Starting phenix.real_space_refine on Tue Feb 20 23:22:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z10_6865/02_2024/5z10_6865.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z10_6865/02_2024/5z10_6865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z10_6865/02_2024/5z10_6865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z10_6865/02_2024/5z10_6865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z10_6865/02_2024/5z10_6865.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5z10_6865/02_2024/5z10_6865.pdb" } resolution = 3.97 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= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 18924 2.51 5 N 4998 2.21 5 O 5103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 973": "OD1" <-> "OD2" Residue "A PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1024": "NH1" <-> "NH2" Residue "A ARG 1031": "NH1" <-> "NH2" Residue "A PHE 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1151": "OD1" <-> "OD2" Residue "A PHE 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1211": "OD1" <-> "OD2" Residue "A PHE 1297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1308": "OD1" <-> "OD2" Residue "A ARG 1318": "NH1" <-> "NH2" Residue "A PHE 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1416": "OE1" <-> "OE2" Residue "A GLU 1537": "OE1" <-> "OE2" Residue "A ARG 1552": "NH1" <-> "NH2" Residue "A ARG 1553": "NH1" <-> "NH2" Residue "A ARG 1724": "NH1" <-> "NH2" Residue "A TYR 1782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1786": "OD1" <-> "OD2" Residue "A PHE 1794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2104": "NH1" <-> "NH2" Residue "A TYR 2175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2264": "OD1" <-> "OD2" Residue "A ARG 2295": "NH1" <-> "NH2" Residue "A ASP 2314": "OD1" <-> "OD2" Residue "A ARG 2318": "NH1" <-> "NH2" Residue "A GLU 2343": "OE1" <-> "OE2" Residue "A TYR 2375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2377": "NH1" <-> "NH2" Residue "A ARG 2402": "NH1" <-> "NH2" Residue "A ARG 2406": "NH1" <-> "NH2" Residue "A ASP 2425": "OD1" <-> "OD2" Residue "A PHE 2449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2546": "NH1" <-> "NH2" Residue "B PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 973": "OD1" <-> "OD2" Residue "B PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1024": "NH1" <-> "NH2" Residue "B ARG 1031": "NH1" <-> "NH2" Residue "B PHE 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1151": "OD1" <-> "OD2" Residue "B PHE 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1211": "OD1" <-> "OD2" Residue "B PHE 1297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1308": "OD1" <-> "OD2" Residue "B ARG 1318": "NH1" <-> "NH2" Residue "B PHE 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1416": "OE1" <-> "OE2" Residue "B GLU 1537": "OE1" <-> "OE2" Residue "B ARG 1552": "NH1" <-> "NH2" Residue "B ARG 1553": "NH1" <-> "NH2" Residue "B ARG 1724": "NH1" <-> "NH2" Residue "B TYR 1782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1786": "OD1" <-> "OD2" Residue "B PHE 1794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2104": "NH1" <-> "NH2" Residue "B TYR 2175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 2235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 2264": "OD1" <-> "OD2" Residue "B ARG 2295": "NH1" <-> "NH2" Residue "B ASP 2314": "OD1" <-> "OD2" Residue "B ARG 2318": "NH1" <-> "NH2" Residue "B GLU 2343": "OE1" <-> "OE2" Residue "B TYR 2375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2377": "NH1" <-> "NH2" Residue "B ARG 2402": "NH1" <-> "NH2" Residue "B ARG 2406": "NH1" <-> "NH2" Residue "B ASP 2425": "OD1" <-> "OD2" Residue "B PHE 2449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 2546": "NH1" <-> "NH2" Residue "C PHE 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 973": "OD1" <-> "OD2" Residue "C PHE 986": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1024": "NH1" <-> "NH2" Residue "C ARG 1031": "NH1" <-> "NH2" Residue "C PHE 1039": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1151": "OD1" <-> "OD2" Residue "C PHE 1170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1211": "OD1" <-> "OD2" Residue "C PHE 1297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1308": "OD1" <-> "OD2" Residue "C ARG 1318": "NH1" <-> "NH2" Residue "C PHE 1413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1416": "OE1" <-> "OE2" Residue "C GLU 1537": "OE1" <-> "OE2" Residue "C ARG 1552": "NH1" <-> "NH2" Residue "C ARG 1553": "NH1" <-> "NH2" Residue "C ARG 1724": "NH1" <-> "NH2" Residue "C TYR 1782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1786": "OD1" <-> "OD2" Residue "C PHE 1794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1995": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2022": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2095": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2104": "NH1" <-> "NH2" Residue "C TYR 2175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 2264": "OD1" <-> "OD2" Residue "C ARG 2295": "NH1" <-> "NH2" Residue "C ASP 2314": "OD1" <-> "OD2" Residue "C ARG 2318": "NH1" <-> "NH2" Residue "C GLU 2343": "OE1" <-> "OE2" Residue "C TYR 2375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2377": "NH1" <-> "NH2" Residue "C ARG 2402": "NH1" <-> "NH2" Residue "C ARG 2406": "NH1" <-> "NH2" Residue "C ASP 2425": "OD1" <-> "OD2" Residue "C PHE 2449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 2546": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29142 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1304, 9714 Classifications: {'peptide': 1304} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 283} Link IDs: {'PTRANS': 47, 'TRANS': 1256} Chain breaks: 16 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1096 Unresolved non-hydrogen angles: 1432 Unresolved non-hydrogen dihedrals: 930 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 3, 'TYR:plan': 17, 'ASN:plan1': 9, 'TRP:plan': 9, 'HIS:plan': 6, 'PHE:plan': 20, 'GLU:plan': 9, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 570 Chain: "B" Number of atoms: 9714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1304, 9714 Classifications: {'peptide': 1304} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 283} Link IDs: {'PTRANS': 47, 'TRANS': 1256} Chain breaks: 16 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1096 Unresolved non-hydrogen angles: 1432 Unresolved non-hydrogen dihedrals: 930 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 3, 'TYR:plan': 17, 'ASN:plan1': 9, 'TRP:plan': 9, 'HIS:plan': 6, 'PHE:plan': 20, 'GLU:plan': 9, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 570 Chain: "C" Number of atoms: 9714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1304, 9714 Classifications: {'peptide': 1304} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 283} Link IDs: {'PTRANS': 47, 'TRANS': 1256} Chain breaks: 16 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 1096 Unresolved non-hydrogen angles: 1432 Unresolved non-hydrogen dihedrals: 930 Unresolved non-hydrogen chiralities: 131 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 3, 'TYR:plan': 17, 'ASN:plan1': 9, 'TRP:plan': 9, 'HIS:plan': 6, 'PHE:plan': 20, 'GLU:plan': 9, 'ARG:plan': 20} Unresolved non-hydrogen planarities: 570 Time building chain proxies: 15.63, per 1000 atoms: 0.54 Number of scatterers: 29142 At special positions: 0 Unit cell: (211.2, 199.32, 154.44, 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 117 16.00 O 5103 8.00 N 4998 7.00 C 18924 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A2437 " - pdb=" SG CYS A2441 " distance=2.05 Simple disulfide: pdb=" SG CYS B2437 " - pdb=" SG CYS B2441 " distance=2.05 Simple disulfide: pdb=" SG CYS C2437 " - pdb=" SG CYS C2441 " distance=2.06 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: 12.07 Conformation dependent library (CDL) restraints added in 5.7 seconds 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7500 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 9 sheets defined 65.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.09 Creating SS restraints... Processing helix chain 'A' and resid 577 through 585 removed outlier: 3.587A pdb=" N ILE A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 607 through 624 removed outlier: 3.733A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 650 removed outlier: 3.821A pdb=" N VAL A 650 " --> pdb=" O VAL A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 706 Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 785 through 821 removed outlier: 4.579A pdb=" N SER A 789 " --> pdb=" O ASP A 785 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 840 Processing helix chain 'A' and resid 845 through 866 removed outlier: 3.754A pdb=" N CYS A 851 " --> pdb=" O PRO A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 950 removed outlier: 3.672A pdb=" N GLN A 925 " --> pdb=" O LEU A 921 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN A 926 " --> pdb=" O GLY A 922 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N HIS A 927 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 930 " --> pdb=" O ASN A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 983 Processing helix chain 'A' and resid 989 through 1006 removed outlier: 4.036A pdb=" N MET A1006 " --> pdb=" O ILE A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1023 removed outlier: 3.847A pdb=" N ARG A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1053 Proline residue: A1034 - end of helix removed outlier: 4.718A pdb=" N LEU A1045 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TYR A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1092 through 1111 Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 3.717A pdb=" N ILE A1144 " --> pdb=" O PRO A1141 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS A1145 " --> pdb=" O ASN A1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1141 through 1145' Processing helix chain 'A' and resid 1150 through 1159 removed outlier: 4.339A pdb=" N ALA A1156 " --> pdb=" O MET A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1173 removed outlier: 3.500A pdb=" N VAL A1167 " --> pdb=" O TRP A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1199 removed outlier: 3.508A pdb=" N LEU A1185 " --> pdb=" O GLY A1181 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N THR A1196 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A1199 " --> pdb=" O GLY A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1224 removed outlier: 4.204A pdb=" N VAL A1220 " --> pdb=" O TYR A1216 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A1221 " --> pdb=" O ASN A1217 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE A1222 " --> pdb=" O VAL A1218 " (cutoff:3.500A) Processing helix chain 'A' and resid 1279 through 1299 removed outlier: 4.189A pdb=" N ASP A1283 " --> pdb=" O GLY A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1315 removed outlier: 3.504A pdb=" N ASP A1308 " --> pdb=" O HIS A1304 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU A1309 " --> pdb=" O VAL A1305 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A1310 " --> pdb=" O SER A1306 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA A1311 " --> pdb=" O ALA A1307 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1362 removed outlier: 3.512A pdb=" N GLY A1319 " --> pdb=" O GLN A1315 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN A1336 " --> pdb=" O ASN A1332 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A1337 " --> pdb=" O PHE A1333 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A1358 " --> pdb=" O ALA A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1415 Processing helix chain 'A' and resid 1505 through 1545 removed outlier: 5.734A pdb=" N HIS A1526 " --> pdb=" O ALA A1522 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS A1527 " --> pdb=" O PHE A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1669 removed outlier: 3.855A pdb=" N GLN A1669 " --> pdb=" O PHE A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1686 Processing helix chain 'A' and resid 1688 through 1701 removed outlier: 3.586A pdb=" N TYR A1692 " --> pdb=" O GLU A1688 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS A1699 " --> pdb=" O ILE A1695 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A1701 " --> pdb=" O LEU A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1705 through 1707 No H-bonds generated for 'chain 'A' and resid 1705 through 1707' Processing helix chain 'A' and resid 1708 through 1719 removed outlier: 3.941A pdb=" N VAL A1712 " --> pdb=" O LEU A1708 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A1713 " --> pdb=" O VAL A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1728 through 1743 removed outlier: 3.756A pdb=" N PHE A1736 " --> pdb=" O THR A1732 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A1741 " --> pdb=" O THR A1737 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1801 removed outlier: 3.743A pdb=" N LYS A1784 " --> pdb=" O ASP A1780 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL A1788 " --> pdb=" O LYS A1784 " (cutoff:3.500A) Processing helix chain 'A' and resid 1958 through 1966 removed outlier: 3.745A pdb=" N PHE A1962 " --> pdb=" O LEU A1958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1979 