Starting phenix.real_space_refine on Fri Dec 8 02:28:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txb_41679/12_2023/8txb_41679.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txb_41679/12_2023/8txb_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_41679/12_2023/8txb_41679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txb_41679/12_2023/8txb_41679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txb_41679/12_2023/8txb_41679.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txb_41679/12_2023/8txb_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 20.86, 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: 15.43 Conformation dependent library (CDL) restraints added in 7.5 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: 5.16 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: 26.41 Time building geometry restraints manager: 17.19 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: 1.230 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: 0.030 Extract box with map and model: 8.430 Check model and map are aligned: 0.620 Set scattering table: 0.360 Process input model: 116.800 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.260 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: 132.960 ------------------------------------------------------------------------------- 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 : 4.458 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 outliers start: 34 outliers final: 10 residues processed: 370 average time/residue: 0.4707 time to fit residues: 310.2841 Evaluate side-chains 222 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 212 time to evaluate : 4.465 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.3985 time to fit residues: 13.3456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 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 ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1503 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C 758 ASN ** 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 D1563 GLN D1672 GLN D1823 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 56268 Z= 0.244 Angle : 0.686 14.805 77572 Z= 0.346 Chirality : 0.042 0.220 9212 Planarity : 0.007 0.102 10148 Dihedral : 5.344 52.862 8052 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.78 % Favored : 91.40 % Rotamer: Outliers : 2.69 % Allowed : 15.46 % Favored : 81.85 % 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: -2.62 (0.09), residues: 7536 helix: -1.37 (0.30), residues: 284 sheet: -1.02 (0.11), residues: 1844 loop : -2.18 (0.08), residues: 5408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1614 HIS 0.007 0.001 HIS C1272 PHE 0.029 0.001 PHE D1601 TYR 0.015 0.001 TYR A1017 ARG 0.006 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 384 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 224 time to evaluate : 4.557 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 outliers start: 160 outliers final: 60 residues processed: 373 average time/residue: 0.4723 time to fit residues: 317.6584 Evaluate side-chains 258 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 198 time to evaluate : 4.537 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 60 outliers final: 1 residues processed: 60 average time/residue: 0.4187 time to fit residues: 53.3998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 381 optimal weight: 5.9990 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: 20.0000 chunk 742 optimal weight: 10.0000 chunk 612 optimal weight: 50.0000 chunk 682 optimal weight: 20.0000 chunk 234 optimal weight: 4.9990 chunk 551 optimal weight: 30.0000 overall best weight: 12.1996 ------------------------------------------------------------------------------- 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 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 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 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 721 ASN C 758 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** ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1212 GLN D1487 ASN ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 56268 Z= 0.456 Angle : 0.782 14.014 77572 Z= 0.402 Chirality : 0.045 0.248 9212 Planarity : 0.007 0.088 10148 Dihedral : 6.055 54.628 8052 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.65 % Favored : 89.62 % Rotamer: Outliers : 3.38 % Allowed : 15.57 % Favored : 81.05 % 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: -2.54 (0.09), residues: 7536 helix: -1.28 (0.30), residues: 280 sheet: -0.90 (0.12), residues: 1796 loop : -2.15 (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 A1272 PHE 0.041 0.002 PHE B1605 TYR 0.023 0.002 TYR C1029 ARG 0.013 0.001 ARG D1766 *********************** 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 401 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 200 time to evaluate : 4.483 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 outliers start: 201 outliers final: 91 residues processed: 393 average time/residue: 0.4570 time to fit residues: 325.3784 Evaluate side-chains 272 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 181 time to evaluate : 4.433 Switching outliers to nearest non-outliers outliers start: 91 outliers final: 0 residues processed: 91 average time/residue: 0.3903 time to fit residues: 73.5638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 679 optimal weight: 10.0000 chunk 517 optimal weight: 20.0000 chunk 356 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 328 optimal weight: 9.9990 chunk 461 optimal weight: 6.9990 chunk 690 optimal weight: 20.0000 chunk 730 optimal weight: 9.9990 chunk 360 optimal weight: 9.9990 chunk 654 optimal weight: 30.0000 chunk 196 optimal weight: 9.