Starting phenix.real_space_refine on Sun Apr 14 19:55:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teu_41202/04_2024/8teu_41202.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teu_41202/04_2024/8teu_41202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teu_41202/04_2024/8teu_41202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teu_41202/04_2024/8teu_41202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teu_41202/04_2024/8teu_41202.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8teu_41202/04_2024/8teu_41202.pdb" } resolution = 4.01 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= 0.000 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 546 5.16 5 C 61608 2.51 5 N 16972 2.21 5 O 17633 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 595": "OE1" <-> "OE2" Residue "G PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 30": "OE1" <-> "OE2" Residue "G TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 345": "OD1" <-> "OD2" Residue "G ASP 486": "OD1" <-> "OD2" Residue "G TYR 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 429": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 910": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 310": "OE1" <-> "OE2" Residue "I PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 784": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 867": "OD1" <-> "OD2" Residue "I GLU 962": "OE1" <-> "OE2" Residue "I PHE 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 728": "OE1" <-> "OE2" Residue "J PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 1206": "OD1" <-> "OD2" Residue "J TYR 1259": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 753": "OD1" <-> "OD2" Residue "K ASP 761": "OD1" <-> "OD2" Residue "K PHE 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 1305": "OE1" <-> "OE2" Residue "K GLU 1348": "OE1" <-> "OE2" Residue "L ASP 169": "OD1" <-> "OD2" Residue "L GLU 248": "OE1" <-> "OE2" Residue "L TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 592": "OE1" <-> "OE2" Residue "L TYR 983": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 1258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 1308": "OE1" <-> "OE2" Residue "M PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 521": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 1296": "OD1" <-> "OD2" Residue "T PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 20": "OD1" <-> "OD2" Residue "V TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 196": "OD1" <-> "OD2" Residue "W PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 280": "OD1" <-> "OD2" Residue "X PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 292": "OD1" <-> "OD2" Residue "X PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 121": "OD1" <-> "OD2" Residue "Z ASP 246": "OD1" <-> "OD2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 96759 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 5830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 5830 Classifications: {'peptide': 722} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 674} Chain breaks: 5 Chain: "C" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 332 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Chain: "E" Number of atoms: 3992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3992 Classifications: {'peptide': 495} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 470} Chain breaks: 5 Chain: "F" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 710 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain breaks: 1 Chain: "G" Number of atoms: 3862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3862 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 21, 'TRANS': 449} Chain breaks: 1 Chain: "H" Number of atoms: 10391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1309, 10391 Classifications: {'peptide': 1309} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 75, 'TRANS': 1232} Chain breaks: 2 Chain: "I" Number of atoms: 10693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 10693 Classifications: {'peptide': 1350} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 78, 'TRANS': 1271} Chain breaks: 1 Chain: "J" Number of atoms: 10433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1317, 10433 Classifications: {'peptide': 1317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 76, 'TRANS': 1240} Chain breaks: 1 Chain: "K" Number of atoms: 10259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1296, 10259 Classifications: {'peptide': 1296} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 76, 'TRANS': 1219} Chain breaks: 2 Chain: "L" Number of atoms: 10693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 10693 Classifications: {'peptide': 1350} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 78, 'TRANS': 1271} Chain breaks: 1 Chain: "M" Number of atoms: 10693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 10693 Classifications: {'peptide': 1350} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 78, 'TRANS': 1271} Chain breaks: 1 Chain: "N" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "O" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "P" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "Q" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "R" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "S" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 513 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "T" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1939 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain breaks: 1 Chain: "U" Number of atoms: 2317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2317 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 276} Chain breaks: 1 Chain: "V" Number of atoms: 2292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2292 Classifications: {'peptide': 288} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Chain: "W" Number of atoms: 2325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2325 Classifications: {'peptide': 290} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 278} Chain: "X" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2334 Classifications: {'peptide': 295} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 278} Chain breaks: 1 Chain: "Y" Number of atoms: 2266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2266 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 271} Chain breaks: 2 Chain: "Z" Number of atoms: 2320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2320 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 276} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 35.43, per 1000 atoms: 0.37 Number of scatterers: 96759 At special positions: 0 Unit cell: (212.16, 296.48, 261.12, 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 546 16.00 O 17633 8.00 N 16972 7.00 C 61608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A1576 " - pdb=" SG CYS A1892 " distance=2.03 Simple disulfide: pdb=" SG CYS A1633 " - pdb=" SG CYS A2179 " distance=2.03 Simple disulfide: pdb=" SG CYS A1697 " - pdb=" SG CYS A1747 " distance=2.03 Simple disulfide: pdb=" SG CYS H1292 " - pdb=" SG CYS H1303 " distance=2.01 Simple disulfide: pdb=" SG CYS I1292 " - pdb=" SG CYS I1303 " distance=2.03 Simple disulfide: pdb=" SG CYS J1292 " - pdb=" SG CYS J1303 " distance=2.03 Simple disulfide: pdb=" SG CYS K1292 " - pdb=" SG CYS K1303 " distance=2.03 Simple disulfide: pdb=" SG CYS L1292 " - pdb=" SG CYS L1303 " distance=2.03 Simple disulfide: pdb=" SG CYS M1292 " - pdb=" SG CYS M1303 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.04 Conformation dependent library (CDL) restraints added in 13.3 seconds 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23232 Finding SS restraints... Secondary structure from input PDB file: 540 helices and 104 sheets defined 47.9% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.52 Creating SS restraints... Processing helix chain 'A' and resid 1444 through 1466 removed outlier: 3.902A pdb=" N GLN A1464 " --> pdb=" O LEU A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1471 through 1494 removed outlier: 3.685A pdb=" N GLN A1475 " --> pdb=" O ASP A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1543 Processing helix chain 'A' and resid 1548 through 1552 Processing helix chain 'A' and resid 1563 through 1576 removed outlier: 3.739A pdb=" N CYS A1576 " --> pdb=" O LEU A1572 " (cutoff:3.500A) Processing helix chain 'A' and resid 1603 through 1608 Processing helix chain 'A' and resid 1612 through 1622 removed outlier: 3.930A pdb=" N ALA A1619 " --> pdb=" O PHE A1615 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A1620 " --> pdb=" O LYS A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1634 Processing helix chain 'A' and resid 1643 through 1662 removed outlier: 3.514A pdb=" N VAL A1655 " --> pdb=" O VAL A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1662 through 1669 removed outlier: 3.588A pdb=" N TYR A1669 " --> pdb=" O GLN A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1671 through 1678 removed outlier: 3.739A pdb=" N LEU A1675 " --> pdb=" O LEU A1671 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS A1678 " --> pdb=" O TYR A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1686 through 1708 removed outlier: 4.065A pdb=" N LEU A1690 " --> pdb=" O GLU A1686 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN A1706 " --> pdb=" O THR A1702 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG A1707 " --> pdb=" O ALA A1703 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE A1708 " --> pdb=" O TRP A1704 " (cutoff:3.500A) Processing helix chain 'A' and resid 1742 through 1754 removed outlier: 3.561A pdb=" N TYR A1754 " --> pdb=" O ILE A1750 " (cutoff:3.500A) Processing helix chain 'A' and resid 1755 through 1764 removed outlier: 4.373A pdb=" N TYR A1759 " --> pdb=" O PRO A1755 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A1762 " --> pdb=" O ILE A1758 " (cutoff:3.500A) Processing helix chain 'A' and resid 1765 through 1777 Proline residue: A1771 - end of helix removed outlier: 3.636A pdb=" N LEU A1777 " --> pdb=" O LEU A1773 " (cutoff:3.500A) Processing helix chain 'A' and resid 1779 through 1787 Processing helix chain 'A' and resid 1807 through 1811 removed outlier: 3.530A pdb=" N GLN A1810 " --> pdb=" O THR A1807 " (cutoff:3.500A) Processing helix chain 'A' and resid 1816 through 1821 Processing helix chain 'A' and resid 1823 through 1830 Processing helix chain 'A' and resid 1841 through 1854 Processing helix chain 'A' and resid 1855 through 1866 Processing helix chain 'A' and resid 1869 through 1874 removed outlier: 4.275A pdb=" N THR A1873 " --> pdb=" O TYR A1870 " (cutoff:3.500A) Processing helix chain 'A' and resid 1876 through 1892 removed outlier: 4.226A pdb=" N LEU A1880 " --> pdb=" O SER A1876 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N VAL A1881 " --> pdb=" O VAL A1877 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N CYS A1892 " --> pdb=" O PHE A1888 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1941 removed outlier: 3.766A pdb=" N GLN A1940 " --> pdb=" O ASP A1936 " (cutoff:3.500A) Processing helix chain 'A' and resid 1943 through 1955 Processing helix chain 'A' and resid 1985 through 1995 removed outlier: 3.704A pdb=" N GLN A1992 " --> pdb=" O PHE A1988 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ARG A1993 " --> pdb=" O LEU A1989 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG A1995 " --> pdb=" O ILE A1991 " (cutoff:3.500A) Processing helix chain 'A' and resid 2000 through 2005 Processing helix chain 'A' and resid 2010 through 2030 removed outlier: 3.529A pdb=" N PHE A2030 " --> pdb=" O ASP A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2109 through 2114 Processing helix chain 'A' and resid 2150 through 2156 Processing helix chain 'A' and resid 2159 through 2165 Processing helix chain 'A' and resid 2179 through 2184 removed outlier: 3.953A pdb=" N VAL A2184 " --> pdb=" O ARG A2180 " (cutoff:3.500A) Processing helix chain 'A' and resid 2203 through 2239 removed outlier: 3.875A pdb=" N LEU A2208 " --> pdb=" O THR A2204 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A2209 " --> pdb=" O GLN A2205 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU A2216 " --> pdb=" O GLU A2212 " (cutoff:3.500A) Processing helix chain 'C' and resid 2207 through 2239 Processing helix chain 'E' and resid 27 through 45 removed outlier: 4.099A pdb=" N GLY E 45 " --> pdb=" O THR E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 92 removed outlier: 3.767A pdb=" N LEU E 68 " --> pdb=" O GLU E 64 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY E 69 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N HIS E 70 " --> pdb=" O ARG E 66 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG E 71 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN E 73 " --> pdb=" O GLY E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 211 removed outlier: 3.673A pdb=" N ALA E 211 " --> pdb=" O MET E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 231 Processing helix chain 'E' and resid 232 through 240 Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 275 through 295 removed outlier: 3.623A pdb=" N ALA E 279 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR E 287 " --> pdb=" O LEU E 283 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA E 290 " --> pdb=" O ALA E 286 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU E 291 " --> pdb=" O TYR E 287 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY E 294 " --> pdb=" O ALA E 290 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG E 295 " --> pdb=" O LEU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 307 Processing helix chain 'E' and resid 307 through 325 Proline residue: E 313 - end of helix Processing helix chain 'E' and resid 365 through 375 removed outlier: 3.641A pdb=" N LYS E 373 " --> pdb=" O ARG E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 417 removed outlier: 4.361A pdb=" N GLY E 414 " --> pdb=" O ARG E 410 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 448 removed outlier: 3.796A pdb=" N SER E 432 " --> pdb=" O GLN E 428 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY E 433 " --> pdb=" O TYR E 429 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU E 434 " --> pdb=" O LEU E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 474 removed outlier: 6.671A pdb=" N SER E 468 " --> pdb=" O ASP E 464 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ASP E 469 " --> pdb=" O LEU E 465 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA E 470 " --> pdb=" O LEU E 466 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 506 removed outlier: 3.939A pdb=" N PHE E 500 " --> pdb=" O ARG E 496 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU E 501 " --> pdb=" O ASN E 497 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG E 503 " --> pdb=" O GLU E 499 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR E 504 " --> pdb=" O PHE E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 513 Processing helix chain 'E' and resid 517 through 522 Processing helix chain 'E' and resid 523 through 537 removed outlier: 4.359A pdb=" N LEU E 527 " --> pdb=" O PRO E 523 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU E 528 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 575 removed outlier: 4.088A pdb=" N ASP E 568 " --> pdb=" O ASN E 564 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET E 570 " --> pdb=" O VAL E 566 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER E 575 " --> pdb=" O PHE E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 604 removed outlier: 3.929A pdb=" N ARG E 600 " --> pdb=" O HIS E 596 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU E 601 " --> pdb=" O GLY E 597 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU E 602 " --> pdb=" O LEU E 598 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 620 Processing helix chain 'E' and resid 623 through 634 removed outlier: 3.924A pdb=" N TYR E 629 " --> pdb=" O TYR E 625 " (cutoff:3.500A) Processing helix chain 'F' and resid 27 through 45 removed outlier: 4.265A pdb=" N VAL F 40 " --> pdb=" O GLU F 36 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY F 45 " --> pdb=" O THR F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 89 removed outlier: 3.539A pdb=" N GLN F 63 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU F 89 " --> pdb=" O GLU F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 92 No H-bonds generated for 'chain 'F' and resid 90 through 92' Processing helix chain 'G' and resid 2 through 15 Processing helix chain 'G' and resid 33 through 39 Processing helix chain 'G' and resid 62 through 66 Processing helix chain 'G' and resid 74 through 77 removed outlier: 3.703A pdb=" N GLY G 77 " --> pdb=" O ASP G 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 74 through 77' Processing helix chain 'G' and resid 78 through 89 removed outlier: 3.733A pdb=" N PHE G 82 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP G 89 " --> pdb=" O GLU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 110 Processing helix chain 'G' and resid 165 through 169 Processing helix chain 'G' and resid 171 through 176 removed outlier: 3.948A pdb=" N ASN G 176 " --> pdb=" O MET G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 310 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 346 through 362 removed outlier: 3.554A pdb=" N ALA G 362 " --> pdb=" O ARG G 358 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 382 Processing helix chain 'G' and resid 399 through 418 removed outlier: 4.126A pdb=" N VAL G 403 " --> pdb=" O SER G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 422 through 432 Proline residue: G 430 - end of helix Processing helix chain 'G' and resid 434 through 448 removed outlier: 4.253A pdb=" N ALA G 438 " --> pdb=" O ARG G 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 453 through 459 Processing helix chain 'G' and resid 546 through 550 removed outlier: 3.909A pdb=" N GLY G 549 " --> pdb=" O THR G 546 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU G 550 " --> pdb=" O LEU G 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 546 through 550' Processing helix chain 'G' and resid 551 through 559 removed outlier: 3.609A pdb=" N LEU G 555 " --> pdb=" O ALA G 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 10 removed outlier: 3.560A pdb=" N LEU H 7 " --> pdb=" O ASN H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 30 Processing helix chain 'H' and resid 42 through 46 removed outlier: 4.124A pdb=" N ARG H 45 " --> pdb=" O ASP H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 74 removed outlier: 3.547A pdb=" N ALA H 72 " --> pdb=" O SER H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 86 removed outlier: 4.679A pdb=" N ASN H 84 " --> pdb=" O HIS H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 140 Processing helix chain 'H' and resid 146 through 187 removed outlier: 3.510A pdb=" N LYS H 150 " --> pdb=" O THR H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 199 Processing helix chain 'H' and resid 208 through 227 removed outlier: 3.642A pdb=" N LEU H 227 " --> pdb=" O MET H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 233 Processing helix chain 'H' and resid 235 through 250 removed outlier: 4.349A pdb=" N ALA H 250 " --> pdb=" O LEU H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 276 through 287 Processing helix chain 'H' and resid 371 through 375 removed outlier: 3.880A pdb=" N ARG H 374 " --> pdb=" O ASN H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 419 through 424 Processing helix chain 'H' and resid 441 through 450 removed outlier: 4.758A pdb=" N LYS H 447 " --> pdb=" O VAL H 443 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N THR H 448 " --> pdb=" O ASP H 444 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS H 450 " --> pdb=" O LEU