT: B 876 VAL cc_start: 0.9362 (OUTLIER) cc_final: 0.9127 (m) REVERT: B 999 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7992 (tpt) REVERT: B 1456 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8643 (p) REVERT: B 1459 MET cc_start: 0.8315 (pmm) cc_final: 0.7801 (pmm) REVERT: B 1515 THR cc_start: 0.6968 (m) cc_final: 0.6746 (p) REVERT: B 1539 MET cc_start: 0.8828 (mmp) cc_final: 0.6892 (mpp) REVERT: C 271 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8438 (mt) REVERT: C 437 MET cc_start: 0.7885 (tpt) cc_final: 0.7624 (mmm) REVERT: C 611 PHE cc_start: 0.3070 (OUTLIER) cc_final: 0.1645 (m-10) REVERT: C 757 LEU cc_start: 0.9052 (tp) cc_final: 0.8680 (tp) REVERT: C 903 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8889 (tt) REVERT: C 966 MET cc_start: 0.8104 (tpp) cc_final: 0.6972 (mtt) REVERT: C 1080 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8447 (p) REVERT: C 1393 GLU cc_start: 0.8773 (pm20) cc_final: 0.8471 (pm20) REVERT: C 1441 LEU cc_start: 0.9144 (pt) cc_final: 0.8846 (pp) REVERT: C 1801 PHE cc_start: 0.8181 (m-10) cc_final: 0.7904 (m-10) REVERT: D 437 MET cc_start: 0.7964 (tpp) cc_final: 0.7224 (tpp) REVERT: D 1101 MET cc_start: 0.7916 (ttp) cc_final: 0.7108 (tmm) REVERT: D 1490 MET cc_start: 0.8712 (pmm) cc_final: 0.8181 (pmm) REVERT: D 1567 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.8531 (mmtp) REVERT: D 1694 LEU cc_start: 0.8919 (mt) cc_final: 0.8636 (mp) REVERT: D 1844 SER cc_start: 0.8994 (m) cc_final: 0.8545 (t) outliers start: 167 outliers final: 60 residues processed: 384 average time/residue: 0.4916 time to fit residues: 340.3608 Evaluate side-chains 269 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 198 time to evaluate : 4.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1189 ILE Chi-restraints excluded: chain A residue 1227 ARG Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 876 VAL Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1167 ASN Chi-restraints excluded: chain B residue 1172 VAL Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1265 SER Chi-restraints excluded: chain B residue 1377 SER Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1456 THR Chi-restraints excluded: chain B residue 1461 VAL Chi-restraints excluded: chain B residue 1562 ILE Chi-restraints excluded: chain B residue 1617 SER Chi-restraints excluded: chain B residue 1643 ASN Chi-restraints excluded: chain B residue 1677 THR Chi-restraints excluded: chain B residue 1678 THR Chi-restraints excluded: chain B residue 1721 THR Chi-restraints excluded: chain B residue 1731 THR Chi-restraints excluded: chain B residue 1829 THR Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain C residue 673 THR Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 903 ILE Chi-restraints excluded: chain C residue 1052 CYS Chi-restraints excluded: chain C residue 1080 VAL Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1472 SER Chi-restraints excluded: chain C residue 1603 ASP Chi-restraints excluded: chain C residue 1731 THR Chi-restraints excluded: chain C residue 1834 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain D residue 1052 CYS Chi-restraints excluded: chain D residue 1084 VAL Chi-restraints excluded: chain D residue 1213 CYS Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1558 ASP Chi-restraints excluded: chain D residue 1567 LYS Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1748 THR Chi-restraints excluded: chain D residue 1811 CYS Chi-restraints excluded: chain D residue 1812 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 381 optimal weight: 7.9990 chunk 213 optimal weight: 20.0000 chunk 571 optimal weight: 20.0000 chunk 467 optimal weight: 30.0000 chunk 189 optimal weight: 20.0000 chunk 687 optimal weight: 30.0000 chunk 742 optimal weight: 20.0000 chunk 612 optimal weight: 40.0000 chunk 682 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 chunk 551 optimal weight: 9.9990 overall best weight: 12.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 GLN A 847 HIS A1025 ASN A1379 ASN ** A1706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 847 HIS B1049 GLN ** B1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1597 GLN ** B1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1706 GLN ** B1757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN ** C1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1212 GLN ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1810 GLN D1823 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 56268 Z= 0.468 Angle : 0.776 13.754 77572 Z= 0.399 Chirality : 0.045 0.232 9212 Planarity : 0.007 0.083 10148 Dihedral : 6.149 54.850 8060 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.74 % Allowed : 9.75 % Favored : 89.50 % Rotamer: Outliers : 4.28 % Allowed : 15.19 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 1.26 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.09), residues: 7536 helix: -1.24 (0.30), residues: 280 sheet: -0.85 (0.12), residues: 1796 loop : -2.13 (0.08), residues: 5460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B1614 HIS 0.012 0.002 HIS A 993 PHE 0.041 0.002 PHE B1605 TYR 0.032 0.002 TYR B1208 ARG 0.007 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 196 time to evaluate : 4.413 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: A 613 VAL cc_start: 0.0047 (OUTLIER) cc_final: -0.0407 (t) REVERT: A 642 ASN cc_start: 0.6647 (p0) cc_final: 0.6398 (p0) REVERT: A 723 PHE cc_start: 0.6302 (OUTLIER) cc_final: 0.5970 (m-10) REVERT: A 938 MET cc_start: 0.7882 (tpt) cc_final: 0.7531 (tpt) REVERT: A 1539 MET cc_start: 0.7652 (mmp) cc_final: 0.7451 (mmp) REVERT: A 1721 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8209 (p) REVERT: A 1809 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7473 (ptm160) REVERT: B 290 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8882 (mm-40) REVERT: B 723 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.5390 (m-80) REVERT: B 938 MET cc_start: 0.8002 (tpt) cc_final: 0.7726 (tpt) REVERT: B 1456 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8755 (p) REVERT: B 1459 MET cc_start: 0.8314 (pmm) cc_final: 0.7682 (pmm) REVERT: B 1511 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8751 (pp) REVERT: C 271 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8589 (mt) REVERT: C 387 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8940 (pp) REVERT: C 437 MET cc_start: 0.7800 (tpt) cc_final: 0.7404 (mmm) REVERT: C 611 PHE cc_start: 0.2688 (OUTLIER) cc_final: 0.2168 (m-80) REVERT: C 757 LEU cc_start: 0.9236 (tp) cc_final: 0.8914 (tp) REVERT: C 966 MET cc_start: 0.8553 (tpp) cc_final: 0.7049 (mtt) REVERT: C 1108 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8829 (p) REVERT: C 1393 GLU cc_start: 0.9179 (pm20) cc_final: 0.8919 (pm20) REVERT: C 1441 LEU cc_start: 0.9317 (pt) cc_final: 0.9055 (pp) REVERT: C 1497 MET cc_start: 0.9571 (mmt) cc_final: 0.9352 (mmt) REVERT: C 1691 GLN cc_start: 0.8341 (mp10) cc_final: 0.8100 (pm20) REVERT: C 1801 PHE cc_start: 0.8389 (m-10) cc_final: 0.8037 (m-80) REVERT: D 209 ILE cc_start: 0.9568 (OUTLIER) cc_final: 0.8950 (mt) REVERT: D 471 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8222 (t70) REVERT: D 719 ILE cc_start: 0.0174 (OUTLIER) cc_final: -0.0091 (mt) REVERT: D 1101 MET cc_start: 0.8112 (ttp) cc_final: 0.7619 (tmm) REVERT: D 1379 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7533 (p0) REVERT: D 1447 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8066 (mt0) REVERT: D 1490 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8403 (pmm) REVERT: D 1567 LYS cc_start: 0.9501 (OUTLIER) cc_final: 0.8472 (mmtt) REVERT: D 1694 LEU cc_start: 0.9115 (mt) cc_final: 0.8730 (mt) outliers start: 255 outliers final: 130 residues processed: 436 average time/residue: 0.4423 time to fit residues: 349.4822 Evaluate side-chains 328 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 179 time to evaluate : 4.