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- 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 589 GLN ** A 593 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 GLN A1701 GLN ** A1706 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** ** B1506 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** C 721 ASN C1061 ASN C1197 ASN C1238 ASN C1602 ASN ** C1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1672 GLN D1823 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 56268 Z= 0.348 Angle : 0.707 16.332 77572 Z= 0.358 Chirality : 0.043 0.286 9212 Planarity : 0.007 0.077 10148 Dihedral : 5.884 51.766 8052 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.74 % Allowed : 8.82 % Favored : 90.43 % Rotamer: Outliers : 2.15 % Allowed : 17.51 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 1.13 % Twisted General : 0.07 % 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: -2.36 (0.09), residues: 7536 helix: -1.14 (0.30), residues: 280 sheet: -0.78 (0.12), residues: 1796 loop : -2.01 (0.08), residues: 5460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1614 HIS 0.009 0.002 HIS A1272 PHE 0.033 0.002 PHE D1601 TYR 0.022 0.002 TYR D1325 ARG 0.008 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 318 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 190 time to evaluate : 4.439 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 outliers start: 128 outliers final: 49 residues processed: 308 average time/residue: 0.4602 time to fit residues: 258.8267 Evaluate side-chains 224 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 175 time to evaluate : 4.473 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.3983 time to fit residues: 42.7579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 608 optimal weight: 30.0000 chunk 414 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 544 optimal weight: 30.0000 chunk 301 optimal weight: 7.9990 chunk 623 optimal weight: 20.0000 chunk 505 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 373 optimal weight: 4.9990 chunk 655 optimal weight: 30.0000 chunk 184 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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** ** A1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1487 ASN ** A1706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 556 ASN B 847 HIS ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1506 ASN ** B1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1647 ASN ** 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 758 ASN ** C1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1672 GLN C1972 GLN ** D1276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1487 ASN ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 56268 Z= 0.271 Angle : 0.670 16.270 77572 Z= 0.335 Chirality : 0.042 0.239 9212 Planarity : 0.006 0.080 10148 Dihedral : 5.626 49.552 8052 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.02 % Favored : 90.30 % Rotamer: Outliers : 1.70 % Allowed : 18.18 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 1.13 % 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: -2.17 (0.09), residues: 7536 helix: -0.88 (0.31), residues: 284 sheet: -0.65 (0.12), residues: 1792 loop : -1.88 (0.08), residues: 5460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1614 HIS 0.006 0.001 HIS A1272 PHE 0.038 0.002 PHE D1601 TYR 0.021 0.001 TYR D1325 ARG 0.006 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 285 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 184 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 101 outliers final: 46 residues processed: 274 average time/residue: 0.5013 time to fit residues: 252.2130 Evaluate side-chains 215 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 169 time to evaluate : 4.468 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 0.4283 time to fit residues: 43.3939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 245 optimal weight: 6.9990 chunk 658 optimal weight: 10.0000 chunk 144 optimal weight: 0.0570 chunk 429 optimal weight: 50.0000 chunk 180 optimal weight: 0.3980 chunk 731 optimal weight: 20.0000 chunk 607 optimal weight: 30.0000 chunk 338 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 384 optimal weight: 7.9990 overall best weight: 4.2904 ------------------------------------------------------------------------------- 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 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN A 987 GLN ** A1706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1891 ASN B 417 GLN B1167 ASN ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1643 ASN ** 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** ** C1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1672 GLN C1972 GLN D1156 GLN ** D1276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1487 ASN ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1783 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3210 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= 0.216 Angle : 0.649 16.447 77572 Z= 0.322 Chirality : 0.042 0.206 9212 Planarity : 0.006 0.082 10148 Dihedral : 5.402 48.588 8052 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.24 % Favored : 91.16 % Rotamer: Outliers : 1.06 % Allowed : 19.22 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 1.01 % 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: -1.99 (0.09), residues: 7536 helix: -0.53 (0.32), residues: 280 sheet: -0.55 (0.12), residues: 1832 loop : -1.76 (0.08), residues: 5424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 771 HIS 0.005 0.001 HIS A1272 PHE 0.037 0.001 PHE D1601 TYR 0.018 0.001 TYR D 824 ARG 0.004 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 240 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 177 time to evaluate : 4.