H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 456 removed outlier: 3.963A pdb=" N HIS H 455 " --> pdb=" O HIS H 451 " (cutoff:3.500A) Processing helix chain 'H' and resid 457 through 468 Processing helix chain 'H' and resid 472 through 480 removed outlier: 3.640A pdb=" N LEU H 478 " --> pdb=" O ALA H 474 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU H 480 " --> pdb=" O GLN H 476 " (cutoff:3.500A) Processing helix chain 'H' and resid 490 through 500 Proline residue: H 496 - end of helix Processing helix chain 'H' and resid 508 through 515 removed outlier: 4.070A pdb=" N GLN H 514 " --> pdb=" O ASN H 510 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP H 515 " --> pdb=" O GLU H 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 517 through 522 removed outlier: 4.601A pdb=" N TYR H 522 " --> pdb=" O VAL H 518 " (cutoff:3.500A) Processing helix chain 'H' and resid 526 through 532 removed outlier: 4.331A pdb=" N TYR H 530 " --> pdb=" O ILE H 527 " (cutoff:3.500A) Processing helix chain 'H' and resid 557 through 561 Processing helix chain 'H' and resid 567 through 582 Processing helix chain 'H' and resid 590 through 603 Processing helix chain 'H' and resid 608 through 618 removed outlier: 3.846A pdb=" N LEU H 612 " --> pdb=" O GLU H 608 " (cutoff:3.500A) Processing helix chain 'H' and resid 620 through 642 removed outlier: 3.574A pdb=" N LEU H 626 " --> pdb=" O ASP H 622 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR H 629 " --> pdb=" O LEU H 625 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE H 630 " --> pdb=" O LEU H 626 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 658 Processing helix chain 'H' and resid 660 through 664 removed outlier: 3.744A pdb=" N ASP H 663 " --> pdb=" O HIS H 660 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY H 664 " --> pdb=" O LEU H 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 660 through 664' Processing helix chain 'H' and resid 667 through 689 removed outlier: 3.678A pdb=" N TYR H 674 " --> pdb=" O LEU H 670 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA H 689 " --> pdb=" O THR H 685 " (cutoff:3.500A) Processing helix chain 'H' and resid 702 through 708 removed outlier: 3.717A pdb=" N TYR H 706 " --> pdb=" O PRO H 702 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL H 707 " --> pdb=" O LEU H 703 " (cutoff:3.500A) Processing helix chain 'H' and resid 753 through 759 Processing helix chain 'H' and resid 774 through 787 Processing helix chain 'H' and resid 787 through 794 removed outlier: 3.557A pdb=" N ALA H 791 " --> pdb=" O CYS H 787 " (cutoff:3.500A) Processing helix chain 'H' and resid 803 through 812 Processing helix chain 'H' and resid 814 through 819 Processing helix chain 'H' and resid 845 through 854 removed outlier: 3.840A pdb=" N VAL H 853 " --> pdb=" O GLN H 849 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY H 854 " --> pdb=" O ARG H 850 " (cutoff:3.500A) Processing helix chain 'H' and resid 854 through 862 Processing helix chain 'H' and resid 871 through 881 Processing helix chain 'H' and resid 882 through 886 Processing helix chain 'H' and resid 900 through 905 removed outlier: 3.899A pdb=" N GLN H 905 " --> pdb=" O HIS H 901 " (cutoff:3.500A) Processing helix chain 'H' and resid 930 through 932 No H-bonds generated for 'chain 'H' and resid 930 through 932' Processing helix chain 'H' and resid 945 through 953 Processing helix chain 'H' and resid 953 through 963 Processing helix chain 'H' and resid 964 through 967 Processing helix chain 'H' and resid 988 through 998 removed outlier: 3.873A pdb=" N SER H 992 " --> pdb=" O ARG H 988 " (cutoff:3.500A) Processing helix chain 'H' and resid 1001 through 1012 removed outlier: 4.256A pdb=" N VAL H1005 " --> pdb=" O VAL H1001 " (cutoff:3.500A) Processing helix chain 'H' and resid 1016 through 1026 Processing helix chain 'H' and resid 1112 through 1117 Processing helix chain 'H' and resid 1124 through 1135 Processing helix chain 'H' and resid 1144 through 1153 Processing helix chain 'H' and resid 1182 through 1188 removed outlier: 3.545A pdb=" N PHE H1186 " --> pdb=" O VAL H1183 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE H1188 " --> pdb=" O TYR H1185 " (cutoff:3.500A) Processing helix chain 'H' and resid 1198 through 1202 Processing helix chain 'H' and resid 1206 through 1216 Processing helix chain 'H' and resid 1238 through 1245 removed outlier: 3.554A pdb=" N TYR H1244 " --> pdb=" O SER H1240 " (cutoff:3.500A) Processing helix chain 'H' and resid 1245 through 1253 removed outlier: 3.662A pdb=" N ARG H1251 " --> pdb=" O ARG H1247 " (cutoff:3.500A) Processing helix chain 'H' and resid 1262 through 1267 Processing helix chain 'H' and resid 1267 through 1274 Processing helix chain 'H' and resid 1277 through 1288 Processing helix chain 'H' and resid 1313 through 1319 removed outlier: 3.890A pdb=" N LEU H1317 " --> pdb=" O ASN H1313 " (cutoff:3.500A) Processing helix chain 'H' and resid 1329 through 1339 Processing helix chain 'H' and resid 1342 through 1346 Processing helix chain 'H' and resid 1362 through 1368 Processing helix chain 'I' and resid 3 through 8 removed outlier: 3.847A pdb=" N LEU I 7 " --> pdb=" O ASN I 3 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU I 8 " --> pdb=" O TRP I 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 3 through 8' Processing helix chain 'I' and resid 22 through 29 removed outlier: 3.711A pdb=" N SER I 26 " --> pdb=" O HIS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.541A pdb=" N ARG I 45 " --> pdb=" O ASP I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 75 removed outlier: 4.177A pdb=" N ALA I 74 " --> pdb=" O GLY I 70 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA I 75 " --> pdb=" O LEU I 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 70 through 75' Processing helix chain 'I' and resid 81 through 85 removed outlier: 4.217A pdb=" N ASN I 84 " --> pdb=" O HIS I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 140 removed outlier: 3.635A pdb=" N ARG I 140 " --> pdb=" O LEU I 136 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 187 removed outlier: 3.585A pdb=" N LYS I 186 " --> pdb=" O THR I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 189 through 199 Processing helix chain 'I' and resid 208 through 226 Processing helix chain 'I' and resid 228 through 233 Processing helix chain 'I' and resid 235 through 250 removed outlier: 3.577A pdb=" N ALA I 250 " --> pdb=" O LEU I 246 " (cutoff:3.500A) Processing helix chain 'I' and resid 276 through 287 Processing helix chain 'I' and resid 308 through 319 Processing helix chain 'I' and resid 324 through 335 Processing helix chain 'I' and resid 342 through 347 Processing helix chain 'I' and resid 371 through 375 removed outlier: 3.936A pdb=" N ARG I 374 " --> pdb=" O ASN I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 424 Processing helix chain 'I' and resid 445 through 450 removed outlier: 3.693A pdb=" N CYS I 450 " --> pdb=" O LEU I 446 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 456 removed outlier: 3.957A pdb=" N HIS I 455 " --> pdb=" O HIS I 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 468 removed outlier: 3.914A pdb=" N GLY I 468 " --> pdb=" O PHE I 464 " (cutoff:3.500A) Processing helix chain 'I' and resid 472 through 480 removed outlier: 3.694A pdb=" N GLU I 480 " --> pdb=" O GLN I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 491 through 493 No H-bonds generated for 'chain 'I' and resid 491 through 493' Processing helix chain 'I' and resid 494 through 501 removed outlier: 3.870A pdb=" N PHE I 498 " --> pdb=" O ARG I 494 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR I 499 " --> pdb=" O ILE I 495 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL I 501 " --> pdb=" O HIS I 497 " (cutoff:3.500A) Processing helix chain 'I' and resid 508 through 515 removed outlier: 4.088A pdb=" N ASP I 515 " --> pdb=" O GLU I 511 " (cutoff:3.500A) Processing helix chain 'I' and resid 526 through 532 removed outlier: 3.927A pdb=" N TYR I 530 " --> pdb=" O ILE I 527 " (cutoff:3.500A) Processing helix chain 'I' and resid 557 through 561 Processing helix chain 'I' and resid 567 through 582 Processing helix chain 'I' and resid 590 through 602 Processing helix chain 'I' and resid 607 through 618 removed outlier: 4.357A pdb=" N TYR I 611 " --> pdb=" O PRO I 607 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N HIS I 618 " --> pdb=" O ASP I 614 " (cutoff:3.500A) Processing helix chain 'I' and resid 620 through 642 removed outlier: 3.661A pdb=" N LEU I 626 " --> pdb=" O ASP I 622 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N THR I 629 " --> pdb=" O LEU I 625 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N PHE I 630 " --> pdb=" O LEU I 626 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG I 633 " --> pdb=" O THR I 629 " (cutoff:3.500A) Processing helix chain 'I' and resid 650 through 661 Processing helix chain 'I' and resid 667 through 689 removed outlier: 3.712A pdb=" N ALA I 689 " --> pdb=" O THR I 685 " (cutoff:3.500A) Processing helix chain 'I' and resid 702 through 708 removed outlier: 3.547A pdb=" N ASN I 708 " --> pdb=" O SER I 704 " (cutoff:3.500A) Processing helix chain 'I' and resid 740 through 742 No H-bonds generated for 'chain 'I' and resid 740 through 742' Processing helix chain 'I' and resid 753 through 759 Processing helix chain 'I' and resid 774 through 787 Processing helix chain 'I' and resid 787 through 794 removed outlier: 3.518A pdb=" N ALA I 791 " --> pdb=" O CYS I 787 " (cutoff:3.500A) Processing helix chain 'I' and resid 803 through 813 removed outlier: 3.991A pdb=" N VAL I 809 " --> pdb=" O LYS I 805 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR I 813 " --> pdb=" O VAL I 809 " (cutoff:3.500A) Processing helix chain 'I' and resid 814 through 819 removed outlier: 3.989A pdb=" N LEU I 818 " --> pdb=" O ARG I 814 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU I 819 " --> pdb=" O PRO I 815 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 814 through 819' Processing helix chain 'I' and resid 846 through 854 Processing helix chain 'I' and resid 854 through 862 Processing helix chain 'I' and resid 871 through 881 removed outlier: 3.798A pdb=" N LEU I 881 " --> pdb=" O ARG I 877 " (cutoff:3.500A) Processing helix chain 'I' and resid 882 through 886 Processing helix chain 'I' and resid 900 through 905 removed outlier: 3.973A pdb=" N GLN I 905 " --> pdb=" O HIS I 901 " (cutoff:3.500A) Processing helix chain 'I' and resid 927 through 932 removed outlier: 4.283A pdb=" N ILE I 931 " --> pdb=" O LYS I 928 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N GLU I 932 " --> pdb=" O THR I 929 " (cutoff:3.500A) Processing helix chain 'I' and resid 945 through 953 Processing helix chain 'I' and resid 953 through 963 Processing helix chain 'I' and resid 964 through 967 Processing helix chain 'I' and resid 988 through 998 removed outlier: 4.244A pdb=" N SER I 992 " --> pdb=" O ARG I 988 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR I 997 " --> pdb=" O ARG I 993 " (cutoff:3.500A) Processing helix chain 'I' and resid 1001 through 1011 Processing helix chain 'I' and resid 1016 through 1026 Processing helix chain 'I' and resid 1112 through 1117 Processing helix chain 'I' and resid 1124 through 1136 Processing helix chain 'I' and resid 1143 through 1154 removed outlier: 3.920A pdb=" N SER I1149 " --> pdb=" O THR I1145 " (cutoff:3.500A) Processing helix chain 'I' and resid 1182 through 1188 removed outlier: 4.082A pdb=" N ILE I1188 " --> pdb=" O TYR I1185 " (cutoff:3.500A) Processing helix chain 'I' and resid 1206 through 1216 Processing helix chain 'I' and resid 1230 through 1235 removed outlier: 3.576A pdb=" N GLN I1235 " --> pdb=" O PRO I1231 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1245 Processing helix chain 'I' and resid 1245 through 1250 Processing helix chain 'I' and resid 1262 through 1267 Processing helix chain 'I' and resid 1267 through 1275 Processing helix chain 'I' and resid 1277 through 1289 Processing helix chain 'I' and resid 1314 through 1319 removed outlier: 3.501A pdb=" N THR I1318 " --> pdb=" O PRO I1314 " (cutoff:3.500A) Processing helix chain 'I' and resid 1329 through 1339 removed outlier: 3.600A pdb=" N MET I1333 " --> pdb=" O THR I1329 " (cutoff:3.500A) Processing helix chain 'I' and resid 1342 through 1346 removed outlier: 3.791A pdb=" N ALA I1345 " --> pdb=" O GLY I1342 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR I1346 " --> pdb=" O ALA I1343 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 1342 through 1346' Processing helix chain 'I' and resid 1361 through 1366 Processing helix chain 'J' and resid 42 through 47 removed outlier: 4.200A pdb=" N ARG J 45 " --> pdb=" O ASP J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 73 removed outlier: 3.546A pdb=" N SER J 69 " --> pdb=" O PHE J 66 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY J 70 " --> pdb=" O LEU J 67 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU J 71 " --> pdb=" O THR J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 141 Processing helix chain 'J' and resid 146 through 187 Processing helix chain 'J' and resid 189 through 200 Processing helix chain 'J' and resid 208 through 226 Processing helix chain 'J' and resid 228 through 233 Processing helix chain 'J' and resid 235 through 250 removed outlier: 4.108A pdb=" N ALA J 250 " --> pdb=" O LEU J 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 287 Processing helix chain 'J' and resid 308 through 319 Processing helix chain 'J' and resid 324 through 335 Processing helix chain 'J' and resid 342 through 347 Processing helix chain 'J' and resid 402 through 405 Processing helix chain 'J' and resid 419 through 424 Processing helix chain 'J' and resid 445 through 450 removed outlier: 3.534A pdb=" N CYS J 450 " --> pdb=" O LEU J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 456 removed outlier: 4.053A pdb=" N HIS J 455 " --> pdb=" O HIS J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 457 through 468 Processing helix chain 'J' and resid 472 through 474 No H-bonds generated for 'chain 'J' and resid 472 through 474' Processing helix chain 'J' and resid 475 through 480 removed outlier: 3.870A pdb=" N LEU J 479 " --> pdb=" O MET J 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 489 through 493 removed outlier: 4.250A pdb=" N ALA J 492 " --> pdb=" O GLY J 489 " (cutoff:3.500A) Processing helix chain 'J' and resid 494 through 499 removed outlier: 3.537A pdb=" N PHE J 498 " --> pdb=" O ARG J 494 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR J 499 " --> pdb=" O ILE J 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 494 through 499' Processing helix chain 'J' and resid 508 through 513 Processing helix chain 'J' and resid 526 through 531 removed outlier: 4.125A pdb=" N TYR J 530 " --> pdb=" O ILE J 527 " (cutoff:3.500A) Processing helix chain 'J' and resid 557 through 561 Processing helix chain 'J' and resid 567 through 582 Processing helix chain 'J' and resid 590 through 602 Processing helix chain 'J' and resid 608 through 618 removed outlier: 4.027A pdb=" N LEU J 612 " --> pdb=" O GLU J 608 " (cutoff:3.500A) Processing helix chain 'J' and resid 620 through 627 Processing helix chain 'J' and resid 627 through 642 Processing helix chain 'J' and resid 650 through 660 removed outlier: 3.564A pdb=" N VAL J 654 " --> pdb=" O SER J 650 " (cutoff:3.500A) Processing helix chain 'J' and resid 667 through 689 removed outlier: 3.580A pdb=" N ALA J 689 " --> pdb=" O THR J 685 " (cutoff:3.500A) Processing helix chain 'J' and resid 702 through 708 Processing helix chain 'J' and resid 740 through 742 No H-bonds generated for 'chain 'J' and resid 740 through 742' Processing helix chain 'J' and resid 753 through 759 Processing helix chain 'J' and resid 774 through 787 Processing helix chain 'J' and resid 787 through 793 removed outlier: 3.563A pdb=" N ALA J 791 " --> pdb=" O CYS J 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 803 through 813 Processing helix chain 'J' and resid 814 through 819 Processing helix chain 'J' and resid 846 through 854 Processing helix chain 'J' and resid 854 through 862 removed outlier: 4.118A pdb=" N LEU J 860 " --> pdb=" O MET J 856 " (cutoff:3.500A) Processing helix chain 'J' and resid 871 through 881 Processing helix chain 'J' and resid 882 through 886 Processing helix chain 'J' and resid 900 through 905 removed outlier: 4.243A pdb=" N GLN J 905 " --> pdb=" O HIS J 901 " (cutoff:3.500A) Processing helix chain 'J' and resid 945 through 953 removed outlier: 3.581A pdb=" N CYS J 949 " --> pdb=" O ASN J 945 " (cutoff:3.500A) Processing helix chain 'J' and resid 953 through 963 Processing helix chain 'J' and resid 964 through 967 Processing helix chain 'J' and resid 988 through 998 removed outlier: 4.390A pdb=" N SER J 992 " --> pdb=" O ARG J 988 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR J 997 " --> pdb=" O ARG J 993 " (cutoff:3.500A) Processing helix chain 'J' and resid 1001 through 1012 removed outlier: 4.159A pdb=" N VAL J1005 " --> pdb=" O VAL J1001 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET J1006 " --> pdb=" O LEU J1002 " (cutoff:3.500A) Processing helix chain 'J' and resid 1016 through 1026 Processing helix chain 'J' and resid 1112 through 1117 removed outlier: 3.977A pdb=" N VAL J1116 " --> pdb=" O ASP J1112 " (cutoff:3.500A) Processing helix chain 'J' and resid 1124 through 1136 Processing helix chain 'J' and resid 1145 through 1152 removed outlier: 4.065A pdb=" N THR J1152 " --> pdb=" O ILE J1148 " (cutoff:3.500A) Processing helix chain 'J' and resid 1182 through 1188 removed outlier: 3.962A pdb=" N ILE J1188 " --> pdb=" O TYR J1185 " (cutoff:3.500A) Processing helix chain 'J' and resid 1206 through 1216 Processing helix chain 'J' and resid 1230 through 1235 removed outlier: 3.737A pdb=" N GLN J1235 " --> pdb=" O PRO J1231 " (cutoff:3.500A) Processing helix chain 'J' and resid 1238 through 1245 Processing helix chain 'J' and resid 1245 through 1250 Processing helix chain 'J' and resid 1262 through 1267 removed outlier: 3.949A pdb=" N PHE J1266 " --> pdb=" O CYS J1262 " (cutoff:3.500A) Processing helix chain 'J' and resid 1267 through 1275 removed outlier: 3.930A pdb=" N ASN J1275 " --> pdb=" O ILE J1271 " (cutoff:3.500A) Processing helix chain 'J' and resid 1277 through 1289 Processing helix chain 'J' and resid 1313 through 1319 removed outlier: 3.994A pdb=" N LEU J1317 " --> pdb=" O ASN J1313 " (cutoff:3.500A) Processing helix chain 'J' and resid 1329 through 1339 removed outlier: 3.664A pdb=" N MET J1333 " --> pdb=" O THR J1329 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 73 removed outlier: 6.207A pdb=" N GLY K 70 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU K 71 " --> pdb=" O THR K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 removed outlier: 4.073A pdb=" N ASN K 84 " --> pdb=" O HIS K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 140 Processing helix chain 'K' and resid 151 through 186 Processing helix chain 'K' and resid 189 through 200 Processing helix chain 'K' and resid 208 through 227 Processing helix chain 'K' and resid 228 through 233 Processing helix chain 'K' and resid 235 through 250 removed outlier: 3.966A pdb=" N ALA K 250 " --> pdb=" O LEU K 246 " (cutoff:3.500A) Processing helix chain 'K' and resid 276 through 287 Processing helix chain 'K' and resid 308 through 319 Processing helix chain 'K' and resid 324 through 335 Processing helix chain 'K' and resid 372 through 377 removed outlier: 3.555A pdb=" N TYR K 376 " --> pdb=" O LEU K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 419 through 424 Processing helix chain 'K' and resid 442 through 450 removed outlier: 4.496A pdb=" N LYS K 447 " --> pdb=" O VAL K 443 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N THR K 448 " --> pdb=" O ASP K 