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 685 ASN Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 810 VAL Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1081 THR Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1292 PHE Chi-restraints excluded: chain A residue 1293 GLN Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1389 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1447 GLN Chi-restraints excluded: chain A residue 1645 THR Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1697 CYS Chi-restraints excluded: chain A residue 1721 THR Chi-restraints excluded: chain A residue 1748 THR Chi-restraints excluded: chain A residue 1765 CYS Chi-restraints excluded: chain A residue 1808 VAL Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 489 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 575 ILE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 999 MET Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain B residue 1167 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1172 VAL Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1299 THR Chi-restraints excluded: chain B residue 1377 SER Chi-restraints excluded: chain B residue 1379 ASN Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1456 THR Chi-restraints excluded: chain B residue 1461 VAL Chi-restraints excluded: chain B residue 1511 LEU Chi-restraints excluded: chain B residue 1549 ASN Chi-restraints excluded: chain B residue 1558 ASP Chi-restraints excluded: chain B residue 1643 ASN Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1677 THR Chi-restraints excluded: chain B residue 1731 THR Chi-restraints excluded: chain B residue 1766 ARG Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1788 PHE Chi-restraints excluded: chain B residue 1809 ARG Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1829 THR Chi-restraints excluded: chain B residue 1844 SER Chi-restraints excluded: chain B residue 1926 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 229 ASN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 673 THR Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 716 LEU Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 836 VAL Chi-restraints excluded: chain C residue 913 THR Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1108 VAL Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1472 SER Chi-restraints excluded: chain C residue 1549 ASN Chi-restraints excluded: chain C residue 1629 ILE Chi-restraints excluded: chain C residue 1834 SER Chi-restraints excluded: chain C residue 1960 MET Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 402 THR Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 414 SER Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1213 CYS Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1327 THR Chi-restraints excluded: chain D residue 1328 ASP Chi-restraints excluded: chain D residue 1332 THR Chi-restraints excluded: chain D residue 1349 SER Chi-restraints excluded: chain D residue 1379 ASN Chi-restraints excluded: chain D residue 1447 GLN Chi-restraints excluded: chain D residue 1490 MET Chi-restraints excluded: chain D residue 1501 VAL Chi-restraints excluded: chain D residue 1558 ASP Chi-restraints excluded: chain D residue 1567 LYS Chi-restraints excluded: chain D residue 1629 ILE Chi-restraints excluded: chain D residue 1648 THR Chi-restraints excluded: chain D residue 1664 THR Chi-restraints excluded: chain D residue 1678 THR Chi-restraints excluded: chain D residue 1721 THR Chi-restraints excluded: chain D residue 1748 THR Chi-restraints excluded: chain D residue 1804 ASP Chi-restraints excluded: chain D residue 1812 THR Chi-restraints excluded: chain D residue 1823 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 679 optimal weight: 0.6980 chunk 517 optimal weight: 2.9990 chunk 356 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 328 optimal weight: 5.9990 chunk 461 optimal weight: 9.9990 chunk 690 optimal weight: 20.0000 chunk 730 optimal weight: 8.9990 chunk 360 optimal weight: 7.9990 chunk 654 optimal weight: 30.0000 chunk 196 optimal weight: 10.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1701 GLN A1706 GLN ** A1810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 847 HIS B1095 GLN ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1506 ASN ** B1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN C1061 ASN C1238 ASN ** C1602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1972 GLN D1487 ASN ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1672 GLN D1783 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 56268 Z= 0.244 Angle : 0.663 16.017 77572 Z= 0.331 Chirality : 0.042 0.270 9212 Planarity : 0.006 0.076 10148 Dihedral : 5.650 53.954 8060 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.74 % Allowed : 7.78 % Favored : 91.48 % Rotamer: Outliers : 3.44 % Allowed : 17.10 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.09), residues: 7536 helix: -1.02 (0.30), residues: 284 sheet: -0.66 (0.12), residues: 1804 loop : -1.93 (0.08), residues: 5448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B1614 HIS 0.006 0.001 HIS A1272 PHE 0.020 0.001 PHE A 504 TYR 0.021 0.001 TYR D1325 ARG 0.005 0.001 ARG B1359 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 194 time to evaluate : 4.431 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: A 723 PHE cc_start: 0.6343 (OUTLIER) cc_final: 0.6064 (m-10) REVERT: A 1614 TRP cc_start: 0.4621 (OUTLIER) cc_final: 0.3249 (p90) REVERT: A 1721 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8333 (p) REVERT: A 1809 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.7491 (ptm160) REVERT: B 290 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8817 (mp10) REVERT: B 723 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.5465 (m-80) REVERT: B 1456 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8685 (p) REVERT: B 1459 MET cc_start: 0.8235 (pmm) cc_final: 0.7605 (pmm) REVERT: B 1539 MET cc_start: 0.8796 (mmp) cc_final: 0.6326 (mpp) REVERT: B 1766 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8647 (ptp-110) REVERT: C 271 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8507 (mt) REVERT: C 437 MET cc_start: 0.7568 (tpt) cc_final: 0.7212 (mmm) REVERT: C 611 PHE cc_start: 0.2287 (OUTLIER) cc_final: 0.1753 (m-80) REVERT: C 757 LEU cc_start: 0.9211 (tp) cc_final: 0.9004 (tp) REVERT: C 966 MET cc_start: 0.8408 (tpp) cc_final: 0.7075 (mtt) REVERT: C 1080 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8447 (p) REVERT: C 1801 PHE cc_start: 0.8413 (m-10) cc_final: 0.8076 (m-80) REVERT: D 84 ASP cc_start: 0.9167 (t0) cc_final: 0.8949 (t0) REVERT: D 437 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7152 (tpt) REVERT: D 471 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8302 (t70) REVERT: D 719 ILE cc_start: -0.0149 (OUTLIER) cc_final: -0.0395 (mt) REVERT: D 1101 MET cc_start: 0.8112 (ttp) cc_final: 0.7604 (tmm) REVERT: D 1490 MET cc_start: 0.8795 (pmm) cc_final: 0.8266 (pmm) REVERT: D 1567 LYS cc_start: 0.9487 (OUTLIER) cc_final: 0.8395 (mmtt) REVERT: D 1694 LEU cc_start: 0.9145 (mt) cc_final: 0.8779 (mt) outliers start: 205 outliers final: 127 residues processed: 387 average time/residue: 0.4391 time to fit residues: 309.5783 Evaluate side-chains 314 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 172 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 522 LYS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 685 ASN Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 723 PHE Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1389 CYS Chi-restraints excluded: chain A residue 1614 TRP Chi-restraints excluded: chain A residue 1645 THR Chi-restraints excluded: chain A residue 1721 THR Chi-restraints excluded: chain A residue 1748 THR Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1829 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 290 GLN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1167 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1172 VAL Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1201 VAL Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1377 SER Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1439 THR Chi-restraints excluded: chain B residue 1456 THR Chi-restraints excluded: chain B residue 1461 VAL Chi-restraints excluded: chain B residue 1643 ASN Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1677 THR Chi-restraints excluded: chain B residue 1721 THR Chi-restraints excluded: chain B residue 1731 THR Chi-restraints excluded: chain B residue 1766 ARG Chi-restraints excluded: chain B residue 1777 SER Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1788 PHE Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1829 THR Chi-restraints excluded: chain B residue 1844 SER Chi-restraints excluded: chain B residue 1926 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 673 THR Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 807 ASP Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1080 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1357 THR Chi-restraints excluded: chain C residue 1379 ASN Chi-restraints excluded: chain C residue 1439 THR Chi-restraints excluded: chain C residue 1472 SER Chi-restraints excluded: chain C residue 1586 LEU Chi-restraints excluded: chain C residue 1629 ILE Chi-restraints excluded: chain C residue 1731 THR Chi-restraints excluded: chain C residue 1843 LEU Chi-restraints excluded: chain C residue 1926 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 118 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 229 ASN Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 719 ILE Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain D residue 1213 CYS Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1328 ASP Chi-restraints excluded: chain D residue 1330 VAL Chi-restraints excluded: chain D residue 1332 THR Chi-restraints excluded: chain D residue 1349 SER Chi-restraints excluded: chain D residue 1487 ASN Chi-restraints excluded: chain D residue 1512 ARG Chi-restraints excluded: chain D residue 1549 ASN Chi-restraints excluded: chain D residue 1558 ASP Chi-restraints excluded: chain D