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 23 residues processed: 229 average time/residue: 0.4758 time to fit residues: 200.9458 Evaluate side-chains 189 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 4.495 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.3990 time to fit residues: 23.5792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 705 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 416 optimal weight: 30.0000 chunk 534 optimal weight: 20.0000 chunk 413 optimal weight: 30.0000 chunk 615 optimal weight: 0.0980 chunk 408 optimal weight: 7.9990 chunk 728 optimal weight: 10.0000 chunk 456 optimal weight: 10.0000 chunk 444 optimal weight: 9.9990 chunk 336 optimal weight: 9.9990 overall best weight: 7.4188 ------------------------------------------------------------------------------- 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 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN ** A1706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** 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** ** C1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8008 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 56268 Z= 0.301 Angle : 0.678 16.518 77572 Z= 0.339 Chirality : 0.042 0.352 9212 Planarity : 0.006 0.079 10148 Dihedral : 5.515 48.335 8052 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.61 % Allowed : 9.65 % Favored : 89.74 % Rotamer: Outliers : 1.01 % Allowed : 19.69 % Favored : 79.30 % 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: -1.99 (0.09), residues: 7536 helix: -0.43 (0.32), residues: 280 sheet: -0.59 (0.12), residues: 1836 loop : -1.75 (0.08), residues: 5420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C1614 HIS 0.007 0.001 HIS A1272 PHE 0.023 0.002 PHE D1601 TYR 0.027 0.001 TYR C 738 ARG 0.007 0.001 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 235 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 175 time to evaluate : 4.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 25 residues processed: 225 average time/residue: 0.4836 time to fit residues: 198.0952 Evaluate side-chains 188 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 4.782 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.4142 time to fit residues: 25.3962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 450 optimal weight: 6.9990 chunk 290 optimal weight: 20.0000 chunk 435 optimal weight: 30.0000 chunk 219 optimal weight: 8.9990 chunk 143 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 chunk 463 optimal weight: 10.0000 chunk 496 optimal weight: 20.0000 chunk 360 optimal weight: 8.9990 chunk 67 optimal weight: 0.0970 chunk 572 optimal weight: 10.0000 overall best weight: 5.8186 ------------------------------------------------------------------------------- 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 454 GLN A 717 GLN ** A1706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1810 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** 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** ** C1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1972 GLN ** D 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1783 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 56268 Z= 0.251 Angle : 0.662 16.670 77572 Z= 0.329 Chirality : 0.042 0.256 9212 Planarity : 0.006 0.080 10148 Dihedral : 5.443 47.551 8052 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.89 % Favored : 90.53 % Rotamer: Outliers : 0.74 % Allowed : 19.94 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -1.93 (0.09), residues: 7536 helix: -0.34 (0.31), residues: 280 sheet: -0.55 (0.12), residues: 1856 loop : -1.72 (0.08), residues: 5400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 312 HIS 0.006 0.001 HIS A1272 PHE 0.053 0.001 PHE D 702 TYR 0.018 0.001 TYR D 824 ARG 0.005 0.000 ARG D1622 *********************** 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 208 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 4.