through 1994 Processing helix chain 'A' and resid 2016 through 2040 removed outlier: 4.401A pdb=" N LEU A2021 " --> pdb=" O PRO A2017 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE A2022 " --> pdb=" O GLN A2018 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N MET A2023 " --> pdb=" O ALA A2019 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG A2035 " --> pdb=" O MET A2031 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A2036 " --> pdb=" O VAL A2032 " (cutoff:3.500A) Processing helix chain 'A' and resid 2043 through 2061 removed outlier: 4.126A pdb=" N VAL A2055 " --> pdb=" O VAL A2051 " (cutoff:3.500A) Processing helix chain 'A' and resid 2077 through 2100 removed outlier: 3.582A pdb=" N ILE A2088 " --> pdb=" O PHE A2084 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A2089 " --> pdb=" O VAL A2085 " (cutoff:3.500A) Processing helix chain 'A' and resid 2115 through 2126 Processing helix chain 'A' and resid 2131 through 2143 removed outlier: 3.647A pdb=" N TRP A2140 " --> pdb=" O ALA A2136 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP A2142 " --> pdb=" O MET A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2149 through 2174 removed outlier: 3.783A pdb=" N CYS A2154 " --> pdb=" O SER A2150 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A2155 " --> pdb=" O ASN A2151 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ALA A2160 " --> pdb=" O GLU A2156 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A2164 " --> pdb=" O ALA A2160 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A2172 " --> pdb=" O SER A2168 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS A2173 " --> pdb=" O ARG A2169 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A2174 " --> pdb=" O GLU A2170 " (cutoff:3.500A) Processing helix chain 'A' and resid 2184 through 2205 removed outlier: 3.939A pdb=" N TYR A2189 " --> pdb=" O LYS A2185 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU A2194 " --> pdb=" O GLY A2190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE A2195 " --> pdb=" O MET A2191 " (cutoff:3.500A) Processing helix chain 'A' and resid 2206 through 2208 No H-bonds generated for 'chain 'A' and resid 2206 through 2208' Processing helix chain 'A' and resid 2252 through 2262 Processing helix chain 'A' and resid 2266 through 2276 removed outlier: 4.134A pdb=" N TYR A2276 " --> pdb=" O PHE A2272 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2279 No H-bonds generated for 'chain 'A' and resid 2277 through 2279' Processing helix chain 'A' and resid 2297 through 2311 Processing helix chain 'A' and resid 2348 through 2358 Processing helix chain 'A' and resid 2421 through 2426 Processing helix chain 'A' and resid 2466 through 2482 Processing helix chain 'A' and resid 2500 through 2517 removed outlier: 4.119A pdb=" N LEU A2506 " --> pdb=" O ARG A2502 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG A2514 " --> pdb=" O ILE A2510 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU A2515 " --> pdb=" O PHE A2511 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A2516 " --> pdb=" O LEU A2512 " (cutoff:3.500A) Processing helix chain 'A' and resid 2518 through 2522 removed outlier: 3.741A pdb=" N GLU A2522 " --> pdb=" O LEU A2519 " (cutoff:3.500A) Processing helix chain 'A' and resid 2525 through 2535 removed outlier: 3.820A pdb=" N SER A2535 " --> pdb=" O PHE A2531 " (cutoff:3.500A) Processing helix chain 'A' and resid 2536 through 2541 Processing helix chain 'B' and resid 577 through 585 removed outlier: 3.587A pdb=" N ILE B 581 " --> pdb=" O LEU B 577 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR B 585 " --> pdb=" O ILE B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 596 Processing helix chain 'B' and resid 607 through 624 removed outlier: 3.734A pdb=" N MET B 611 " --> pdb=" O LYS B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 650 removed outlier: 3.821A pdb=" N VAL B 650 " --> pdb=" O VAL B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 706 Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'B' and resid 785 through 821 removed outlier: 4.578A pdb=" N SER B 789 " --> pdb=" O ASP B 785 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU B 807 " --> pdb=" O ARG B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 840 Processing helix chain 'B' and resid 845 through 866 removed outlier: 3.754A pdb=" N CYS B 851 " --> pdb=" O PRO B 847 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 950 removed outlier: 3.672A pdb=" N GLN B 925 " --> pdb=" O LEU B 921 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASN B 926 " --> pdb=" O GLY B 922 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N HIS B 927 " --> pdb=" O TYR B 923 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE B 930 " --> pdb=" O ASN B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 983 Processing helix chain 'B' and resid 989 through 1006 removed outlier: 4.036A pdb=" N MET B1006 " --> pdb=" O ILE B1002 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1023 removed outlier: 3.847A pdb=" N ARG B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1053 Proline residue: B1034 - end of helix removed outlier: 4.719A pdb=" N LEU B1045 " --> pdb=" O THR B1041 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TYR B1046 " --> pdb=" O LEU B1042 " (cutoff:3.500A) Processing helix chain 'B' and resid 1092 through 1111 Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.717A pdb=" N ILE B1144 " --> pdb=" O PRO B1141 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS B1145 " --> pdb=" O ASN B1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1141 through 1145' Processing helix chain 'B' and resid 1150 through 1159 removed outlier: 4.339A pdb=" N ALA B1156 " --> pdb=" O MET B1152 " (cutoff:3.500A) Processing helix chain 'B' and resid 1163 through 1173 removed outlier: 3.500A pdb=" N VAL B1167 " --> pdb=" O TRP B1163 " (cutoff:3.500A) Processing helix chain 'B' and resid 1181 through 1199 removed outlier: 3.508A pdb=" N LEU B1185 " --> pdb=" O GLY B1181 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR B1196 " --> pdb=" O LEU B1192 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR B1197 " --> pdb=" O LEU B1193 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU B1199 " --> pdb=" O GLY B1195 " (cutoff:3.500A) Processing helix chain 'B' and resid 1202 through 1224 removed outlier: 4.205A pdb=" N VAL B1220 " --> pdb=" O TYR B1216 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE B1221 " --> pdb=" O ASN B1217 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE B1222 " --> pdb=" O VAL B1218 " (cutoff:3.500A) Processing helix chain 'B' and resid 1279 through 1299 removed outlier: 4.190A pdb=" N ASP B1283 " --> pdb=" O GLY B1279 " (cutoff:3.500A) Processing helix chain 'B' and resid 1302 through 1315 removed outlier: 3.505A pdb=" N ASP B1308 " --> pdb=" O HIS B1304 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU B1309 " --> pdb=" O VAL B1305 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS B1310 " --> pdb=" O SER B1306 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B1311 " --> pdb=" O ALA B1307 " (cutoff:3.500A) Processing helix chain 'B' and resid 1315 through 1362 removed outlier: 3.512A pdb=" N GLY B1319 " --> pdb=" O GLN B1315 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B1336 " --> pdb=" O ASN B1332 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE B1337 " --> pdb=" O PHE B1333 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS B1358 " --> pdb=" O ALA B1354 " (cutoff:3.500A) Processing helix chain 'B' and resid 1411 through 1415 Processing helix chain 'B' and resid 1505 through 1545 removed outlier: 5.735A pdb=" N HIS B1526 " --> pdb=" O ALA B1522 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS B1527 " --> pdb=" O PHE B1523 " (cutoff:3.500A) Processing helix chain 'B' and resid 1656 through 1669 removed outlier: 3.856A pdb=" N GLN B1669 " --> pdb=" O PHE B1665 " (cutoff:3.500A) Processing helix chain 'B' and resid 1672 through 1686 Processing helix chain 'B' and resid 1688 through 1701 removed outlier: 3.587A pdb=" N TYR B1692 " --> pdb=" O GLU B1688 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS B1699 " --> pdb=" O ILE B1695 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B1701 " --> pdb=" O LEU B1697 " (cutoff:3.500A) Processing helix chain 'B' and resid 1705 through 1707 No H-bonds generated for 'chain 'B' and resid 1705 through 1707' Processing helix chain 'B' and resid 1708 through 1719 removed outlier: 3.941A pdb=" N VAL B1712 " --> pdb=" O LEU B1708 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU B1713 " --> pdb=" O VAL B1709 " (cutoff:3.500A) Processing helix chain 'B' and resid 1728 through 1743 removed outlier: 3.756A pdb=" N PHE B1736 " --> pdb=" O THR B1732 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL B1741 " --> pdb=" O THR B1737 " (cutoff:3.500A) Processing helix chain 'B' and resid 1780 through 1801 removed outlier: 3.743A pdb=" N LYS B1784 " --> pdb=" O ASP B1780 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B1788 " --> pdb=" O LYS B1784 " (cutoff:3.500A) Processing helix chain 'B' and resid 1958 through 1966 removed outlier: 3.745A pdb=" N PHE B1962 " --> pdb=" O LEU B1958 " (cutoff:3.500A) Processing helix chain 'B' and resid 1979 through 1994 Processing helix chain 'B' and resid 2016 through 2040 removed outlier: 4.401A pdb=" N LEU B2021 " --> pdb=" O PRO B2017 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N PHE B2022 " --> pdb=" O GLN B2018 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N MET B2023 " --> pdb=" O ALA B2019 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG B2035 " --> pdb=" O MET B2031 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA B2036 " --> pdb=" O VAL B2032 " (cutoff:3.500A) Processing helix chain 'B' and resid 2043 through 2061 removed outlier: 4.127A pdb=" N VAL B2055 " --> pdb=" O VAL B2051 " (cutoff:3.500A) Processing helix chain 'B' and resid 2077 through 2100 removed outlier: 3.582A pdb=" N ILE B2088 " --> pdb=" O PHE B2084 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR B2089 " --> pdb=" O VAL B2085 " (cutoff:3.500A) Processing helix chain 'B' and resid 2115 through 2126 Processing helix chain 'B' and resid 2131 through 2143 removed outlier: 3.647A pdb=" N TRP B2140 " --> pdb=" O ALA B2136 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N TRP B2142 " --> pdb=" O MET B2138 " (cutoff:3.500A) Processing helix chain 'B' and resid 2149 through 2174 removed outlier: 3.783A pdb=" N CYS B2154 " --> pdb=" O SER B2150 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL B2155 " --> pdb=" O ASN B2151 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA B2160 " --> pdb=" O GLU B2156 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B2164 " --> pdb=" O ALA B2160 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B2172 " --> pdb=" O SER B2168 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B2173 " --> pdb=" O ARG B2169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS B2174 " --> pdb=" O GLU B2170 " (cutoff:3.500A) Processing helix chain 'B' and resid 2184 through 2205 removed outlier: 3.940A pdb=" N TYR B2189 " --> pdb=" O LYS B2185 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU B2194 " --> pdb=" O GLY B2190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE B2195 " --> pdb=" O MET B2191 " (cutoff:3.500A) Processing helix chain 'B' and resid 2206 through 2208 No H-bonds generated for 'chain 'B' and resid 2206 through 2208' Processing helix chain 'B' and resid 2252 through 2262 Processing helix chain 'B' and resid 2266 through 2276 removed outlier: 4.134A pdb=" N TYR B2276 " --> pdb=" O PHE B2272 " (cutoff:3.500A) Processing helix chain 'B' and resid 2277 through 2279 No H-bonds generated for 'chain 'B' and resid 2277 through 2279' Processing helix chain 'B' and resid 2297 through 2311 Processing helix chain 'B' and resid 2348 through 2358 Processing helix chain 'B' and resid 2421 through 2426 Processing helix chain 'B' and resid 2466 through 2482 Processing helix chain 'B' and resid 2500 through 2517 removed outlier: 4.118A pdb=" N LEU B2506 " --> pdb=" O ARG B2502 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B2514 " --> pdb=" O ILE B2510 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU B2515 " --> pdb=" O PHE B2511 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR B2516 " --> pdb=" O LEU B2512 " (cutoff:3.500A) Processing helix chain 'B' and resid 2518 through 2522 removed outlier: 3.742A pdb=" N GLU B2522 " --> pdb=" O LEU B2519 " (cutoff:3.500A) Processing helix chain 'B' and resid 2525 through 2535 removed outlier: 3.821A pdb=" N SER B2535 " --> pdb=" O PHE B2531 " (cutoff:3.500A) Processing helix chain 'B' and resid 2536 through 2541 Processing helix chain 'C' and resid 577 through 585 removed outlier: 3.587A pdb=" N ILE C 581 " --> pdb=" O LEU C 577 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR C 585 " --> pdb=" O ILE C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 596 Processing helix chain 'C' and resid 607 through 624 removed outlier: 3.733A pdb=" N MET C 611 " --> pdb=" O LYS C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 650 removed outlier: 3.821A pdb=" N VAL C 650 " --> pdb=" O VAL C 646 