444 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 456 removed outlier: 4.054A pdb=" N HIS K 455 " --> pdb=" O HIS K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 457 through 468 removed outlier: 3.762A pdb=" N GLY K 468 " --> pdb=" O PHE K 464 " (cutoff:3.500A) Processing helix chain 'K' and resid 472 through 480 removed outlier: 4.084A pdb=" N ARG K 477 " --> pdb=" O PRO K 473 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU K 478 " --> pdb=" O ALA K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 494 through 501 removed outlier: 3.709A pdb=" N PHE K 498 " --> pdb=" O ARG K 494 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR K 499 " --> pdb=" O ILE K 495 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL K 501 " --> pdb=" O HIS K 497 " (cutoff:3.500A) Processing helix chain 'K' and resid 508 through 515 removed outlier: 3.932A pdb=" N ASP K 515 " --> pdb=" O GLU K 511 " (cutoff:3.500A) Processing helix chain 'K' and resid 519 through 523 removed outlier: 3.686A pdb=" N TYR K 522 " --> pdb=" O THR K 519 " (cutoff:3.500A) Processing helix chain 'K' and resid 526 through 532 removed outlier: 3.903A pdb=" N LEU K 529 " --> pdb=" O ASN K 526 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR K 530 " --> pdb=" O ILE K 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 557 through 561 Processing helix chain 'K' and resid 567 through 582 Processing helix chain 'K' and resid 590 through 602 removed outlier: 3.627A pdb=" N LEU K 594 " --> pdb=" O TYR K 590 " (cutoff:3.500A) Processing helix chain 'K' and resid 607 through 618 removed outlier: 4.523A pdb=" N TYR K 611 " --> pdb=" O PRO K 607 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU K 612 " --> pdb=" O GLU K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 620 through 627 Processing helix chain 'K' and resid 627 through 642 Processing helix chain 'K' and resid 650 through 661 Processing helix chain 'K' and resid 667 through 689 removed outlier: 3.696A pdb=" N ALA K 689 " --> pdb=" O THR K 685 " (cutoff:3.500A) Processing helix chain 'K' and resid 708 through 712 Processing helix chain 'K' and resid 753 through 759 Processing helix chain 'K' and resid 774 through 787 Processing helix chain 'K' and resid 787 through 794 removed outlier: 3.848A pdb=" N ALA K 791 " --> pdb=" O CYS K 787 " (cutoff:3.500A) Processing helix chain 'K' and resid 803 through 812 removed outlier: 3.847A pdb=" N ASP K 810 " --> pdb=" O THR K 806 " (cutoff:3.500A) Processing helix chain 'K' and resid 814 through 819 removed outlier: 3.598A pdb=" N LEU K 818 " --> pdb=" O ARG K 814 " (cutoff:3.500A) Processing helix chain 'K' and resid 845 through 854 Processing helix chain 'K' and resid 854 through 862 Processing helix chain 'K' and resid 871 through 882 removed outlier: 3.770A pdb=" N ALA K 882 " --> pdb=" O GLU K 878 " (cutoff:3.500A) Processing helix chain 'K' and resid 883 through 885 No H-bonds generated for 'chain 'K' and resid 883 through 885' Processing helix chain 'K' and resid 902 through 906 removed outlier: 3.719A pdb=" N GLN K 905 " --> pdb=" O ALA K 902 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY K 906 " --> pdb=" O GLN K 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 902 through 906' Processing helix chain 'K' and resid 945 through 953 removed outlier: 3.566A pdb=" N CYS K 949 " --> pdb=" O ASN K 945 " (cutoff:3.500A) Processing helix chain 'K' and resid 953 through 963 Processing helix chain 'K' and resid 964 through 968 removed outlier: 3.749A pdb=" N ARG K 968 " --> pdb=" O HIS K 965 " (cutoff:3.500A) Processing helix chain 'K' and resid 988 through 996 removed outlier: 3.824A pdb=" N SER K 992 " --> pdb=" O ARG K 988 " (cutoff:3.500A) Processing helix chain 'K' and resid 1001 through 1011 removed outlier: 3.597A pdb=" N VAL K1005 " --> pdb=" O VAL K1001 " (cutoff:3.500A) Processing helix chain 'K' and resid 1016 through 1026 Processing helix chain 'K' and resid 1112 through 1117 removed outlier: 3.553A pdb=" N VAL K1116 " --> pdb=" O ASP K1112 " (cutoff:3.500A) Processing helix chain 'K' and resid 1124 through 1135 Processing helix chain 'K' and resid 1145 through 1152 Processing helix chain 'K' and resid 1182 through 1186 Processing helix chain 'K' and resid 1206 through 1216 Processing helix chain 'K' and resid 1238 through 1245 Processing helix chain 'K' and resid 1245 through 1252 removed outlier: 3.827A pdb=" N ARG K1251 " --> pdb=" O ARG K1247 " (cutoff:3.500A) Processing helix chain 'K' and resid 1262 through 1267 Processing helix chain 'K' and resid 1267 through 1274 Processing helix chain 'K' and resid 1277 through 1288 Processing helix chain 'K' and resid 1313 through 1319 removed outlier: 3.958A pdb=" N LEU K1317 " --> pdb=" O ASN K1313 " (cutoff:3.500A) Processing helix chain 'K' and resid 1329 through 1339 removed outlier: 3.596A pdb=" N MET K1333 " --> pdb=" O THR K1329 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY K1339 " --> pdb=" O THR K1335 " (cutoff:3.500A) Processing helix chain 'K' and resid 1361 through 1370 removed outlier: 3.709A pdb=" N SER K1365 " --> pdb=" O PRO K1361 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU K1367 " --> pdb=" O GLN K1363 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER K1370 " --> pdb=" O MET K1366 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 10 removed outlier: 3.690A pdb=" N LEU L 7 " --> pdb=" O ASN L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 29 Processing helix chain 'L' and resid 42 through 46 removed outlier: 3.944A pdb=" N ARG L 45 " --> pdb=" O ASP L 42 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 73 Processing helix chain 'L' and resid 82 through 84 No H-bonds generated for 'chain 'L' and resid 82 through 84' Processing helix chain 'L' and resid 133 through 141 Processing helix chain 'L' and resid 146 through 185 Processing helix chain 'L' and resid 189 through 200 Processing helix chain 'L' and resid 208 through 226 Processing helix chain 'L' and resid 228 through 233 Processing helix chain 'L' and resid 235 through 250 removed outlier: 4.128A pdb=" N ALA L 250 " --> pdb=" O LEU L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 287 Processing helix chain 'L' and resid 308 through 319 Processing helix chain 'L' and resid 324 through 335 Processing helix chain 'L' and resid 342 through 348 removed outlier: 3.538A pdb=" N GLY L 348 " --> pdb=" O LEU L 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 419 through 424 Processing helix chain 'L' and resid 441 through 450 removed outlier: 4.580A pdb=" N LYS L 447 " --> pdb=" O VAL L 443 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N THR L 448 " --> pdb=" O ASP L 444 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS L 450 " --> pdb=" O LEU L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 456 removed outlier: 3.902A pdb=" N HIS L 455 " --> pdb=" O HIS L 451 " (cutoff:3.500A) Processing helix chain 'L' and resid 457 through 468 Processing helix chain 'L' and resid 472 through 480 removed outlier: 3.631A pdb=" N GLU L 480 " --> pdb=" O GLN L 476 " (cutoff:3.500A) Processing helix chain 'L' and resid 494 through 499 Processing helix chain 'L' and resid 508 through 514 removed outlier: 3.634A pdb=" N GLN L 514 " --> pdb=" O ASN L 510 " (cutoff:3.500A) Processing helix chain 'L' and resid 519 through 523 removed outlier: 3.726A pdb=" N TYR L 522 " --> pdb=" O THR L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 526 through 531 removed outlier: 3.596A pdb=" N LEU L 529 " --> pdb=" O ASN L 526 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR L 530 " --> pdb=" O ILE L 527 " (cutoff:3.500A) Processing helix chain 'L' and resid 557 through 561 Processing helix chain 'L' and resid 567 through 582 Processing helix chain 'L' and resid 590 through 602 removed outlier: 3.604A pdb=" N LEU L 594 " --> pdb=" O TYR L 590 " (cutoff:3.500A) Processing helix chain 'L' and resid 608 through 618 removed outlier: 3.998A pdb=" N LEU L 612 " --> pdb=" O GLU L 608 " (cutoff:3.500A) Processing helix chain 'L' and resid 620 through 627 Processing helix chain 'L' and resid 627 through 642 removed outlier: 3.683A pdb=" N HIS L 640 " --> pdb=" O VAL L 636 " (cutoff:3.500A) Processing helix chain 'L' and resid 650 through 661 Processing helix chain 'L' and resid 667 through 689 removed outlier: 3.859A pdb=" N LEU L 671 " --> pdb=" O PRO L 667 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA L 689 " --> pdb=" O THR L 685 " (cutoff:3.500A) Processing helix chain 'L' and resid 702 through 708 removed outlier: 3.690A pdb=" N TYR L 706 " --> pdb=" O PRO L 702 " (cutoff:3.500A) Processing helix chain 'L' and resid 753 through 759 removed outlier: 3.519A pdb=" N LEU L 757 " --> pdb=" O ASP L 753 " (cutoff:3.500A) Processing helix chain 'L' and resid 774 through 787 Processing helix chain 'L' and resid 787 through 794 removed outlier: 3.680A pdb=" N ALA L 791 " --> pdb=" O CYS L 787 " (cutoff:3.500A) Processing helix chain 'L' and resid 803 through 813 removed outlier: 3.599A pdb=" N TYR L 813 " --> pdb=" O VAL L 809 " (cutoff:3.500A) Processing helix chain 'L' and resid 814 through 819 removed outlier: 4.056A pdb=" N LEU L 818 " --> pdb=" O ARG L 814 " (cutoff:3.500A) Processing helix chain 'L' and resid 846 through 854 Processing helix chain 'L' and resid 854 through 862 Processing helix chain 'L' and resid 871 through 883 removed outlier: 3.662A pdb=" N ALA L 875 " --> pdb=" O PRO L 871 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA L 882 " --> pdb=" O GLU L 878 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL L 883 " --> pdb=" O LEU L 879 " (cutoff:3.500A) Processing helix chain 'L' and resid 884 through 886 No H-bonds generated for 'chain 'L' and resid 884 through 886' Processing helix chain 'L' and resid 930 through 932 No H-bonds generated for 'chain 'L' and resid 930 through 932' Processing helix chain 'L' and resid 945 through 953 removed outlier: 3.876A pdb=" N CYS L 949 " --> pdb=" O ASN L 945 " (cutoff:3.500A) Processing helix chain 'L' and resid 953 through 963 removed outlier: 3.560A pdb=" N LYS L 957 " --> pdb=" O SER L 953 " (cutoff:3.500A) Processing helix chain 'L' and resid 964 through 967 Processing helix chain 'L' and resid 988 through 998 removed outlier: 4.395A pdb=" N SER L 992 " --> pdb=" O ARG L 988 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR L 997 " --> pdb=" O ARG L 993 " (cutoff:3.500A) Processing helix chain 'L' and resid 1001 through 1011 removed outlier: 3.940A pdb=" N VAL L1005 " --> pdb=" O VAL L1001 " (cutoff:3.500A) Processing helix chain 'L' and resid 1016 through 1026 Processing helix chain 'L' and resid 1112 through 1117 removed outlier: 3.753A pdb=" N VAL L1116 " --> pdb=" O ASP L1112 " (cutoff:3.500A) Processing helix chain 'L' and resid 1124 through 1136 Processing helix chain 'L' and resid 1144 through 1153 removed outlier: 4.048A pdb=" N PHE L1153 " --> pdb=" O SER L1149 " (cutoff:3.500A) Processing helix chain 'L' and resid 1182 through 1187 Processing helix chain 'L' and resid 1198 through 1202 Processing helix chain 'L' and resid 1206 through 1216 Processing helix chain 'L' and resid 1230 through 1235 removed outlier: 3.751A pdb=" N GLN L1235 " --> pdb=" O PRO L1231 " (cutoff:3.500A) Processing helix chain 'L' and resid 1238 through 1245 Processing helix chain 'L' and resid 1245 through 1250 Processing helix chain 'L' and resid 1262 through 1267 Processing helix chain 'L' and resid 1267 through 1273 Processing helix chain 'L' and resid 1277 through 1288 removed outlier: 3.615A pdb=" N LEU L1287 " --> pdb=" O ASP L1283 " (cutoff:3.500A) Processing helix chain 'L' and resid 1314 through 1319 removed outlier: 3.662A pdb=" N THR L1318 " --> pdb=" O PRO L1314 " (cutoff:3.500A) Processing helix chain 'L' and resid 1329 through 1339 removed outlier: 3.538A pdb=" N MET L1333 " --> pdb=" O THR L1329 " (cutoff:3.500A) Processing helix chain 'L' and resid 1361 through 1369 removed outlier: 3.778A pdb=" N LEU L1367 " --> pdb=" O GLN L1363 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 10 removed outlier: 3.622A pdb=" N LEU M 7 " --> pdb=" O ASN M 3 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU M 8 " --> pdb=" O TRP M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 29 removed outlier: 3.537A pdb=" N GLU M 29 " --> pdb=" O THR M 25 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 46 removed outlier: 3.919A pdb=" N ARG M 45 " --> pdb=" O ASP M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 73 Processing helix chain 'M' and resid 82 through 86 Processing helix chain 'M' and resid 133 through 141 Processing helix chain 'M' and resid 146 through 186 removed outlier: 3.704A pdb=" N LYS M 186 " --> pdb=" O THR M 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 200 removed outlier: 3.617A pdb=" N VAL M 193 " --> pdb=" O PRO M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 201 through 203 No H-bonds generated for 'chain 'M' and resid 201 through 203' Processing helix chain 'M' and resid 208 through 226 Processing helix chain 'M' and resid 228 through 233 Processing helix chain 'M' and resid 235 through 250 removed outlier: 4.112A pdb=" N ALA M 250 " --> pdb=" O LEU M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 276 through 287 Processing helix chain 'M' and resid 308 through 319 Processing helix chain 'M' and resid 324 through 335 Processing helix chain 'M' and resid 344 through 348 Processing helix chain 'M' and resid 372 through 377 removed outlier: 3.714A pdb=" N TYR M 376 " --> pdb=" O LEU M 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 406 removed outlier: 3.607A pdb=" N ARG M 405 " --> pdb=" O PRO M 402 " (cutoff:3.500A) Processing helix chain 'M' and resid 419 through 424 Processing helix chain 'M' and resid 445 through 450 removed outlier: 3.948A pdb=" N CYS M 450 " --> pdb=" O LEU M 446 " (cutoff:3.500A) Processing helix chain 'M' and resid 451 through 456 Processing helix chain 'M' and resid 457 through 468 Processing helix chain 'M' and resid 472 through 480 removed outlier: 3.863A pdb=" N ARG M 477 " --> pdb=" O PRO M 473 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU M 478 " --> pdb=" O ALA M 474 " (cutoff:3.500A) Processing helix chain 'M' and resid 490 through 493 Processing helix chain 'M' and resid 494 through 501 removed outlier: 4.079A pdb=" N TYR M 499 " --> pdb=" O ILE M 495 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL M 501 " --> pdb=" O HIS M 497 " (cutoff:3.500A) Processing helix chain 'M' and resid 508 through 515 removed outlier: 3.523A pdb=" N GLN M 514 " --> pdb=" O ASN M 510 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP M 515 " --> pdb=" O GLU M 511 " (cutoff:3.500A) Processing helix chain 'M' and resid 528 through 532 Processing helix chain 'M' and resid 557 through 561 Processing helix chain 'M' and resid 567 through 582 Processing helix chain 'M' and resid 590 through 603 Processing helix chain 'M' and resid 608 through 618 removed outlier: 3.961A pdb=" N LEU M 612 " --> pdb=" O GLU M 608 " (cutoff:3.500A) Processing helix chain 'M' and resid 620 through 627 Processing helix chain 'M' and resid 627 through 642 Processing helix chain 'M' and resid 650 through 660 removed outlier: 3.750A pdb=" N VAL M 654 " --> pdb=" O SER M 650 " (cutoff:3.500A) Processing helix chain 'M' and resid 667 through 689 removed outlier: 3.647A pdb=" N LEU M 671 " --> pdb=" O PRO M 667 " (cutoff:3.500A) Processing helix chain 'M' and resid 702 through 708 removed outlier: 3.568A pdb=" N TYR M 706 " --> pdb=" O PRO M 702 " (cutoff:3.500A) Processing helix chain 'M' and resid 753 through 760 removed outlier: 3.706A pdb=" N LEU M 757 " --> pdb=" O ASP M 753 " (cutoff:3.500A) Processing helix chain 'M' and resid 774 through 787 Processing helix chain 'M' and resid 787 through 794 removed outlier: 3.582A pdb=" N ALA M 791 " --> pdb=" O CYS M 787 " (cutoff:3.500A) Processing helix chain 'M' and resid 803 through 813 removed outlier: 3.544A pdb=" N TYR M 813 " --> pdb=" O VAL M 809 " (cutoff:3.500A) Processing helix chain 'M' and resid 814 through 819 Processing helix chain 'M' and resid 846 through 854 removed outlier: 3.785A pdb=" N ARG M 850 " --> pdb=" O ILE M 846 " (cutoff:3.500A) Processing helix chain 'M' and resid 854 through 861 Processing helix chain 'M' and resid 871 through 881 removed outlier: 3.970A pdb=" N ARG M 877 " --> pdb=" O LEU M 873 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU M 881 " --> pdb=" O ARG M 877 " (cutoff:3.500A) Processing helix chain 'M' and resid 882 through 885 Processing helix chain 'M' and resid 945 through 952 removed outlier: 3.542A pdb=" N CYS M 949 " --> pdb=" O ASN M 945 " (cutoff:3.500A) Processing helix chain 'M' and resid 953 through 963 Processing helix chain 'M' and resid 964 through 967 Processing helix chain 'M' and resid 988 through 998 removed outlier: 4.292A pdb=" N SER M 992 " --> pdb=" O ARG M 988 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG M 993 " --> pdb=" O SER M 989 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR M 997 " --> pdb=" O ARG M 993 " (cutoff:3.500A) Processing helix chain 'M' and resid 1001 through 1011 removed outlier: 3.676A pdb=" N VAL M1005 " --> pdb=" O VAL M1001 " (cutoff:3.500A) Processing helix chain 'M' and resid 1016 through 1026 Processing helix chain 'M' and resid 1112 through 1117 removed outlier: 3.897A pdb=" N VAL M1116 " --> pdb=" O ASP M1112 " (cutoff:3.500A) Processing helix chain 'M' and resid 1124 through 1136 Processing helix chain 'M' and resid 1143 through 1153 Processing helix chain 'M' and resid 1183 through 1188 removed outlier: 3.699A pdb=" N LYS M1187 " --> pdb=" O VAL M1183 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE M1188 " --> pdb=" O ASN M1184 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1183 through 1188' Processing helix chain 'M' and resid 1206 through 1216 Processing helix chain 'M' and resid 1238 through 1245 Processing helix chain 'M' and resid 1245 through 1252 removed outlier: 3.555A pdb=" N ARG M1251 " --> pdb=" O ARG M1247 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU M1252 " --> pdb=" O HIS M1248 " (cutoff:3.500A) Processing helix chain 'M' and resid 1262 through 1267 removed outlier: 3.596A pdb=" N PHE M1266 " --> pdb=" O CYS M1262 " (cutoff:3.500A) Processing helix chain 'M' and resid 1267 through 1275 removed outlier: 3.547A pdb=" N ASN M1275 " --> pdb=" O ILE M1271 " (cutoff:3.500A) Processing helix chain 'M' and resid 1277 through 1288 removed outlier: 3.501A pdb=" N LEU M1287 " --> pdb=" O ASP M1283 " (cutoff:3.500A) Processing helix chain 'M' and resid 1313 through 1319 removed outlier: 4.122A pdb=" N LEU M1317 " --> pdb=" O ASN M1313 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR M1318 " --> pdb=" O PRO M1314 " (cutoff:3.500A) Processing helix chain 'M' and resid 1329 through 1339 removed outlier: 3.674A pdb=" N MET M1333 " --> pdb=" O THR M1329 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 25 removed outlier: 3.630A pdb=" N HIS N 18 " --> pdb=" O ARG N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 50 removed outlier: 4.206A pdb=" N SER N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N LYS N 46 " --> pdb=" O THR N 42 " (cutoff:3.500A) Processing helix chain 'N' and resid 56 through 72 removed outlier: 3.959A pdb=" N PHE N 60 " --> pdb=" O ASP N 56 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG N 72 " --> pdb=" O VAL N 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 25 Processing helix chain 'O' and resid 37 through 50 removed outlier: 3.619A pdb=" N THR O 42 " --> pdb=" O PRO O 38 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS O 46 " --> pdb=" O THR O 42 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG O 49 " --> pdb=" O SER O 45 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET O 50 " --> pdb=" O LYS O 46 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 