residue 1567 LYS Chi-restraints excluded: chain D residue 1664 THR Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1721 THR Chi-restraints excluded: chain D residue 1748 THR Chi-restraints excluded: chain D residue 1804 ASP Chi-restraints excluded: chain D residue 1812 THR Chi-restraints excluded: chain D residue 1823 ASN Chi-restraints excluded: chain D residue 1834 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 608 optimal weight: 20.0000 chunk 414 optimal weight: 40.0000 chunk 10 optimal weight: 9.9990 chunk 544 optimal weight: 20.0000 chunk 301 optimal weight: 5.9990 chunk 623 optimal weight: 30.0000 chunk 505 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 373 optimal weight: 0.0270 chunk 655 optimal weight: 30.0000 chunk 184 optimal weight: 0.0370 overall best weight: 5.2122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 476 ASN B 847 HIS ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 ASN C1602 ASN ** C1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1691 GLN ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1783 ASN D1823 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 56268 Z= 0.238 Angle : 0.645 16.059 77572 Z= 0.321 Chirality : 0.042 0.230 9212 Planarity : 0.006 0.079 10148 Dihedral : 5.503 54.232 8060 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.70 % Allowed : 8.51 % Favored : 90.79 % Rotamer: Outliers : 3.44 % Allowed : 17.22 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 1.01 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.09), residues: 7536 helix: -0.76 (0.31), residues: 284 sheet: -0.54 (0.12), residues: 1800 loop : -1.83 (0.08), residues: 5452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 771 HIS 0.006 0.001 HIS A1272 PHE 0.019 0.001 PHE C 504 TYR 0.020 0.001 TYR D1325 ARG 0.005 0.000 ARG D1622 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 176 time to evaluate : 4.436 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: A 189 MET cc_start: 0.9023 (mtm) cc_final: 0.8422 (mpp) REVERT: A 1101 MET cc_start: 0.8585 (mmt) cc_final: 0.7864 (mmt) REVERT: A 1614 TRP cc_start: 0.4791 (OUTLIER) cc_final: 0.3293 (p90) REVERT: A 1721 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8315 (p) REVERT: A 1809 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7444 (ptm160) REVERT: B 611 PHE cc_start: 0.4960 (OUTLIER) cc_final: 0.3707 (m-80) REVERT: B 723 PHE cc_start: 0.6275 (OUTLIER) cc_final: 0.5365 (m-80) REVERT: B 1456 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8711 (p) REVERT: B 1459 MET cc_start: 0.8224 (pmm) cc_final: 0.7601 (pmm) REVERT: B 1766 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8674 (ptp-110) REVERT: C 271 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8484 (mt) REVERT: C 437 MET cc_start: 0.7655 (tpt) cc_final: 0.7237 (mmm) REVERT: C 611 PHE cc_start: 0.2429 (OUTLIER) cc_final: 0.1936 (m-80) REVERT: C 792 MET cc_start: 0.7104 (ppp) cc_final: 0.6850 (ppp) REVERT: C 966 MET cc_start: 0.8456 (tpp) cc_final: 0.7024 (mtt) REVERT: C 1080 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8480 (p) REVERT: C 1493 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8952 (ttm170) REVERT: C 1497 MET cc_start: 0.9492 (mmt) cc_final: 0.9274 (mmp) REVERT: C 1801 PHE cc_start: 0.8465 (m-10) cc_final: 0.8134 (m-80) REVERT: D 84 ASP cc_start: 0.9200 (t0) cc_final: 0.8981 (t0) REVERT: D 437 MET cc_start: 0.7622 (OUTLIER) cc_final: 0.6985 (tpt) REVERT: D 691 MET cc_start: 0.4488 (ptp) cc_final: 0.4244 (ptp) REVERT: D 757 LEU cc_start: 0.8596 (tp) cc_final: 0.7807 (pt) REVERT: D 1101 MET cc_start: 0.8107 (ttp) cc_final: 0.7588 (tmm) REVERT: D 1379 ASN cc_start: 0.7867 (OUTLIER) cc_final: 0.7407 (p0) REVERT: D 1447 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8042 (mt0) REVERT: D 1567 LYS cc_start: 0.9490 (OUTLIER) cc_final: 0.8411 (mmtt) REVERT: D 1614 TRP cc_start: 0.4913 (OUTLIER) cc_final: 0.4112 (p90) REVERT: D 1694 LEU cc_start: 0.9121 (mt) cc_final: 0.8765 (mt) outliers start: 205 outliers final: 140 residues processed: 368 average time/residue: 0.4305 time to fit residues: 291.5207 Evaluate side-chains 325 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 169 time to evaluate : 4.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 522 LYS Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1389 CYS Chi-restraints excluded: chain A residue 1447 GLN Chi-restraints excluded: chain A residue 1614 TRP Chi-restraints excluded: chain A residue 1645 THR Chi-restraints excluded: chain A residue 1697 CYS Chi-restraints excluded: chain A residue 1721 THR Chi-restraints excluded: chain A residue 1748 THR Chi-restraints excluded: chain A residue 1765 CYS Chi-restraints excluded: chain A residue 1788 PHE Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1829 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain B residue 1167 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1172 VAL Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1299 THR Chi-restraints excluded: chain B residue 1328 ASP Chi-restraints excluded: chain B residue 1377 SER Chi-restraints excluded: chain B residue 1379 ASN Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1439 THR Chi-restraints excluded: chain B residue 1456 THR Chi-restraints excluded: chain B residue 1461 VAL Chi-restraints excluded: chain B residue 1549 ASN Chi-restraints excluded: chain B residue 1558 ASP Chi-restraints excluded: chain B residue 1643 ASN Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1677 THR Chi-restraints excluded: chain B residue 1721 THR Chi-restraints excluded: chain B residue 1731 THR Chi-restraints excluded: chain B residue 1766 ARG Chi-restraints excluded: chain B residue 1777 SER Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1788 PHE Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1829 THR Chi-restraints excluded: chain B residue 1926 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 673 THR Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 737 VAL Chi-restraints excluded: chain C residue 807 ASP Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 1052 CYS Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1080 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1357 THR Chi-restraints excluded: chain C residue 1379 ASN Chi-restraints excluded: chain C residue 1439 THR Chi-restraints excluded: chain C residue 1472 SER Chi-restraints excluded: chain C residue 1493 ARG Chi-restraints excluded: chain C residue 1586 LEU Chi-restraints excluded: chain C residue 1629 ILE Chi-restraints excluded: chain C residue 1677 THR Chi-restraints excluded: chain C residue 1721 THR Chi-restraints excluded: chain C residue 1731 THR Chi-restraints excluded: chain C residue 1834 SER Chi-restraints excluded: chain C residue 1843 LEU Chi-restraints excluded: chain C residue 1926 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 229 ASN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 913 THR Chi-restraints excluded: chain D residue 1006 VAL Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain D residue 1213 CYS Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1330 VAL Chi-restraints excluded: chain D residue 1332 THR Chi-restraints excluded: chain D residue 1349 SER Chi-restraints excluded: chain D residue 1379 ASN Chi-restraints excluded: chain D residue 1447 GLN Chi-restraints excluded: chain D residue 1549 ASN Chi-restraints excluded: chain D residue 1558 ASP Chi-restraints excluded: chain D residue 1567 LYS Chi-restraints excluded: chain D residue 1586 LEU Chi-restraints excluded: chain D residue 1614 TRP Chi-restraints excluded: chain D residue 1664 THR Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1678 THR Chi-restraints excluded: chain D residue 1721 THR Chi-restraints excluded: chain D residue 1748 THR Chi-restraints excluded: chain D residue 1811 CYS Chi-restraints excluded: chain D residue 1812 THR Chi-restraints excluded: chain D residue 1834 SER Chi-restraints excluded: chain D residue 1904 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 245 optimal weight: 8.9990 chunk 658 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 429 optimal weight: 50.0000 chunk 180 optimal weight: 3.9990 chunk 731 optimal weight: 2.9990 chunk 607 optimal weight: 0.9990 chunk 338 optimal weight: 8.9990 chunk 60 optimal weight: 9.9990 chunk 241 optimal weight: 10.0000 chunk 384 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN ** A1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1487 ASN A1810 GLN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 847 HIS ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1647 ASN ** B1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 ASN C1672 GLN C1972 GLN ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1783 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 56268 Z= 0.205 Angle : 0.628 16.087 77572 Z= 0.310 Chirality : 0.041 0.213 9212 Planarity : 0.006 0.090 10148 Dihedral : 5.231 47.544 8057 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.15 % Favored : 91.23 % Rotamer: Outliers : 3.38 % Allowed : 17.52 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.09), residues: 7536 helix: -0.49 (0.31), residues: 284 sheet: -0.52 (0.12), residues: 1800 loop : -1.71 (0.08), residues: 5452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 771 HIS 0.005 0.001 HIS A1272 PHE 0.018 0.001 PHE A 504 TYR 0.017 0.001 TYR D1325 ARG 0.005 0.000 ARG B1359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 173 time to evaluate : 5.504 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: A 1101 MET cc_start: 0.8861 (mmt) cc_final: 0.8290 (mmt) REVERT: A 1519 MET cc_start: 0.8202 (tpp) cc_final: 0.7790 (tpp) REVERT: A 1614 TRP cc_start: 0.4791 (OUTLIER) cc_final: 0.3219 (p90) REVERT: A 1721 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8330 (p) REVERT: A 1809 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7409 (ptm160) REVERT: B 611 PHE cc_start: 0.5020 (OUTLIER) cc_final: 0.3794 (m-80) REVERT: B 723 PHE cc_start: 0.6319 (OUTLIER) cc_final: 0.5297 (m-80) REVERT: B 1080 VAL cc_start: 0.8843 (OUTLIER) cc_final: 0.8627 (p) REVERT: B 1201 VAL cc_start: 0.9585 (OUTLIER) cc_final: 0.9367 (t) REVERT: B 1456 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8731 (p) REVERT: B 1459 MET cc_start: 0.8256 (pmm) cc_final: 0.7734 (pmm) REVERT: B 1539 MET cc_start: 0.8677 (mmp) cc_final: 0.6394 (mpp) REVERT: C 271 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8516 (mt) REVERT: C 437 MET cc_start: 0.7568 (tpt) cc_final: 0.7097 (mmm) REVERT: C 611 PHE cc_start: 0.2574 (OUTLIER) cc_final: 0.2128 (m-80) REVERT: C 757 LEU cc_start: 0.9057 (tp) cc_final: 0.8318 (tp) REVERT: C 966 MET cc_start: 0.8439 (tpp) cc_final: 0.7078 (mtt) REVERT: C 1080 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8329 (p) REVERT: C 1493 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8930 (ttm170) REVERT: C 1497 MET cc_start: 0.9468 (mmt) cc_final: 0.9233 (mmp) REVERT: C 1801 PHE cc_start: 0.8459 (m-10) cc_final: 0.8146 (m-10) REVERT: D 84 ASP cc_start: 0.9224 (t0) cc_final: 0.8986 (t0) REVERT: D 375 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9249 (mp) REVERT: D 437 MET cc_start: 0.7566 (tpt) cc_final: 0.6833 (tpt) REVERT: D 691 MET cc_start: 0.4663 (ptp) cc_final: 0.4384 (ptt) REVERT: D 757 LEU cc_start: 0.8598 (tp) cc_final: 0.7814 (pt) REVERT: D 1101 MET cc_start: 0.8045 (ttp) cc_final: 0.7477 (tmm) REVERT: D 1379 ASN cc_start: 0.7768 (OUTLIER) cc_final: 0.7313 (p0) REVERT: D 1447 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: D 1567 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.8468 (mmtt) REVERT: D 1614 TRP cc_start: 0.4880 (OUTLIER) cc_final: 0.4111 (p90) REVERT: D 1694 LEU cc_start: 0.9128 (mt) cc_final: 0.8758 (mt) outliers start: 201 outliers final: 151 residues processed: 361 average time/residue: 0.4487 time to fit residues: 296.4903 Evaluate side-chains 335 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 167 time to evaluate : 4.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 522 LYS Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 685 ASN Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1389 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1447 GLN Chi-restraints excluded: chain A residue 1614 TRP Chi-restraints excluded: chain A residue 1645 THR Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1697 CYS Chi-restraints excluded: chain A residue 1721 THR Chi-restraints excluded: chain A residue 1765 CYS Chi-restraints excluded: chain A residue 1788 PHE Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1829 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1167 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1172 VAL Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1201 VAL Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1299 THR Chi-restraints excluded: chain B residue 1328 ASP Chi-restraints excluded: chain B residue 1377 SER Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1439 THR Chi-restraints excluded: chain B residue 1456 THR Chi-restraints excluded: chain B residue 1461 VAL Chi-restraints excluded: chain B residue 1549 ASN Chi-restraints excluded: chain B residue 1558 ASP Chi-restraints excluded: chain B residue 1643 ASN Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1677 THR Chi-restraints excluded: chain B residue 1697 CYS Chi-restraints excluded: chain B residue 1721 THR Chi-restraints excluded: chain B residue 1731 THR Chi-restraints excluded: chain B residue 1763 THR Chi-restraints excluded: chain B residue 1777 SER Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1788 PHE Chi-restraints excluded: chain B residue 1844 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 673 THR Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 1052 CYS Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1080 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1379 ASN Chi-restraints excluded: chain C residue 1439 THR Chi-restraints excluded: chain C residue 1472 SER Chi-restraints excluded: chain C residue 1493 ARG Chi-restraints excluded: chain C residue 1586 LEU Chi-restraints excluded: chain C residue 1629 ILE Chi-restraints excluded: chain C residue 1677 THR Chi-restraints excluded: chain C residue 1731 THR Chi-restraints excluded: chain C residue 1834 SER Chi-restraints excluded: chain C residue 1843 LEU Chi-restraints excluded: chain C residue 1926 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 ASN Chi-restraints excluded: chain D residue 254 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 1006 VAL Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain D residue 1213 CYS Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1299 THR Chi-restraints excluded: chain D residue 1325 TYR Chi-restraints excluded: chain D residue 1328 ASP Chi-restraints excluded: chain D residue 1330 VAL Chi-restraints excluded: chain D residue 1332 THR Chi-restraints excluded: chain D residue 1349 SER Chi-restraints excluded: chain D residue 1379 ASN Chi-restraints excluded: chain D residue 1447 GLN Chi-restraints excluded: chain D residue 1545 THR Chi-restraints excluded: chain D residue 1549 ASN Chi-restraints excluded: chain D residue 1558 ASP Chi-restraints excluded: chain D residue 1567 LYS Chi-restraints excluded: chain D residue 1586 LEU Chi-restraints excluded: chain D residue 1614 TRP Chi-restraints excluded: chain D residue 1664 THR Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1721 THR Chi-restraints excluded: chain D residue 1748 THR Chi-restraints excluded: chain D residue 1765 CYS Chi-restraints excluded: chain D residue 1811 CYS Chi-restraints excluded: chain D residue 1812 THR Chi-restraints excluded: chain D residue 1834 SER Chi-restraints excluded: chain D residue 1904 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 705 optimal weight: 0.0040 chunk 82 optimal weight: 9.9990 chunk 416 optimal weight: 30.0000 chunk 534 optimal weight: 40.0000 chunk 413 optimal weight: 40.0000 chunk 615 optimal weight: 9.9990 chunk 408 optimal weight: 5.9990 chunk 728 optimal weight: 0.5980 chunk 456 optimal weight: 9.9990 chunk 444 optimal weight: 9.9990 chunk 336 optimal weight: 6.9990 overall best weight: 4.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN B 847 HIS ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1757 ASN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 ASN C1672 GLN C1972 GLN ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 56268 Z= 0.220 Angle : 0.627 15.917 77572 Z= 0.308 Chirality : 0.041 0.201 9212 Planarity : 0.006 0.100 10148 Dihedral : 5.150 47.139 8057 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.61 % Allowed : 8.69 % Favored : 90.70 % Rotamer: Outliers : 3.78 % Allowed : 17.64 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.09), residues: 7536 helix: -0.26 (0.32), residues: 284 sheet: -0.38 (0.12), residues: 1804 loop : -1.62 (0.08), residues: 5448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 771 HIS 0.005 0.001 HIS A1272 PHE 0.017 0.001 PHE A 504 TYR 0.017 0.001 TYR D1325 ARG 0.005 0.000 ARG D1622 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 173 time to evaluate : 5.762 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: A 189 MET cc_start: 0.8982 (mtm) cc_final: 0.8694 (mpp) REVERT: A 833 PHE cc_start: 0.8294 (m-80) cc_final: 0.7628 (t80) REVERT: A 851 ASN cc_start: 0.7869 (OUTLIER) cc_final: 0.7611 (m-40) REVERT: A 1101 MET cc_start: 0.8931 (mmt) cc_final: 0.8400 (mmt) REVERT: A 1519 MET cc_start: 0.8297 (tpp) cc_final: 0.7989 (tpp) REVERT: A 1614 TRP cc_start: 0.4794 (OUTLIER) cc_final: 0.3165 (p90) REVERT: A 1721 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8324 (p) REVERT: A 1809 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7382 (ptm160) REVERT: B 230 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8578 (mm) REVERT: B 611 PHE cc_start: 0.4876 (OUTLIER) cc_final: 0.3735 (m-80) REVERT: B 723 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.5297 (m-80) REVERT: B 1080 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8632 (p) REVERT: B 1208 TYR cc_start: 0.5039 (OUTLIER) cc_final: 0.4504 (m-10) REVERT: B 1456 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8730 (p) REVERT: B 1459 MET cc_start: 0.8259 (pmm) cc_final: 0.7746 (pmm) REVERT: B 1519 MET cc_start: 0.8209 (ppp) cc_final: 0.7815 (tmm) REVERT: B 1539 MET cc_start: 0.8498 (mmp) cc_final: 0.6172 (mpp) REVERT: B 1614 TRP cc_start: 0.4441 (OUTLIER) cc_final: 0.1760 (m-10) REVERT: C 271 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8531 (mt) REVERT: C 437 MET cc_start: 0.7612 (tpt) cc_final: 0.7138 (mmm) REVERT: C 611 PHE cc_start: 0.2611 (OUTLIER) cc_final: 0.2159 (m-80) REVERT: C 738 TYR cc_start: 0.3882 (t80) cc_final: 0.3336 (m-80) REVERT: C 757 LEU cc_start: 0.9138 (tp) cc_final: 0.8463 (tp) REVERT: C 966 MET cc_start: 0.8523 (tpp) cc_final: 0.7124 (mtt) REVERT: C 1080 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8328 (p) REVERT: C 1459 MET cc_start: 0.8017 (pmm) cc_final: 0.7409 (pmm) REVERT: C 1497 MET cc_start: 0.9452 (mmt) cc_final: 0.9229 (mmp) REVERT: C 1801 PHE cc_start: 0.8455 (m-10) cc_final: 0.8145 (m-10) REVERT: D 84 ASP cc_start: 0.9254 (t0) cc_final: 0.8991 (t0) REVERT: D 375 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9223 (mp) REVERT: D 437 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.6834 (tpt) REVERT: D 691 MET cc_start: 0.4907 (ptp) cc_final: 0.4703 (ptt) REVERT: D 757 LEU cc_start: 0.8731 (tp) cc_final: 0.8066 (pt) REVERT: D 903 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9036 (pt) REVERT: D 1101 MET cc_start: 0.8076 (ttp) cc_final: 0.7500 (tmm) REVERT: D 1379 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7311 (p0) REVERT: D 1447 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8027 (mt0) REVERT: D 1481 GLN cc_start: 0.6437 (OUTLIER) cc_final: 0.6122 (pm20) REVERT: D 1567 LYS cc_start: 0.9504 (OUTLIER) cc_final: 0.8479 (mmtt) REVERT: D 1611 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8176 (mtmt) REVERT: D 1614 TRP cc_start: 0.4690 (OUTLIER) cc_final: 0.3945 (p90) REVERT: D 1694 LEU cc_start: 0.9136 (mt) cc_final: 0.8760 (mt) outliers start: 225 outliers final: 171 residues processed: 380 average time/residue: 0.4414 time to fit residues: 307.6327 Evaluate side-chains 360 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 166 time to evaluate : 4.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 685 ASN Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1389 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1447 GLN Chi-restraints excluded: chain A residue 1614 TRP Chi-restraints excluded: chain A residue 1645 THR Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1697 CYS Chi-restraints excluded: chain A residue 1721 THR Chi-restraints excluded: chain A residue 1765 CYS Chi-restraints excluded: chain A residue 1788 PHE Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1829 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain B residue 1167 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1208 TYR Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1299 THR Chi-restraints excluded: chain B residue 1328 ASP Chi-restraints excluded: chain B residue 1377 SER Chi-restraints excluded: chain B residue 1379 ASN Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1439 THR Chi-restraints excluded: chain B residue 1456 THR Chi-restraints excluded: chain B residue 1461 VAL Chi-restraints excluded: chain B residue 1549 ASN Chi-restraints excluded: chain B residue 1558 ASP Chi-restraints excluded: chain B residue 1614 TRP Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1643 ASN Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1677 THR Chi-restraints excluded: chain B residue 1697 CYS Chi-restraints excluded: chain B residue 1721 THR Chi-restraints excluded: chain B residue 1731 THR Chi-restraints excluded: chain B residue 1763 THR Chi-restraints excluded: chain B residue 1777 SER Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1788 PHE Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1829 THR Chi-restraints excluded: chain B residue 1844 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 673 THR Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 1052 CYS Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1080 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1379 ASN Chi-restraints excluded: chain C residue 1439 THR Chi-restraints excluded: chain C residue 1472 SER Chi-restraints excluded: chain C residue 1493 ARG Chi-restraints excluded: chain C residue 1586 LEU Chi-restraints excluded: chain C residue 1677 THR Chi-restraints excluded: chain C residue 1721 THR Chi-restraints excluded: chain C residue 1731 THR Chi-restraints excluded: chain C residue 1834 SER Chi-restraints excluded: chain C residue 1843 LEU Chi-restraints excluded: chain C residue 1926 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 229 ASN Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 708 THR Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 903 ILE Chi-restraints excluded: chain D residue 1006 VAL Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain D residue 1213 CYS Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1299 THR Chi-restraints excluded: chain D residue 1325 TYR Chi-restraints excluded: chain D residue 1328 ASP Chi-restraints excluded: chain D residue 1330 VAL Chi-restraints excluded: chain D residue 1332 THR Chi-restraints excluded: chain D residue 1349 SER Chi-restraints excluded: chain D residue 1379 ASN Chi-restraints excluded: chain D residue 1441 LEU Chi-restraints excluded: chain D residue 1447 GLN Chi-restraints excluded: chain D residue 1481 GLN Chi-restraints excluded: chain D residue 1501 VAL Chi-restraints excluded: chain D residue 1545 THR Chi-restraints excluded: chain D residue 1549 ASN Chi-restraints excluded: chain D residue 1558 ASP Chi-restraints excluded: chain D residue 1567 LYS Chi-restraints excluded: chain D residue 1586 LEU Chi-restraints excluded: chain D residue 1611 LYS Chi-restraints excluded: chain D residue 1614 TRP Chi-restraints excluded: chain D residue 1664 THR Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1678 THR Chi-restraints excluded: chain D residue 1697 CYS Chi-restraints excluded: chain D residue 1721 THR Chi-restraints excluded: chain D residue 1732 LYS Chi-restraints excluded: chain D residue 1748 THR Chi-restraints excluded: chain D residue 1765 CYS Chi-restraints excluded: chain D residue 1788 PHE Chi-restraints excluded: chain D residue 1811 CYS Chi-restraints excluded: chain D residue 1812 THR Chi-restraints excluded: chain D residue 1823 ASN Chi-restraints excluded: chain D residue 1834 SER Chi-restraints excluded: chain D residue 1904 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 450 optimal weight: 5.9990 chunk 290 optimal weight: 20.0000 chunk 435 optimal weight: 30.0000 chunk 219 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 463 optimal weight: 3.9990 chunk 496 optimal weight: 20.0000 chunk 360 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 572 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 847 HIS ** B1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN ** C 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 ASN C1972 GLN D 758 ASN D1156 GLN ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1783 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 56268 Z= 0.247 Angle : 0.636 15.885 77572 Z= 0.314 Chirality : 0.041 0.367 9212 Planarity : 0.006 0.100 10148 Dihedral : 5.196 46.504 8057 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.82 % Favored : 90.58 % Rotamer: Outliers : 3.78 % Allowed : 17.86 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.10), residues: 7536 helix: -0.17 (0.32), residues: 284 sheet: -0.35 (0.12), residues: 1812 loop : -1.60 (0.08), residues: 5440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1614 HIS 0.006 0.001 HIS A1272 PHE 0.017 0.001 PHE A 504 TYR 0.019 0.001 TYR D1325 ARG 0.005 0.000 ARG A1390 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 172 time to evaluate : 4.486 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: A 833 PHE cc_start: 0.8330 (m-80) cc_final: 0.7645 (t80) REVERT: A 851 ASN cc_start: 0.7821 (OUTLIER) cc_final: 0.7577 (m-40) REVERT: A 966 MET cc_start: 0.8269 (mmm) cc_final: 0.6567 (mtm) REVERT: A 1101 MET cc_start: 0.9008 (mmt) cc_final: 0.8517 (mmt) REVERT: A 1519 MET cc_start: 0.8228 (tpp) cc_final: 0.7991 (tpp) REVERT: A 1614 TRP cc_start: 0.4913 (OUTLIER) cc_final: 0.3194 (p90) REVERT: A 1721 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8336 (p) REVERT: A 1809 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7388 (ptm160) REVERT: B 230 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8670 (mm) REVERT: B 611 PHE cc_start: 0.4925 (OUTLIER) cc_final: 0.3790 (m-80) REVERT: B 723 PHE cc_start: 0.6293 (OUTLIER) cc_final: 0.5289 (m-80) REVERT: B 1208 TYR cc_start: 0.5115 (OUTLIER) cc_final: 0.4522 (m-10) REVERT: B 1353 ILE cc_start: 0.9218 (OUTLIER) cc_final: 0.8819 (tp) REVERT: B 1456 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8737 (p) REVERT: B 1459 MET cc_start: 