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 706 Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 785 through 821 removed outlier: 4.579A pdb=" N SER C 789 " --> pdb=" O ASP C 785 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU C 807 " --> pdb=" O ARG C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 840 Processing helix chain 'C' and resid 845 through 866 removed outlier: 3.753A pdb=" N CYS C 851 " --> pdb=" O PRO C 847 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 950 removed outlier: 3.673A pdb=" N GLN C 925 " --> pdb=" O LEU C 921 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN C 926 " --> pdb=" O GLY C 922 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N HIS C 927 " --> pdb=" O TYR C 923 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE C 930 " --> pdb=" O ASN C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 983 Processing helix chain 'C' and resid 989 through 1006 removed outlier: 4.036A pdb=" N MET C1006 " --> pdb=" O ILE C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1023 removed outlier: 3.847A pdb=" N ARG C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1027 through 1053 Proline residue: C1034 - end of helix removed outlier: 4.718A pdb=" N LEU C1045 " --> pdb=" O THR C1041 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N TYR C1046 " --> pdb=" O LEU C1042 " (cutoff:3.500A) Processing helix chain 'C' and resid 1092 through 1111 Processing helix chain 'C' and resid 1141 through 1145 removed outlier: 3.717A pdb=" N ILE C1144 " --> pdb=" O PRO C1141 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS C1145 " --> pdb=" O ASN C1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1141 through 1145' Processing helix chain 'C' and resid 1150 through 1159 removed outlier: 4.339A pdb=" N ALA C1156 " --> pdb=" O MET C1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 1163 through 1173 removed outlier: 3.500A pdb=" N VAL C1167 " --> pdb=" O TRP C1163 " (cutoff:3.500A) Processing helix chain 'C' and resid 1181 through 1199 removed outlier: 3.508A pdb=" N LEU C1185 " --> pdb=" O GLY C1181 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR C1197 " --> pdb=" O LEU C1193 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C1199 " --> pdb=" O GLY C1195 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1224 removed outlier: 4.205A pdb=" N VAL C1220 " --> pdb=" O TYR C1216 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C1221 " --> pdb=" O ASN C1217 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ILE C1222 " --> pdb=" O VAL C1218 " (cutoff:3.500A) Processing helix chain 'C' and resid 1279 through 1299 removed outlier: 4.190A pdb=" N ASP C1283 " --> pdb=" O GLY C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1302 through 1315 removed outlier: 3.505A pdb=" N ASP C1308 " --> pdb=" O HIS C1304 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU C1309 " --> pdb=" O VAL C1305 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C1310 " --> pdb=" O SER C1306 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA C1311 " --> pdb=" O ALA C1307 " (cutoff:3.500A) Processing helix chain 'C' and resid 1315 through 1362 removed outlier: 3.512A pdb=" N GLY C1319 " --> pdb=" O GLN C1315 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLN C1336 " --> pdb=" O ASN C1332 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C1337 " --> pdb=" O PHE C1333 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS C1358 " --> pdb=" O ALA C1354 " (cutoff:3.500A) Processing helix chain 'C' and resid 1411 through 1415 Processing helix chain 'C' and resid 1505 through 1545 removed outlier: 5.735A pdb=" N HIS C1526 " --> pdb=" O ALA C1522 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS C1527 " --> pdb=" O PHE C1523 " (cutoff:3.500A) Processing helix chain 'C' and resid 1656 through 1669 removed outlier: 3.855A pdb=" N GLN C1669 " --> pdb=" O PHE C1665 " (cutoff:3.500A) Processing helix chain 'C' and resid 1672 through 1686 Processing helix chain 'C' and resid 1688 through 1701 removed outlier: 3.586A pdb=" N TYR C1692 " --> pdb=" O GLU C1688 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS C1699 " --> pdb=" O ILE C1695 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C1701 " --> pdb=" O LEU C1697 " (cutoff:3.500A) Processing helix chain 'C' and resid 1705 through 1707 No H-bonds generated for 'chain 'C' and resid 1705 through 1707' Processing helix chain 'C' and resid 1708 through 1719 removed outlier: 3.941A pdb=" N VAL C1712 " --> pdb=" O LEU C1708 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU C1713 " --> pdb=" O VAL C1709 " (cutoff:3.500A) Processing helix chain 'C' and resid 1728 through 1743 removed outlier: 3.757A pdb=" N PHE C1736 " --> pdb=" O THR C1732 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C1741 " --> pdb=" O THR C1737 " (cutoff:3.500A) Processing helix chain 'C' and resid 1780 through 1801 removed outlier: 3.743A pdb=" N LYS C1784 " --> pdb=" O ASP C1780 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL C1788 " --> pdb=" O LYS C1784 " (cutoff:3.500A) Processing helix chain 'C' and resid 1958 through 1966 removed outlier: 3.745A pdb=" N PHE C1962 " --> pdb=" O LEU C1958 " (cutoff:3.500A) Processing helix chain 'C' and resid 1979 through 1994 Processing helix chain 'C' and resid 2016 through 2040 removed outlier: 4.401A pdb=" N LEU C2021 " --> pdb=" O PRO C2017 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N PHE C2022 " --> pdb=" O GLN C2018 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N MET C2023 " --> pdb=" O ALA C2019 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ARG C2035 " --> pdb=" O MET C2031 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA C2036 " --> pdb=" O VAL C2032 " (cutoff:3.500A) Processing helix chain 'C' and resid 2043 through 2061 removed outlier: 4.127A pdb=" N VAL C2055 " --> pdb=" O VAL C2051 " (cutoff:3.500A) Processing helix chain 'C' and resid 2077 through 2100 removed outlier: 3.582A pdb=" N ILE C2088 " --> pdb=" O PHE C2084 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR C2089 " --> pdb=" O VAL C2085 " (cutoff:3.500A) Processing helix chain 'C' and resid 2115 through 2126 Processing helix chain 'C' and resid 2131 through 2143 removed outlier: 3.646A pdb=" N TRP C2140 " --> pdb=" O ALA C2136 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TRP C2142 " --> pdb=" O MET C2138 " (cutoff:3.500A) Processing helix chain 'C' and resid 2149 through 2174 removed outlier: 3.781A pdb=" N CYS C2154 " --> pdb=" O SER C2150 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL C2155 " --> pdb=" O ASN C2151 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA C2160 " --> pdb=" O GLU C2156 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE C2164 " --> pdb=" O ALA C2160 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU C2172 " --> pdb=" O SER C2168 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C2173 " --> pdb=" O ARG C2169 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS C2174 " --> pdb=" O GLU C2170 " (cutoff:3.500A) Processing helix chain 'C' and resid 2184 through 2205 removed outlier: 3.939A pdb=" N TYR C2189 " --> pdb=" O LYS C2185 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU C2194 " --> pdb=" O GLY C2190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE C2195 " --> pdb=" O MET C2191 " (cutoff:3.500A) Processing helix chain 'C' and resid 2206 through 2208 No H-bonds generated for 'chain 'C' and resid 2206 through 2208' Processing helix chain 'C' and resid 2252 through 2262 Processing helix chain 'C' and resid 2266 through 2276 removed outlier: 4.135A pdb=" N TYR C2276 " --> pdb=" O PHE C2272 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2279 No H-bonds generated for 'chain 'C' and resid 2277 through 2279' Processing helix chain 'C' and resid 2297 through 2311 Processing helix chain 'C' and resid 2348 through 2358 Processing helix chain 'C' and resid 2421 through 2426 Processing helix chain 'C' and resid 2466 through 2482 Processing helix chain 'C' and resid 2500 through 2517 removed outlier: 4.118A pdb=" N LEU C2506 " --> pdb=" O ARG C2502 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG C2514 " --> pdb=" O ILE C2510 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU C2515 " --> pdb=" O PHE C2511 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C2516 " --> pdb=" O LEU C2512 " (cutoff:3.500A) Processing helix chain 'C' and resid 2518 through 2522 removed outlier: 3.741A pdb=" N GLU C2522 " --> pdb=" O LEU C2519 " (cutoff:3.500A) Processing helix chain 'C' and resid 2525 through 2535 removed outlier: 3.820A pdb=" N SER C2535 " --> pdb=" O PHE C2531 " (cutoff:3.500A) Processing helix chain 'C' and resid 2536 through 2541 Processing sheet with id=AA1, first strand: chain 'A' and resid 2239 through 2243 removed outlier: 3.575A pdb=" N VAL A2226 " --> pdb=" O ALA A2243 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TRP A2321 " --> pdb=" O GLU A2338 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A2338 " --> pdb=" O TRP A2321 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2248 through 2250 removed outlier: 7.090A pdb=" N ILE A2376 " --> pdb=" O PHE A2449 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2401 through 2406 Processing sheet with id=AA4, first strand: chain 'B' and resid 2239 through 2243 removed outlier: 3.575A pdb=" N VAL B2226 " --> pdb=" O ALA B2243 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TRP B2321 " --> pdb=" O GLU B2338 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU B2338 " --> pdb=" O TRP B2321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2248 through 2250 removed outlier: 7.090A pdb=" N ILE B2376 " --> pdb=" O PHE B2449 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 2401 through 2406 Processing sheet with id=AA7, first strand: chain 'C' and resid 2239 through 2243 removed outlier: 3.575A pdb=" N VAL C2226 " --> pdb=" O ALA C2243 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N TRP C2321 " --> pdb=" O GLU C2338 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU C2338 " --> pdb=" O TRP C2321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2248 through 2250 removed outlier: 7.090A pdb=" N ILE C2376 " --> pdb=" O PHE C2449 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2401 through 2406 1809 hydrogen bonds defined for protein. 5355 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: 10.44 Time building geometry restraints manager: 12.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9251 1.34 - 1.46: 6447 1.46 - 1.58: 13876 1.58 - 1.70: 0 1.70 - 1.82: 186 Bond restraints: 29760 Sorted by residual: bond pdb=" CB TRP A2082 " pdb=" CG TRP A2082 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.05e+00 bond pdb=" CB TRP B2082 " pdb=" CG TRP B2082 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.05e+00 bond pdb=" CB TRP C2082 " pdb=" CG TRP C2082 " ideal model delta sigma weight residual 1.498 1.429 0.069 3.10e-02 1.04e+03 5.01e+00 bond pdb=" C GLU C2496 " pdb=" N LEU C2497 " ideal model delta sigma weight residual 1.331 1.281 0.050 2.83e-02 1.25e+03 3.11e+00 bond pdb=" C GLU B2496 " pdb=" N LEU B2497 " ideal model delta sigma weight residual 1.331 1.281 0.050 2.83e-02 1.25e+03 3.09e+00 ... (remaining 29755 not shown) Histogram of bond angle deviations from ideal: 98.92 - 106.01: 574 106.01 - 113.10: 15782 113.10 - 120.19: 11906 120.19 - 127.28: 11947 127.28 - 134.38: 294 Bond angle restraints: 40503 Sorted by residual: angle pdb=" C LEU B2106 " pdb=" N GLY B2107 " pdb=" CA GLY B2107 " ideal model delta sigma weight residual 121.41 132.72 -11.31 1.96e+00 2.60e-01 3.33e+01 angle pdb=" C LEU A2106 " pdb=" N GLY A2107 " pdb=" CA GLY A2107 " ideal model delta sigma weight residual 121.41 132.72 -11.31 1.96e+00 2.60e-01 3.33e+01 angle pdb=" C LEU C2106 " pdb=" N GLY C2107 " pdb=" CA GLY C2107 " ideal model delta sigma weight residual 121.41 132.70 -11.29 1.96e+00 2.60e-01 3.32e+01 angle pdb=" CB ILE C1280 " pdb=" CG1 ILE C1280 " pdb=" CD1 ILE C1280 " ideal model delta sigma weight residual 113.80 122.89 -9.09 2.10e+00 2.27e-01 1.87e+01 angle pdb=" CB ILE B1280 " pdb=" CG1 ILE B1280 " pdb=" CD1 ILE B1280 " ideal model delta sigma weight residual 113.80 122.85 -9.05 2.10e+00 2.27e-01 1.86e+01 ... (remaining 40498 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 15499 17.80 - 35.60: 1719 35.60 - 53.40: 248 53.40 - 71.20: 54 71.20 - 89.00: 42 Dihedral angle restraints: 17562 sinusoidal: 6072 harmonic: 11490 Sorted by residual: dihedral pdb=" CA ARG C1724 " pdb=" C ARG C1724 " pdb=" N PRO C1725 " pdb=" CA PRO C1725 " ideal model delta harmonic sigma weight residual -180.00 -144.27 -35.73 0 5.00e+00 4.00e-02 5.11e+01 dihedral pdb=" CA ARG A1724 " pdb=" C ARG A1724 " pdb=" N PRO A1725 " pdb=" CA PRO A1725 " ideal model delta harmonic sigma weight residual -180.00 -144.28 -35.72 0 5.00e+00 4.00e-02 5.10e+01 dihedral pdb=" CA ARG B1724 " pdb=" C ARG B1724 " pdb=" N PRO B1725 " pdb=" CA PRO B1725 " ideal model delta harmonic sigma weight residual 180.00 -144.29 -35.71 0 5.00e+00 4.00e-02 5.10e+01 ... (remaining 17559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3828 0.072 - 0.143: 768 0.143 - 0.215: 97 0.215 - 0.287: 20 0.287 - 0.359: 3 Chirality restraints: 4716 Sorted by residual: chirality pdb=" CG