73 removed outlier: 3.712A pdb=" N PHE O 60 " --> pdb=" O ASP O 56 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG O 72 " --> pdb=" O VAL O 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 24 removed outlier: 4.113A pdb=" N VAL P 21 " --> pdb=" O LYS P 17 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL P 22 " --> pdb=" O HIS P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 43 removed outlier: 3.607A pdb=" N ALA P 41 " --> pdb=" O HIS P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 48 Processing helix chain 'P' and resid 56 through 73 removed outlier: 4.026A pdb=" N PHE P 60 " --> pdb=" O ASP P 56 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 24 Processing helix chain 'Q' and resid 37 through 48 removed outlier: 3.766A pdb=" N LYS Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR Q 48 " --> pdb=" O LEU Q 44 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 72 removed outlier: 4.054A pdb=" N PHE Q 60 " --> pdb=" O ASP Q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 25 removed outlier: 3.808A pdb=" N HIS R 18 " --> pdb=" O ARG R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 removed outlier: 3.896A pdb=" N THR R 42 " --> pdb=" O PRO R 38 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N MET R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU R 44 " --> pdb=" O LEU R 40 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS R 46 " --> pdb=" O THR R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 72 Processing helix chain 'S' and resid 14 through 25 Processing helix chain 'S' and resid 37 through 48 removed outlier: 4.250A pdb=" N SER S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS S 46 " --> pdb=" O THR S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 72 removed outlier: 3.728A pdb=" N ARG S 72 " --> pdb=" O VAL S 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 58 Processing helix chain 'T' and resid 84 through 89 removed outlier: 3.840A pdb=" N GLY T 88 " --> pdb=" O LEU T 84 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE T 89 " --> pdb=" O TYR T 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 84 through 89' Processing helix chain 'T' and resid 95 through 106 Processing helix chain 'T' and resid 108 through 121 removed outlier: 3.511A pdb=" N GLY T 121 " --> pdb=" O TRP T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 125 through 127 No H-bonds generated for 'chain 'T' and resid 125 through 127' Processing helix chain 'T' and resid 211 through 223 removed outlier: 4.176A pdb=" N GLY T 221 " --> pdb=" O ASP T 217 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS T 222 " --> pdb=" O VAL T 218 " (cutoff:3.500A) Processing helix chain 'T' and resid 223 through 237 Processing helix chain 'U' and resid 17 through 27 Processing helix chain 'U' and resid 44 through 46 No H-bonds generated for 'chain 'U' and resid 44 through 46' Processing helix chain 'U' and resid 57 through 68 removed outlier: 3.579A pdb=" N ASN U 67 " --> pdb=" O GLY U 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 140 through 158 removed outlier: 3.880A pdb=" N LEU U 158 " --> pdb=" O GLY U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 161 through 173 removed outlier: 3.652A pdb=" N ALA U 167 " --> pdb=" O GLU U 163 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 211 removed outlier: 3.583A pdb=" N ALA U 211 " --> pdb=" O VAL U 207 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 226 removed outlier: 3.749A pdb=" N MET U 216 " --> pdb=" O SER U 212 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR U 217 " --> pdb=" O GLU U 213 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL U 219 " --> pdb=" O THR U 215 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ARG U 220 " --> pdb=" O MET U 216 " (cutoff:3.500A) Processing helix chain 'U' and resid 228 through 240 removed outlier: 4.179A pdb=" N ARG U 240 " --> pdb=" O GLU U 236 " (cutoff:3.500A) Processing helix chain 'U' and resid 260 through 280 removed outlier: 3.626A pdb=" N ASP U 280 " --> pdb=" O ARG U 276 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 27 removed outlier: 4.243A pdb=" N LEU V 27 " --> pdb=" O LYS V 23 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 46 No H-bonds generated for 'chain 'V' and resid 44 through 46' Processing helix chain 'V' and resid 47 through 51 removed outlier: 4.289A pdb=" N GLN V 50 " --> pdb=" O GLY V 47 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 68 removed outlier: 4.403A pdb=" N LEU V 61 " --> pdb=" O GLY V 57 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG V 62 " --> pdb=" O TYR V 58 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN V 67 " --> pdb=" O GLY V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 140 through 160 removed outlier: 4.100A pdb=" N LEU V 158 " --> pdb=" O GLY V 154 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP V 159 " --> pdb=" O LEU V 155 " (cutoff:3.500A) Processing helix chain 'V' and resid 162 through 173 Processing helix chain 'V' and resid 194 through 224 removed outlier: 4.779A pdb=" N MET V 216 " --> pdb=" O SER V 212 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR V 217 " --> pdb=" O GLU V 213 " (cutoff:3.500A) Processing helix chain 'V' and resid 228 through 246 Processing helix chain 'V' and resid 260 through 278 removed outlier: 3.774A pdb=" N LEU V 278 " --> pdb=" O MET V 274 " (cutoff:3.500A) Processing helix chain 'V' and resid 278 through 283 removed outlier: 3.689A pdb=" N ILE V 282 " --> pdb=" O LEU V 278 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG V 283 " --> pdb=" O ASP V 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 278 through 283' Processing helix chain 'W' and resid 2 through 7 Processing helix chain 'W' and resid 18 through 28 Processing helix chain 'W' and resid 55 through 57 No H-bonds generated for 'chain 'W' and resid 55 through 57' Processing helix chain 'W' and resid 84 through 89 removed outlier: 3.666A pdb=" N ILE W 89 " --> pdb=" O TYR W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 95 through 106 Processing helix chain 'W' and resid 108 through 121 removed outlier: 3.672A pdb=" N ASP W 119 " --> pdb=" O LEU W 115 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLY W 121 " --> pdb=" O TRP W 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 124 through 128 removed outlier: 3.516A pdb=" N ARG W 128 " --> pdb=" O LEU W 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 124 through 128' Processing helix chain 'W' and resid 211 through 223 Processing helix chain 'W' and resid 223 through 237 Processing helix chain 'W' and resid 257 through 259 No H-bonds generated for 'chain 'W' and resid 257 through 259' Processing helix chain 'X' and resid 17 through 26 Processing helix chain 'X' and resid 48 through 52 Processing helix chain 'X' and resid 57 through 67 removed outlier: 3.913A pdb=" N ASN X 67 " --> pdb=" O GLY X 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 140 through 157 Processing helix chain 'X' and resid 161 through 173 Processing helix chain 'X' and resid 190 through 211 Processing helix chain 'X' and resid 212 through 226 removed outlier: 4.227A pdb=" N VAL X 219 " --> pdb=" O THR X 215 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG X 220 " --> pdb=" O MET X 216 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 238 removed outlier: 3.573A pdb=" N LEU X 237 " --> pdb=" O LYS X 233 " (cutoff:3.500A) Processing helix chain 'X' and resid 260 through 280 Processing helix chain 'Y' and resid 17 through 27 removed outlier: 3.566A pdb=" N LEU Y 27 " --> pdb=" O LYS Y 23 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 46 No H-bonds generated for 'chain 'Y' and resid 44 through 46' Processing helix chain 'Y' and resid 48 through 52 Processing helix chain 'Y' and resid 57 through 68 removed outlier: 3.606A pdb=" N LEU Y 61 " --> pdb=" O GLY Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 140 through 156 Processing helix chain 'Y' and resid 157 through 160 removed outlier: 3.978A pdb=" N ARG Y 160 " --> pdb=" O SER Y 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 157 through 160' Processing helix chain 'Y' and resid 162 through 174 removed outlier: 3.757A pdb=" N THR Y 174 " --> pdb=" O GLN Y 170 " (cutoff:3.500A) Processing helix chain 'Y' and resid 194 through 226 removed outlier: 3.906A pdb=" N SER Y 212 " --> pdb=" O ALA Y 208 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU Y 213 " --> pdb=" O ASN Y 209 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N MET Y 216 " --> pdb=" O SER Y 212 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR Y 217 " --> pdb=" O GLU Y 213 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR Y 218 " --> pdb=" O LEU Y 214 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG Y 220 " --> pdb=" O MET Y 216 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS Y 221 " --> pdb=" O THR Y 217 " (cutoff:3.500A) Processing helix chain 'Y' and resid 229 through 245 Processing helix chain 'Y' and resid 260 through 283 removed outlier: 3.677A pdb=" N GLN Y 277 " --> pdb=" O VAL Y 273 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASP Y 280 " --> pdb=" O ARG Y 276 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LEU Y 281 " --> pdb=" O GLN Y 277 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 22 Processing helix chain 'Z' and resid 23 through 26 Processing helix chain 'Z' and resid 34 through 41 removed outlier: 3.933A pdb=" N LEU Z 38 " --> pdb=" O HIS Z 34 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS Z 41 " --> pdb=" O ILE Z 37 " (cutoff:3.500A) Processing helix chain 'Z' and resid 47 through 69 Processing helix chain 'Z' and resid 73 through 94 removed outlier: 3.670A pdb=" N GLU Z 79 " --> pdb=" O SER Z 75 " (cutoff:3.500A) Processing helix chain 'Z' and resid 98 through 111 removed outlier: 3.602A pdb=" N ALA Z 102 " --> pdb=" O ASP Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 117 through 141 Processing helix chain 'Z' and resid 160 through 177 Processing helix chain 'Z' and resid 194 through 240 Processing helix chain 'Z' and resid 244 through 255 Processing helix chain 'Z' and resid 260 through 274 removed outlier: 3.872A pdb=" N ASP Z 274 " --> pdb=" O LEU Z 270 " (cutoff:3.500A) Processing helix chain 'Z' and resid 274 through 279 removed outlier: 3.983A pdb=" N TYR Z 278 " --> pdb=" O ASP Z 274 " (cutoff:3.500A) Processing helix chain 'Z' and resid 280 through 282 No H-bonds generated for 'chain 'Z' and resid 280 through 282' Processing sheet with id=AA1, first strand: chain 'A' and resid 1594 through 1597 removed outlier: 7.823A pdb=" N VAL A1588 " --> pdb=" O VAL A1910 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N VAL A1910 " --> pdb=" O VAL A1588 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1641 through 1642 Processing sheet with id=AA3, first strand: chain 'A' and resid 1738 through 1741 removed outlier: 6.042A pdb=" N LEU A1739 " --> pdb=" O VAL A2067 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 1803 through 1806 removed outlier: 6.866A pdb=" N ILE A1973 " --> pdb=" O ASP A1966 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ASP A1966 " --> pdb=" O ILE A1973 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL A1975 " --> pdb=" O VAL A1964 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A1964 " --> pdb=" O VAL A1975 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N ARG A1977 " --> pdb=" O VAL A1962 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A1962 " --> pdb=" O ARG A1977 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N CYS A1959 " --> pdb=" O VAL A2040 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N TYR A2042 " --> pdb=" O CYS A1959 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N GLY A1961 " --> pdb=" O TYR A2042 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU A2039 " --> pdb=" O VAL A2052 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL A2052 " --> pdb=" O LEU A2039 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE A2041 " --> pdb=" O VAL A2050 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2105 through 2106 Processing sheet with id=AA6, first strand: chain 'E' and resid 14 through 15 Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 5 Processing sheet with id=AA8, first strand: chain 'E' and resid 182 through 184 Processing sheet with id=AA9, first strand: chain 'G' and resid 94 through 97 removed outlier: 8.140A pdb=" N TYR G 331 " --> pdb=" O PRO G 22 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N HIS G 24 " --> pdb=" O LEU G 329 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG G 315 " --> pdb=" O VAL G 328 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TRP G 330 " --> pdb=" O ARG G 313 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG G 313 " --> pdb=" O TRP G 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 90 through 91 removed outlier: 3.626A pdb=" N LEU G 151 " --> pdb=" O ARG G 159 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG G 159 " --> pdb=" O LEU G 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AB3, first strand: chain 'G' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'G' and resid 502 through 505 removed outlier: 5.844A pdb=" N VAL G 485 " --> pdb=" O ARG G 479 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ARG G 479 " --> pdb=" O VAL G 485 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LEU G 487 " --> pdb=" O VAL G 477 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N VAL G 477 " --> pdb=" O LEU G 487 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL G 489 " --> pdb=" O ALA G 475 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR G 474 " --> pdb=" O VAL G 525 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 13 through 15 removed outlier: 5.833A pdb=" N VAL H 13 " --> pdb=" O CYS L 58 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS K 90 " --> pdb=" O ILE L 53 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY L 55 " --> pdb=" O LYS K 90 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU K 92 " --> pdb=" O GLY L 55 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE L 57 " --> pdb=" O LEU K 92 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN L 59 " --> pdb=" O HIS K 94 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLN K 96 " --> pdb=" O ASN L 59 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR K 119 " --> pdb=" O ASP K1085 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP K1085 " --> pdb=" O TYR K 119 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE K1081 " --> pdb=" O SER K 123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 33 through 39 removed outlier: 6.173A pdb=" N ALA H 34 " --> pdb=" O THR K 117 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR K 117 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR H 38 " --> pdb=" O THR K 113 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N TYR K 119 " --> pdb=" O ASP K1085 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASP K1085 " --> pdb=" O TYR K 119 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE K1081 " --> pdb=" O SER K 123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 303 through 304 removed outlier: 6.493A pdb=" N ILE I 78 " --> pdb=" O ILE I1059 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASP I1085 " --> pdb=" O TYR I 119 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR I 119 " --> pdb=" O ASP I1085 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LYS I 90 " --> pdb=" O GLU H 51 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE H 53 " --> pdb=" O LYS I 90 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU I 92 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY H 55 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N HIS I 94 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE H 57 " --> pdb=" O HIS I 94 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLN I 96 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN H 59 " --> pdb=" O GLN I 96 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLY L 14 " --> pdb=" O LEU I 339 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 320 through 322 removed outlier: 6.192A pdb=" N GLU H 51 " --> pdb=" O ILE I 321 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N LYS I 90 " --> pdb=" O GLU H 51 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ILE H 53 " --> pdb=" O LYS I 90 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU I 92 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY H 55 " --> pdb=" O LEU I 92 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N HIS I 94 " --> pdb=" O GLY H 55 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE H 57 " --> pdb=" O HIS I 94 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N GLN I 96 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASN H 59 " --> pdb=" O GLN I 96 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR L 38 " --> pdb=" O THR I 113 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA L 34 " --> pdb=" O THR I 117 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 121 through 122 removed outlier: 6.493A pdb=" N ILE H 78 " --> pdb=" O ILE H1059 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY H 303 " --> pdb=" O ALA H 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AC2, first strand: chain 'H' and resid 1063 through 1068 Processing sheet with id=AC3, first strand: chain 'H' and resid 262 through 263 removed outlier: 4.182A pdb=" N THR H 262 " --> pdb=" O SER H 297 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASP H 358 " --> pdb=" O MET H 369 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU H 370 " --> pdb=" O MET H 273 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 1092 through 1102 removed outlier: 7.101A pdb=" N ASP H1045 " --> pdb=" O ALA H1097 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL H1099 " --> pdb=" O GLU H1043 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLU H1043 " --> pdb=" O VAL H1099 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG H1101 " --> pdb=" O THR H1041 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR H1041 " --> pdb=" O ARG H1101 " (cutoff:3.500A) removed outlier: 8.992A pdb=" N LEU H1322 " --> pdb=" O ASP H 390 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR H 392 " --> pdb=" O LEU H1322 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 415 through 416 Processing sheet with id=AC6, first strand: chain 'H' and resid 428 through 431 Processing sheet with id=AC7, first strand: chain 'H' and resid 537 through 544 Processing sheet with id=AC8, first strand: chain 'H' and resid 719 through 720 removed outlier: 3.509A pdb=" N LYS H 891 " --> pdb=" O TYR H 918 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 744 through 745 Processing sheet with id=AD1, first strand: chain 'H' and resid 921 through 923 Processing sheet with id=AD2, first strand: chain 'H' and resid 1290 through 1291 Processing sheet with id=AD3, first strand: chain 'H' and resid 1326 through 1327 Processing sheet with id=AD4, first strand: chain 'J' and resid 303 through 304 removed outlier: 4.317A pdb=" N ASP J1085 " --> pdb=" O TYR J 119 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N TYR J 119 " --> pdb=" O ASP J1085 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE J 114 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL J 95 " --> pdb=" O ILE J 114 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLY J 89 " --> pdb=" O SER J 120 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LYS J 122 " --> pdb=" O THR J 87 " (cutoff:3.500A) removed outlier: 11.579A pdb=" N THR J 87 " --> pdb=" O LYS J 122 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N PHE I 50 " --> pdb=" O THR J 88 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LYS J 90 " --> pdb=" O PHE I 50 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ALA I 52 " --> pdb=" O LYS J 90 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU J 92 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N PHE I 54 " --> pdb=" O LEU J 92 " (cutoff:3.500A) removed outlier: 12.652A pdb=" N HIS J 94 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 9.667A pdb=" N THR I 56 " --> pdb=" O HIS J 94 " (cutoff:3.500A) removed outlier: 12.521A pdb=" N GLN J 96 " --> pdb=" O THR I 56 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLU I 51 " --> pdb=" O ILE J 321 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 125 through 132 removed outlier: 4.778A pdb=" N VAL I1064 " --> pdb=" O TYR W 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 262 through 263 removed outlier: 5.211A pdb=" N ASP I 358 " --> pdb=" O MET I 369 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE I 368 " --> pdb=" O SER I 270 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL I 272 " --> pdb=" O ILE I 368 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU I 370 " --> pdb=" O VAL I 272 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL I 274 " --> pdb=" O GLU I 370 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 1092 through 1102 removed outlier: 7.290A pdb=" N ASP I1045 " --> pdb=" O ALA I1097 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL I1099 " --> pdb=" O GLU I1043 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLU I1043 " --> pdb=" O VAL I1099 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ARG I1101 " --> pdb=" O THR I1041 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR I1041 " --> pdb=" O ARG I1101 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N LEU I1322 " --> pdb=" O ASP I 390 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR I 392 " --> pdb=" O LEU I1322 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 415 through 416 Processing sheet with id=AD9, first strand: chain 'I' and resid 437 through 440 Processing sheet with id=AE1, first strand: chain 'I' and resid 537 through 544 Processing sheet with id=AE2, first strand: chain 'I' and resid 719 through 720 Processing sheet with id=AE3, first strand: chain 'I' and resid 744 through 746 Processing sheet with id=AE4, first strand: chain 'I' and resid 921 through 923 removed outlier: 4.043A pdb=" N GLY I 799 " --> pdb=" O VAL I 937 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 125 through 132 Processing sheet with id=AE6, first strand: chain 'J' and resid 262 through 263 removed outlier: 3.646A pdb=" N THR J 262 " --> pdb=" O SER J 297 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASP J 358 " --> pdb=" O MET J 369 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY J 271 " --> pdb=" O THR J 366 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1092 through 1102 removed outlier: 7.382A pdb=" N SER J1092 " --> pdb=" O GLY J1051 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY J1051 " --> pdb=" O SER J1092 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N THR J1094 " --> pdb=" O TYR J1049 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR J1049 " --> pdb=" O THR J1094 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL J1096 " --> pdb=" O LEU J1047 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU J1047 " --> pdb=" O VAL J1096 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N GLU J1043 " --> pdb=" O ASN J1100 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL J1102 " --> pdb=" O THR J1041 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N THR J1041 " --> pdb=" O VAL J1102 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU J1034 " --> pdb=" O VAL J 397 " (cutoff:3.500A) removed outlier: 9.168A pdb=" N LEU J1322 " --> pdb=" O ASP J 390 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR J 392 " --> pdb=" O LEU J1322 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 437 through 441 removed outlier: 3.567A pdb=" N SER J1326 " --> pdb=" O VAL J1356 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU J1348 " --> pdb=" O VAL J1355 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 537 through 544 Processing sheet with id=AF1, first strand: chain 'J' and resid 719 through 720 Processing sheet with id=AF2, first strand: chain 'J' and resid 744 through 746 Processing sheet with id=AF3, first strand: chain 'J' and resid 921 through 923 removed outlier: 3.523A pdb=" N CYS J 921 " --> pdb=" O LEU J 800 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU J 800 " --> pdb=" O CYS J 921 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 102 through 103 removed outlier: 3.505A pdb=" N VAL L1077 " --> pdb=" O ILE L 127 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 262 through 263 Processing sheet with id=AF6, first strand: chain 'K' and resid 291 through 299 removed outlier: 13.406A pdb=" N SER K 356 " --> pdb=" O ASN K 371 " (cutoff:3.500A) removed outlier: 10.484A pdb=" N ASN K 371 " --> pdb=" O SER K 356 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ASP K 358 " --> pdb=" O MET K 369 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY K 271 " --> pdb=" O THR K 366 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 1092 through 1102 removed outlier: 7.613A pdb=" N SER K1092 " --> pdb=" O GLY K1051 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLY K1051 " --> pdb=" O SER K1092 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N THR K1094 " --> pdb=" O TYR K1049 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N TYR K1049 " --> pdb=" O THR K1094 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL K1096 " --> pdb=" O LEU K1047 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU K1047 " --> pdb=" O VAL K1096 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN K1100 " --> pdb=" O GLU K1043 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU K1043 " --> pdb=" O ASN K1100 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL K1102 " --> pdb=" O THR K1041 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR K1041 " --> pdb=" O VAL K1102 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N LEU K1322 " --> pdb=" O ASP K 390 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR K 392 " --> pdb=" O LEU K1322 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 407 through 408 Processing sheet with id=AF9, first strand: chain 'K' and resid 427 through 431 Processing sheet with id=AG1, first strand: chain 'K' and resid 537 through 544 Processing sheet with id=AG2, first strand: chain 'K' and resid 697 through 698 Processing sheet with id=AG3, first strand: chain 'K' and resid 719 through 720 Processing sheet with id=AG4, first strand: chain 'K' and resid 723 through 724 removed outlier: 6.951A pdb=" N LEU K 723 " --> pdb=" O ALA K 773 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'K' and resid 745 through 746 removed outlier: 6.218A pdb=" N GLU K 745 " --> pdb=" O VAL K 768 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'K' and resid 921 through 923 Processing sheet with id=AG7, first strand: chain 'K' and resid 1326 through 1327 Processing sheet with id=AG8, first strand: chain 'L' and resid 303 through 305 removed outlier: 4.484A pdb=" N ASP L1085 " --> pdb=" O TYR L 119 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TYR L 119 " --> pdb=" O ASP L1085 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLY L 89 " --> pdb=" O SER L 120 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N LYS L 122 " --> pdb=" O THR L 87 " (cutoff:3.500A) removed outlier: 12.382A pdb=" N THR L 87 " --> pdb=" O LYS L 122 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ALA M 52 " --> pdb=" O THR L 87 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY L 89 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N PHE M 54 " --> pdb=" O GLY L 89 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N MET L 91 " --> pdb=" O PHE M 54 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N THR M 56 " --> pdb=" O MET L 91 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE L 93 " --> pdb=" O THR M 56 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N CYS M 58 " --> pdb=" O PHE L 93 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL L 95 " --> pdb=" O CYS M 58 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 102 through 103 removed outlier: 3.655A pdb=" N ILE M 125 " --> pdb=" O GLN M1079 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 262 through 263 removed outlier: 3.677A pdb=" N THR L 262 " --> pdb=" O SER L 297 " (cutoff:3.500A) removed outlier: 13.744A pdb=" N SER L 356 " --> pdb=" O ASN L 371 " (cutoff:3.500A) removed outlier: 10.732A pdb=" N ASN L 371 " --> pdb=" O SER L 356 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ASP L 358 " --> pdb=" O MET L 369 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY L 271 " --> pdb=" O THR L 366 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 1092 through 1102 removed outlier: 3.521A pdb=" N ALA L1097 " --> pdb=" O ASP L1045 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASP L1045 " --> pdb=" O ALA L1097 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL L1099 " --> pdb=" O GLU L1043 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU L1043 " --> pdb=" O VAL L1099 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ARG L1101 " --> pdb=" O THR L1041 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N THR L1041 " --> pdb=" O ARG L1101 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N LEU L1322 " --> pdb=" O ASP L 390 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR L 392 " --> pdb=" O LEU L1322 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 407 through 408 Processing sheet with id=AH4, first strand: chain 'L' and resid 428 through 431 Processing sheet with id=AH5, first strand: chain 'L' and resid 537 through 544 Processing sheet with id=AH6, first strand: chain 'L' and resid 719 through 720 Processing sheet with id=AH7, first strand: chain 'L' and resid 744 through 746 Processing sheet with id=AH8, first strand: chain 'L' and resid 921 through 923 Processing sheet with id=AH9, first strand: chain 'L' and resid 1326 through 1327 Processing sheet with id=AI1, first strand: chain 'M' and resid 121 through 122 removed outlier: 6.040A pdb=" N HIS M 76 " --> pdb=" O VAL M1057 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE M1059 " --> pdb=" O HIS M 76 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE M 78 " --> pdb=" O ILE M1059 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'M' and resid 90 through 92 Processing sheet with id=AI3, first strand: chain 'M' and resid 95 through 96 Processing sheet with id=AI4, first strand: chain 'M' and resid 291 through 298 removed outlier: 4.370A pdb=" N ASP M 358 " --> pdb=" O MET M 369 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER M 275 " --> pdb=" O GLU M 370 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'M' and resid 1092 through 1102 removed outlier: 3.590A pdb=" N ALA M1097 " --> pdb=" O ASP M1045 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N ASP M1045 " --> pdb=" O ALA M1097 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL M1099 " --> pdb=" O GLU M1043 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N GLU M1043 " --> pdb=" O VAL M1099 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ARG M1101 " --> pdb=" O THR M1041 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N THR M1041 " --> pdb=" O ARG M1101 " (cutoff:3.500A) removed outlier: 8.949A pdb=" N LEU M1322 " --> pdb=" O ASP M 390 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR M 392 " --> pdb=" O LEU M1322 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'M' and resid 437 through 441 Processing sheet with id=AI7, first strand: chain 'M' and resid 537 through 544 Processing sheet with id=AI8, first strand: chain 'M' and resid 719 through 720 Processing sheet with id=AI9, first strand: chain 'M' and resid 744 through 746 Processing sheet with id=AJ1, first strand: chain 'M' and resid 921 through 923 Processing sheet with id=AJ2, first strand: chain 'T' and resid 46 through 53 removed outlier: 3.756A pdb=" N ARG T 151 " --> pdb=" O LEU T 46 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ALA T 48 " --> pdb=" O VAL T 149 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL T 149 " --> pdb=" O ALA T 48 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N PHE T 50 " --> pdb=" O THR T 147 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N THR T 147 " --> pdb=" O PHE T 50 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL T 52 " --> pdb=" O LEU T 145 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N LEU T 145 " --> pdb=" O VAL T 52 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N MET T 150 " --> pdb=" O LEU T 283 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU T 283 " --> pdb=" O MET T 150 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY T 152 " --> pdb=" O VAL T 281 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU T 282 " --> pdb=" O LEU T 251 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU T 251 " --> pdb=" O GLU T 282 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N GLY T 246 " --> pdb=" O TYR T 191 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR T 191 " --> pdb=" O GLY T 246 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE T 248 " --> pdb=" O ILE T 189 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N ILE T 189 " --> pdb=" O ILE T 248 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS T 250 " --> pdb=" O LEU T 187 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU T 187 " --> pdb=" O LYS T 250 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY T 252 " --> pdb=" O VAL T 185 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N VAL T 185 " --> pdb=" O GLY T 252 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR T 206 " --> pdb=" O LEU T 173 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'T' and resid 79 through 83 removed outlier: 6.354A pdb=" N LEU T 67 " --> pdb=" O LEU T 132 " (cutoff:3.500A) removed outlier: 11.779A pdb=" N LEU T 132 " --> pdb=" O ARG T 151 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ARG T 151 " --> pdb=" O LEU T 132 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N MET T 150 " --> pdb=" O LEU T 283 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU T 283 " --> pdb=" O MET T 150 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY T 152 " --> pdb=" O VAL T 281 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU T 282 " --> pdb=" O LEU T 251 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU T 251 " --> pdb=" O GLU T 282 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'T' and resid 165 through 168 removed outlier: 3.570A pdb=" N LEU T 269 " --> pdb=" O HIS T 266 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N HIS T 266 " --> pdb=" O LEU T 269 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'U' and resid 9 through 11 removed outlier: 3.582A pdb=" N THR U 11 " --> pdb=" O ILE U 41 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'U' and resid 31 through 34 Processing sheet with id=AJ7, first strand: chain 'U' and resid 91 through 94 removed outlier: 3.595A pdb=" N PHE U 288 " --> pdb=" O LEU U 108 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'U' and resid 115 through 116 removed outlier: 3.712A pdb=" N THR U 183 " --> pdb=" O PHE U 115 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'U' and resid 126 through 127 removed outlier: 3.645A pdb=" N TRP U 130 " --> pdb=" O LEU U 127 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'V' and resid 31 through 34 removed outlier: 8.489A pdb=" N ILE V 41 " --> pdb=" O ASN V 7 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE V 9 " --> pdb=" O ILE V 41 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'V' and resid 91 through 95 removed outlier: 3.608A pdb=" N PHE V 288 " --> pdb=" O LEU V 108 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'V' and resid 174 through 177 Processing sheet with id=AK4, first strand: chain 'V' and resid 188 through 189 Processing sheet with id=AK5, first strand: chain 'W' and resid 47 through 53 removed outlier: 6.789A pdb=" N LEU W 145 " --> pdb=" O VAL W 138 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL W 138 " --> pdb=" O LEU W 145 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR W 147 " --> pdb=" O LYS W 136 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU W 67 " --> pdb=" O LEU W 132 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'W' and resid 165 through 168 Processing sheet with id=AK7, first strand: chain 'W' and resid 172 through 173 removed outlier: 3.704A pdb=" N ARG W 199 " --> pdb=" O ASP W 192 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN W 183 " --> pdb=" O TRP W 253 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP W 253 " --> pdb=" O GLN W 183 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL W 185 " --> pdb=" O LEU W 251 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU W 251 " --> pdb=" O GLU W 282 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLU W 282 " --> pdb=" O LEU W 251 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'W' and resid 172 through 173 removed outlier: 3.704A pdb=" N ARG W 199 " --> pdb=" O ASP W 192 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLN W 183 " --> pdb=" O TRP W 253 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N TRP W 253 " --> pdb=" O GLN W 183 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL W 185 " --> pdb=" O LEU W 251 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'X' and resid 31 through 34 removed outlier: 7.959A pdb=" N ILE X 41 " --> pdb=" O ASN X 7 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE X 9 " --> pdb=" O ILE X 41 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'X' and resid 91 through 95 Processing sheet with id=AL2, first strand: chain 'X' and resid 174 through 177 Processing sheet with id=AL3, first strand: chain 'Y' and resid 31 through 34 removed outlier: 4.205A pdb=" N LEU Y 82 " --> pdb=" O ARG Y 74 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL Y 76 " --> pdb=" O GLN Y 80 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLN Y 80 " --> pdb=" O VAL Y 76 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N PHE Y 9 " --> pdb=" O ILE Y 41 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'Y' and resid 91 through 95 removed outlier: 8.125A pdb=" N SER Y 299 " --> pdb=" O VAL Y 293 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL Y 293 " --> pdb=" O SER Y 299 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N THR Y 301 " --> pdb=" O CYS Y 291 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'Y' and resid 188 through 189 4299 hydrogen bonds defined for protein. 