0.8259 (pmm) cc_final: 0.7743 (pmm) REVERT: B 1519 MET cc_start: 0.8279 (ppp) cc_final: 0.7904 (tmm) REVERT: B 1539 MET cc_start: 0.8690 (mmp) cc_final: 0.6138 (mtt) REVERT: B 1614 TRP cc_start: 0.4340 (OUTLIER) cc_final: 0.1856 (m-10) REVERT: C 271 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8553 (mt) REVERT: C 387 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8955 (pp) REVERT: C 437 MET cc_start: 0.7604 (tpt) cc_final: 0.6915 (mmm) REVERT: C 611 PHE cc_start: 0.2758 (OUTLIER) cc_final: 0.2392 (m-80) REVERT: C 738 TYR cc_start: 0.3848 (t80) cc_final: 0.3312 (m-80) REVERT: C 966 MET cc_start: 0.8604 (tpp) cc_final: 0.7125 (mtt) REVERT: C 1080 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8334 (p) REVERT: C 1572 MET cc_start: 0.9043 (tpp) cc_final: 0.8793 (tpp) REVERT: C 1801 PHE cc_start: 0.8501 (m-10) cc_final: 0.8184 (m-10) REVERT: D 375 ILE cc_start: 0.9491 (OUTLIER) cc_final: 0.9244 (mp) REVERT: D 437 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.6901 (tpt) REVERT: D 702 PHE cc_start: 0.3056 (OUTLIER) cc_final: 0.2503 (p90) REVERT: D 757 LEU cc_start: 0.8819 (tp) cc_final: 0.8175 (pt) REVERT: D 790 CYS cc_start: 0.7942 (m) cc_final: 0.7659 (m) REVERT: D 903 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9024 (pt) REVERT: D 1101 MET cc_start: 0.8083 (ttp) cc_final: 0.7521 (tmm) REVERT: D 1372 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7902 (tp-100) REVERT: D 1379 ASN cc_start: 0.7854 (OUTLIER) cc_final: 0.7360 (p0) REVERT: D 1447 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8059 (mt0) REVERT: D 1481 GLN cc_start: 0.6445 (OUTLIER) cc_final: 0.6136 (pm20) REVERT: D 1493 ARG cc_start: 0.9392 (OUTLIER) cc_final: 0.8798 (ttp80) REVERT: D 1567 LYS cc_start: 0.9515 (OUTLIER) cc_final: 0.8456 (mmtm) REVERT: D 1614 TRP cc_start: 0.4783 (OUTLIER) cc_final: 0.4052 (p90) REVERT: D 1694 LEU cc_start: 0.9152 (mt) cc_final: 0.8757 (mt) outliers start: 225 outliers final: 172 residues processed: 380 average time/residue: 0.4376 time to fit residues: 305.6236 Evaluate side-chains 365 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 167 time to evaluate : 4.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 392 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 685 ASN Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 851 ASN Chi-restraints excluded: chain A residue 913 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1166 THR Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1302 LEU Chi-restraints excluded: chain A residue 1324 THR Chi-restraints excluded: chain A residue 1353 ILE Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1389 CYS Chi-restraints excluded: chain A residue 1439 THR Chi-restraints excluded: chain A residue 1447 GLN Chi-restraints excluded: chain A residue 1614 TRP Chi-restraints excluded: chain A residue 1645 THR Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1697 CYS Chi-restraints excluded: chain A residue 1721 THR Chi-restraints excluded: chain A residue 1765 CYS Chi-restraints excluded: chain A residue 1788 PHE Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1829 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 705 SER Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 723 PHE Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 951 THR Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1160 THR Chi-restraints excluded: chain B residue 1167 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1191 SER Chi-restraints excluded: chain B residue 1208 TYR Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1299 THR Chi-restraints excluded: chain B residue 1328 ASP Chi-restraints excluded: chain B residue 1353 ILE Chi-restraints excluded: chain B residue 1377 SER Chi-restraints excluded: chain B residue 1379 ASN Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1439 THR Chi-restraints excluded: chain B residue 1456 THR Chi-restraints excluded: chain B residue 1461 VAL Chi-restraints excluded: chain B residue 1549 ASN Chi-restraints excluded: chain B residue 1558 ASP Chi-restraints excluded: chain B residue 1614 TRP Chi-restraints excluded: chain B residue 1626 THR Chi-restraints excluded: chain B residue 1643 ASN Chi-restraints excluded: chain B residue 1668 MET Chi-restraints excluded: chain B residue 1677 THR Chi-restraints excluded: chain B residue 1697 CYS Chi-restraints excluded: chain B residue 1721 THR Chi-restraints excluded: chain B residue 1731 THR Chi-restraints excluded: chain B residue 1763 THR Chi-restraints excluded: chain B residue 1777 SER Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1788 PHE Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1829 THR Chi-restraints excluded: chain B residue 1844 SER Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 303 SER Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 491 THR Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 673 THR Chi-restraints excluded: chain C residue 711 THR Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1080 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1251 THR Chi-restraints excluded: chain C residue 1332 THR Chi-restraints excluded: chain C residue 1379 ASN Chi-restraints excluded: chain C residue 1439 THR Chi-restraints excluded: chain C residue 1472 SER Chi-restraints excluded: chain C residue 1586 LEU Chi-restraints excluded: chain C residue 1629 ILE Chi-restraints excluded: chain C residue 1677 THR Chi-restraints excluded: chain C residue 1721 THR Chi-restraints excluded: chain C residue 1731 THR Chi-restraints excluded: chain C residue 1843 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 271 LEU Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 570 ILE Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 702 PHE Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 903 ILE Chi-restraints excluded: chain D residue 1069 ILE Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain D residue 1213 CYS Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1299 THR Chi-restraints excluded: chain D residue 1325 TYR Chi-restraints excluded: chain D residue 1328 ASP Chi-restraints excluded: chain D residue 1330 VAL Chi-restraints excluded: chain D residue 1332 THR Chi-restraints excluded: chain D residue 1349 SER Chi-restraints excluded: chain D residue 1372 GLN Chi-restraints excluded: chain D residue 1379 ASN Chi-restraints excluded: chain D residue 1441 LEU Chi-restraints excluded: chain D residue 1447 GLN Chi-restraints excluded: chain D residue 1481 GLN Chi-restraints excluded: chain D residue 1493 ARG Chi-restraints excluded: chain D residue 1501 VAL Chi-restraints excluded: chain D residue 1531 THR Chi-restraints excluded: chain D residue 1545 THR Chi-restraints excluded: chain D residue 1549 ASN Chi-restraints excluded: chain D residue 1558 ASP Chi-restraints excluded: chain D residue 1567 LYS Chi-restraints excluded: chain D residue 1586 LEU Chi-restraints excluded: chain D residue 1614 TRP Chi-restraints excluded: chain D residue 1664 THR Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1678 THR Chi-restraints excluded: chain D residue 1697 CYS Chi-restraints excluded: chain D residue 1721 THR Chi-restraints excluded: chain D residue 1732 LYS Chi-restraints excluded: chain D residue 1748 THR Chi-restraints excluded: chain D residue 1765 CYS Chi-restraints excluded: chain D residue 1811 CYS Chi-restraints excluded: chain D residue 1812 THR Chi-restraints excluded: chain D residue 1823 ASN Chi-restraints excluded: chain D residue 1834 SER Chi-restraints excluded: chain D residue 1904 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 662 optimal weight: 30.0000 chunk 698 optimal weight: 1.9990 chunk 636 optimal weight: 6.9990 chunk 679 optimal weight: 0.0980 chunk 697 optimal weight: 1.9990 chunk 408 optimal weight: 9.9990 chunk 295 optimal weight: 30.0000 chunk 533 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 613 optimal weight: 9.9990 chunk 642 optimal weight: 0.2980 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 ASN ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1212 GLN ** B1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 446 ASN C 556 ASN C 721 ASN ** C 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 ASN D1421 GLN ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 56268 Z= 0.173 Angle : 0.624 16.286 77572 Z= 0.305 Chirality : 0.041 0.281 9212 Planarity : 0.006 0.097 10148 Dihedral : 4.946 45.236 8057 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.60 % Favored : 91.81 % Rotamer: Outliers : 2.96 % Allowed : 18.73 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.10), residues: 7536 helix: 0.16 (0.33), residues: 280 sheet: -0.23 (0.12), residues: 1820 loop : -1.54 (0.08), residues: 5436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 312 HIS 0.004 0.001 HIS D 411 PHE 0.021 0.001 PHE D1788 TYR 0.015 0.001 TYR D1325 ARG 0.005 0.000 ARG C1493 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 174 time to evaluate : 4.505 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: A 833 PHE