LEU A1673 " pdb=" CB LEU A1673 " pdb=" CD1 LEU A1673 " pdb=" CD2 LEU A1673 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CG LEU B1673 " pdb=" CB LEU B1673 " pdb=" CD1 LEU B1673 " pdb=" CD2 LEU B1673 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CG LEU C1673 " pdb=" CB LEU C1673 " pdb=" CD1 LEU C1673 " pdb=" CD2 LEU C1673 " both_signs ideal model delta sigma weight residual False -2.59 -2.23 -0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 4713 not shown) Planarity restraints: 5148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C1715 " -0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C PHE C1715 " 0.059 2.00e-02 2.50e+03 pdb=" O PHE C1715 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU C1716 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B1715 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C PHE B1715 " -0.059 2.00e-02 2.50e+03 pdb=" O PHE B1715 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU B1716 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A1715 " 0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C PHE A1715 " -0.059 2.00e-02 2.50e+03 pdb=" O PHE A1715 " 0.022 2.00e-02 2.50e+03 pdb=" N LEU A1716 " 0.020 2.00e-02 2.50e+03 ... (remaining 5145 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5648 2.77 - 3.30: 28036 3.30 - 3.83: 48779 3.83 - 4.37: 52525 4.37 - 4.90: 87088 Nonbonded interactions: 222076 Sorted by model distance: nonbonded pdb=" OG SER B2535 " pdb=" OG1 THR B2538 " model vdw 2.234 2.440 nonbonded pdb=" OG SER A2535 " pdb=" OG1 THR A2538 " model vdw 2.234 2.440 nonbonded pdb=" OG SER C2535 " pdb=" OG1 THR C2538 " model vdw 2.234 2.440 nonbonded pdb=" O ILE C2213 " pdb=" OG SER C2457 " model vdw 2.266 2.440 nonbonded pdb=" O ILE A2213 " pdb=" OG SER A2457 " model vdw 2.267 2.440 ... (remaining 222071 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' } 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.130 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 77.980 Find NCS groups from input model: 1.610 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 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 : 0.006 0.070 29760 Z= 0.410 Angle : 1.052 13.827 40503 Z= 0.576 Chirality : 0.059 0.359 4716 Planarity : 0.008 0.083 5148 Dihedral : 15.591 88.997 10053 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.79 % Allowed : 8.27 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.13 % Twisted General : 0.08 % 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: -4.80 (0.10), residues: 3810 helix: -2.57 (0.08), residues: 2439 sheet: -2.62 (0.32), residues: 210 loop : -4.32 (0.14), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B1717 HIS 0.009 0.002 HIS B1403 PHE 0.050 0.003 PHE C1039 TYR 0.034 0.003 TYR C1184 ARG 0.008 0.001 ARG A2534 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 550 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1363 GLN cc_start: 0.8279 (tp40) cc_final: 0.8058 (tt0) REVERT: A 1518 ARG cc_start: 0.8137 (ttm110) cc_final: 0.7837 (ptp90) REVERT: A 1519 TRP cc_start: 0.8463 (t60) cc_final: 0.8142 (t60) REVERT: A 1690 LEU cc_start: 0.8163 (pt) cc_final: 0.7746 (tt) REVERT: A 1697 LEU cc_start: 0.9024 (tp) cc_final: 0.8606 (mt) REVERT: A 1698 ASN cc_start: 0.8052 (p0) cc_final: 0.7723 (p0) REVERT: A 1731 MET cc_start: 0.8159 (mmt) cc_final: 0.7931 (mmp) REVERT: A 1984 ASP cc_start: 0.7520 (t70) cc_final: 0.7150 (t0) REVERT: A 2157 ASP cc_start: 0.8220 (t70) cc_final: 0.7974 (t0) REVERT: A 2181 GLN cc_start: 0.7891 (mp10) cc_final: 0.7663 (mp10) REVERT: A 2210 MET cc_start: 0.8052 (tpt) cc_final: 0.7487 (tmm) REVERT: A 2214 ARG cc_start: 0.5612 (mtm180) cc_final: 0.5018 (mmm-85) REVERT: A 2270 MET cc_start: 0.5398 (mmt) cc_final: 0.4784 (mmp) REVERT: A 2304 MET cc_start: 0.8403 (ttp) cc_final: 0.8031 (ttt) REVERT: A 2449 PHE cc_start: 0.6930 (m-80) cc_final: 0.6522 (m-80) REVERT: B 1690 LEU cc_start: 0.8379 (pt) cc_final: 0.7924 (tt) REVERT: B 1697 LEU cc_start: 0.9147 (tp) cc_final: 0.8823 (mt) REVERT: B 1698 ASN cc_start: 0.8228 (p0) cc_final: 0.7953 (p0) REVERT: B 1984 ASP cc_start: 0.7671 (t70) cc_final: 0.7408 (t0) REVERT: B 2119 LEU cc_start: 0.9532 (tp) cc_final: 0.9302 (tt) REVERT: B 2139 ASP cc_start: 0.7448 (t0) cc_final: 0.7129 (t0) REVERT: B 2157 ASP cc_start: 0.8226 (t70) cc_final: 0.7942 (t0) REVERT: B 2210 MET cc_start: 0.7982 (tpt) cc_final: 0.7196 (tmm) REVERT: B 2272 PHE cc_start: 0.6947 (t80) cc_final: 0.6201 (t80) REVERT: C 1519 TRP cc_start: 0.8427 (t60) cc_final: 0.7942 (t60) REVERT: C 1538 ARG cc_start: 0.9459 (ttm110) cc_final: 0.9135 (ttp80) REVERT: C 1690 LEU cc_start: 0.7978 (pt) cc_final: 0.7698 (tt) REVERT: C 1697 LEU cc_start: 0.8926 (tp) cc_final: 0.8397 (mt) REVERT: C 1700 MET cc_start: 0.7184 (ppp) cc_final: 0.6845 (ppp) REVERT: C 1731 MET cc_start: 0.8354 (mmt) cc_final: 0.8134 (mmm) REVERT: C 1989 ILE cc_start: 0.8972 (mt) cc_final: 0.8750 (mp) REVERT: C 2119 LEU cc_start: 0.9520 (tp) cc_final: 0.9316 (tt) REVERT: C 2133 GLU cc_start: 0.7837 (pm20) cc_final: 0.7557 (pm20) REVERT: C 2157 ASP cc_start: 0.8206 (t70) cc_final: 0.7953 (t0) REVERT: C 2210 MET cc_start: 0.8250 (tpt) cc_final: 0.7663 (tpt) REVERT: C 2214 ARG cc_start: 0.5424 (mtm180) cc_final: 0.5209 (mmm-85) REVERT: C 2272 PHE cc_start: 0.6919 (t80) cc_final: 0.6490 (t80) REVERT: C 2382 PRO cc_start: 0.8935 (Cg_endo) cc_final: 0.8679 (Cg_exo) REVERT: C 2446 MET cc_start: 0.8482 (ppp) cc_final: 0.8250 (ppp) outliers start: 21 outliers final: 5 residues processed: 568 average time/residue: 0.3967 time to fit residues: 360.5882 Evaluate side-chains 400 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 395 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain B residue 1280 ILE Chi-restraints excluded: chain B residue 2333 VAL Chi-restraints excluded: chain C residue 1280 ILE Chi-restraints excluded: chain C residue 2333 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 0.9990 chunk 295 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 199 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 chunk 227 optimal weight: 0.8980 chunk 354 optimal weight: 0.0060 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1315 GLN A1668 GLN A1669 GLN A1686 HIS ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2018 GLN A2058 HIS A2177 GLN A2254 GLN ** A2262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2271 GLN A2306 GLN ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2389 GLN ** A2409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2442 ASN ** B1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1315 GLN B1668 GLN B1669 GLN B1686 HIS ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2018 GLN B2058 HIS B2177 GLN ** B2262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2306 GLN ** B2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2391 GLN ** B2409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2442 ASN ** C1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1315 GLN C1668 GLN C1669 GLN C1686 HIS ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2018 GLN C2058 HIS C2177 GLN ** C2262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2306 GLN ** C2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2391 GLN ** C2409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2442 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29760 Z= 0.198 Angle : 0.683 9.885 40503 Z= 0.359 Chirality : 0.042 0.243 4716 Planarity : 0.005 0.071 5148 Dihedral : 6.548 39.155 4181 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 2.19 % Allowed : 15.86 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.12), residues: 3810 helix: -1.13 (0.09), residues: 2493 sheet: -2.31 (0.32), residues: 207 loop : -3.83 (0.16), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 836 HIS 0.010 0.001 HIS C1145 PHE 0.031 0.002 PHE A1039 TYR 0.023 0.002 TYR B2375 ARG 0.005 0.000 ARG A2104 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 448 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1170 PHE cc_start: 0.9236 (t80) cc_final: 0.9028 (t80) REVERT: A 1297 PHE cc_start: 0.9185 (m-80) cc_final: 0.8923 (m-80) REVERT: A 1518 ARG cc_start: 0.8051 (ttm110) cc_final: 0.7790 (ptp90) REVERT: A 1519 TRP cc_start: 0.8495 (t60) cc_final: 0.8240 (t60) REVERT: A 1690 LEU cc_start: 0.8105 (pt) cc_final: 0.7664 (tt) REVERT: A 1697 LEU cc_start: 0.8895 (tp) cc_final: 0.8564 (mt) REVERT: A 1731 MET cc_start: 0.8312 (mmt) cc_final: 0.8102 (mmm) REVERT: A 2104 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7028 (tpt90) REVERT: A 2157 ASP cc_start: 0.8202 (t70) cc_final: 0.7988 (t0) REVERT: A 2159 TYR cc_start: 0.8668 (t80) cc_final: 0.8438 (t80) REVERT: A 2181 GLN cc_start: 0.7779 (mp10) cc_final: 0.7555 (mp10) REVERT: A 2210 MET cc_start: 0.7922 (tpt) cc_final: 0.7438 (tmm) REVERT: A 2214 ARG cc_start: 0.5662 (mtm180) cc_final: 0.5073 (mmm-85) REVERT: A 2270 MET cc_start: 0.5754 (mmt) cc_final: 0.4663 (mmp) REVERT: A 2271 GLN cc_start: 0.8521 (tp40) cc_final: 0.8236 (mm-40) REVERT: A 2446 MET cc_start: 0.8005 (ppp) cc_final: 0.7639 (ppp) REVERT: A 2517 ARG cc_start: 0.8563 (mmt90) cc_final: 0.8346 (mmt90) REVERT: B 1170 PHE cc_start: 0.9216 (t80) cc_final: 0.8750 (t80) REVERT: B 1287 PHE cc_start: 0.9083 (t80) cc_final: 0.8754 (t80) REVERT: B 1411 ASP cc_start: 0.6917 (t70) cc_final: 0.6535 (t0) REVERT: B 1690 LEU cc_start: 0.8249 (pt) cc_final: 0.7737 (tt) REVERT: B 1697 LEU cc_start: 0.9019 (tp) cc_final: 0.8781 (mt) REVERT: B 2022 PHE cc_start: 0.7710 (t80) cc_final: 0.7465 (t80) REVERT: B 2104 ARG cc_start: 0.7546 (OUTLIER) cc_final: 0.7107 (tpt90) REVERT: B 2139 ASP cc_start: 0.7138 (t0) cc_final: 0.6673 (t0) REVERT: B 2157 ASP cc_start: 0.8139 (t70) cc_final: 0.7801 (t0) REVERT: B 2210 MET cc_start: 0.7280 (tpt) cc_final: 0.7038 (tmm) REVERT: B 2271 GLN cc_start: 0.8365 (tp-100) cc_final: 0.8114 (mm-40) REVERT: B 2272 PHE cc_start: 0.6905 (t80) cc_final: 0.6345 (t80) REVERT: B 2352 ARG cc_start: 0.7134 (mmm160) cc_final: 0.6411 (mmm160) REVERT: B 2446 MET cc_start: 0.8183 (ppp) cc_final: 0.7877 (ppp) REVERT: B 2485 PHE cc_start: 0.6498 (m-10) cc_final: 0.6263 (m-80) REVERT: C 1349 MET cc_start: 0.8060 (mmm) cc_final: 0.7762 (mmm) REVERT: C 1519 TRP cc_start: 0.8407 (t60) cc_final: 0.8102 (t60) REVERT: C 1690 LEU cc_start: 0.8205 (pt) cc_final: 0.7715 (tt) REVERT: C 1697 LEU cc_start: 0.8885 (tp) cc_final: 0.8192 (mt) REVERT: C 1989 ILE cc_start: 0.8927 (mt) cc_final: 0.8705 (mp) REVERT: C 2104 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7336 (tpt90) REVERT: C 2119 LEU cc_start: 0.9511 (tp) cc_final: 0.9254 (tp) REVERT: C 2157 ASP cc_start: 0.8241 (t70) cc_final: 0.7956 (t0) REVERT: C 2271 GLN cc_start: 0.8470 (tp-100) cc_final: 0.8025 (mm-40) REVERT: C 2272 PHE cc_start: 0.6895 (t80) cc_final: 0.6418 (t80) REVERT: C 2382 PRO cc_start: 0.8898 (Cg_endo) cc_final: 0.8621 (Cg_exo) outliers start: 58 outliers final: 29 residues processed: 484 average time/residue: 0.3629 time to fit residues: 291.8481 Evaluate side-chains 426 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 394 time to evaluate : 3.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1976 VAL Chi-restraints excluded: chain A residue 2104 ARG Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2332 THR Chi-restraints excluded: chain A residue 2473 ILE Chi-restraints excluded: chain A residue 2488 ILE Chi-restraints excluded: chain A residue 2510 ILE Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1702 THR Chi-restraints excluded: chain B residue 1976 VAL Chi-restraints excluded: chain B residue 2044 LEU Chi-restraints excluded: chain B residue 2104 ARG Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2510 ILE Chi-restraints excluded: chain B residue 2539 MET Chi-restraints excluded: chain C residue 1178 SER Chi-restraints excluded: chain C residue 1323 TYR Chi-restraints excluded: chain C residue 1689 LEU Chi-restraints excluded: chain C residue 1702 THR Chi-restraints excluded: chain C residue 1991 ILE Chi-restraints excluded: chain C residue 2104 ARG Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2203 ILE Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2449 PHE Chi-restraints excluded: chain C residue 2510 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 241 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 354 optimal weight: 0.9980 chunk 383 optimal weight: 0.5980 chunk 315 optimal weight: 0.9990 chunk 351 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN A2262 GLN A2303 GLN ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2391 GLN ** A2409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1669 GLN ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2254 GLN ** B2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN ** C2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29760 Z= 0.225 Angle : 0.660 13.995 40503 Z= 0.343 Chirality : 0.043 0.314 4716 Planarity : 0.005 0.062 5148 Dihedral : 5.908 35.897 4173 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.13 % Allowed : 17.93 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.13), residues: 3810 helix: -0.44 (0.10), residues: 2544 sheet: -1.98 (0.34), residues: 207 loop : -3.76 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B2082 HIS 0.005 0.001 HIS A1403 PHE 0.030 0.002 PHE A1039 TYR 0.019 0.002 TYR C2533 