12144 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: 62.36 Time building geometry restraints manager: 32.35 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: 32057 1.34 - 1.46: 22023 1.46 - 1.58: 44007 1.58 - 1.70: 0 1.70 - 1.83: 863 Bond restraints: 98950 Sorted by residual: bond pdb=" CA ASN V 79 " pdb=" C ASN V 79 " ideal model delta sigma weight residual 1.523 1.564 -0.041 1.34e-02 5.57e+03 9.18e+00 bond pdb=" C GLY U 117 " pdb=" N PRO U 118 " ideal model delta sigma weight residual 1.337 1.354 -0.018 9.80e-03 1.04e+04 3.28e+00 bond pdb=" CA THR E 269 " pdb=" C THR E 269 " ideal model delta sigma weight residual 1.524 1.501 0.023 1.27e-02 6.20e+03 3.23e+00 bond pdb=" CA GLY U 117 " pdb=" C GLY U 117 " ideal model delta sigma weight residual 1.511 1.523 -0.012 6.90e-03 2.10e+04 3.16e+00 bond pdb=" CA ASP E 271 " pdb=" C ASP E 271 " ideal model delta sigma weight residual 1.525 1.498 0.027 1.63e-02 3.76e+03 2.75e+00 ... (remaining 98945 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.24: 2352 105.24 - 112.46: 51424 112.46 - 119.68: 32700 119.68 - 126.90: 46798 126.90 - 134.13: 1334 Bond angle restraints: 134608 Sorted by residual: angle pdb=" N TYR E 270 " pdb=" CA TYR E 270 " pdb=" C TYR E 270 " ideal model delta sigma weight residual 112.72 102.50 10.22 1.14e+00 7.69e-01 8.03e+01 angle pdb=" C ASP M 753 " pdb=" N VAL M 754 " pdb=" CA VAL M 754 " ideal model delta sigma weight residual 120.24 124.35 -4.11 6.30e-01 2.52e+00 4.25e+01 angle pdb=" C SER K 752 " pdb=" N ASP K 753 " pdb=" CA ASP K 753 " ideal model delta sigma weight residual 121.54 133.37 -11.83 1.91e+00 2.74e-01 3.84e+01 angle pdb=" C ARG L 988 " pdb=" N SER L 989 " pdb=" CA SER L 989 " ideal model delta sigma weight residual 120.09 127.19 -7.10 1.25e+00 6.40e-01 3.22e+01 angle pdb=" C CYS X 291 " pdb=" N ASP X 292 " pdb=" CA ASP X 292 " ideal model delta sigma weight residual 121.54 132.05 -10.51 1.91e+00 2.74e-01 3.03e+01 ... (remaining 134603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 53603 17.95 - 35.90: 4858 35.90 - 53.86: 1034 53.86 - 71.81: 195 71.81 - 89.76: 98 Dihedral angle restraints: 59788 sinusoidal: 24041 harmonic: 35747 Sorted by residual: dihedral pdb=" CB CYS L1292 " pdb=" SG CYS L1292 " pdb=" SG CYS L1303 " pdb=" CB CYS L1303 " ideal model delta sinusoidal sigma weight residual 93.00 179.40 -86.40 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CA ASN J 794 " pdb=" C ASN J 794 " pdb=" N ASN J 795 " pdb=" CA ASN J 795 " ideal model delta harmonic sigma weight residual 180.00 139.99 40.01 0 5.00e+00 4.00e-02 6.40e+01 dihedral pdb=" CA ASN H1100 " pdb=" C ASN H1100 " pdb=" N ARG H1101 " pdb=" CA ARG H1101 " ideal model delta harmonic sigma weight residual 180.00 140.15 39.85 0 5.00e+00 4.00e-02 6.35e+01 ... (remaining 59785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 14596 0.087 - 0.173: 916 0.173 - 0.260: 5 0.260 - 0.346: 1 0.346 - 0.433: 1 Chirality restraints: 15519 Sorted by residual: chirality pdb=" CB THR T 137 " pdb=" CA THR T 137 " pdb=" OG1 THR T 137 " pdb=" CG2 THR T 137 " both_signs ideal model delta sigma weight residual False 2.55 2.12 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CB THR W 137 " pdb=" CA THR W 137 " pdb=" OG1 THR W 137 " pdb=" CG2 THR W 137 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CG LEU X 150 " pdb=" CB LEU X 150 " pdb=" CD1 LEU X 150 " pdb=" CD2 LEU X 150 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 15516 not shown) Planarity restraints: 17313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR L 870 " 0.047 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO L 871 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO L 871 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO L 871 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1526 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C GLU A1526 " 0.046 2.00e-02 2.50e+03 pdb=" O GLU A1526 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A1527 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 595 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.93e+00 pdb=" CD GLU E 595 " 0.046 2.00e-02 2.50e+03 pdb=" OE1 GLU E 595 " -0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU E 595 " -0.016 2.00e-02 2.50e+03 ... (remaining 17310 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 1083 2.66 - 3.22: 92071 3.22 - 3.78: 147499 3.78 - 4.34: 202077 4.34 - 4.90: 331888 Nonbonded interactions: 774618 Sorted by model distance: nonbonded pdb=" ND2 ASN J 795 " pdb=" O HIS J 969 " model vdw 2.095 2.520 nonbonded pdb=" O CYS L 450 " pdb=" OH TYR L1122 " model vdw 2.112 2.440 nonbonded pdb=" OD2 ASP L1070 " pdb=" OH TYR W 155 " model vdw 2.165 2.440 nonbonded pdb=" OH TYR H1098 " pdb=" OD1 ASN H1369 " model vdw 2.166 2.440 nonbonded pdb=" NH2 ARG G 53 " pdb=" O ALA G 58 " model vdw 2.166 2.520 ... (remaining 774613 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 'H' and (resid 47 through 140 or resid 150 through 822 or resid 845 throu \ gh 1370)) selection = (chain 'I' and (resid 47 through 140 or resid 150 through 305 or resid 350 throu \ gh 822 or resid 845 through 1370)) selection = (chain 'J' and (resid 47 through 140 or resid 150 through 305 or resid 350 throu \ gh 822 or resid 845 through 1370)) selection = (chain 'K' and (resid 47 through 305 or resid 350 through 822 or resid 845 throu \ gh 1370)) selection = (chain 'L' and (resid 47 through 140 or resid 150 through 305 or resid 350 throu \ gh 822 or resid 845 through 1370)) selection = (chain 'M' and (resid 47 through 140 or resid 150 through 305 or resid 350 throu \ gh 822 or resid 845 through 1370)) } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } ncs_group { reference = (chain 'U' and (resid 6 through 115 or resid 122 through 241 or resid 255 or res \ id 259 through 306)) selection = (chain 'V' and (resid 6 through 115 or resid 122 through 241 or resid 245 or res \ id 259 through 306)) selection = (chain 'X' and (resid 6 through 115 or resid 122 through 241 or resid 255 or res \ id 259 through 306)) selection = (chain 'Y' and (resid 6 through 241 or resid 243 or resid 259 through 306)) } 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: 2.670 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: 0.130 Extract box with map and model: 13.750 Check model and map are aligned: 1.080 Set scattering table: 0.690 Process input model: 218.840 Find NCS groups from input model: 5.730 Set up NCS constraints: 0.500 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: 0.020 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 246.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 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 : 0.003 0.044 98950 Z= 0.172 Angle : 0.668 11.829 134608 Z= 0.368 Chirality : 0.042 0.433 15519 Planarity : 0.005 0.071 17313 Dihedral : 14.822 89.760 36529 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.12 % Favored : 95.76 % Rotamer: Outliers : 0.11 % Allowed : 12.02 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.42 (0.07), residues: 12037 helix: 0.31 (0.07), residues: 4751 sheet: 0.05 (0.12), residues: 1670 loop : -0.82 (0.08), residues: 5616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP J 576 HIS 0.010 0.001 HIS I 713 PHE 0.022 0.001 PHE E 498 TYR 0.034 0.001 TYR V 162 ARG 0.015 0.001 ARG A2023 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2761 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 2749 time to evaluate : 7.935 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 1464 GLN cc_start: 0.5348 (mm-40) cc_final: 0.4909 (mm-40) REVERT: A 1472 PHE cc_start: 0.3092 (p90) cc_final: 0.2877 (p90) REVERT: A 1473 ARG cc_start: 0.5257 (tmt170) cc_final: 0.3861 (mmm160) REVERT: A 1491 LYS cc_start: 0.4538 (tppt) cc_final: 0.4168 (mmmt) REVERT: A 1527 ARG cc_start: 0.4016 (ttp80) cc_final: 0.3704 (tmm160) REVERT: A 1568 MET cc_start: 0.3160 (tpt) cc_final: 0.2853 (ptt) REVERT: A 1616 LYS cc_start: 0.4305 (tttt) cc_final: 0.3924 (pttp) REVERT: A 1641 VAL cc_start: 0.4855 (t) cc_final: 0.4487 (p) REVERT: A 1669 TYR cc_start: 0.4075 (t80) cc_final: 0.3333 (t80) REVERT: A 1802 LYS cc_start: 0.2941 (tptt) cc_final: 0.2713 (mmmt) REVERT: A 1829 LEU cc_start: 0.3936 (mt) cc_final: 0.3614 (mp) REVERT: A 1841 LEU cc_start: 0.4778 (mt) cc_final: 0.4015 (tt) REVERT: A 1894 MET cc_start: 0.4666 (pmm) cc_final: 0.3005 (mmp) REVERT: A 1910 VAL cc_start: 0.6518 (t) cc_final: 0.6092 (t) REVERT: A 1913 MET cc_start: 0.3752 (tmm) cc_final: 0.2492 (tpp) REVERT: A 1981 TYR cc_start: 0.2846 (t80) cc_final: 0.2226 (t80) REVERT: A 1992 GLN cc_start: 0.5571 (mm-40) cc_final: 0.3753 (pt0) REVERT: A 2001 GLN cc_start: 0.4668 (pm20) cc_final: 0.4456 (pm20) REVERT: A 2018 GLN cc_start: 0.5146 (tt0) cc_final: 0.4905 (pt0) REVERT: A 2025 ARG cc_start: 0.4426 (mtp180) cc_final: 0.3712 (tmm160) REVERT: A 2026 ASP cc_start: 0.4324 (m-30) cc_final: 0.4076 (m-30) REVERT: C 2236 ARG cc_start: 0.4385 (ttp80) cc_final: 0.4134 (mtp-110) REVERT: E 36 GLU cc_start: 0.5923 (mt-10) cc_final: 0.5683 (mt-10) REVERT: E 64 GLU cc_start: 0.6655 (tp30) cc_final: 0.6343 (mm-30) REVERT: E 207 MET cc_start: 0.4841 (mmm) cc_final: 0.3203 (tmm) REVERT: E 225 LEU cc_start: 0.5785 (mt) cc_final: 0.5558 (mt) REVERT: E 234 ARG cc_start: 0.4286 (tpt170) cc_final: 0.3980 (mtp85) REVERT: E 247 PHE cc_start: 0.4818 (m-80) cc_final: 0.4268 (t80) REVERT: E 271 ASP cc_start: 0.4029 (OUTLIER) cc_final: 0.3745 (t0) REVERT: E 272 CYS cc_start: 0.4783 (OUTLIER) cc_final: 0.4369 (p) REVERT: E 349 MET cc_start: 0.3177 (OUTLIER) cc_final: 0.1369 (ppp) REVERT: E 356 HIS cc_start: 0.3002 (p-80) cc_final: 0.2236 (t-90) REVERT: E 570 MET cc_start: 0.5066 (mtt) cc_final: 0.4640 (mmm) REVERT: F 42 MET cc_start: 0.4741 (tpp) cc_final: 0.3399 (ppp) REVERT: F 65 LEU cc_start: 0.7117 (tt) cc_final: 0.6882 (tp) REVERT: G 70 ASP cc_start: 0.2699 (m-30) cc_final: 0.2425 (m-30) REVERT: G 82 PHE cc_start: 0.6771 (t80) cc_final: 0.6422 (t80) REVERT: G 364 GLU cc_start: 0.7125 (pm20) cc_final: 0.6690 (pm20) REVERT: G 374 GLU cc_start: 0.5509 (mm-30) cc_final: 0.5227 (mm-30) REVERT: G 389 ARG cc_start: 0.6786 (mmt-90) cc_final: 0.5964 (mtp85) REVERT: G 411 LEU cc_start: 0.7551 (tp) cc_final: 0.7082 (tp) REVERT: G 444 ARG cc_start: 0.7151 (tmm-80) cc_final: 0.6817 (tmm-80) REVERT: G 507 ARG cc_start: 0.7242 (ptm160) cc_final: 0.6334 (ptm-80) REVERT: G 562 PHE cc_start: 0.6118 (t80) cc_final: 0.5545 (t80) REVERT: G 576 ARG cc_start: 0.5887 (mmm-85) cc_final: 0.5526 (mmt90) REVERT: G 577 GLN cc_start: 0.6044 (tt0) cc_final: 0.5352 (pp30) REVERT: H 47 ASN cc_start: 0.7465 (p0) cc_final: 0.7209 (p0) REVERT: H 67 LEU cc_start: 0.7894 (mt) cc_final: 0.7670 (mt) REVERT: H 81 HIS cc_start: 0.7368 (t-170) cc_final: 0.5858 (m90) REVERT: H 82 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6528 (m-30) REVERT: H 87 THR cc_start: 0.6105 (m) cc_final: 0.5899 (t) REVERT: H 91 MET cc_start: 0.7516 (tpp) cc_final: 0.6874 (tpt) REVERT: H 130 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6897 (mt-10) REVERT: H 181 GLN cc_start: 0.5833 (mm-40) cc_final: 0.5557 (mm-40) REVERT: H 210 ILE cc_start: 0.8586 (mm) cc_final: 0.8364 (mm) REVERT: H 284 MET cc_start: 0.7106 (mmp) cc_final: 0.6705 (mmp) REVERT: H 370 GLU cc_start: 0.6732 (tp30) cc_final: 0.6070 (tp30) REVERT: H 373 ARG cc_start: 0.7798 (tpt170) cc_final: 0.7094 (tpt-90) REVERT: H 493 ARG cc_start: 0.6832 (ttm110) cc_final: 0.6605 (ptp-110) REVERT: H 589 ASP cc_start: 0.8202 (t0) cc_final: 0.7832 (t0) REVERT: H 598 LYS cc_start: 0.7717 (tmtt) cc_final: 0.6505 (ttpp) REVERT: H 757 LEU cc_start: 0.8175 (mt) cc_final: 0.7906 (mt) REVERT: H 792 MET cc_start: 0.8257 (tpp) cc_final: 0.8042 (tpp) REVERT: H 844 ASP cc_start: 0.5412 (p0) cc_final: 0.4357 (m-30) REVERT: H 845 SER cc_start: 0.7014 (t) cc_final: 0.6724 (t) REVERT: H 919 ASN cc_start: 0.6895 (t0) cc_final: 0.6633 (t0) REVERT: H 958 ARG cc_start: 0.6888 (mtt180) cc_final: 0.6657 (mtt180) REVERT: H 967 HIS cc_start: 0.7746 (t70) cc_final: 0.7385 (t-90) REVERT: H 1011 MET cc_start: 0.7582 (mtp) cc_final: 0.7359 (mtp) REVERT: H 1034 LEU cc_start: 0.8285 (mp) cc_final: 0.8082 (mp) REVERT: H 1287 LEU cc_start: 0.7997 (tp) cc_final: 0.7622 (mm) REVERT: H 1362 LEU cc_start: 0.7619 (tp) cc_final: 0.7399 (tp) REVERT: I 1 MET cc_start: 0.6903 (mtm) cc_final: 0.6001 (mtt) REVERT: I 30 GLU cc_start: 0.6829 (tt0) cc_final: 0.6528 (tp30) REVERT: I 60 ARG cc_start: 0.6307 (mtp180) cc_final: 0.5925 (ptp-110) REVERT: I 81 HIS cc_start: 0.7513 (m-70) cc_final: 0.7136 (m-70) REVERT: I 108 THR cc_start: 0.6022 (t) cc_final: 0.5776 (t) REVERT: I 169 ASP cc_start: 0.8310 (t70) cc_final: 0.7933 (t0) REVERT: I 246 LEU cc_start: 0.8339 (tp) cc_final: 0.7967 (mt) REVERT: I 256 ASP cc_start: 0.6348 (t0) cc_final: 0.6130 (t0) REVERT: I 383 ASP cc_start: 0.7922 (t0) cc_final: 0.7709 (t0) REVERT: I 467 ARG cc_start: 0.7400 (mtp85) cc_final: 0.6490 (mtp-110) REVERT: I 478 LEU cc_start: 0.6631 (tt) cc_final: 0.6035 (tt) REVERT: I 514 GLN cc_start: 0.7171 (tp40) cc_final: 0.6187 (tp40) REVERT: I 526 ASN cc_start: 0.7893 (t0) cc_final: 0.7479 (t0) REVERT: I 528 THR cc_start: 0.8441 (p) cc_final: 0.8154 (t) REVERT: I 961 THR cc_start: 0.7898 (p) cc_final: 0.7677 (m) REVERT: I 975 LEU cc_start: 0.8212 (mp) cc_final: 0.7779 (mp) REVERT: I 1109 ARG cc_start: 0.6521 (mtm180) cc_final: 0.5727 (mtt180) REVERT: I 1115 ARG cc_start: 0.6382 (mpt-90) cc_final: 0.5937 (mpt-90) REVERT: I 1128 ASP cc_start: 0.5819 (t70) cc_final: 0.5535 (t70) REVERT: I 1129 ARG cc_start: 0.6838 (mtm110) cc_final: 0.6626 (tpp-160) REVERT: I 1250 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6248 (mt-10) REVERT: I 1259 TYR cc_start: 0.6465 (t80) cc_final: 0.5968 (t80) REVERT: I 1267 ASN cc_start: 0.7348 (m-40) cc_final: 0.7117 (m110) REVERT: I 1294 ARG cc_start: 0.6583 (mmm-85) cc_final: 0.5962 (tpp-160) REVERT: J 61 LEU cc_start: 0.6899 (mp) cc_final: 0.6398 (mt) REVERT: J 205 GLN cc_start: 0.6400 (tt0) cc_final: 0.6004 (tm-30) REVERT: J 231 ASN cc_start: 0.7643 (m110) cc_final: 0.6599 (t0) REVERT: J 248 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6698 (mt-10) REVERT: J 346 GLN cc_start: 0.6226 (tt0) cc_final: 0.5937 (mm110) REVERT: J 361 ARG cc_start: 0.6896 (tpp-160) cc_final: 0.6156 (mmt90) REVERT: J 400 TYR cc_start: 0.7147 (t80) cc_final: 0.6809 (t80) REVERT: J 407 TYR cc_start: 0.7737 (p90) cc_final: 0.7160 (p90) REVERT: J 435 ARG cc_start: 0.7419 (tpp80) cc_final: 0.7214 (tpp80) REVERT: J 488 MET cc_start: 0.5842 (mmt) cc_final: 0.5359 (tpp) REVERT: J 527 ILE cc_start: 0.8571 (mm) cc_final: 0.8363 (mm) REVERT: J 598 LYS cc_start: 0.7475 (ptmt) cc_final: 0.7272 (tptm) REVERT: J 628 ARG cc_start: 0.7335 (mtp85) cc_final: 0.6816 (mtp85) REVERT: J 669 GLN cc_start: 0.6294 (mp10) cc_final: 0.5339 (mt0) REVERT: J 693 LEU cc_start: 0.8211 (mp) cc_final: 0.7899 (mt) REVERT: J 697 GLN cc_start: 0.7577 (mm110) cc_final: 0.6301 (mp10) REVERT: J 856 MET cc_start: 0.7137 (ttm) cc_final: 0.6818 (ttp) REVERT: J 874 GLN cc_start: 0.6906 (pt0) cc_final: 0.5993 (mm110) REVERT: J 914 GLN cc_start: 0.6452 (mt0) cc_final: 0.6193 (mt0) REVERT: J 1011 MET cc_start: 0.8153 (mtt) cc_final: 0.7950 (mtm) REVERT: J 1050 SER cc_start: 0.8913 (t) cc_final: 0.8696 (t) REVERT: J 1061 ASN cc_start: 0.7504 (t0) cc_final: 0.7019 (m-40) REVERT: J 1270 GLU cc_start: 0.7050 (mt-10) cc_final: 0.6793 (mt-10) REVERT: J 1278 LEU cc_start: 0.8832 (tp) cc_final: 0.8628 (tp) REVERT: K 61 LEU cc_start: 0.7392 (mp) cc_final: 0.7065 (tp) REVERT: K 80 PHE cc_start: 0.8010 (t80) cc_final: 0.7576 (t80) REVERT: K 164 LEU cc_start: 0.7561 (mt) cc_final: 0.7327 (mt) REVERT: K 259 THR cc_start: 0.7502 (p) cc_final: 0.7273 (t) REVERT: K 270 SER cc_start: 0.7941 (m) cc_final: 0.7701 (t) REVERT: K 273 MET cc_start: 0.7976 (mtp) cc_final: 0.7656 (mtp) REVERT: K 371 ASN cc_start: 0.6699 (p0) cc_final: 0.6311 (p0) REVERT: K 373 ARG cc_start: 0.6813 (tpp-160) cc_final: 0.6503 (tpp-160) REVERT: K 403 GLU cc_start: 0.6943 (mt-10) cc_final: 0.6580 (mt-10) REVERT: K 583 ARG cc_start: 0.7521 (ttt180) cc_final: 0.7000 (ttt-90) REVERT: K 626 LEU cc_start: 0.7521 (tp) cc_final: 0.7079 (tt) REVERT: K 809 VAL cc_start: 0.9260 (m) cc_final: 0.8861 (p) REVERT: K 885 PHE cc_start: 0.6827 (m-80) cc_final: 0.6319 (m-80) REVERT: K 933 TYR cc_start: 0.6137 (m-80) cc_final: 0.5776 (m-80) REVERT: K 993 ARG cc_start: 0.7859 (tpp80) cc_final: 0.7097 (mmm160) REVERT: K 1013 TYR cc_start: 0.7717 (m-80) cc_final: 0.7178 (m-80) REVERT: K 1181 MET cc_start: 0.6758 (ttt) cc_final: 0.6480 (ttt) REVERT: K 1184 ASN cc_start: 0.8265 (m110) cc_final: 0.7983 (m110) REVERT: K 1206 ASP cc_start: 0.7785 (t0) cc_final: 0.5766 (m-30) REVERT: K 1260 SER cc_start: 0.6666 (t) cc_final: 0.6250 (p) REVERT: L 84 ASN cc_start: 0.7687 (m-40) cc_final: 0.7435 (m-40) REVERT: L 140 ARG cc_start: 0.6421 (mmt180) cc_final: 0.6079 (mmt90) REVERT: L 241 LYS cc_start: 0.8454 (tptt) cc_final: 0.8070 (tptt) REVERT: L 268 LYS cc_start: 0.7491 (mmtp) cc_final: 0.7041 (ttpt) REVERT: L 290 HIS cc_start: 0.5252 (m90) cc_final: 0.4863 (m-70) REVERT: L 502 ARG cc_start: 0.6850 (mmt90) cc_final: 0.6544 (mmt90) REVERT: L 625 LEU cc_start: 0.7675 (mm) cc_final: 0.7350 (mt) REVERT: L 656 LEU cc_start: 0.8035 (mp) cc_final: 0.7790 (mt) REVERT: L 693 LEU cc_start: 0.7856 (mp) cc_final: 0.7596 (mp) REVERT: L 733 VAL cc_start: 0.7792 (t) cc_final: 0.7526 (m) REVERT: L 771 TYR cc_start: 0.6418 (t80) cc_final: 0.6191 (t80) REVERT: L 1006 MET cc_start: 0.7313 (mmm) cc_final: 0.7037 (mmt) REVERT: L 1048 LEU cc_start: 0.8624 (tp) cc_final: 0.8349 (tt) REVERT: L 1092 SER cc_start: 0.8661 (m) cc_final: 0.8267 (t) REVERT: L 1175 ILE cc_start: 0.8254 (pt) cc_final: 0.7506 (mt) REVERT: L 1182 ASP cc_start: 0.5989 (t0) cc_final: 0.5771 (t0) REVERT: L 1219 GLU cc_start: 0.6298 (mp0) cc_final: 0.5855 (mp0) REVERT: L 1230 ASN cc_start: 0.8293 (t0) cc_final: 0.8064 (t0) REVERT: L 1308 GLU cc_start: 0.6713 (pm20) cc_final: 0.5630 (pm20) REVERT: L 1330 LEU cc_start: 0.8207 (mt) cc_final: 0.7560 (mp) REVERT: M 1 MET cc_start: 0.5343 (ttp) cc_final: 0.5061 (ttt) REVERT: M 240 LEU cc_start: 0.8223 (tp) cc_final: 0.7994 (tp) REVERT: M 467 ARG cc_start: 0.7683 (mtp85) cc_final: 0.6827 (ttt180) REVERT: M 488 MET cc_start: 0.7148 (ptp) cc_final: 0.6931 (ptm) REVERT: M 512 MET cc_start: 0.8183 (mtm) cc_final: 0.7951 (mtp) REVERT: M 532 GLU cc_start: 0.7292 (tp30) cc_final: 0.6775 (tp30) REVERT: M 625 LEU cc_start: 0.7890 (mt) cc_final: 0.7217 (tp) REVERT: M 675 ARG cc_start: 0.6448 (ptm160) cc_final: 0.6194 (ptm160) REVERT: M 732 VAL cc_start: 0.8639 (t) cc_final: 0.8419 (p) REVERT: M 778 TRP cc_start: 0.8107 (t-100) cc_final: 0.7854 (t-100) REVERT: M 786 LEU cc_start: 0.7031 (mt) cc_final: 0.6738 (mp) REVERT: M 803 ASN cc_start: 0.7375 (t0) cc_final: 0.6848 (t0) REVERT: M 937 VAL cc_start: 0.7508 (p) cc_final: 0.7133 (m) REVERT: M 954 ASP cc_start: 0.7365 (t70) cc_final: 0.7026 (t0) REVERT: M 955 ASP cc_start: 0.7449 (m-30) cc_final: 0.7166 (t70) REVERT: M 957 LYS cc_start: 0.7635 (ttpp) cc_final: 0.7379 (ttpp) REVERT: M 979 PHE cc_start: 0.6957 (m-10) cc_final: 0.6716 (m-10) REVERT: M 1013 TYR cc_start: 0.7394 (m-80) cc_final: 0.7187 (m-80) REVERT: M 1080 ASN cc_start: 0.8044 (t0) cc_final: 0.7841 (t0) REVERT: M 1106 MET cc_start: 0.7742 (mtm) cc_final: 0.7157 (mtm) REVERT: M 1271 ILE cc_start: 0.6731 (mt) cc_final: 0.6358 (mt) REVERT: M 1308 GLU cc_start: 0.6505 (pt0) cc_final: 0.6231 (mm-30) REVERT: M 1358 GLU cc_start: 0.6591 (pt0) cc_final: 0.6135 (pt0) REVERT: M 1360 ILE cc_start: 0.7772 (tt) cc_final: 0.7434 (tt) REVERT: O 63 ASP cc_start: 0.6630 (t0) cc_final: 0.6408 (t0) REVERT: P 75 ARG cc_start: 0.2866 (tmm160) cc_final: 0.2570 (tpt170) REVERT: Q 43 MET cc_start: 0.5298 (mmp) cc_final: 0.5042 (mmp) REVERT: R 19 ARG cc_start: 0.5184 (ptp90) cc_final: 0.4928 (mtt180) REVERT: S 70 VAL cc_start: 0.7831 (p) cc_final: 0.7600 (p) REVERT: T 51 PHE cc_start: 0.4716 (m-80) cc_final: 0.3680 (m-80) REVERT: T 71 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7209 (mt-10) REVERT: T 287 ARG cc_start: 0.6254 (tpm170) cc_final: 0.5691 (mtp180) REVERT: U 68 MET cc_start: 0.8017 (ttm) cc_final: 0.7746 (ttm) REVERT: U 79 ASN cc_start: 0.6806 (t0) cc_final: 0.6276 (m-40) REVERT: U 80 GLN cc_start: 0.5996 (tt0) cc_final: 0.4683 (mm-40) REVERT: U 147 ASN cc_start: 0.7053 (m-40) cc_final: 0.6669 (m-40) REVERT: U 153 MET cc_start: 0.7430 (tpp) cc_final: 0.6911 (tpt) REVERT: U 197 MET cc_start: 0.7129 (mtm) cc_final: 0.6842 (mtp) REVERT: U 204 MET cc_start: 0.7483 (mtm) cc_final: 0.7197 (mtm) REVERT: U 279 ASP cc_start: 0.7196 (t0) cc_final: 0.6526 (t70) REVERT: U 298 LYS cc_start: 0.7719 (mmpt) cc_final: 0.7149 (mmmm) REVERT: V 27 LEU cc_start: 0.7052 (pt) cc_final: 0.6716 (pp) REVERT: V 50 GLN cc_start: 0.8325 (pt0) cc_final: 0.7491 (pt0) REVERT: V 68 MET cc_start: 0.5557 (ttp) cc_final: 0.5315 (ttt) REVERT: V 153 MET cc_start: 0.7566 (ttm) cc_final: 0.7207 (ttp) REVERT: V 172 LEU cc_start: 0.7459 (mm) cc_final: 0.6991 (mt) REVERT: V 197 MET cc_start: 0.7147 (mmm) cc_final: 0.6793 (tpp) REVERT: V 204 MET cc_start: 0.7132 (ttp) cc_final: 0.6928 (ttm) REVERT: V 244 GLU cc_start: 0.5545 (mm-30) cc_final: 0.4749 (mt-10) REVERT: V 279 ASP cc_start: 0.5825 (m-30) cc_final: 0.5173 (m-30) REVERT: W 70 MET cc_start: 0.6794 (ppp) cc_final: 0.6441 (ptt) REVERT: W 169 LYS cc_start: 0.7280 (mtmt) cc_final: 0.6862 (pttt) REVERT: W 268 GLU cc_start: 0.6207 (mp0) cc_final: 0.5984 (mp0) REVERT: X 20 ASP cc_start: 0.5949 (m-30) cc_final: 0.5715 (m-30) REVERT: X 26 LYS cc_start: 0.6904 (mttt) cc_final: 0.6372 (mtmt) REVERT: X 77 GLU cc_start: 0.7667 (pt0) cc_final: 0.7384 (pt0) REVERT: X 189 ILE cc_start: 0.5088 (mm) cc_final: 0.4808 (mm) REVERT: X 206 MET cc_start: 0.7140 (mmm) cc_final: 0.6713 (mmm) REVERT: X 273 VAL cc_start: 0.8025 (t) cc_final: 0.7800 (t) REVERT: X 298 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7519 (mttp) REVERT: Y 131 GLU cc_start: 0.6272 (tt0) cc_final: 0.6025 (tt0) REVERT: Y 194 LEU cc_start: 0.8043 (mt) cc_final: 0.7723 (mp) REVERT: Y 215 THR cc_start: 0.6718 (t) cc_final: 0.6449 (t) REVERT: Y 217 THR cc_start: 0.7025 (m) cc_final: 0.6745 (p) REVERT: Y 230 LEU cc_start: 0.7872 (pp) cc_final: 0.7219 (tp) REVERT: Z 90 ARG cc_start: 0.8067 (tpp80) cc_final: 0.7258 (tpp80) REVERT: Z 138 MET cc_start: 0.7908 (mtm) cc_final: 0.7643 (mtm) REVERT: Z 219 GLU cc_start: 0.6356 (mm-30) cc_final: 0.5868 (tp30) REVERT: Z 282 PHE cc_start: 0.5540 (m-80) cc_final: 0.5121 (m-80) outliers start: 12 outliers final: 4 residues processed: 2758 average time/residue: 0.9224 time to fit residues: 4301.1673 Evaluate side-chains 1938 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1930 time to evaluate : 8.