cc_start: 0.8275 (m-80) cc_final: 0.7535 (t80) REVERT: A 966 MET cc_start: 0.7970 (mmm) cc_final: 0.6560 (mtm) REVERT: A 1101 MET cc_start: 0.8938 (mmt) cc_final: 0.8571 (mmt) REVERT: A 1519 MET cc_start: 0.8292 (tpp) cc_final: 0.8040 (tpp) REVERT: A 1614 TRP cc_start: 0.4813 (OUTLIER) cc_final: 0.3087 (p90) REVERT: A 1809 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7427 (ptm160) REVERT: B 230 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8613 (mm) REVERT: B 611 PHE cc_start: 0.5001 (OUTLIER) cc_final: 0.3992 (m-80) REVERT: B 1456 THR cc_start: 0.8992 (OUTLIER) cc_final: 0.8689 (p) REVERT: B 1459 MET cc_start: 0.8219 (pmm) cc_final: 0.7791 (pmm) REVERT: B 1519 MET cc_start: 0.8109 (ppp) cc_final: 0.7656 (tmm) REVERT: B 1539 MET cc_start: 0.8549 (mmp) cc_final: 0.6250 (mpp) REVERT: B 1614 TRP cc_start: 0.4413 (OUTLIER) cc_final: 0.1882 (m-10) REVERT: C 271 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8485 (mt) REVERT: C 387 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8862 (pp) REVERT: C 437 MET cc_start: 0.7495 (tpt) cc_final: 0.7028 (mmm) REVERT: C 611 PHE cc_start: 0.2895 (OUTLIER) cc_final: 0.2503 (m-80) REVERT: C 738 TYR cc_start: 0.3962 (t80) cc_final: 0.3395 (m-80) REVERT: C 757 LEU cc_start: 0.9042 (mt) cc_final: 0.8472 (tp) REVERT: C 792 MET cc_start: 0.7179 (ppp) cc_final: 0.6880 (ppp) REVERT: C 966 MET cc_start: 0.8520 (tpp) cc_final: 0.7144 (mtt) REVERT: C 1080 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8197 (p) REVERT: C 1459 MET cc_start: 0.8066 (pmm) cc_final: 0.7417 (pmm) REVERT: C 1572 MET cc_start: 0.9045 (tpp) cc_final: 0.8731 (tpp) REVERT: C 1801 PHE cc_start: 0.8501 (m-10) cc_final: 0.8183 (m-10) REVERT: D 375 ILE cc_start: 0.9498 (OUTLIER) cc_final: 0.9258 (mp) REVERT: D 437 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.6896 (tpt) REVERT: D 691 MET cc_start: 0.4170 (ptt) cc_final: 0.3142 (ptm) REVERT: D 702 PHE cc_start: 0.3111 (OUTLIER) cc_final: 0.2520 (p90) REVERT: D 757 LEU cc_start: 0.8748 (tp) cc_final: 0.8133 (pt) REVERT: D 903 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.9004 (pt) REVERT: D 1372 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7953 (tp40) REVERT: D 1379 ASN cc_start: 0.7704 (OUTLIER) cc_final: 0.7278 (p0) REVERT: D 1447 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: D 1481 GLN cc_start: 0.6409 (OUTLIER) cc_final: 0.6111 (pm20) REVERT: D 1493 ARG cc_start: 0.9393 (OUTLIER) cc_final: 0.8717 (ttp80) REVERT: D 1567 LYS cc_start: 0.9475 (OUTLIER) cc_final: 0.8411 (mmtm) REVERT: D 1611 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8183 (mtmt) REVERT: D 1614 TRP cc_start: 0.4687 (OUTLIER) cc_final: 0.4013 (p90) REVERT: D 1694 LEU cc_start: 0.9159 (mt) cc_final: 0.8759 (mt) outliers start: 176 outliers final: 133 residues processed: 337 average time/residue: 0.4484 time to fit residues: 275.4792 Evaluate side-chains 319 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 164 time to evaluate : 4.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 703 THR Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1108 VAL Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1389 CYS Chi-restraints excluded: chain A residue 1447 GLN Chi-restraints excluded: chain A residue 1614 TRP Chi-restraints excluded: chain A residue 1645 THR Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1697 CYS Chi-restraints excluded: chain A residue 1765 CYS Chi-restraints excluded: chain A residue 1788 PHE Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1829 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 784 SER Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 913 THR Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1167 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1299 THR Chi-restraints excluded: chain B residue 1328 ASP Chi-restraints excluded: chain B residue 1377 SER Chi-restraints excluded: chain B residue 1379 ASN Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1439 THR Chi-restraints excluded: chain B residue 1456 THR Chi-restraints excluded: chain B residue 1461 VAL Chi-restraints excluded: chain B residue 1558 ASP Chi-restraints excluded: chain B residue 1614 TRP Chi-restraints excluded: chain B residue 1643 ASN Chi-restraints excluded: chain B residue 1677 THR Chi-restraints excluded: chain B residue 1697 CYS Chi-restraints excluded: chain B residue 1721 THR Chi-restraints excluded: chain B residue 1777 SER Chi-restraints excluded: chain B residue 1784 LEU Chi-restraints excluded: chain B residue 1788 PHE Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1829 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 658 ILE Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 1052 CYS Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1080 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1379 ASN Chi-restraints excluded: chain C residue 1439 THR Chi-restraints excluded: chain C residue 1472 SER Chi-restraints excluded: chain C residue 1586 LEU Chi-restraints excluded: chain C residue 1629 ILE Chi-restraints excluded: chain C residue 1721 THR Chi-restraints excluded: chain C residue 1731 THR Chi-restraints excluded: chain C residue 1843 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 702 PHE Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 903 ILE Chi-restraints excluded: chain D residue 1069 ILE Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain D residue 1213 CYS Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1299 THR Chi-restraints excluded: chain D residue 1325 TYR Chi-restraints excluded: chain D residue 1328 ASP Chi-restraints excluded: chain D residue 1330 VAL Chi-restraints excluded: chain D residue 1372 GLN Chi-restraints excluded: chain D residue 1379 ASN Chi-restraints excluded: chain D residue 1447 GLN Chi-restraints excluded: chain D residue 1481 GLN Chi-restraints excluded: chain D residue 1493 ARG Chi-restraints excluded: chain D residue 1531 THR Chi-restraints excluded: chain D residue 1545 THR Chi-restraints excluded: chain D residue 1558 ASP Chi-restraints excluded: chain D residue 1567 LYS Chi-restraints excluded: chain D residue 1586 LEU Chi-restraints excluded: chain D residue 1611 LYS Chi-restraints excluded: chain D residue 1614 TRP Chi-restraints excluded: chain D residue 1664 THR Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1678 THR Chi-restraints excluded: chain D residue 1697 CYS Chi-restraints excluded: chain D residue 1721 THR Chi-restraints excluded: chain D residue 1732 LYS Chi-restraints excluded: chain D residue 1748 THR Chi-restraints excluded: chain D residue 1811 CYS Chi-restraints excluded: chain D residue 1812 THR Chi-restraints excluded: chain D residue 1904 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 676 optimal weight: 7.9990 chunk 445 optimal weight: 0.7980 chunk 718 optimal weight: 9.9990 chunk 438 optimal weight: 50.0000 chunk 340 optimal weight: 9.9990 chunk 499 optimal weight: 20.0000 chunk 753 optimal weight: 50.0000 chunk 693 optimal weight: 0.3980 chunk 599 optimal weight: 0.9990 chunk 62 optimal weight: 0.0020 chunk 463 optimal weight: 5.9990 overall best weight: 1.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 ASN ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 ASN ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1783 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 56268 Z= 0.166 Angle : 0.619 16.349 77572 Z= 0.302 Chirality : 0.041 0.341 9212 Planarity : 0.006 0.087 10148 Dihedral : 4.818 48.213 8057 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.50 % Favored : 91.96 % Rotamer: Outliers : 2.50 % Allowed : 19.20 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.10), residues: 7536 helix: 0.35 (0.33), residues: 280 sheet: -0.07 (0.12), residues: 1788 loop : -1.49 (0.08), residues: 5468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1397 HIS 0.004 0.001 HIS D 411 PHE 0.031 0.001 PHE C1537 TYR 0.018 0.001 TYR D 824 ARG 0.004 0.000 ARG B1359 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15072 Ramachandran restraints generated. 