ARG 0.007 0.000 ARG C1360 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 433 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1152 MET cc_start: 0.8917 (mtm) cc_final: 0.8392 (mtm) REVERT: A 1297 PHE cc_start: 0.9182 (m-80) cc_final: 0.8692 (m-80) REVERT: A 1519 TRP cc_start: 0.8492 (t60) cc_final: 0.8229 (t60) REVERT: A 1690 LEU cc_start: 0.8259 (pt) cc_final: 0.7731 (tt) REVERT: A 1731 MET cc_start: 0.8211 (mmt) cc_final: 0.8004 (mmp) REVERT: A 2104 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7208 (tpt90) REVERT: A 2157 ASP cc_start: 0.8241 (t70) cc_final: 0.7996 (t70) REVERT: A 2181 GLN cc_start: 0.7789 (mp10) cc_final: 0.7517 (mp10) REVERT: A 2210 MET cc_start: 0.7880 (tpt) cc_final: 0.7389 (tmm) REVERT: A 2214 ARG cc_start: 0.5671 (mtm180) cc_final: 0.5097 (mmm-85) REVERT: A 2256 TYR cc_start: 0.7572 (t80) cc_final: 0.7286 (t80) REVERT: A 2270 MET cc_start: 0.5736 (mmt) cc_final: 0.5211 (mmt) REVERT: A 2271 GLN cc_start: 0.8580 (tp40) cc_final: 0.8234 (mm-40) REVERT: A 2446 MET cc_start: 0.7867 (ppp) cc_final: 0.7618 (ppp) REVERT: A 2517 ARG cc_start: 0.8664 (mmt90) cc_final: 0.8414 (mmt90) REVERT: B 1170 PHE cc_start: 0.9240 (t80) cc_final: 0.8831 (t80) REVERT: B 1287 PHE cc_start: 0.9072 (t80) cc_final: 0.8730 (t80) REVERT: B 1288 PHE cc_start: 0.8332 (t80) cc_final: 0.7948 (t80) REVERT: B 1292 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8496 (mt) REVERT: B 1518 ARG cc_start: 0.7848 (ptt180) cc_final: 0.7534 (ptt90) REVERT: B 1690 LEU cc_start: 0.8395 (pt) cc_final: 0.7834 (tt) REVERT: B 2022 PHE cc_start: 0.7776 (t80) cc_final: 0.7506 (t80) REVERT: B 2104 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7266 (tpt90) REVERT: B 2157 ASP cc_start: 0.8199 (t70) cc_final: 0.7891 (t0) REVERT: B 2270 MET cc_start: 0.6150 (mmt) cc_final: 0.5608 (mmt) REVERT: B 2271 GLN cc_start: 0.8460 (tp-100) cc_final: 0.8136 (mm-40) REVERT: B 2272 PHE cc_start: 0.6997 (t80) cc_final: 0.6584 (t80) REVERT: B 2323 PHE cc_start: 0.8876 (m-80) cc_final: 0.8533 (m-80) REVERT: B 2446 MET cc_start: 0.8207 (ppp) cc_final: 0.7988 (ppp) REVERT: C 1226 MET cc_start: 0.8540 (mtm) cc_final: 0.8203 (mpp) REVERT: C 1518 ARG cc_start: 0.7824 (ptt180) cc_final: 0.7528 (ptt90) REVERT: C 1519 TRP cc_start: 0.8422 (t60) cc_final: 0.8129 (t60) REVERT: C 1690 LEU cc_start: 0.8224 (pt) cc_final: 0.7723 (tt) REVERT: C 1787 LEU cc_start: 0.8477 (pp) cc_final: 0.8064 (pp) REVERT: C 1989 ILE cc_start: 0.8985 (mt) cc_final: 0.8757 (mp) REVERT: C 1993 PHE cc_start: 0.8338 (t80) cc_final: 0.8115 (t80) REVERT: C 2104 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7396 (tpt90) REVERT: C 2119 LEU cc_start: 0.9549 (tp) cc_final: 0.9332 (tp) REVERT: C 2133 GLU cc_start: 0.7860 (pm20) cc_final: 0.7504 (pm20) REVERT: C 2271 GLN cc_start: 0.8593 (tp-100) cc_final: 0.8102 (mm-40) REVERT: C 2272 PHE cc_start: 0.6758 (t80) cc_final: 0.6548 (t80) REVERT: C 2382 PRO cc_start: 0.8846 (Cg_endo) cc_final: 0.8556 (Cg_exo) REVERT: C 2515 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7523 (tm-30) outliers start: 83 outliers final: 44 residues processed: 486 average time/residue: 0.3549 time to fit residues: 289.9916 Evaluate side-chains 446 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 398 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 2085 VAL Chi-restraints excluded: chain A residue 2104 ARG Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2262 GLN Chi-restraints excluded: chain A residue 2332 THR Chi-restraints excluded: chain A residue 2449 PHE Chi-restraints excluded: chain A residue 2510 ILE Chi-restraints excluded: chain B residue 1167 VAL Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1286 CYS Chi-restraints excluded: chain B residue 1292 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1701 VAL Chi-restraints excluded: chain B residue 1702 THR Chi-restraints excluded: chain B residue 1791 MET Chi-restraints excluded: chain B residue 1976 VAL Chi-restraints excluded: chain B residue 2023 MET Chi-restraints excluded: chain B residue 2085 VAL Chi-restraints excluded: chain B residue 2104 ARG Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2172 GLU Chi-restraints excluded: chain B residue 2510 ILE Chi-restraints excluded: chain C residue 1167 VAL Chi-restraints excluded: chain C residue 1168 VAL Chi-restraints excluded: chain C residue 1178 SER Chi-restraints excluded: chain C residue 1302 PHE Chi-restraints excluded: chain C residue 1323 TYR Chi-restraints excluded: chain C residue 1540 LEU Chi-restraints excluded: chain C residue 1676 LEU Chi-restraints excluded: chain C residue 1689 LEU Chi-restraints excluded: chain C residue 1702 THR Chi-restraints excluded: chain C residue 1726 SER Chi-restraints excluded: chain C residue 2085 VAL Chi-restraints excluded: chain C residue 2088 ILE Chi-restraints excluded: chain C residue 2104 ARG Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2172 GLU Chi-restraints excluded: chain C residue 2207 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 356 optimal weight: 0.7980 chunk 376 optimal weight: 9.9990 chunk 186 optimal weight: 0.0970 chunk 337 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1669 GLN ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1799 GLN ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2409 GLN ** B1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1799 GLN B2254 GLN ** B2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2409 GLN ** C1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1669 GLN ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1799 GLN C2303 GLN ** C2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2409 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29760 Z= 0.175 Angle : 0.624 13.884 40503 Z= 0.320 Chirality : 0.043 0.463 4716 Planarity : 0.005 0.058 5148 Dihedral : 5.498 32.684 4173 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.79 % Allowed : 19.97 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.14), residues: 3810 helix: -0.01 (0.10), residues: 2544 sheet: -1.62 (0.36), residues: 207 loop : -3.55 (0.17), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C2082 HIS 0.005 0.001 HIS A1403 PHE 0.028 0.001 PHE A1039 TYR 0.013 0.001 TYR B1184 ARG 0.006 0.000 ARG A2104 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 470 time to evaluate : 3.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1152 MET cc_start: 0.8851 (mtm) cc_final: 0.8420 (mtm) REVERT: A 1297 PHE cc_start: 0.9171 (m-80) cc_final: 0.8877 (m-80) REVERT: A 1519 TRP cc_start: 0.8418 (t60) cc_final: 0.8174 (t60) REVERT: A 1690 LEU cc_start: 0.8220 (pt) cc_final: 0.7646 (tt) REVERT: A 2104 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7233 (tpt90) REVERT: A 2157 ASP cc_start: 0.8127 (t70) cc_final: 0.7875 (t0) REVERT: A 2181 GLN cc_start: 0.8040 (mp10) cc_final: 0.7718 (mp10) REVERT: A 2210 MET cc_start: 0.7785 (tpt) cc_final: 0.7324 (tmm) REVERT: A 2214 ARG cc_start: 0.5451 (mtm180) cc_final: 0.5044 (mmm-85) REVERT: A 2256 TYR cc_start: 0.7709 (t80) cc_final: 0.7467 (t80) REVERT: A 2270 MET cc_start: 0.5861 (mmt) cc_final: 0.5447 (mmt) REVERT: A 2271 GLN cc_start: 0.8655 (tp40) cc_final: 0.8211 (mm-40) REVERT: A 2370 HIS cc_start: 0.6966 (m-70) cc_final: 0.6736 (m-70) REVERT: A 2446 MET cc_start: 0.7980 (ppp) cc_final: 0.7742 (ppp) REVERT: A 2517 ARG cc_start: 0.8678 (mmt90) cc_final: 0.8437 (mmt90) REVERT: B 1170 PHE cc_start: 0.9199 (t80) cc_final: 0.8783 (t80) REVERT: B 1287 PHE cc_start: 0.9085 (t80) cc_final: 0.8772 (t80) REVERT: B 1518 ARG cc_start: 0.7617 (ptt180) cc_final: 0.7322 (ptt90) REVERT: B 1690 LEU cc_start: 0.8369 (pt) cc_final: 0.7780 (tt) REVERT: B 1976 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8819 (m) REVERT: B 2022 PHE cc_start: 0.7669 (t80) cc_final: 0.7421 (t80) REVERT: B 2104 ARG cc_start: 0.7928 (OUTLIER) cc_final: 0.7456 (tpt90) REVERT: B 2157 ASP cc_start: 0.8169 (t70) cc_final: 0.7900 (t0) REVERT: B 2270 MET cc_start: 0.5931 (mmt) cc_final: 0.5378 (mmt) REVERT: B 2271 GLN cc_start: 0.8516 (tp-100) cc_final: 0.8099 (mm-40) REVERT: B 2272 PHE cc_start: 0.7001 (t80) cc_final: 0.6602 (t80) REVERT: B 2323 PHE cc_start: 0.8810 (m-80) cc_final: 0.8446 (m-80) REVERT: B 2446 MET cc_start: 0.8150 (ppp) cc_final: 0.7901 (ppp) REVERT: C 1199 LEU cc_start: 0.9147 (mt) cc_final: 0.8914 (mt) REVERT: C 1226 MET cc_start: 0.8510 (mtm) cc_final: 0.8197 (mpp) REVERT: C 1518 ARG cc_start: 0.7722 (ptt180) cc_final: 0.7416 (ptt90) REVERT: C 1519 TRP cc_start: 0.8414 (t60) cc_final: 0.8126 (t60) REVERT: C 1690 LEU cc_start: 0.8251 (pt) cc_final: 0.7783 (tt) REVERT: C 1786 ASP cc_start: 0.9178 (t70) cc_final: 0.8871 (t0) REVERT: C 2023 MET cc_start: 0.7131 (mtm) cc_final: 0.6753 (mtp) REVERT: C 2086 LYS cc_start: 0.8644 (ptpp) cc_final: 0.8436 (ptpp) REVERT: C 2104 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7424 (tpt90) REVERT: C 2133 GLU cc_start: 0.7842 (pm20) cc_final: 0.7433 (pm20) REVERT: C 2264 ASP cc_start: 0.8148 (t0) cc_final: 0.7787 (t0) REVERT: C 2271 GLN cc_start: 0.8551 (tp-100) cc_final: 0.8130 (mm-40) REVERT: C 2382 PRO cc_start: 0.8801 (Cg_endo) cc_final: 0.8498 (Cg_exo) outliers start: 74 outliers final: 44 residues processed: 523 average time/residue: 0.3487 time to fit residues: 307.3629 Evaluate side-chains 467 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 419 time to evaluate : 3.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1168 VAL Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1701 VAL Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 2016 VAL Chi-restraints excluded: chain A residue 2085 VAL Chi-restraints excluded: chain A residue 2104 ARG Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2262 GLN Chi-restraints excluded: chain A residue 2449 PHE Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain A residue 2510 ILE Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1296 ILE Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1701 VAL Chi-restraints excluded: chain B residue 1702 THR Chi-restraints excluded: chain B residue 1976 VAL Chi-restraints excluded: chain B residue 2016 VAL Chi-restraints excluded: chain B residue 2023 MET Chi-restraints excluded: chain B residue 2085 VAL Chi-restraints excluded: chain B residue 2104 ARG Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2134 LEU Chi-restraints excluded: chain B residue 2226 VAL Chi-restraints excluded: chain B residue 2471 VAL Chi-restraints excluded: chain B residue 2510 ILE Chi-restraints excluded: chain C residue 1292 LEU Chi-restraints excluded: chain C residue 1323 TYR Chi-restraints excluded: chain C residue 1651 ASP Chi-restraints excluded: chain C residue 1676 LEU Chi-restraints excluded: chain C residue 1689 LEU Chi-restraints excluded: chain C residue 1702 THR Chi-restraints excluded: chain C residue 1726 SER Chi-restraints excluded: chain C residue 1966 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2085 VAL Chi-restraints excluded: chain C residue 2104 ARG Chi-restraints excluded: chain C residue 2128 VAL Chi-restraints excluded: chain C residue 2172 GLU Chi-restraints excluded: chain C residue 2226 VAL Chi-restraints excluded: chain C residue 2332 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 2.9990 chunk 213 optimal weight: 0.9980 chunk 5 optimal weight: 40.0000 chunk 280 optimal weight: 30.0000 chunk 155 optimal weight: 20.0000 chunk 321 optimal weight: 6.9990 chunk 260 optimal weight: 50.0000 chunk 0 optimal weight: 50.0000 chunk 192 optimal weight: 4.9990 chunk 338 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2404 GLN ** B1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2254 GLN B2303 GLN ** B2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN ** C2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2389 GLN C2404 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29760 Z= 0.312 Angle : 0.685 13.852 40503 Z= 0.355 Chirality : 0.044 0.391 4716 Planarity : 0.005 0.055 5148 Dihedral : 5.426 31.828 4173 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.44 % Allowed : 21.82 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3810 helix: 0.16 (0.10), residues: 2529 sheet: -1.61 (0.35), residues: 207 loop : -3.43 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B2082 HIS 0.007 0.001 HIS A1403 PHE 0.044 0.002 PHE A1189 TYR 0.025 0.002 TYR C2533 ARG 0.007 0.001 ARG A2104 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 429 time to evaluate : 3.