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 13 residues processed: 201 average time/residue: 0.4989 time to fit residues: 183.3054 Evaluate side-chains 171 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 4.803 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4841 time to fit residues: 17.9638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 636 optimal weight: 0.1980 chunk 679 optimal weight: 8.9990 chunk 697 optimal weight: 5.9990 chunk 408 optimal weight: 9.9990 chunk 295 optimal weight: 7.9990 chunk 533 optimal weight: 0.0670 chunk 208 optimal weight: 20.0000 chunk 613 optimal weight: 3.9990 chunk 642 optimal weight: 40.0000 overall best weight: 3.6524 ------------------------------------------------------------------------------- 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 ** A1706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1810 GLN B1212 GLN ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1810 GLN ** 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 556 ASN ** C1379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1972 GLN ** D 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1421 GLN ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1783 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 56268 Z= 0.204 Angle : 0.649 16.218 77572 Z= 0.320 Chirality : 0.042 0.233 9212 Planarity : 0.006 0.080 10148 Dihedral : 5.246 46.816 8052 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.54 % Allowed : 8.60 % Favored : 90.86 % Rotamer: Outliers : 0.35 % Allowed : 20.23 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.00 % Twisted Proline : 0.88 % 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: -1.81 (0.10), residues: 7536 helix: -0.08 (0.32), residues: 280 sheet: -0.49 (0.12), residues: 1868 loop : -1.63 (0.08), residues: 5388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 677 HIS 0.005 0.001 HIS D 411 PHE 0.043 0.001 PHE C 702 TYR 0.015 0.001 TYR A1017 ARG 0.006 0.000 ARG D1493 *********************** 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 188 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 4.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 183 average time/residue: 0.5050 time to fit residues: 171.1981 Evaluate side-chains 165 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 158 time to evaluate : 4.523 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3983 time to fit residues: 11.4140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 676 optimal weight: 30.0000 chunk 445 optimal weight: 1.9990 chunk 718 optimal weight: 20.0000 chunk 438 optimal weight: 40.0000 chunk 340 optimal weight: 10.0000 chunk 499 optimal weight: 20.0000 chunk 753 optimal weight: 50.0000 chunk 693 optimal weight: 0.3980 chunk 599 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 463 optimal weight: 9.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- 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 847 HIS ** A1706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1810 GLN ** 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 556 ASN C1972 GLN ** D 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1783 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 56268 Z= 0.233 Angle : 0.655 16.076 77572 Z= 0.322 Chirality : 0.042 0.227 9212 Planarity : 0.006 0.080 10148 Dihedral : 5.235 46.608 8052 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.52 % Allowed : 9.06 % Favored : 90.42 % Rotamer: Outliers : 0.25 % Allowed : 20.35 % Favored : 79.40 % 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 (0.10), residues: 7536 helix: 0.00 (0.32), residues: 280 sheet: -0.44 (0.12), residues: 1860 loop : -1.61 (0.08), residues: 5396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1614 HIS 0.005 0.001 HIS D 411 PHE 0.033 0.001 PHE C 702 TYR 0.016 0.001 TYR D 824 ARG 0.007 0.000 ARG D1493 ********************** 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 175 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 4.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 170 average time/residue: 0.5119 time to fit residues: 160.4945 Evaluate side-chains 162 residues out of total 6000 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 5.228 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4329 time to fit residues: 11.7368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 367 optimal weight: 8.9990 chunk 476 optimal weight: 4.9990 chunk 638 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 553 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 600 optimal weight: 20.0000 chunk 251 optimal weight: 0.0170 chunk 616 optimal weight: 50.0000 chunk 76 optimal weight: 9.9990 overall best weight: 5.4026 ------------------------------------------------------------------------------- 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 A1706 GLN ** B1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1810 GLN ** C 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN C1972 GLN ** D 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1783 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.056051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.045185 restraints weight = 452338.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.046291 restraints weight = 225406.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.046998 restraints weight = 135861.362| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 56268 Z= 0.238 Angle : 0.655 15.985 77572 Z= 0.323 Chirality : 0.042 0.222 9212 Planarity : 0.006 0.079 10148 Dihedral : 5.225 45.674 8052 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.96 % Favored : 90.53 % Rotamer: Outliers : 0.25 % Allowed : 20.38 % Favored : 79.37 % 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: -1.74 (0.10), residues: 7536 helix: 0.07 (0.32), residues: 280 sheet: -0.43 (0.12), residues: 1868 loop : -1.60 (0.08), residues: 5388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D1614 HIS 0.006 0.001 HIS C 411 PHE 0.034 0.001 PHE C 702 TYR 0.014 0.001 TYR A1017 ARG 0.008 0.000 ARG D 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7099.03 seconds wall clock time: 130 minutes 8.92 seconds (7808.92 seconds total)