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1206 random chunks: chunk 1018 optimal weight: 2.9990 chunk 914 optimal weight: 0.3980 chunk 507 optimal weight: 20.0000 chunk 312 optimal weight: 20.0000 chunk 616 optimal weight: 4.9990 chunk 488 optimal weight: 8.9990 chunk 945 optimal weight: 20.0000 chunk 365 optimal weight: 3.9990 chunk 574 optimal weight: 20.0000 chunk 703 optimal weight: 4.9990 chunk 1095 optimal weight: 9.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2020 GLN A2234 HIS E 19 HIS ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN G 148 HIS G 321 GLN H 153 ASN ** H 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 510 ASN H 643 GLN H 740 ASN ** H 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 940 HIS H1000 ASN I 22 HIS I 199 ASN I 281 GLN I 541 HIS I 560 ASN I 697 GLN ** I 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1061 ASN J 497 HIS J 571 HIS J 581 HIS ** J 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J1003 HIS ** J1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1141 GLN J1353 ASN K 111 GLN K 231 ASN K 388 ASN K 541 HIS K 981 HIS K1080 ASN K1319 GLN K1350 HIS L 49 HIS L 181 GLN L 541 HIS L 620 ASN L 749 HIS L 919 ASN ** L 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1029 HIS ** L1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 497 HIS ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1060 ASN M1061 ASN ** M1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 126 HIS U 14 HIS U 39 HIS ** U 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 84 HIS Z 187 ASN Z 191 HIS Z 256 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 98950 Z= 0.222 Angle : 0.659 13.543 134608 Z= 0.337 Chirality : 0.044 0.279 15519 Planarity : 0.005 0.074 17313 Dihedral : 5.618 89.446 13396 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.26 % Favored : 95.66 % Rotamer: Outliers : 0.21 % Allowed : 4.76 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.39 (0.07), residues: 12037 helix: 0.43 (0.07), residues: 4806 sheet: -0.12 (0.12), residues: 1784 loop : -0.85 (0.08), residues: 5447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP G 514 HIS 0.028 0.001 HIS A2234 PHE 0.040 0.002 PHE J 672 TYR 0.030 0.002 TYR A1899 ARG 0.011 0.001 ARG M 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2457 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 2435 time to evaluate : 8.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1464 GLN cc_start: 0.5621 (mm-40) cc_final: 0.5001 (mm-40) REVERT: A 1472 PHE cc_start: 0.3103 (p90) cc_final: 0.2876 (p90) REVERT: A 1473 ARG cc_start: 0.5323 (tmt170) cc_final: 0.3833 (mtp180) REVERT: A 1493 ARG cc_start: 0.2629 (mmt180) cc_final: 0.2183 (mmm160) REVERT: A 1540 LEU cc_start: 0.5451 (mm) cc_final: 0.5234 (mm) REVERT: A 1616 LYS cc_start: 0.5016 (tttt) cc_final: 0.4600 (pttp) REVERT: A 1641 VAL cc_start: 0.4891 (t) cc_final: 0.4568 (p) REVERT: A 1669 TYR cc_start: 0.3515 (t80) cc_final: 0.3193 (t80) REVERT: A 1740 ARG cc_start: 0.3982 (ttp80) cc_final: 0.3718 (ttp80) REVERT: A 1802 LYS cc_start: 0.3064 (tptt) cc_final: 0.2729 (mmmt) REVERT: A 1841 LEU cc_start: 0.4598 (mt) cc_final: 0.4234 (tt) REVERT: A 1894 MET cc_start: 0.3625 (pmm) cc_final: 0.3047 (mmp) REVERT: A 1913 MET cc_start: 0.4123 (tmm) cc_final: 0.3560 (tpt) REVERT: A 1992 GLN cc_start: 0.5609 (mm-40) cc_final: 0.3833 (pt0) REVERT: A 2018 GLN cc_start: 0.5291 (tt0) cc_final: 0.4994 (pt0) REVERT: A 2059 PHE cc_start: 0.2373 (p90) cc_final: 0.0929 (p90) REVERT: E 207 MET cc_start: 0.4157 (mmm) cc_final: 0.2882 (tmm) REVERT: E 234 ARG cc_start: 0.4514 (tpt170) cc_final: 0.3893 (mtp85) REVERT: E 247 PHE cc_start: 0.4770 (m-80) cc_final: 0.4250 (t80) REVERT: E 349 MET cc_start: 0.2390 (mtt) cc_final: 0.0749 (ppp) REVERT: E 356 HIS cc_start: 0.2368 (p-80) cc_final: 0.1741 (t-170) REVERT: E 570 MET cc_start: 0.5320 (mtt) cc_final: 0.4865 (mmm) REVERT: F 42 MET cc_start: 0.2765 (mmt) cc_final: 0.2071 (ppp) REVERT: G 70 ASP cc_start: 0.2492 (m-30) cc_final: 0.2234 (m-30) REVERT: G 364 GLU cc_start: 0.7095 (pm20) cc_final: 0.6349 (pm20) REVERT: G 374 GLU cc_start: 0.5526 (mm-30) cc_final: 0.5162 (mm-30) REVERT: G 389 ARG cc_start: 0.6448 (mmt-90) cc_final: 0.5669 (mtp85) REVERT: G 411 LEU cc_start: 0.7709 (tp) cc_final: 0.7305 (tp) REVERT: G 484 GLN cc_start: 0.7177 (tp-100) cc_final: 0.6948 (tp40) REVERT: G 507 ARG cc_start: 0.7295 (ptm160) cc_final: 0.6490 (ptm-80) REVERT: G 513 ARG cc_start: 0.5448 (mtp-110) cc_final: 0.5238 (ttt90) REVERT: G 562 PHE cc_start: 0.5170 (t80) cc_final: 0.4965 (t80) REVERT: G 576 ARG cc_start: 0.5605 (mmm-85) cc_final: 0.5201 (mmt90) REVERT: G 577 GLN cc_start: 0.5982 (tt0) cc_final: 0.5348 (pp30) REVERT: H 81 HIS cc_start: 0.7436 (t-170) cc_final: 0.5730 (m90) REVERT: H 91 MET cc_start: 0.7649 (tpp) cc_final: 0.6982 (tpt) REVERT: H 110 ARG cc_start: 0.5238 (tmt170) cc_final: 0.4000 (mmp-170) REVERT: H 210 ILE cc_start: 0.8491 (mm) cc_final: 0.8139 (mm) REVERT: H 274 VAL cc_start: 0.8688 (m) cc_final: 0.8360 (m) REVERT: H 357 MET cc_start: 0.6674 (pmm) cc_final: 0.6469 (pmm) REVERT: H 359 VAL cc_start: 0.8324 (t) cc_final: 0.8111 (m) REVERT: H 371 ASN cc_start: 0.7762 (t0) cc_final: 0.7187 (t0) REVERT: H 372 LEU cc_start: 0.8168 (mt) cc_final: 0.7930 (mt) REVERT: H 493 ARG cc_start: 0.6911 (ttm110) cc_final: 0.6532 (ptp-110) REVERT: H 589 ASP cc_start: 0.7977 (t0) cc_final: 0.7665 (t0) REVERT: H 598 LYS cc_start: 0.7847 (tmtt) cc_final: 0.6782 (ttpp) REVERT: H 733 VAL cc_start: 0.7386 (t) cc_final: 0.6644 (t) REVERT: H 844 ASP cc_start: 0.5846 (p0) cc_final: 0.4507 (m-30) REVERT: H 845 SER cc_start: 0.7327 (t) cc_final: 0.6848 (t) REVERT: H 849 GLN cc_start: 0.6996 (pt0) cc_final: 0.6712 (pt0) REVERT: H 900 ASP cc_start: 0.7084 (p0) cc_final: 0.6685 (m-30) REVERT: H 919 ASN cc_start: 0.6898 (t0) cc_final: 0.6682 (m-40) REVERT: H 967 HIS cc_start: 0.7731 (t70) cc_final: 0.7456 (t-90) REVERT: H 1072 SER cc_start: 0.7360 (t) cc_final: 0.7138 (t) REVERT: H 1138 GLU cc_start: 0.5313 (mm-30) cc_final: 0.4940 (mp0) REVERT: H 1156 MET cc_start: 0.6911 (mmm) cc_final: 0.6319 (mmm) REVERT: H 1320 GLU cc_start: 0.6546 (mt-10) cc_final: 0.5550 (mm-30) REVERT: H 1362 LEU cc_start: 0.7620 (tp) cc_final: 0.7177 (tp) REVERT: I 1 MET cc_start: 0.6873 (mtm) cc_final: 0.6227 (mtt) REVERT: I 60 ARG cc_start: 0.6145 (mtp180) cc_final: 0.5830 (ptp-110) REVERT: I 81 HIS cc_start: 0.7427 (m-70) cc_final: 0.6973 (m-70) REVERT: I 150 LYS cc_start: 0.8224 (mmtp) cc_final: 0.7913 (mttt) REVERT: I 169 ASP cc_start: 0.8324 (t70) cc_final: 0.8002 (t0) REVERT: I 246 LEU cc_start: 0.8405 (tp) cc_final: 0.8142 (mt) REVERT: I 284 MET cc_start: 0.6631 (mmm) cc_final: 0.6413 (mmm) REVERT: I 467 ARG cc_start: 0.7396 (mtp85) cc_final: 0.6464 (mtp-110) REVERT: I 514 GLN cc_start: 0.7272 (tp40) cc_final: 0.6357 (tp40) REVERT: I 527 ILE cc_start: 0.8063 (pt) cc_final: 0.7693 (pt) REVERT: I 736 ARG cc_start: 0.5945 (ttm110) cc_final: 0.5537 (ttm110) REVERT: I 878 GLU cc_start: 0.7489 (mt-10) cc_final: 0.6563 (tm-30) REVERT: I 975 LEU cc_start: 0.7762 (mp) cc_final: 0.7494 (mp) REVERT: I 1099 VAL cc_start: 0.8028 (p) cc_final: 0.7719 (p) REVERT: I 1115 ARG cc_start: 0.6130 (mpt-90) cc_final: 0.5861 (mpt-90) REVERT: I 1156 MET cc_start: 0.6402 (ttm) cc_final: 0.6115 (ttp) REVERT: I 1250 GLU cc_start: 0.6757 (mt-10) cc_final: 0.6396 (mt-10) REVERT: I 1259 TYR cc_start: 0.6412 (t80) cc_final: 0.5978 (t80) REVERT: I 1287 LEU cc_start: 0.6267 (mm) cc_final: 0.6063 (mm) REVERT: I 1294 ARG cc_start: 0.6880 (mmm-85) cc_final: 0.6072 (tpp-160) REVERT: I 1360 ILE cc_start: 0.8721 (pt) cc_final: 0.8414 (pt) REVERT: I 1365 SER cc_start: 0.7619 (p) cc_final: 0.7186 (m) REVERT: J 92 LEU cc_start: 0.8236 (mt) cc_final: 0.7770 (mp) REVERT: J 126 THR cc_start: 0.6064 (t) cc_final: 0.5760 (t) REVERT: J 185 ARG cc_start: 0.6899 (ptp-170) cc_final: 0.6217 (ptp-110) REVERT: J 231 ASN cc_start: 0.7764 (m110) cc_final: 0.6791 (t0) REVERT: J 420 VAL cc_start: 0.8335 (p) cc_final: 0.8089 (p) REVERT: J 475 MET cc_start: 0.7353 (mmm) cc_final: 0.7088 (mmm) REVERT: J 488 MET cc_start: 0.5639 (mmt) cc_final: 0.5060 (tpp) REVERT: J 584 LEU cc_start: 0.8012 (mt) cc_final: 0.7482 (mt) REVERT: J 628 ARG cc_start: 0.7257 (mtp85) cc_final: 0.6727 (mtp85) REVERT: J 638 MET cc_start: 0.6960 (mmp) cc_final: 0.6599 (mmm) REVERT: J 669 GLN cc_start: 0.6436 (mp10) cc_final: 0.5141 (mt0) REVERT: J 693 LEU cc_start: 0.8216 (mp) cc_final: 0.7965 (mt) REVERT: J 697 GLN cc_start: 0.7147 (mm110) cc_final: 0.5838 (mp10) REVERT: J 731 GLN cc_start: 0.7449 (pt0) cc_final: 0.6549 (pt0) REVERT: J 789 MET cc_start: 0.7914 (tpp) cc_final: 0.7660 (tpp) REVERT: J 856 MET cc_start: 0.7270 (ttm) cc_final: 0.6620 (ttp) REVERT: J 963 PHE cc_start: 0.5690 (m-80) cc_final: 0.5484 (m-80) REVERT: J 1006 MET cc_start: 0.7819 (mtt) cc_final: 0.7570 (mtt) REVERT: J 1270 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6815 (mt-10) REVERT: J 1353 ASN cc_start: 0.8444 (m-40) cc_final: 0.8161 (m-40) REVERT: K 61 LEU cc_start: 0.7371 (mp) cc_final: 0.7081 (tp) REVERT: K 91 MET cc_start: 0.8566 (mtp) cc_final: 0.8156 (mtp) REVERT: K 157 MET cc_start: 0.5919 (tmm) cc_final: 0.5661 (tmm) REVERT: K 259 THR cc_start: 0.7675 (p) cc_final: 0.7051 (t) REVERT: K 447 LYS cc_start: 0.7441 (ttmm) cc_final: 0.7108 (ttmt) REVERT: K 475 MET cc_start: 0.7663 (mmp) cc_final: 0.7000 (mmm) REVERT: K 537 PHE cc_start: 0.7888 (m-80) cc_final: 0.7607 (m-80) REVERT: K 544 GLU cc_start: 0.6473 (tp30) cc_final: 0.6085 (tp30) REVERT: K 809 VAL cc_start: 0.8885 (m) cc_final: 0.8595 (p) REVERT: K 918 TYR cc_start: 0.6745 (t80) cc_final: 0.6182 (t80) REVERT: K 933 TYR cc_start: 0.6104 (m-80) cc_final: 0.5903 (m-10) REVERT: K 993 ARG cc_start: 0.7761 (tpp80) cc_final: 0.7119 (mmm160) REVERT: K 1024 THR cc_start: 0.8188 (m) cc_final: 0.7960 (p) REVERT: K 1150 MET cc_start: 0.6850 (ptm) cc_final: 0.6444 (tmm) REVERT: K 1184 ASN cc_start: 0.8307 (m110) cc_final: 0.8082 (m110) REVERT: K 1206 ASP cc_start: 0.7885 (t0) cc_final: 0.5714 (m-30) REVERT: K 1260 SER cc_start: 0.6701 (t) cc_final: 0.6143 (p) REVERT: K 1284 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6361 (mt-10) REVERT: K 1358 GLU cc_start: 0.6467 (pt0) cc_final: 0.6089 (mt-10) REVERT: L 140 ARG cc_start: 0.6508 (mmt180) cc_final: 0.5992 (mmt90) REVERT: L 141 GLU cc_start: 0.6213 (tm-30) cc_final: 0.5949 (tm-30) REVERT: L 186 LYS cc_start: 0.6972 (tmtt) cc_final: 0.6177 (tppt) REVERT: L 241 LYS cc_start: 0.8345 (tptt) cc_final: 0.7968 (tptt) REVERT: L 268 LYS cc_start: 0.7423 (mmtp) cc_final: 0.6899 (ttpt) REVERT: L 386 GLU cc_start: 0.6484 (mt-10) cc_final: 0.6275 (mt-10) REVERT: L 475 MET cc_start: 0.5989 (mmp) cc_final: 0.3658 (tpp) REVERT: L 527 ILE cc_start: 0.7869 (mp) cc_final: 0.7663 (pt) REVERT: L 625 LEU cc_start: 0.7838 (mm) cc_final: 0.7475 (mm) REVERT: L 656 LEU cc_start: 0.8029 (mp) cc_final: 0.7736 (mt) REVERT: L 684 VAL cc_start: 0.7973 (p) cc_final: 0.7187 (p) REVERT: L 693 LEU cc_start: 0.7759 (mp) cc_final: 0.7485 (mp) REVERT: L 802 LEU cc_start: 0.7152 (mt) cc_final: 0.6922 (mt) REVERT: L 1092 SER cc_start: 0.8654 (m) cc_final: 0.8359 (m) REVERT: L 1175 ILE cc_start: 0.8333 (pt) cc_final: 0.7796 (mt) REVERT: L 1225 PHE cc_start: 0.6961 (m-10) cc_final: 0.6574 (m-10) REVERT: L 1308 GLU cc_start: 0.6904 (pm20) cc_final: 0.6079 (pm20) REVERT: L 1330 LEU cc_start: 0.8130 (mt) cc_final: 0.7832 (mp) REVERT: M 146 THR cc_start: 0.8312 (t) cc_final: 0.8040 (m) REVERT: M 255 LEU cc_start: 0.6945 (tp) cc_final: 0.6675 (mt) REVERT: M 320 SER cc_start: 0.7150 (t) cc_final: 0.6920 (m) REVERT: M 467 ARG cc_start: 0.7651 (mtp85) cc_final: 0.6874 (ttt180) REVERT: M 488 MET cc_start: 0.7301 (ptp) cc_final: 0.6945 (ptm) REVERT: M 493 ARG cc_start: 0.7498 (mtt-85) cc_final: 0.7086 (mpt-90) REVERT: M 512 MET cc_start: 0.8360 (mtm) cc_final: 0.7978 (mtp) REVERT: M 532 GLU cc_start: 0.7280 (tp30) cc_final: 0.6836 (tp30) REVERT: M 625 LEU cc_start: 0.7745 (mt) cc_final: 0.7515 (mt) REVERT: M 675 ARG cc_start: 0.6409 (ptm160) cc_final: 0.6126 (ptm160) REVERT: M 719 PHE cc_start: 0.7304 (m-80) cc_final: 0.6850 (m-10) REVERT: M 732 VAL cc_start: 0.8592 (t) cc_final: 0.8213 (p) REVERT: M 778 TRP cc_start: 0.8327 (t-100) cc_final: 0.7892 (t-100) REVERT: M 786 LEU cc_start: 0.7151 (mt) cc_final: 0.6803 (mp) REVERT: M 863 ASP cc_start: 0.6966 (p0) cc_final: 0.5563 (m-30) REVERT: M 1022 LEU cc_start: 0.7435 (mt) cc_final: 0.7081 (mp) REVERT: M 1043 GLU cc_start: 0.6182 (pt0) cc_final: 0.5682 (mt-10) REVERT: M 1106 MET cc_start: 0.7658 (mtm) cc_final: 0.7343 (mtm) REVERT: M 1308 GLU cc_start: 0.6755 (pt0) cc_final: 0.6184 (mm-30) REVERT: M 1358 GLU cc_start: 0.6708 (pt0) cc_final: 0.6155 (pt0) REVERT: N 43 MET cc_start: 0.6588 (mmm) cc_final: 0.5686 (mmp) REVERT: N 61 LYS cc_start: 0.7792 (mttt) cc_final: 0.7455 (mttt) REVERT: Q 22 VAL cc_start: 0.6966 (t) cc_final: 0.6669 (t) REVERT: R 19 ARG cc_start: 0.5461 (ptp-110) cc_final: 0.5070 (mtt180) REVERT: T 51 PHE cc_start: 0.4645 (m-80) cc_final: 0.3664 (m-80) REVERT: T 70 MET cc_start: 0.8141 (ptm) cc_final: 0.7825 (ptt) REVERT: U 26 LYS cc_start: 0.6179 (tttm) cc_final: 0.5765 (pttm) REVERT: U 80 GLN cc_start: 0.5417 (tt0) cc_final: 0.4776 (mm-40) REVERT: U 140 MET cc_start: 0.6583 (tpt) cc_final: 0.6169 (tpp) REVERT: U 147 ASN cc_start: 0.7045 (m-40) cc_final: 0.6720 (m-40) REVERT: U 153 MET cc_start: 0.7555 (tpp) cc_final: 0.6989 (tpp) REVERT: U 197 MET cc_start: 0.7280 (mtm) cc_final: 0.6324 (ttm) REVERT: U 279 ASP cc_start: 0.7254 (t0) cc_final: 0.6398 (t70) REVERT: U 298 LYS cc_start: 0.7344 (mmpt) cc_final: 0.7083 (mmmm) REVERT: V 27 LEU cc_start: 0.7013 (pt) cc_final: 0.6630 (pp) REVERT: V 40 LEU cc_start: 0.6879 (tp) cc_final: 0.6661 (tp) REVERT: V 73 MET cc_start: 0.7176 (tmm) cc_final: 0.6840 (tmm) REVERT: V 147 ASN cc_start: 0.7866 (m110) cc_final: 0.7580 (m110) REVERT: V 172 LEU cc_start: 0.7199 (mm) cc_final: 0.6953 (mt) REVERT: V 244 GLU cc_start: 0.5695 (mm-30) cc_final: 0.4757 (mt-10) REVERT: V 264 GLU cc_start: 0.7333 (tm-30) cc_final: 0.6846 (tm-30) REVERT: V 279 ASP cc_start: 0.6015 (m-30) cc_final: 0.5383 (m-30) REVERT: W 42 ASP cc_start: 0.7472 (p0) cc_final: 0.7209 (p0) REVERT: W 56 LEU cc_start: 0.8235 (mt) cc_final: 0.7951 (mt) REVERT: W 169 LYS cc_start: 0.7641 (mtmt) cc_final: 0.7306 (pttp) REVERT: W 182 LEU cc_start: 0.6157 (tt) cc_final: 0.5480 (tt) REVERT: X 206 MET cc_start: 0.7013 (mmm) cc_final: 0.6664 (mmm) REVERT: Y 131 GLU cc_start: 0.6181 (tt0) cc_final: 0.5857 (tt0) REVERT: Y 151 LEU cc_start: 0.7467 (tp) cc_final: 0.6868 (tp) REVERT: Y 153 MET cc_start: 0.8336 (ptp) cc_final: 0.7858 (ptp) REVERT: Y 215 THR cc_start: 0.6873 (t) cc_final: 0.6562 (t) REVERT: Y 217 THR cc_start: 0.7121 (m) cc_final: 0.6774 (p) REVERT: Y 230 LEU cc_start: 0.7669 (pp) cc_final: 0.7061 (tp) REVERT: Z 40 LYS cc_start: 0.4846 (tppp) cc_final: 0.4142 (mmtm) REVERT: Z 79 GLU cc_start: 0.5435 (tp30) cc_final: 0.5102 (tp30) REVERT: Z 84 CYS cc_start: 0.5761 (m) cc_final: 0.5425 (m) REVERT: Z 90 ARG cc_start: 0.7595 (tpp80) cc_final: 0.7335 (tpp80) REVERT: Z 138 MET cc_start: 0.7893 (mtm) cc_final: 0.7644 (mtm) REVERT: Z 151 THR cc_start: 0.6626 (p) cc_final: 0.6349 (t) REVERT: Z 194 THR cc_start: 0.6531 (t) cc_final: 0.6312 (t) REVERT: Z 282 PHE cc_start: 0.5764 (m-80) cc_final: 0.5269 (m-80) outliers start: 22 outliers final: 8 residues processed: 2452 average time/residue: 0.9011 time to fit residues: 3764.6835 Evaluate side-chains 1836 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1828 time to evaluate : 8.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1206 random chunks: chunk 608 optimal weight: 20.0000 chunk 339 optimal weight: 9.9990 chunk 911 optimal weight: 30.0000 chunk 745 optimal weight: 9.9990 chunk 302 optimal weight: 5.9990 chunk 1097 optimal weight: 0.1980 chunk 1185 optimal weight: 40.0000 chunk 977 optimal weight: 8.9990 chunk 1088 optimal weight: 0.4980 chunk 374 optimal weight: 20.0000 chunk 880 optimal weight: 3.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1681 HIS A1886 GLN ** A2047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2234 HIS C2234 HIS E 93 GLN E 188 GLN F 22 ASN ** G 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 571 HIS H 643 GLN H 726 ASN H 740 ASN ** H 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 967 HIS H1000 ASN I 217 GLN I 281 GLN I 849 GLN I 874 GLN I 915 HIS I 985 ASN J 311 ASN J 649 HIS ** J 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1082 ASN K 231 ASN K 326 ASN K 526 ASN K1080 ASN K1133 HIS K1166 HIS L 194 GLN L 541 HIS ** L 945 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1029 HIS ** L1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 422 ASN M 451 HIS ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 985 ASN M1060 ASN M1082 ASN M1133 HIS M1309 GLN M1313 ASN N 20 HIS R 20 HIS S 20 HIS T 79 HIS U 14 HIS ** U 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 HIS ** W 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 249 GLN Z 256 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 98950 Z= 0.222 Angle : 0.627 14.019 134608 Z= 0.321 Chirality : 0.043 0.323 15519 Planarity : 0.005 0.068 17313 Dihedral : 5.444 86.995 13396 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.54 % Favored : 95.40 % Rotamer: Outliers : 0.10 % Allowed : 4.30 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.08), residues: 12037 helix: 0.53 (0.07), residues: 4808 sheet: -0.25 (0.12), residues: 1771 loop : -0.83 (0.09), residues: 5458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP G 514 HIS 0.010 0.001 HIS L 969 PHE 0.024 0.002 PHE A2075 TYR 0.024 0.002 TYR L1254 ARG 0.013 0.000 ARG T 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2286 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2275 time to evaluate : 8.