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1152 MET cc_start: 0.8908 (mtm) cc_final: 0.8586 (mtm) REVERT: A 1297 PHE cc_start: 0.9194 (m-80) cc_final: 0.8892 (m-80) REVERT: A 1519 TRP cc_start: 0.8499 (t60) cc_final: 0.8171 (t60) REVERT: A 1690 LEU cc_start: 0.8322 (pt) cc_final: 0.7778 (tt) REVERT: A 1696 ILE cc_start: 0.9564 (mm) cc_final: 0.9283 (mt) REVERT: A 2104 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7358 (tpt90) REVERT: A 2157 ASP cc_start: 0.8397 (t70) cc_final: 0.8183 (t70) REVERT: A 2181 GLN cc_start: 0.7847 (mp10) cc_final: 0.7569 (mp10) REVERT: A 2210 MET cc_start: 0.7854 (tpt) cc_final: 0.7345 (tmm) REVERT: A 2214 ARG cc_start: 0.5642 (mtm180) cc_final: 0.5034 (mmm-85) REVERT: A 2272 PHE cc_start: 0.6278 (t80) cc_final: 0.5919 (t80) REVERT: A 2326 ASP cc_start: 0.8128 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: A 2370 HIS cc_start: 0.7009 (m-70) cc_final: 0.6770 (m-70) REVERT: A 2446 MET cc_start: 0.8173 (ppp) cc_final: 0.7938 (ppp) REVERT: B 1170 PHE cc_start: 0.9239 (t80) cc_final: 0.8873 (t80) REVERT: B 1287 PHE cc_start: 0.9123 (t80) cc_final: 0.8822 (t80) REVERT: B 1518 ARG cc_start: 0.7721 (ptt180) cc_final: 0.7404 (ptt90) REVERT: B 1690 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.7922 (tt) REVERT: B 1716 LEU cc_start: 0.8411 (mm) cc_final: 0.8183 (mp) REVERT: B 2022 PHE cc_start: 0.7888 (t80) cc_final: 0.7611 (t80) REVERT: B 2050 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7480 (tp-100) REVERT: B 2104 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7464 (tpt90) REVERT: B 2157 ASP cc_start: 0.8234 (t70) cc_final: 0.7982 (t0) REVERT: B 2210 MET cc_start: 0.8048 (tmm) cc_final: 0.7789 (tmm) REVERT: B 2270 MET cc_start: 0.6096 (mmt) cc_final: 0.5529 (mmt) REVERT: B 2271 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8173 (mm-40) REVERT: B 2272 PHE cc_start: 0.7045 (t80) cc_final: 0.6717 (t80) REVERT: B 2323 PHE cc_start: 0.8820 (m-80) cc_final: 0.8455 (m-80) REVERT: B 2404 GLN cc_start: 0.7032 (mt0) cc_final: 0.6291 (mm110) REVERT: C 1201 LYS cc_start: 0.8991 (mmtm) cc_final: 0.8662 (mmtm) REVERT: C 1226 MET cc_start: 0.8478 (mtm) cc_final: 0.8149 (mpp) REVERT: C 1519 TRP cc_start: 0.8473 (t60) cc_final: 0.8066 (t60) REVERT: C 1675 LEU cc_start: 0.8941 (tp) cc_final: 0.8670 (tt) REVERT: C 1690 LEU cc_start: 0.8213 (pt) cc_final: 0.7677 (tt) REVERT: C 1786 ASP cc_start: 0.9120 (t70) cc_final: 0.8896 (t0) REVERT: C 2104 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7380 (tpt90) REVERT: C 2133 GLU cc_start: 0.8214 (pm20) cc_final: 0.7780 (pm20) REVERT: C 2264 ASP cc_start: 0.8326 (t0) cc_final: 0.8045 (t0) REVERT: C 2271 GLN cc_start: 0.8588 (tp-100) cc_final: 0.8165 (mm-40) REVERT: C 2382 PRO cc_start: 0.8785 (Cg_endo) cc_final: 0.8478 (Cg_exo) REVERT: C 2539 MET cc_start: 0.8893 (ttp) cc_final: 0.8637 (ttm) outliers start: 91 outliers final: 59 residues processed: 486 average time/residue: 0.3431 time to fit residues: 280.6106 Evaluate side-chains 471 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 406 time to evaluate : 4.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 2016 VAL Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2085 VAL Chi-restraints excluded: chain A residue 2104 ARG Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2172 GLU Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2326 ASP Chi-restraints excluded: chain A residue 2449 PHE Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain A residue 2510 ILE Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1286 CYS Chi-restraints excluded: chain B residue 1296 ILE Chi-restraints excluded: chain B residue 1520 LEU Chi-restraints excluded: chain B residue 1540 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 1701 VAL Chi-restraints excluded: chain B residue 1702 THR Chi-restraints excluded: chain B residue 1976 VAL Chi-restraints excluded: chain B residue 1987 ASP Chi-restraints excluded: chain B residue 2016 VAL Chi-restraints excluded: chain B residue 2023 MET Chi-restraints excluded: chain B residue 2050 GLN Chi-restraints excluded: chain B residue 2055 VAL Chi-restraints excluded: chain B residue 2085 VAL Chi-restraints excluded: chain B residue 2104 ARG Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2172 GLU Chi-restraints excluded: chain B residue 2199 LEU Chi-restraints excluded: chain B residue 2226 VAL Chi-restraints excluded: chain B residue 2471 VAL Chi-restraints excluded: chain B residue 2510 ILE Chi-restraints excluded: chain C residue 1178 SER Chi-restraints excluded: chain C residue 1286 CYS Chi-restraints excluded: chain C residue 1292 LEU Chi-restraints excluded: chain C residue 1323 TYR Chi-restraints excluded: chain C residue 1540 LEU Chi-restraints excluded: chain C residue 1651 ASP Chi-restraints excluded: chain C residue 1689 LEU Chi-restraints excluded: chain C residue 1702 THR Chi-restraints excluded: chain C residue 1726 SER Chi-restraints excluded: chain C residue 1966 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2021 LEU Chi-restraints excluded: chain C residue 2085 VAL Chi-restraints excluded: chain C residue 2104 ARG Chi-restraints excluded: chain C residue 2172 GLU Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2226 VAL Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2471 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 1.9990 chunk 339 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 221 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 377 optimal weight: 10.0000 chunk 313 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 124 optimal weight: 0.5980 chunk 198 optimal weight: 0.0470 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1334 HIS ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2409 GLN ** B1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1334 HIS ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2254 GLN ** B2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2409 GLN ** C1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1334 HIS ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN ** C2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2409 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29760 Z= 0.166 Angle : 0.632 16.187 40503 Z= 0.320 Chirality : 0.043 0.456 4716 Planarity : 0.004 0.053 5148 Dihedral : 5.127 28.291 4173 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.51 % Allowed : 22.35 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3810 helix: 0.47 (0.10), residues: 2538 sheet: -1.32 (0.35), residues: 213 loop : -3.25 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B2082 HIS 0.005 0.001 HIS C1403 PHE 0.032 0.002 PHE A1189 TYR 0.013 0.001 TYR A1184 ARG 0.006 0.000 ARG C2214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 469 time to evaluate : 3.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1152 MET cc_start: 0.8865 (mtm) cc_final: 0.8567 (mtm) REVERT: A 1297 PHE cc_start: 0.9167 (m-80) cc_final: 0.8805 (m-80) REVERT: A 1519 TRP cc_start: 0.8474 (t60) cc_final: 0.8165 (t60) REVERT: A 1690 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7782 (tt) REVERT: A 1696 ILE cc_start: 0.9489 (mm) cc_final: 0.9133 (mt) REVERT: A 2050 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7870 (tp40) REVERT: A 2104 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7324 (tpt90) REVERT: A 2157 ASP cc_start: 0.8182 (t70) cc_final: 0.7935 (t0) REVERT: A 2159 TYR cc_start: 0.8642 (t80) cc_final: 0.8404 (t80) REVERT: A 2181 GLN cc_start: 0.8081 (mp10) cc_final: 0.7773 (mp10) REVERT: A 2210 MET cc_start: 0.7721 (tpt) cc_final: 0.7230 (tmm) REVERT: A 2326 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7581 (m-30) REVERT: A 2370 HIS cc_start: 0.6950 (m-70) cc_final: 0.6694 (m-70) REVERT: A 2395 GLU cc_start: 0.5548 (OUTLIER) cc_final: 0.4954 (mp0) REVERT: A 2436 ASP cc_start: 0.7663 (p0) cc_final: 0.7295 (p0) REVERT: A 2446 MET cc_start: 0.8100 (ppp) cc_final: 0.7882 (ppp) REVERT: A 2517 ARG cc_start: 0.8703 (mmt90) cc_final: 0.8485 (mmt90) REVERT: B 1170 PHE cc_start: 0.9239 (t80) cc_final: 0.8843 (t80) REVERT: B 1287 PHE cc_start: 0.9085 (t80) cc_final: 0.8818 (t80) REVERT: B 1518 ARG cc_start: 0.7597 (ptt180) cc_final: 0.7305 (ptt90) REVERT: B 1690 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7831 (tt) REVERT: B 2022 PHE cc_start: 0.7687 (t80) cc_final: 0.7428 (t80) REVERT: B 2050 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.8006 (tp40) REVERT: B 2104 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7563 (tpt90) REVERT: B 2157 ASP cc_start: 0.8176 (t70) cc_final: 0.7935 (t0) REVERT: B 2172 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7270 (tm-30) REVERT: B 2210 MET cc_start: 0.7856 (tmm) cc_final: 0.7277 (tmm) REVERT: B 2270 MET cc_start: 0.6073 (mmt) cc_final: 0.5687 (mmt) REVERT: B 2271 GLN cc_start: 0.8581 (tp-100) cc_final: 0.8126 (mm-40) REVERT: B 2272 PHE cc_start: 0.6975 (t80) cc_final: 0.6592 (t80) REVERT: B 2304 MET cc_start: 0.8043 (ttp) cc_final: 0.7834 (ttt) REVERT: B 2323 PHE cc_start: 0.8841 (m-80) cc_final: 0.8578 (m-10) REVERT: B 2395 GLU cc_start: 0.6306 (OUTLIER) cc_final: 0.5933 (tt0) REVERT: B 2404 GLN cc_start: 0.6917 (mt0) cc_final: 0.6040 (mm-40) REVERT: B 2446 MET cc_start: 0.8313 (ppp) cc_final: 0.8046 (ppp) REVERT: C 1201 LYS cc_start: 0.9084 (mmtm) cc_final: 0.8774 (mmtm) REVERT: C 1519 TRP cc_start: 0.8406 (t60) cc_final: 0.8031 (t60) REVERT: C 1675 LEU cc_start: 0.8909 (tp) cc_final: 0.8626 (tt) REVERT: C 1690 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7724 (tt) REVERT: C 1786 ASP cc_start: 0.9101 (t70) cc_final: 0.8883 (t0) REVERT: C 2104 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7426 (tpt90) REVERT: C 2133 GLU cc_start: 0.7909 (pm20) cc_final: 0.7433 (pm20) REVERT: C 2134 LEU cc_start: 0.9215 (mt) cc_final: 0.9009 (mt) REVERT: C 2271 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8195 (mm-40) REVERT: C 2382 PRO cc_start: 0.8729 (Cg_endo) cc_final: 0.8429 (Cg_exo) outliers start: 93 outliers final: 45 residues processed: 532 average time/residue: 0.3377 time to fit residues: 304.1320 Evaluate side-chains 487 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 430 time to evaluate : 3.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1302 PHE Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 2016 VAL Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2050 GLN Chi-restraints excluded: chain A residue 2085 VAL Chi-restraints excluded: chain A residue 2104 ARG Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2326 ASP Chi-restraints excluded: chain A residue 2336 THR Chi-restraints excluded: chain A residue 2395 GLU Chi-restraints excluded: chain A residue 2449 PHE Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain A residue 2510 ILE Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1296 ILE Chi-restraints excluded: chain B residue 1520 LEU Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 1702 THR Chi-restraints excluded: chain B residue 2023 MET Chi-restraints excluded: chain B residue 2044 LEU Chi-restraints excluded: chain B residue 2050 GLN Chi-restraints excluded: chain B residue 2085 VAL Chi-restraints excluded: chain B residue 2104 ARG Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2134 LEU Chi-restraints excluded: chain B residue 2172 GLU Chi-restraints excluded: chain B residue 2226 VAL Chi-restraints excluded: chain B residue 2395 GLU Chi-restraints excluded: chain B residue 2510 ILE Chi-restraints excluded: chain C residue 1178 SER Chi-restraints excluded: chain C residue 1292 LEU Chi-restraints excluded: chain C residue 1302 PHE Chi-restraints excluded: chain C residue 1323 TYR Chi-restraints excluded: chain C residue 1689 LEU Chi-restraints excluded: chain C residue 1690 LEU Chi-restraints excluded: chain C residue 1702 THR Chi-restraints excluded: chain C residue 1966 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2085 VAL Chi-restraints excluded: chain C residue 2104 ARG Chi-restraints excluded: chain C residue 2172 GLU Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2226 VAL Chi-restraints excluded: chain C residue 2336 THR Chi-restraints excluded: chain C residue 2471 VAL Chi-restraints excluded: chain C residue 2533 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 275 optimal weight: 4.9990 chunk 213 optimal weight: 0.6980 chunk 317 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 375 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 229 optimal weight: 7.9990 chunk 173 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 ASN A1668 GLN ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1668 GLN ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2254 GLN ** B2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1558 GLN ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN ** C2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 29760 Z= 0.351 Angle : 0.724 16.301 40503 Z= 0.371 Chirality : 0.045 0.414 4716 Planarity : 0.005 0.051 5148 Dihedral : 5.199 28.642 4173 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.59 % Allowed : 23.67 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3810 helix: 0.49 (0.10), residues: 2520 sheet: -1.32 (0.35), residues: 213 loop : -3.25 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B2082 HIS 0.008 0.001 HIS C1403 PHE 0.042 0.002 PHE C1189 TYR 0.037 0.002 TYR C2533 ARG 0.008 0.001 ARG C2534 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 429 time to evaluate : 3.