7536 Oldfield, 0 Emsley, 7536 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 172 time to evaluate : 4.437 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: A 966 MET cc_start: 0.7966 (mmm) cc_final: 0.6584 (mtm) REVERT: A 1101 MET cc_start: 0.8914 (mmt) cc_final: 0.8548 (mmt) REVERT: A 1519 MET cc_start: 0.8288 (tpp) cc_final: 0.8042 (tpp) REVERT: A 1614 TRP cc_start: 0.4732 (OUTLIER) cc_final: 0.3069 (p90) REVERT: A 1809 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7466 (ptm160) REVERT: B 230 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8621 (mm) REVERT: B 611 PHE cc_start: 0.5042 (OUTLIER) cc_final: 0.3991 (m-80) REVERT: B 1456 THR cc_start: 0.8976 (OUTLIER) cc_final: 0.8672 (p) REVERT: B 1459 MET cc_start: 0.8219 (pmm) cc_final: 0.7834 (pmm) REVERT: B 1519 MET cc_start: 0.8034 (ppp) cc_final: 0.7563 (tmm) REVERT: B 1539 MET cc_start: 0.8510 (mmp) cc_final: 0.6222 (mpp) REVERT: B 1614 TRP cc_start: 0.4350 (OUTLIER) cc_final: 0.1845 (m-10) REVERT: C 271 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8492 (mt) REVERT: C 387 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8839 (pp) REVERT: C 437 MET cc_start: 0.7440 (tpt) cc_final: 0.6915 (mmm) REVERT: C 611 PHE cc_start: 0.3024 (OUTLIER) cc_final: 0.2704 (m-80) REVERT: C 738 TYR cc_start: 0.4005 (t80) cc_final: 0.3404 (m-80) REVERT: C 757 LEU cc_start: 0.9058 (mt) cc_final: 0.8475 (tp) REVERT: C 792 MET cc_start: 0.7192 (ppp) cc_final: 0.6900 (ppp) REVERT: C 966 MET cc_start: 0.8484 (tpp) cc_final: 0.7172 (mtt) REVERT: C 1080 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8290 (p) REVERT: C 1572 MET cc_start: 0.8992 (tpp) cc_final: 0.8774 (tpp) REVERT: C 1801 PHE cc_start: 0.8508 (m-10) cc_final: 0.8195 (m-10) REVERT: D 375 ILE cc_start: 0.9496 (OUTLIER) cc_final: 0.9253 (mp) REVERT: D 437 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.6882 (tpt) REVERT: D 691 MET cc_start: 0.4111 (ptt) cc_final: 0.3049 (ptm) REVERT: D 702 PHE cc_start: 0.3098 (OUTLIER) cc_final: 0.2519 (p90) REVERT: D 757 LEU cc_start: 0.8741 (tp) cc_final: 0.8147 (pt) REVERT: D 903 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9071 (pt) REVERT: D 1372 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8042 (tp40) REVERT: D 1378 MET cc_start: 0.9388 (mmm) cc_final: 0.9182 (mmm) REVERT: D 1379 ASN cc_start: 0.7600 (OUTLIER) cc_final: 0.7170 (p0) REVERT: D 1447 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7978 (mt0) REVERT: D 1481 GLN cc_start: 0.6405 (OUTLIER) cc_final: 0.6096 (pm20) REVERT: D 1493 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.8761 (ttp80) REVERT: D 1567 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.8437 (mmtt) REVERT: D 1611 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8211 (mtmt) REVERT: D 1614 TRP cc_start: 0.4846 (OUTLIER) cc_final: 0.4181 (p90) REVERT: D 1694 LEU cc_start: 0.9145 (mt) cc_final: 0.8738 (mt) outliers start: 149 outliers final: 114 residues processed: 308 average time/residue: 0.4512 time to fit residues: 253.5061 Evaluate side-chains 300 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 164 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 484 THR Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 808 ILE Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1160 THR Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1237 SER Chi-restraints excluded: chain A residue 1251 THR Chi-restraints excluded: chain A residue 1299 THR Chi-restraints excluded: chain A residue 1379 ASN Chi-restraints excluded: chain A residue 1389 CYS Chi-restraints excluded: chain A residue 1447 GLN Chi-restraints excluded: chain A residue 1614 TRP Chi-restraints excluded: chain A residue 1645 THR Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1765 CYS Chi-restraints excluded: chain A residue 1788 PHE Chi-restraints excluded: chain A residue 1809 ARG Chi-restraints excluded: chain A residue 1829 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 405 PHE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 484 THR Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 611 PHE Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 635 THR Chi-restraints excluded: chain B residue 711 THR Chi-restraints excluded: chain B residue 752 THR Chi-restraints excluded: chain B residue 774 VAL Chi-restraints excluded: chain B residue 808 ILE Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 1054 LEU Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1167 ASN Chi-restraints excluded: chain B residue 1168 VAL Chi-restraints excluded: chain B residue 1251 THR Chi-restraints excluded: chain B residue 1299 THR Chi-restraints excluded: chain B residue 1328 ASP Chi-restraints excluded: chain B residue 1377 SER Chi-restraints excluded: chain B residue 1405 CYS Chi-restraints excluded: chain B residue 1439 THR Chi-restraints excluded: chain B residue 1456 THR Chi-restraints excluded: chain B residue 1558 ASP Chi-restraints excluded: chain B residue 1614 TRP Chi-restraints excluded: chain B residue 1643 ASN Chi-restraints excluded: chain B residue 1677 THR Chi-restraints excluded: chain B residue 1697 CYS Chi-restraints excluded: chain B residue 1721 THR Chi-restraints excluded: chain B residue 1788 PHE Chi-restraints excluded: chain B residue 1824 LEU Chi-restraints excluded: chain B residue 1829 THR Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain C residue 254 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 493 VAL Chi-restraints excluded: chain C residue 611 PHE Chi-restraints excluded: chain C residue 613 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 721 ASN Chi-restraints excluded: chain C residue 816 VAL Chi-restraints excluded: chain C residue 888 ILE Chi-restraints excluded: chain C residue 1052 CYS Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1061 ASN Chi-restraints excluded: chain C residue 1080 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1379 ASN Chi-restraints excluded: chain C residue 1472 SER Chi-restraints excluded: chain C residue 1586 LEU Chi-restraints excluded: chain C residue 1629 ILE Chi-restraints excluded: chain C residue 1721 THR Chi-restraints excluded: chain C residue 1731 THR Chi-restraints excluded: chain C residue 1843 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 405 PHE Chi-restraints excluded: chain D residue 437 MET Chi-restraints excluded: chain D residue 491 THR Chi-restraints excluded: chain D residue 493 VAL Chi-restraints excluded: chain D residue 611 PHE Chi-restraints excluded: chain D residue 635 THR Chi-restraints excluded: chain D residue 689 THR Chi-restraints excluded: chain D residue 702 PHE Chi-restraints excluded: chain D residue 866 VAL Chi-restraints excluded: chain D residue 887 THR Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 903 ILE Chi-restraints excluded: chain D residue 1108 VAL Chi-restraints excluded: chain D residue 1168 VAL Chi-restraints excluded: chain D residue 1184 ASP Chi-restraints excluded: chain D residue 1213 CYS Chi-restraints excluded: chain D residue 1251 THR Chi-restraints excluded: chain D residue 1299 THR Chi-restraints excluded: chain D residue 1325 TYR Chi-restraints excluded: chain D residue 1328 ASP Chi-restraints excluded: chain D residue 1330 VAL Chi-restraints excluded: chain D residue 1372 GLN Chi-restraints excluded: chain D residue 1379 ASN Chi-restraints excluded: chain D residue 1441 LEU Chi-restraints excluded: chain D residue 1447 GLN Chi-restraints excluded: chain D residue 1481 GLN Chi-restraints excluded: chain D residue 1493 ARG Chi-restraints excluded: chain D residue 1545 THR Chi-restraints excluded: chain D residue 1558 ASP Chi-restraints excluded: chain D residue 1567 LYS Chi-restraints excluded: chain D residue 1611 LYS Chi-restraints excluded: chain D residue 1614 TRP Chi-restraints excluded: chain D residue 1664 THR Chi-restraints excluded: chain D residue 1677 THR Chi-restraints excluded: chain D residue 1678 THR Chi-restraints excluded: chain D residue 1697 CYS Chi-restraints excluded: chain D residue 1721 THR Chi-restraints excluded: chain D residue 1748 THR Chi-restraints excluded: chain D residue 1811 CYS Chi-restraints excluded: chain D residue 1812 THR Chi-restraints excluded: chain D residue 1904 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 367 optimal weight: 0.0020 chunk 476 optimal weight: 0.8980 chunk 638 optimal weight: 50.0000 chunk 183 optimal weight: 3.9990 chunk 553 optimal weight: 5.9990 chunk 88 optimal weight: 0.0770 chunk 166 optimal weight: 20.0000 chunk 600 optimal weight: 30.0000 chunk 251 optimal weight: 5.9990 chunk 616 optimal weight: 9.9990 chunk 76 optimal weight: 50.0000 overall best weight: 2.1950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 987 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1212 GLN ** B1095 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 ASN ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1783 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.057373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.046662 restraints weight = 448914.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.047969 restraints weight = 230855.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.048536 restraints weight = 127769.569| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 56268 Z= 0.173 Angle : 0.618 16.101 77572 Z= 0.301 Chirality : 0.041 0.361 9212 Planarity : 0.006 0.091 10148 Dihedral : 4.751 45.360 8057 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.48 % Allowed : 7.47 % Favored : 92.05 % Rotamer: Outliers : 2.47 % Allowed : 19.34 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.10), residues: 7536 helix: 0.48 (0.33), residues: 280 sheet: -0.05 (0.12), residues: 1824 loop : -1.45 (0.08), residues: 5432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1397 HIS 0.004 0.001 HIS D 411 PHE 0.025 0.001 PHE C1537 TYR 0.013 0.001 TYR A1017 ARG 0.004 0.000 ARG B1359 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7397.37 seconds wall clock time: 134 minutes 17.50 seconds (8057.50 seconds total)