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1152 MET cc_start: 0.8900 (mtm) cc_final: 0.8601 (mtm) REVERT: A 1201 LYS cc_start: 0.9108 (mmtm) cc_final: 0.8802 (mmtm) REVERT: A 1297 PHE cc_start: 0.9143 (m-80) cc_final: 0.8782 (m-80) REVERT: A 1519 TRP cc_start: 0.8386 (t60) cc_final: 0.8134 (t60) REVERT: A 1690 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7744 (tt) REVERT: A 2104 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7333 (tpt90) REVERT: A 2157 ASP cc_start: 0.8438 (t70) cc_final: 0.8237 (t70) REVERT: A 2181 GLN cc_start: 0.7858 (mp10) cc_final: 0.7635 (mp10) REVERT: A 2270 MET cc_start: 0.6249 (mmt) cc_final: 0.5986 (mmt) REVERT: A 2272 PHE cc_start: 0.6370 (t80) cc_final: 0.5907 (t80) REVERT: A 2326 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7616 (m-30) REVERT: A 2370 HIS cc_start: 0.6994 (m-70) cc_final: 0.6722 (m-70) REVERT: A 2436 ASP cc_start: 0.7301 (p0) cc_final: 0.6931 (p0) REVERT: A 2446 MET cc_start: 0.8140 (ppp) cc_final: 0.7901 (ppp) REVERT: B 1287 PHE cc_start: 0.9139 (t80) cc_final: 0.8856 (t80) REVERT: B 1518 ARG cc_start: 0.7718 (ptt180) cc_final: 0.7424 (ptt90) REVERT: B 1690 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.7929 (tt) REVERT: B 2022 PHE cc_start: 0.8003 (t80) cc_final: 0.7743 (t80) REVERT: B 2104 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7584 (tpt90) REVERT: B 2157 ASP cc_start: 0.8284 (t70) cc_final: 0.8080 (t0) REVERT: B 2209 PHE cc_start: 0.7800 (t80) cc_final: 0.7518 (t80) REVERT: B 2210 MET cc_start: 0.7953 (tmm) cc_final: 0.7366 (tmm) REVERT: B 2270 MET cc_start: 0.6364 (mmt) cc_final: 0.5749 (mmt) REVERT: B 2271 GLN cc_start: 0.8646 (tp-100) cc_final: 0.8182 (mm-40) REVERT: B 2272 PHE cc_start: 0.7053 (t80) cc_final: 0.6734 (t80) REVERT: B 2323 PHE cc_start: 0.8874 (m-80) cc_final: 0.8575 (m-10) REVERT: B 2404 GLN cc_start: 0.6975 (mt0) cc_final: 0.6090 (mm-40) REVERT: B 2446 MET cc_start: 0.8313 (ppp) cc_final: 0.8076 (ppp) REVERT: C 1201 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8800 (mmtm) REVERT: C 1519 TRP cc_start: 0.8498 (t60) cc_final: 0.8027 (t60) REVERT: C 1675 LEU cc_start: 0.8942 (tp) cc_final: 0.8639 (tt) REVERT: C 1690 LEU cc_start: 0.8248 (pt) cc_final: 0.7784 (tt) REVERT: C 1786 ASP cc_start: 0.9104 (t70) cc_final: 0.8892 (t0) REVERT: C 2104 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7356 (tpt90) REVERT: C 2133 GLU cc_start: 0.8235 (pm20) cc_final: 0.7791 (pm20) REVERT: C 2271 GLN cc_start: 0.8637 (tp-100) cc_final: 0.8226 (mm-40) outliers start: 95 outliers final: 70 residues processed: 487 average time/residue: 0.3425 time to fit residues: 282.5748 Evaluate side-chains 490 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 414 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1149 TYR Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1286 CYS Chi-restraints excluded: chain A residue 1302 PHE Chi-restraints excluded: chain A residue 1540 LEU Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 2016 VAL Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2085 VAL Chi-restraints excluded: chain A residue 2104 ARG Chi-restraints excluded: chain A residue 2123 GLN Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2132 VAL Chi-restraints excluded: chain A residue 2172 GLU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2240 THR Chi-restraints excluded: chain A residue 2326 ASP Chi-restraints excluded: chain A residue 2336 THR Chi-restraints excluded: chain A residue 2449 PHE Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain A residue 2510 ILE Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1286 CYS Chi-restraints excluded: chain B residue 1296 ILE Chi-restraints excluded: chain B residue 1308 ASP Chi-restraints excluded: chain B residue 1520 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 1702 THR Chi-restraints excluded: chain B residue 1987 ASP Chi-restraints excluded: chain B residue 2016 VAL Chi-restraints excluded: chain B residue 2023 MET Chi-restraints excluded: chain B residue 2042 THR Chi-restraints excluded: chain B residue 2085 VAL Chi-restraints excluded: chain B residue 2104 ARG Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2172 GLU Chi-restraints excluded: chain B residue 2199 LEU Chi-restraints excluded: chain B residue 2226 VAL Chi-restraints excluded: chain B residue 2336 THR Chi-restraints excluded: chain B residue 2471 VAL Chi-restraints excluded: chain B residue 2510 ILE Chi-restraints excluded: chain C residue 1149 TYR Chi-restraints excluded: chain C residue 1167 VAL Chi-restraints excluded: chain C residue 1178 SER Chi-restraints excluded: chain C residue 1292 LEU Chi-restraints excluded: chain C residue 1302 PHE Chi-restraints excluded: chain C residue 1308 ASP Chi-restraints excluded: chain C residue 1323 TYR Chi-restraints excluded: chain C residue 1540 LEU Chi-restraints excluded: chain C residue 1651 ASP Chi-restraints excluded: chain C residue 1689 LEU Chi-restraints excluded: chain C residue 1702 THR Chi-restraints excluded: chain C residue 1726 SER Chi-restraints excluded: chain C residue 1966 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2021 LEU Chi-restraints excluded: chain C residue 2042 THR Chi-restraints excluded: chain C residue 2085 VAL Chi-restraints excluded: chain C residue 2104 ARG Chi-restraints excluded: chain C residue 2172 GLU Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2226 VAL Chi-restraints excluded: chain C residue 2249 VAL Chi-restraints excluded: chain C residue 2332 THR Chi-restraints excluded: chain C residue 2336 THR Chi-restraints excluded: chain C residue 2393 ASP Chi-restraints excluded: chain C residue 2471 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 7.9990 chunk 150 optimal weight: 0.6980 chunk 224 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 256 optimal weight: 0.9980 chunk 185 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 295 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1558 GLN ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1558 GLN ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2254 GLN ** B2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN ** C2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29760 Z= 0.196 Angle : 0.656 17.839 40503 Z= 0.331 Chirality : 0.043 0.456 4716 Planarity : 0.004 0.051 5148 Dihedral : 5.013 26.145 4173 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.10 % Allowed : 24.88 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3810 helix: 0.67 (0.11), residues: 2517 sheet: -1.07 (0.35), residues: 231 loop : -3.28 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B2082 HIS 0.006 0.001 HIS C1403 PHE 0.028 0.002 PHE C1189 TYR 0.023 0.001 TYR C2533 ARG 0.008 0.000 ARG A2214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 448 time to evaluate : 3.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1201 LYS cc_start: 0.9075 (mmtm) cc_final: 0.8794 (mmtm) REVERT: A 1519 TRP cc_start: 0.8418 (t60) cc_final: 0.8090 (t60) REVERT: A 1690 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7765 (tt) REVERT: A 2023 MET cc_start: 0.7224 (mtm) cc_final: 0.6648 (ttm) REVERT: A 2104 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7408 (tpt90) REVERT: A 2157 ASP cc_start: 0.8296 (t70) cc_final: 0.8057 (t0) REVERT: A 2270 MET cc_start: 0.6284 (mmt) cc_final: 0.5949 (mmt) REVERT: A 2272 PHE cc_start: 0.6240 (t80) cc_final: 0.5739 (t80) REVERT: A 2326 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: A 2370 HIS cc_start: 0.6911 (m-70) cc_final: 0.6644 (m-70) REVERT: A 2446 MET cc_start: 0.8104 (ppp) cc_final: 0.7859 (ppp) REVERT: A 2515 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7844 (tp30) REVERT: B 1170 PHE cc_start: 0.9098 (t80) cc_final: 0.8818 (t80) REVERT: B 1287 PHE cc_start: 0.9092 (t80) cc_final: 0.8824 (t80) REVERT: B 1518 ARG cc_start: 0.7603 (ptt180) cc_final: 0.7360 (ptt90) REVERT: B 1690 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.7787 (tt) REVERT: B 2022 PHE cc_start: 0.7782 (t80) cc_final: 0.7495 (t80) REVERT: B 2050 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.7688 (tp-100) REVERT: B 2157 ASP cc_start: 0.8184 (t70) cc_final: 0.7946 (t0) REVERT: B 2209 PHE cc_start: 0.7644 (t80) cc_final: 0.7364 (t80) REVERT: B 2210 MET cc_start: 0.7870 (tmm) cc_final: 0.7293 (tmm) REVERT: B 2229 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8527 (t) REVERT: B 2270 MET cc_start: 0.6463 (mmt) cc_final: 0.5766 (mmt) REVERT: B 2271 GLN cc_start: 0.8614 (tp-100) cc_final: 0.8151 (mm-40) REVERT: B 2272 PHE cc_start: 0.6987 (t80) cc_final: 0.6685 (t80) REVERT: B 2323 PHE cc_start: 0.8860 (m-80) cc_final: 0.8625 (m-10) REVERT: B 2395 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.5969 (tt0) REVERT: B 2404 GLN cc_start: 0.6897 (mt0) cc_final: 0.6064 (mm-40) REVERT: B 2446 MET cc_start: 0.8238 (ppp) cc_final: 0.7984 (ppp) REVERT: C 1152 MET cc_start: 0.8715 (mtm) cc_final: 0.8480 (mtm) REVERT: C 1201 LYS cc_start: 0.9085 (mmtm) cc_final: 0.8802 (mmtm) REVERT: C 1519 TRP cc_start: 0.8571 (t60) cc_final: 0.7988 (t60) REVERT: C 1675 LEU cc_start: 0.8870 (tp) cc_final: 0.8553 (tt) REVERT: C 1690 LEU cc_start: 0.8282 (pt) cc_final: 0.7827 (tt) REVERT: C 1786 ASP cc_start: 0.9080 (t70) cc_final: 0.8873 (t0) REVERT: C 2028 PHE cc_start: 0.9057 (m-80) cc_final: 0.8849 (m-10) REVERT: C 2104 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7406 (tpt90) REVERT: C 2133 GLU cc_start: 0.7962 (pm20) cc_final: 0.7507 (pm20) REVERT: C 2271 GLN cc_start: 0.8674 (tp-100) cc_final: 0.8238 (mm-40) outliers start: 82 outliers final: 53 residues processed: 504 average time/residue: 0.3477 time to fit residues: 296.8882 Evaluate side-chains 487 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 426 time to evaluate : 3.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1302 PHE Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 2016 VAL Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2085 VAL Chi-restraints excluded: chain A residue 2104 ARG Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2172 GLU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2228 VAL Chi-restraints excluded: chain A residue 2326 ASP Chi-restraints excluded: chain A residue 2336 THR Chi-restraints excluded: chain A residue 2449 PHE Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain A residue 2510 ILE Chi-restraints excluded: chain B residue 1155 VAL Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1296 ILE Chi-restraints excluded: chain B residue 1308 ASP Chi-restraints excluded: chain B residue 1520 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 1702 THR Chi-restraints excluded: chain B residue 1987 ASP Chi-restraints excluded: chain B residue 2016 VAL Chi-restraints excluded: chain B residue 2023 MET Chi-restraints excluded: chain B residue 2042 THR Chi-restraints excluded: chain B residue 2050 GLN Chi-restraints excluded: chain B residue 2085 VAL Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2172 GLU Chi-restraints excluded: chain B residue 2226 VAL Chi-restraints excluded: chain B residue 2229 THR Chi-restraints excluded: chain B residue 2395 GLU Chi-restraints excluded: chain B residue 2510 ILE Chi-restraints excluded: chain C residue 1178 SER Chi-restraints excluded: chain C residue 1286 CYS Chi-restraints excluded: chain C residue 1292 LEU Chi-restraints excluded: chain C residue 1302 PHE Chi-restraints excluded: chain C residue 1323 TYR Chi-restraints excluded: chain C residue 1651 ASP Chi-restraints excluded: chain C residue 1689 LEU Chi-restraints excluded: chain C residue 1702 THR Chi-restraints excluded: chain C residue 1726 SER Chi-restraints excluded: chain C residue 1966 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2042 THR Chi-restraints excluded: chain C residue 2085 VAL Chi-restraints excluded: chain C residue 2104 ARG Chi-restraints excluded: chain C residue 2172 GLU Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2226 VAL Chi-restraints excluded: chain C residue 2336 THR Chi-restraints excluded: chain C residue 2471 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 0.0980 chunk 360 optimal weight: 7.9990 chunk 328 optimal weight: 0.6980 chunk 350 optimal weight: 0.9980 chunk 210 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 316 optimal weight: 7.9990 chunk 331 optimal weight: 0.8980 chunk 349 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2254 GLN ** B2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2385 ASN ** C1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2254 GLN ** C2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29760 Z= 0.180 Angle : 0.654 18.370 40503 Z= 0.327 Chirality : 0.043 0.443 4716 Planarity : 0.004 0.052 5148 Dihedral : 4.862 23.930 4173 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 3.21 % Allowed : 24.65 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3810 helix: 0.85 (0.11), residues: 2502 sheet: -0.93 (0.34), residues: 249 loop : -3.19 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B2082 HIS 0.006 0.001 HIS C2490 PHE 0.036 0.001 PHE A1287 TYR 0.020 0.001 TYR C2533 ARG 0.007 0.000 ARG A2214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 453 time to evaluate : 3.524 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: A 836 TRP cc_start: 0.7450 (m100) cc_final: 0.6765 (m100) REVERT: A 1185 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8510 (mp) REVERT: A 1189 PHE cc_start: 0.7327 (m-10) cc_final: 0.7117 (m-10) REVERT: A 1201 LYS cc_start: 0.9050 (mmtm) cc_final: 0.8774 (mmtm) REVERT: A 1519 TRP cc_start: 0.8427 (t60) cc_final: 0.8062 (t60) REVERT: A 1690 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7593 (tt) REVERT: A 2050 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7859 (tp-100) REVERT: A 2104 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7365 (tpt90) REVERT: A 2270 MET cc_start: 0.6387 (mmt) cc_final: 0.6040 (mmt) REVERT: A 2272 PHE cc_start: 0.6218 (t80) cc_final: 0.5680 (t80) REVERT: A 2326 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: A 2370 HIS cc_start: 0.6857 (m-70) cc_final: 0.6581 (m-70) REVERT: B 1170 PHE cc_start: 0.9083 (t80) cc_final: 0.8750 (t80) REVERT: B 1287 PHE cc_start: 0.9074 (t80) cc_final: 0.8810 (t80) REVERT: B 1518 ARG cc_start: 0.7659 (ptt180) cc_final: 0.7402 (ptt90) REVERT: B 1690 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7816 (tt) REVERT: B 2022 PHE cc_start: 0.7886 (t80) cc_final: 0.7597 (t80) REVERT: B 2050 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8008 (tp40) REVERT: B 2157 ASP cc_start: 0.8202 (t70) cc_final: 0.7984 (t0) REVERT: B 2210 MET cc_start: 0.7823 (tmm) cc_final: 0.7298 (tmm) REVERT: B 2270 MET cc_start: 0.6620 (mmt) cc_final: 0.5917 (mmt) REVERT: B 2271 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8141 (mm-40) REVERT: B 2272 PHE cc_start: 0.6923 (t80) cc_final: 0.6583 (t80) REVERT: B 2323 PHE cc_start: 0.8867 (m-80) cc_final: 0.8637 (m-10) REVERT: B 2404 GLN cc_start: 0.6712 (mt0) cc_final: 0.5962 (mm-40) REVERT: B 2432 ILE cc_start: 0.8924 (pp) cc_final: 0.8628 (pp) REVERT: B 2446 MET cc_start: 0.8273 (ppp) cc_final: 0.8045 (ppp) REVERT: B 2479 LYS cc_start: 0.8535 (mttt) cc_final: 0.7796 (mmtt) REVERT: C 1201 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8858 (mmtm) REVERT: C 1519 TRP cc_start: 0.8533 (t60) cc_final: 0.7989 (t60) REVERT: C 1675 LEU cc_start: 0.8797 (tp) cc_final: 0.8495 (tt) REVERT: C 1690 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7810 (tt) REVERT: C 1786 ASP cc_start: 0.9106 (t70) cc_final: 0.8885 (t0) REVERT: C 2104 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7435 (tpt90) REVERT: C 2133 GLU cc_start: 0.7927 (pm20) cc_final: 0.7487 (pm20) REVERT: C 2210 MET cc_start: 0.6648 (OUTLIER) cc_final: 0.6434 (tmm) REVERT: C 2254 GLN cc_start: 0.9578 (mt0) cc_final: 0.9253 (pp30) REVERT: C 2271 GLN cc_start: 0.8686 (tp-100) cc_final: 0.8217 (mm-40) REVERT: C 2309 TYR cc_start: 0.8167 (OUTLIER) cc_final: 0.7901 (m-10) REVERT: C 2452 LYS cc_start: 0.7551 (tppt) cc_final: 0.7347 (tppt) outliers start: 85 outliers final: 53 residues processed: 508 average time/residue: 0.3518 time to fit residues: 302.5895 Evaluate side-chains 498 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 434 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1302 PHE Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 2016 VAL Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2050 GLN Chi-restraints excluded: chain A residue 2085 VAL Chi-restraints excluded: chain A residue 2104 ARG Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2172 GLU Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2326 ASP Chi-restraints excluded: chain A residue 2336 THR Chi-restraints excluded: chain A residue 2449 PHE Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1296 ILE Chi-restraints excluded: chain B residue 1308 ASP Chi-restraints excluded: chain B residue 1520 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 1702 THR Chi-restraints excluded: chain B residue 1987 ASP Chi-restraints excluded: chain B residue 2016 VAL Chi-restraints excluded: chain B residue 2023 MET Chi-restraints excluded: chain B residue 2042 THR Chi-restraints excluded: chain B residue 2050 GLN Chi-restraints excluded: chain B residue 2085 VAL Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2134 LEU Chi-restraints excluded: chain B residue 2172 GLU Chi-restraints excluded: chain B residue 2226 VAL Chi-restraints excluded: chain B residue 2336 THR Chi-restraints excluded: chain B residue 2510 ILE Chi-restraints excluded: chain C residue 1178 SER Chi-restraints excluded: chain C residue 1292 LEU Chi-restraints excluded: chain C residue 1302 PHE Chi-restraints excluded: chain C residue 1323 TYR Chi-restraints excluded: chain C residue 1651 ASP Chi-restraints excluded: chain C residue 1689 LEU Chi-restraints excluded: chain C residue 1690 LEU Chi-restraints excluded: chain C residue 1702 THR Chi-restraints excluded: chain C residue 1966 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2021 LEU Chi-restraints excluded: chain C residue 2042 THR Chi-restraints excluded: chain C residue 2085 VAL Chi-restraints excluded: chain C residue 2104 ARG Chi-restraints excluded: chain C residue 2172 GLU Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2210 MET Chi-restraints excluded: chain C residue 2226 VAL Chi-restraints excluded: chain C residue 2309 TYR Chi-restraints excluded: chain C residue 2336 THR Chi-restraints excluded: chain C residue 2471 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 6.9990 chunk 370 optimal weight: 6.9990 chunk 226 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 257 optimal weight: 0.9980 chunk 388 optimal weight: 0.8980 chunk 357 optimal weight: 0.9990 chunk 309 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 238 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2385 ASN ** B1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2254 GLN ** B2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29760 Z= 0.219 Angle : 0.676 17.598 40503 Z= 0.336 Chirality : 0.044 0.453 4716 Planarity : 0.004 0.051 5148 Dihedral : 4.838 22.744 4173 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.76 % Allowed : 24.92 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.14), residues: 3810 helix: 0.88 (0.11), residues: 2514 sheet: -0.84 (0.34), residues: 249 loop : -3.27 (0.18), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B2082 HIS 0.006 0.001 HIS C1403 PHE 0.030 0.002 PHE B2239 TYR 0.026 0.001 TYR A2159 ARG 0.006 0.000 ARG A2214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 445 time to evaluate : 3.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 836 TRP cc_start: 0.7453 (m100) cc_final: 0.6810 (m100) REVERT: A 1185 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8436 (mp) REVERT: A 1201 LYS cc_start: 0.9063 (mmtm) cc_final: 0.8783 (mmtm) REVERT: A 1690 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7621 (tt) REVERT: A 1696 ILE cc_start: 0.9580 (mm) cc_final: 0.9286 (mt) REVERT: A 2139 ASP cc_start: 0.7453 (t0) cc_final: 0.7226 (t0) REVERT: A 2270 MET cc_start: 0.6364 (mmt) cc_final: 0.6003 (mmt) REVERT: A 2272 PHE cc_start: 0.6245 (t80) cc_final: 0.5749 (t80) REVERT: A 2326 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: A 2370 HIS cc_start: 0.6838 (m-70) cc_final: 0.6568 (m-70) REVERT: A 2446 MET cc_start: 0.7930 (ppp) cc_final: 0.7634 (ppp) REVERT: B 1170 PHE cc_start: 0.9106 (t80) cc_final: 0.8835 (t80) REVERT: B 1287 PHE cc_start: 0.9090 (t80) cc_final: 0.8841 (t80) REVERT: B 1292 LEU cc_start: 0.9032 (mt) cc_final: 0.8627 (mt) REVERT: B 1518 ARG cc_start: 0.7605 (ptt180) cc_final: 0.7387 (ptt90) REVERT: B 1690 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7842 (tt) REVERT: B 2022 PHE cc_start: 0.7977 (t80) cc_final: 0.7718 (t80) REVERT: B 2050 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7975 (tp-100) REVERT: B 2139 ASP cc_start: 0.7183 (t0) cc_final: 0.6934 (t0) REVERT: B 2157 ASP cc_start: 0.8215 (t70) cc_final: 0.7965 (t0) REVERT: B 2209 PHE cc_start: 0.7589 (t80) cc_final: 0.7316 (t80) REVERT: B 2210 MET cc_start: 0.7837 (tmm) cc_final: 0.7285 (tmm) REVERT: B 2254 GLN cc_start: 0.9517 (mt0) cc_final: 0.9276 (pp30) REVERT: B 2270 MET cc_start: 0.6609 (mmt) cc_final: 0.5872 (mmt) REVERT: B 2271 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8154 (mm-40) REVERT: B 2272 PHE cc_start: 0.6934 (t80) cc_final: 0.6622 (t80) REVERT: B 2323 PHE cc_start: 0.8871 (m-80) cc_final: 0.8597 (m-10) REVERT: B 2446 MET cc_start: 0.8236 (ppp) cc_final: 0.7976 (ppp) REVERT: B 2479 LYS cc_start: 0.8550 (mttt) cc_final: 0.7825 (mmtt) REVERT: C 1152 MET cc_start: 0.8673 (mtm) cc_final: 0.8286 (mtm) REVERT: C 1201 LYS cc_start: 0.9077 (mmtm) cc_final: 0.8862 (mmtm) REVERT: C 1519 TRP cc_start: 0.8574 (t60) cc_final: 0.7975 (t60) REVERT: C 1675 LEU cc_start: 0.8796 (tp) cc_final: 0.8492 (tt) REVERT: C 1690 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7793 (tt) REVERT: C 1786 ASP cc_start: 0.9076 (t70) cc_final: 0.8874 (t0) REVERT: C 2022 PHE cc_start: 0.7517 (t80) cc_final: 0.7224 (t80) REVERT: C 2023 MET cc_start: 0.7219 (mtm) cc_final: 0.6918 (mtp) REVERT: C 2028 PHE cc_start: 0.9147 (m-80) cc_final: 0.8896 (m-10) REVERT: C 2104 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7359 (tpt90) REVERT: C 2133 GLU cc_start: 0.8018 (pm20) cc_final: 0.7485 (pm20) REVERT: C 2210 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.6334 (tmm) REVERT: C 2254 GLN cc_start: 0.9580 (mt0) cc_final: 0.9255 (pp30) REVERT: C 2271 GLN cc_start: 0.8697 (tp-100) cc_final: 0.8229 (mm-40) REVERT: C 2309 TYR cc_start: 0.8102 (OUTLIER) cc_final: 0.7888 (m-10) REVERT: C 2479 LYS cc_start: 0.8384 (mttt) cc_final: 0.7598 (mmtt) outliers start: 73 outliers final: 57 residues processed: 489 average time/residue: 0.3528 time to fit residues: 290.9926 Evaluate side-chains 503 residues out of total 3498 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 437 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1185 LEU Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1302 PHE Chi-restraints excluded: chain A residue 1651 ASP Chi-restraints excluded: chain A residue 1690 LEU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 2016 VAL Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2085 VAL Chi-restraints excluded: chain A residue 2128 VAL Chi-restraints excluded: chain A residue 2172 GLU Chi-restraints excluded: chain A residue 2226 VAL Chi-restraints excluded: chain A residue 2326 ASP Chi-restraints excluded: chain A residue 2336 THR Chi-restraints excluded: chain A residue 2449 PHE Chi-restraints excluded: chain A residue 2471 VAL Chi-restraints excluded: chain A residue 2495 GLU Chi-restraints excluded: chain B residue 1213 LEU Chi-restraints excluded: chain B residue 1286 CYS Chi-restraints excluded: chain B residue 1296 ILE Chi-restraints excluded: chain B residue 1308 ASP Chi-restraints excluded: chain B residue 1520 LEU Chi-restraints excluded: chain B residue 1651 ASP Chi-restraints excluded: chain B residue 1676 LEU Chi-restraints excluded: chain B residue 1689 LEU Chi-restraints excluded: chain B residue 1690 LEU Chi-restraints excluded: chain B residue 1702 THR Chi-restraints excluded: chain B residue 1987 ASP Chi-restraints excluded: chain B residue 2016 VAL Chi-restraints excluded: chain B residue 2023 MET Chi-restraints excluded: chain B residue 2042 THR Chi-restraints excluded: chain B residue 2050 GLN Chi-restraints excluded: chain B residue 2085 VAL Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2134 LEU Chi-restraints excluded: chain B residue 2172 GLU Chi-restraints excluded: chain B residue 2203 ILE Chi-restraints excluded: chain B residue 2226 VAL Chi-restraints excluded: chain B residue 2336 THR Chi-restraints excluded: chain B residue 2510 ILE Chi-restraints excluded: chain C residue 1178 SER Chi-restraints excluded: chain C residue 1286 CYS Chi-restraints excluded: chain C residue 1292 LEU Chi-restraints excluded: chain C residue 1302 PHE Chi-restraints excluded: chain C residue 1323 TYR Chi-restraints excluded: chain C residue 1651 ASP Chi-restraints excluded: chain C residue 1689 LEU Chi-restraints excluded: chain C residue 1690 LEU Chi-restraints excluded: chain C residue 1702 THR Chi-restraints excluded: chain C residue 1966 LEU Chi-restraints excluded: chain C residue 1987 ASP Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2021 LEU Chi-restraints excluded: chain C residue 2042 THR Chi-restraints excluded: chain C residue 2085 VAL Chi-restraints excluded: chain C residue 2104 ARG Chi-restraints excluded: chain C residue 2172 GLU Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2210 MET Chi-restraints excluded: chain C residue 2226 VAL Chi-restraints excluded: chain C residue 2309 TYR Chi-restraints excluded: chain C residue 2336 THR Chi-restraints excluded: chain C residue 2471 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 245 optimal weight: 0.9980 chunk 329 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 285 optimal weight: 40.0000 chunk 45 optimal weight: 0.0370 chunk 85 optimal weight: 0.9990 chunk 309 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 318 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2254 GLN ** A2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.154479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.123178 restraints weight = 77682.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.116478 restraints weight = 67920.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.117384 restraints weight = 47631.829| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29760 Z= 0.177 Angle : 0.662 18.370 40503 Z= 0.326 Chirality : 0.043 0.442 4716 Planarity : 0.004 0.053 5148 Dihedral : 4.685 21.370 4173 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.83 % Allowed : 24.99 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.14), residues: 3810 helix: 0.96 (0.11), residues: 2538 sheet: -0.60 (0.34), residues: 249 loop : -3.24 (0.18), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B2082 HIS 0.005 0.001 HIS C1145 PHE 0.045 0.002 PHE B1993 TYR 0.017 0.001 TYR A2159 ARG 0.008 0.000 ARG A1518 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6047.23 seconds wall clock time: 110 minutes 44.89 seconds (6644.89 seconds total)