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 PHE cc_start: 0.2897 (p90) cc_final: 0.2669 (p90) REVERT: A 1473 ARG cc_start: 0.5423 (tmt170) cc_final: 0.4064 (mmm160) REVERT: A 1641 VAL cc_start: 0.4379 (t) cc_final: 0.4072 (p) REVERT: A 1669 TYR cc_start: 0.3399 (t80) cc_final: 0.2878 (t80) REVERT: A 1802 LYS cc_start: 0.3229 (tptt) cc_final: 0.2685 (mmmt) REVERT: A 1841 LEU cc_start: 0.4815 (mt) cc_final: 0.4300 (tt) REVERT: A 1894 MET cc_start: 0.3446 (pmm) cc_final: 0.2929 (mmp) REVERT: A 1913 MET cc_start: 0.4070 (tmm) cc_final: 0.2779 (tmm) REVERT: A 1915 ARG cc_start: 0.4208 (tpt90) cc_final: 0.3385 (ttp-110) REVERT: A 1992 GLN cc_start: 0.5879 (mm-40) cc_final: 0.4054 (pt0) REVERT: A 2059 PHE cc_start: 0.2354 (p90) cc_final: 0.0976 (p90) REVERT: A 2221 LEU cc_start: 0.1724 (mt) cc_final: 0.1375 (mt) REVERT: A 2233 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.5666 (mp10) REVERT: A 2234 HIS cc_start: 0.6749 (OUTLIER) cc_final: 0.5622 (t-90) REVERT: E 207 MET cc_start: 0.4297 (mmm) cc_final: 0.3057 (tmm) REVERT: E 234 ARG cc_start: 0.4942 (tpt170) cc_final: 0.4129 (mtp85) REVERT: E 247 PHE cc_start: 0.4728 (m-80) cc_final: 0.4135 (t80) REVERT: E 349 MET cc_start: 0.1752 (mtt) cc_final: 0.1202 (ppp) REVERT: E 570 MET cc_start: 0.5243 (mtt) cc_final: 0.4699 (mmm) REVERT: F 42 MET cc_start: 0.2629 (mmt) cc_final: 0.2080 (ppp) REVERT: G 364 GLU cc_start: 0.6971 (pm20) cc_final: 0.6522 (pm20) REVERT: G 373 ASP cc_start: 0.7460 (m-30) cc_final: 0.6992 (m-30) REVERT: G 374 GLU cc_start: 0.5445 (mm-30) cc_final: 0.5124 (mm-30) REVERT: G 389 ARG cc_start: 0.6465 (mmt-90) cc_final: 0.5639 (mtp85) REVERT: G 411 LEU cc_start: 0.7752 (tp) cc_final: 0.7313 (tp) REVERT: G 447 ARG cc_start: 0.5797 (tmt-80) cc_final: 0.5588 (tmt-80) REVERT: G 484 GLN cc_start: 0.7235 (tp-100) cc_final: 0.6785 (tp40) REVERT: G 490 GLU cc_start: 0.6736 (tt0) cc_final: 0.6494 (tt0) REVERT: G 507 ARG cc_start: 0.7397 (ptm160) cc_final: 0.6492 (ptm-80) REVERT: G 513 ARG cc_start: 0.5416 (mtp-110) cc_final: 0.5181 (ttt90) REVERT: G 543 SER cc_start: 0.7461 (t) cc_final: 0.6999 (m) REVERT: G 577 GLN cc_start: 0.5841 (tt0) cc_final: 0.5115 (pp30) REVERT: H 81 HIS cc_start: 0.7457 (t-170) cc_final: 0.5742 (m90) REVERT: H 86 LEU cc_start: 0.6947 (mt) cc_final: 0.6597 (mt) REVERT: H 90 LYS cc_start: 0.7458 (mttm) cc_final: 0.6766 (pttp) REVERT: H 91 MET cc_start: 0.7634 (tpp) cc_final: 0.6936 (tpt) REVERT: H 110 ARG cc_start: 0.5320 (tmt170) cc_final: 0.4011 (mmp-170) REVERT: H 141 GLU cc_start: 0.4333 (mp0) cc_final: 0.4127 (mp0) REVERT: H 210 ILE cc_start: 0.8363 (mm) cc_final: 0.8045 (mm) REVERT: H 359 VAL cc_start: 0.8390 (t) cc_final: 0.8123 (m) REVERT: H 387 ARG cc_start: 0.7239 (mmt180) cc_final: 0.7038 (mmt90) REVERT: H 410 VAL cc_start: 0.7941 (t) cc_final: 0.7632 (m) REVERT: H 493 ARG cc_start: 0.6880 (ttm110) cc_final: 0.6470 (ptp-110) REVERT: H 589 ASP cc_start: 0.7941 (t0) cc_final: 0.7689 (t0) REVERT: H 598 LYS cc_start: 0.7873 (tmtt) cc_final: 0.6782 (ttpp) REVERT: H 610 CYS cc_start: 0.7815 (m) cc_final: 0.7570 (m) REVERT: H 844 ASP cc_start: 0.5638 (p0) cc_final: 0.4987 (m-30) REVERT: H 845 SER cc_start: 0.7091 (t) cc_final: 0.6843 (t) REVERT: H 849 GLN cc_start: 0.6994 (pt0) cc_final: 0.6676 (pt0) REVERT: H 900 ASP cc_start: 0.6886 (p0) cc_final: 0.6333 (m-30) REVERT: H 919 ASN cc_start: 0.6761 (t0) cc_final: 0.6484 (m-40) REVERT: H 967 HIS cc_start: 0.7436 (t-90) cc_final: 0.7219 (t-90) REVERT: H 1156 MET cc_start: 0.6870 (mmm) cc_final: 0.5422 (mmm) REVERT: H 1190 ASN cc_start: 0.7032 (m-40) cc_final: 0.6779 (m-40) REVERT: H 1320 GLU cc_start: 0.6170 (mt-10) cc_final: 0.5593 (mm-30) REVERT: H 1362 LEU cc_start: 0.7514 (tp) cc_final: 0.7065 (tp) REVERT: I 1 MET cc_start: 0.6903 (mtm) cc_final: 0.6212 (mtt) REVERT: I 31 MET cc_start: 0.7535 (tpp) cc_final: 0.6880 (ttt) REVERT: I 60 ARG cc_start: 0.6015 (mtp180) cc_final: 0.5806 (ptp-110) REVERT: I 81 HIS cc_start: 0.7356 (m-70) cc_final: 0.7014 (m-70) REVERT: I 150 LYS cc_start: 0.8275 (mmtp) cc_final: 0.7984 (mttt) REVERT: I 169 ASP cc_start: 0.8431 (t70) cc_final: 0.8074 (t0) REVERT: I 213 SER cc_start: 0.8687 (m) cc_final: 0.8476 (m) REVERT: I 467 ARG cc_start: 0.7357 (mtp85) cc_final: 0.6483 (mtp-110) REVERT: I 514 GLN cc_start: 0.7336 (tp40) cc_final: 0.6295 (tp40) REVERT: I 527 ILE cc_start: 0.8121 (pt) cc_final: 0.7836 (pt) REVERT: I 736 ARG cc_start: 0.5816 (ttm110) cc_final: 0.5389 (ttm110) REVERT: I 872 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6747 (mt) REVERT: I 966 TYR cc_start: 0.8487 (m-10) cc_final: 0.8124 (m-80) REVERT: I 1115 ARG cc_start: 0.5908 (mpt-90) cc_final: 0.5667 (mpt-90) REVERT: I 1150 MET cc_start: 0.5112 (mtp) cc_final: 0.4775 (mtp) REVERT: I 1156 MET cc_start: 0.6471 (ttm) cc_final: 0.6201 (ttp) REVERT: I 1250 GLU cc_start: 0.6680 (mt-10) cc_final: 0.6426 (mt-10) REVERT: I 1255 ASN cc_start: 0.8403 (t0) cc_final: 0.8032 (t0) REVERT: I 1287 LEU cc_start: 0.6151 (mm) cc_final: 0.5880 (mm) REVERT: I 1294 ARG cc_start: 0.6919 (mmm-85) cc_final: 0.6251 (ttm170) REVERT: I 1348 GLU cc_start: 0.6870 (pt0) cc_final: 0.6624 (pt0) REVERT: I 1365 SER cc_start: 0.7426 (p) cc_final: 0.7079 (m) REVERT: J 60 ARG cc_start: 0.5019 (mpt180) cc_final: 0.4565 (mpt180) REVERT: J 92 LEU cc_start: 0.8285 (mt) cc_final: 0.7889 (mp) REVERT: J 126 THR cc_start: 0.5759 (t) cc_final: 0.5484 (t) REVERT: J 185 ARG cc_start: 0.6921 (ptp-170) cc_final: 0.6232 (ptp-110) REVERT: J 293 LYS cc_start: 0.7292 (tptp) cc_final: 0.6726 (mmtm) REVERT: J 342 ASP cc_start: 0.4241 (m-30) cc_final: 0.4007 (m-30) REVERT: J 488 MET cc_start: 0.5705 (mmt) cc_final: 0.5157 (tpp) REVERT: J 584 LEU cc_start: 0.7966 (mt) cc_final: 0.7664 (mt) REVERT: J 614 ASP cc_start: 0.6028 (t0) cc_final: 0.5625 (t0) REVERT: J 628 ARG cc_start: 0.7336 (mtp85) cc_final: 0.7066 (mtp85) REVERT: J 638 MET cc_start: 0.6848 (mmp) cc_final: 0.6420 (mmm) REVERT: J 659 GLU cc_start: 0.6047 (pt0) cc_final: 0.5765 (pt0) REVERT: J 669 GLN cc_start: 0.6383 (mp10) cc_final: 0.5134 (mt0) REVERT: J 693 LEU cc_start: 0.8199 (mp) cc_final: 0.7986 (mt) REVERT: J 697 GLN cc_start: 0.7150 (mm110) cc_final: 0.5615 (mp10) REVERT: J 731 GLN cc_start: 0.7417 (pt0) cc_final: 0.6496 (pt0) REVERT: J 856 MET cc_start: 0.7352 (ttm) cc_final: 0.6733 (ttp) REVERT: J 881 LEU cc_start: 0.7752 (mt) cc_final: 0.7516 (mt) REVERT: J 962 GLU cc_start: 0.5224 (tp30) cc_final: 0.4421 (tp30) REVERT: J 963 PHE cc_start: 0.5697 (m-80) cc_final: 0.5381 (m-80) REVERT: J 1156 MET cc_start: 0.6797 (mmm) cc_final: 0.6593 (mmm) REVERT: J 1270 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6791 (mt-10) REVERT: K 61 LEU cc_start: 0.7347 (mp) cc_final: 0.7120 (tp) REVERT: K 63 TRP cc_start: 0.6842 (m100) cc_final: 0.6316 (m100) REVERT: K 91 MET cc_start: 0.8356 (mtp) cc_final: 0.8081 (mtp) REVERT: K 157 MET cc_start: 0.5799 (tmm) cc_final: 0.5586 (tmm) REVERT: K 240 LEU cc_start: 0.7865 (tp) cc_final: 0.7567 (tp) REVERT: K 259 THR cc_start: 0.7408 (p) cc_final: 0.7050 (t) REVERT: K 273 MET cc_start: 0.7918 (mtp) cc_final: 0.7585 (mtp) REVERT: K 411 GLU cc_start: 0.6884 (pm20) cc_final: 0.6561 (pm20) REVERT: K 447 LYS cc_start: 0.7373 (ttmm) cc_final: 0.7084 (ttmt) REVERT: K 638 MET cc_start: 0.6771 (tpp) cc_final: 0.6545 (tpp) REVERT: K 809 VAL cc_start: 0.8893 (m) cc_final: 0.8605 (p) REVERT: K 918 TYR cc_start: 0.6574 (t80) cc_final: 0.6001 (t80) REVERT: K 925 THR cc_start: 0.7585 (p) cc_final: 0.7332 (p) REVERT: K 933 TYR cc_start: 0.6073 (m-80) cc_final: 0.5860 (m-10) REVERT: K 958 ARG cc_start: 0.6644 (mtp180) cc_final: 0.6336 (mmm-85) REVERT: K 993 ARG cc_start: 0.7711 (tpp80) cc_final: 0.7150 (mmm160) REVERT: K 1013 TYR cc_start: 0.7875 (m-80) cc_final: 0.7332 (m-80) REVERT: K 1150 MET cc_start: 0.7085 (ptm) cc_final: 0.6375 (tmm) REVERT: K 1184 ASN cc_start: 0.8187 (m110) cc_final: 0.7946 (m110) REVERT: K 1206 ASP cc_start: 0.7824 (t0) cc_final: 0.7377 (t70) REVERT: K 1284 GLU cc_start: 0.6679 (tm-30) cc_final: 0.6435 (mt-10) REVERT: L 64 VAL cc_start: 0.6125 (p) cc_final: 0.5578 (p) REVERT: L 140 ARG cc_start: 0.6521 (mmt180) cc_final: 0.6100 (mmt90) REVERT: L 141 GLU cc_start: 0.6162 (tm-30) cc_final: 0.5887 (tm-30) REVERT: L 241 LYS cc_start: 0.8632 (tptt) cc_final: 0.8041 (tptt) REVERT: L 268 LYS cc_start: 0.7491 (mmtp) cc_final: 0.6942 (ttpt) REVERT: L 302 TYR cc_start: 0.8026 (m-80) cc_final: 0.7507 (m-80) REVERT: L 512 MET cc_start: 0.8368 (mtp) cc_final: 0.7959 (mtp) REVERT: L 866 THR cc_start: 0.5462 (p) cc_final: 0.5084 (p) REVERT: L 1006 MET cc_start: 0.7705 (mmt) cc_final: 0.6786 (mmt) REVERT: L 1080 ASN cc_start: 0.7535 (t0) cc_final: 0.7125 (t0) REVERT: L 1092 SER cc_start: 0.8747 (m) cc_final: 0.8477 (m) REVERT: L 1106 MET cc_start: 0.7383 (mtp) cc_final: 0.6966 (mtt) REVERT: L 1175 ILE cc_start: 0.8356 (pt) cc_final: 0.7890 (mt) REVERT: L 1330 LEU cc_start: 0.8043 (mt) cc_final: 0.7795 (mp) REVERT: M 146 THR cc_start: 0.7956 (t) cc_final: 0.7681 (m) REVERT: M 296 VAL cc_start: 0.7965 (m) cc_final: 0.7084 (p) REVERT: M 320 SER cc_start: 0.7380 (t) cc_final: 0.7109 (m) REVERT: M 467 ARG cc_start: 0.7665 (mtp85) cc_final: 0.6867 (ttt180) REVERT: M 512 MET cc_start: 0.8277 (mtm) cc_final: 0.7963 (mtp) REVERT: M 675 ARG cc_start: 0.6412 (ptm160) cc_final: 0.6166 (ptm160) REVERT: M 719 PHE cc_start: 0.7241 (m-80) cc_final: 0.6886 (m-10) REVERT: M 732 VAL cc_start: 0.8615 (t) cc_final: 0.8132 (p) REVERT: M 1106 MET cc_start: 0.7703 (mtm) cc_final: 0.7395 (mtm) REVERT: M 1308 GLU cc_start: 0.6873 (pt0) cc_final: 0.6119 (mm-30) REVERT: M 1358 GLU cc_start: 0.6803 (pt0) cc_final: 0.6505 (pt0) REVERT: N 61 LYS cc_start: 0.7846 (mttt) cc_final: 0.7411 (mttt) REVERT: Q 22 VAL cc_start: 0.6772 (t) cc_final: 0.6493 (t) REVERT: R 19 ARG cc_start: 0.5569 (ptp-110) cc_final: 0.5156 (mtt180) REVERT: T 70 MET cc_start: 0.8076 (ptm) cc_final: 0.7742 (ptt) REVERT: T 253 TRP cc_start: 0.5983 (p90) cc_final: 0.5447 (p90) REVERT: U 26 LYS cc_start: 0.6481 (tttm) cc_final: 0.5867 (pttm) REVERT: U 58 TYR cc_start: 0.8088 (t80) cc_final: 0.7821 (t80) REVERT: U 68 MET cc_start: 0.7996 (ttm) cc_final: 0.7786 (ttm) REVERT: U 80 GLN cc_start: 0.5169 (tt0) cc_final: 0.4788 (mm-40) REVERT: U 131 GLU cc_start: 0.6969 (tt0) cc_final: 0.6359 (mt-10) REVERT: U 147 ASN cc_start: 0.7126 (m-40) cc_final: 0.6788 (m-40) REVERT: U 153 MET cc_start: 0.7425 (tpp) cc_final: 0.6999 (tpp) REVERT: U 197 MET cc_start: 0.7296 (mtm) cc_final: 0.6609 (ttm) REVERT: U 279 ASP cc_start: 0.7177 (t0) cc_final: 0.6405 (t70) REVERT: U 298 LYS cc_start: 0.7417 (mmpt) cc_final: 0.6807 (mmtt) REVERT: V 244 GLU cc_start: 0.5596 (mm-30) cc_final: 0.4629 (mt-10) REVERT: V 279 ASP cc_start: 0.5992 (m-30) cc_final: 0.5330 (m-30) REVERT: W 21 VAL cc_start: 0.8105 (m) cc_final: 0.7791 (p) REVERT: W 70 MET cc_start: 0.6812 (ppp) cc_final: 0.6508 (ptt) REVERT: W 169 LYS cc_start: 0.7371 (mtmt) cc_final: 0.7156 (pttp) REVERT: W 275 ARG cc_start: 0.6421 (ttt-90) cc_final: 0.6202 (ttt-90) REVERT: X 51 PHE cc_start: 0.8446 (m-80) cc_final: 0.8238 (m-80) REVERT: X 91 LEU cc_start: 0.8615 (tp) cc_final: 0.8298 (mp) REVERT: X 206 MET cc_start: 0.7041 (mmm) cc_final: 0.6600 (mmm) REVERT: X 273 VAL cc_start: 0.7889 (t) cc_final: 0.7658 (t) REVERT: Y 9 PHE cc_start: 0.7073 (m-80) cc_final: 0.6818 (m-10) REVERT: Y 104 LYS cc_start: 0.7624 (tttp) cc_final: 0.7339 (tttp) REVERT: Y 131 GLU cc_start: 0.6100 (tt0) cc_final: 0.5842 (tt0) REVERT: Y 217 THR cc_start: 0.7032 (m) cc_final: 0.6788 (p) REVERT: Y 230 LEU cc_start: 0.7904 (pp) cc_final: 0.7215 (tp) REVERT: Z 40 LYS cc_start: 0.4893 (tppp) cc_final: 0.4119 (mmtm) REVERT: Z 151 THR cc_start: 0.6443 (p) cc_final: 0.6130 (t) REVERT: Z 178 MET cc_start: 0.7807 (ptt) cc_final: 0.7526 (ptm) REVERT: Z 272 ILE cc_start: 0.7235 (mm) cc_final: 0.6871 (mm) REVERT: Z 282 PHE cc_start: 0.5637 (m-80) cc_final: 0.5384 (m-80) outliers start: 11 outliers final: 1 residues processed: 2285 average time/residue: 0.8963 time to fit residues: 3491.0607 Evaluate side-chains 1803 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1799 time to evaluate : 7.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1206 random chunks: chunk 1083 optimal weight: 5.9990 chunk 824 optimal weight: 9.9990 chunk 569 optimal weight: 9.9990 chunk 121 optimal weight: 30.0000 chunk 523 optimal weight: 3.9990 chunk 736 optimal weight: 20.0000 chunk 1101 optimal weight: 10.0000 chunk 1165 optimal weight: 20.0000 chunk 575 optimal weight: 6.9990 chunk 1043 optimal weight: 0.9980 chunk 314 optimal weight: 0.3980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 643 GLN H 740 ASN ** H 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 HIS I 96 GLN I 158 HIS I 231 ASN ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 874 GLN J 231 ASN ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 581 HIS J 874 GLN ** J 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 914 GLN K 199 ASN ** K 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 476 GLN ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1080 ASN K1111 GLN K1133 HIS L 194 GLN L 304 ASN L 541 HIS L1267 ASN L1309 GLN M 208 ASN M 388 ASN ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 884 GLN M1060 ASN M1133 HIS M1223 GLN N 20 HIS O 18 HIS ** Q 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 183 GLN T 211 HIS T 213 GLN U 36 GLN ** U 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 14 HIS W 40 HIS W 43 HIS X 84 HIS Y 96 ASN Z 47 HIS Z 256 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6816 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 98950 Z= 0.214 Angle : 0.617 14.610 134608 Z= 0.312 Chirality : 0.043 0.423 15519 Planarity : 0.005 0.079 17313 Dihedral : 5.333 84.748 13396 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.66 % Favored : 95.26 % Rotamer: Outliers : 0.05 % Allowed : 3.60 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.33 (0.08), residues: 12037 helix: 0.56 (0.07), residues: 4808 sheet: -0.21 (0.12), residues: 1682 loop : -0.85 (0.08), residues: 5547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP G 514 HIS 0.012 0.001 HIS E 365 PHE 0.035 0.002 PHE K 672 TYR 0.021 0.002 TYR U 44 ARG 0.015 0.000 ARG K 968 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2232 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2227 time to evaluate : 8.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 PHE cc_start: 0.2493 (p90) cc_final: 0.2185 (p90) REVERT: A 1473 ARG cc_start: 0.5359 (tmt170) cc_final: 0.4044 (mmm160) REVERT: A 1616 LYS cc_start: 0.4032 (pttp) cc_final: 0.3823 (pttp) REVERT: A 1641 VAL cc_start: 0.4345 (t) cc_final: 0.4037 (p) REVERT: A 1669 TYR cc_start: 0.3464 (t80) cc_final: 0.3066 (t80) REVERT: A 1707 ARG cc_start: 0.5226 (mtm-85) cc_final: 0.4241 (ttm110) REVERT: A 1802 LYS cc_start: 0.3284 (tptt) cc_final: 0.2630 (mmmt) REVERT: A 1804 PHE cc_start: 0.0765 (p90) cc_final: 0.0237 (p90) REVERT: A 1827 GLN cc_start: 0.3409 (tp40) cc_final: 0.2832 (tp40) REVERT: A 1841 LEU cc_start: 0.4856 (mt) cc_final: 0.4353 (tt) REVERT: A 1894 MET cc_start: 0.3386 (pmm) cc_final: 0.2905 (mmp) REVERT: A 1906 THR cc_start: 0.4847 (t) cc_final: 0.4137 (p) REVERT: A 1913 MET cc_start: 0.4180 (tmm) cc_final: 0.2972 (tmm) REVERT: A 1915 ARG cc_start: 0.4306 (tpt90) cc_final: 0.3573 (ttp-170) REVERT: A 1945 LEU cc_start: 0.4412 (tp) cc_final: 0.3886 (pp) REVERT: A 1981 TYR cc_start: 0.2907 (t80) cc_final: 0.2522 (t80) REVERT: A 1992 GLN cc_start: 0.5862 (mm-40) cc_final: 0.3990 (pt0) REVERT: A 2059 PHE cc_start: 0.2440 (p90) cc_final: 0.0961 (p90) REVERT: A 2221 LEU cc_start: 0.1728 (mt) cc_final: 0.1370 (mt) REVERT: E 207 MET cc_start: 0.4224 (mmm) cc_final: 0.3026 (tmm) REVERT: E 247 PHE cc_start: 0.4951 (m-80) cc_final: 0.4207 (t80) REVERT: E 349 MET cc_start: 0.1857 (mtt) cc_final: 0.1048 (ppp) REVERT: E 364 ARG cc_start: 0.5565 (ttm110) cc_final: 0.5318 (ttm110) REVERT: E 570 MET cc_start: 0.4978 (mtt) cc_final: 0.4161 (mmm) REVERT: F 42 MET cc_start: 0.2553 (mmt) cc_final: 0.2167 (ppp) REVERT: G 364 GLU cc_start: 0.6998 (pm20) cc_final: 0.6590 (pm20) REVERT: G 373 ASP cc_start: 0.7502 (m-30) cc_final: 0.5623 (m-30) REVERT: G 374 GLU cc_start: 0.5530 (mm-30) cc_final: 0.5201 (mm-30) REVERT: G 389 ARG cc_start: 0.6498 (mmt-90) cc_final: 0.5921 (mmt180) REVERT: G 411 LEU cc_start: 0.7756 (tp) cc_final: 0.7149 (tp) REVERT: G 415 MET cc_start: 0.7110 (mmm) cc_final: 0.6644 (mmm) REVERT: G 447 ARG cc_start: 0.5776 (tmt-80) cc_final: 0.5434 (tmt-80) REVERT: G 484 GLN cc_start: 0.7207 (tp-100) cc_final: 0.6919 (tp-100) REVERT: G 507 ARG cc_start: 0.7197 (ptm160) cc_final: 0.6964 (ptm-80) REVERT: G 513 ARG cc_start: 0.5367 (mtp-110) cc_final: 0.5162 (ttt90) REVERT: G 543 SER cc_start: 0.7475 (t) cc_final: 0.7054 (m) REVERT: G 577 GLN cc_start: 0.5797 (tt0) cc_final: 0.5107 (pp30) REVERT: H 81 HIS cc_start: 0.7430 (t-170) cc_final: 0.5784 (m90) REVERT: H 86 LEU cc_start: 0.6915 (mt) cc_final: 0.6705 (mt) REVERT: H 90 LYS cc_start: 0.7359 (mttm) cc_final: 0.6709 (pttp) REVERT: H 91 MET cc_start: 0.7582 (tpp) cc_final: 0.6810 (tpt) REVERT: H 110 ARG cc_start: 0.5258 (tmt170) cc_final: 0.4051 (mmp-170) REVERT: H 210 ILE cc_start: 0.8407 (mm) cc_final: 0.8125 (mm) REVERT: H 359 VAL cc_start: 0.8432 (t) cc_final: 0.8135 (m) REVERT: H 589 ASP cc_start: 0.7917 (t0) cc_final: 0.7606 (t0) REVERT: H 598 LYS cc_start: 0.7676 (tmtt) cc_final: 0.6716 (ttpt) REVERT: H 745 GLU cc_start: 0.7199 (tp30) cc_final: 0.6918 (tp30) REVERT: H 844 ASP cc_start: 0.5617 (p0) cc_final: 0.4930 (m-30) REVERT: H 845 SER cc_start: 0.7558 (t) cc_final: 0.7198 (t) REVERT: H 849 GLN cc_start: 0.6946 (pt0) cc_final: 0.6603 (pt0) REVERT: H 900 ASP cc_start: 0.6835 (p0) cc_final: 0.6386 (m-30) REVERT: H 919 ASN cc_start: 0.6758 (t0) cc_final: 0.6531 (m-40) REVERT: H 1156 MET cc_start: 0.6818 (mmm) cc_final: 0.5897 (mmm) REVERT: H 1254 TYR cc_start: 0.7015 (p90) cc_final: 0.6727 (p90) REVERT: H 1362 LEU cc_start: 0.7433 (tp) cc_final: 0.6947 (tp) REVERT: I 1 MET cc_start: 0.6876 (mtm) cc_final: 0.6209 (mtt) REVERT: I 30 GLU cc_start: 0.6458 (tp30) cc_final: 0.6231 (tp30) REVERT: I 31 MET cc_start: 0.7485 (tpp) cc_final: 0.7155 (ttt) REVERT: I 60 ARG cc_start: 0.6058 (mtp180) cc_final: 0.5843 (ptp-110) REVERT: I 130 GLU cc_start: 0.6163 (pt0) cc_final: 0.5729 (pt0) REVERT: I 169 ASP cc_start: 0.8408 (t70) cc_final: 0.8130 (t0) REVERT: I 291 ILE cc_start: 0.8020 (mt) cc_final: 0.7792 (mt) REVERT: I 467 ARG cc_start: 0.7350 (mtp85) cc_final: 0.6481 (mtp-110) REVERT: I 514 GLN cc_start: 0.7279 (tp40) cc_final: 0.6285 (tp40) REVERT: I 672 PHE cc_start: 0.6131 (m-10) cc_final: 0.5879 (m-10) REVERT: I 736 ARG cc_start: 0.5819 (ttm110) cc_final: 0.5437 (ttm110) REVERT: I 1115 ARG cc_start: 0.5972 (mpt-90) cc_final: 0.5562 (mpt-90) REVERT: I 1150 MET cc_start: 0.5311 (mtp) cc_final: 0.4840 (mtp) REVERT: I 1156 MET cc_start: 0.6429 (ttm) cc_final: 0.6182 (ttp) REVERT: I 1250 GLU cc_start: 0.6620 (mt-10) cc_final: 0.6337 (mt-10) REVERT: I 1255 ASN cc_start: 0.8231 (t0) cc_final: 0.7757 (t0) REVERT: I 1287 LEU cc_start: 0.6076 (mm) cc_final: 0.5757 (mm) REVERT: I 1294 ARG cc_start: 0.6937 (mmm-85) cc_final: 0.6155 (ttm170) REVERT: I 1365 SER cc_start: 0.7400 (p) cc_final: 0.6955 (m) REVERT: J 60 ARG cc_start: 0.5119 (mpt180) cc_final: 0.4614 (mpt180) REVERT: J 126 THR cc_start: 0.5464 (t) cc_final: 0.5166 (t) REVERT: J 185 ARG cc_start: 0.7024 (ptp-170) cc_final: 0.6103 (ptp-110) REVERT: J 293 LYS cc_start: 0.7282 (tptp) cc_final: 0.6801 (mmtt) REVERT: J 475 MET cc_start: 0.7412 (mmm) cc_final: 0.6836 (mtt) REVERT: J 488 MET cc_start: 0.5719 (mmt) cc_final: 0.5348 (tpp) REVERT: J 628 ARG cc_start: 0.7338 (mtp85) cc_final: 0.7004 (mtp85) REVERT: J 638 MET cc_start: 0.6808 (mmp) cc_final: 0.6485 (mmm) REVERT: J 659 GLU cc_start: 0.6096 (pt0) cc_final: 0.5669 (pt0) REVERT: J 669 GLN cc_start: 0.6332 (mp10) cc_final: 0.5167 (mt0) REVERT: J 693 LEU cc_start: 0.8236 (mp) cc_final: 0.7990 (mt) REVERT: J 697 GLN cc_start: 0.6909 (mm110) cc_final: 0.5297 (mp10) REVERT: J 731 GLN cc_start: 0.7569 (pt0) cc_final: 0.6713 (pt0) REVERT: J 856 MET cc_start: 0.7498 (ttm) cc_final: 0.6702 (ttp) REVERT: J 962 GLU cc_start: 0.5596 (tp30) cc_final: 0.5135 (tp30) REVERT: J 963 PHE cc_start: 0.5762 (m-80) cc_final: 0.5504 (m-80) REVERT: J 1156 MET cc_start: 0.6522 (mmm) cc_final: 0.6315 (mmm) REVERT: J 1270 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6864 (mt-10) REVERT: K 61 LEU cc_start: 0.7357 (mp) cc_final: 0.7105 (tp) REVERT: K 63 TRP cc_start: 0.6910 (m100) cc_final: 0.6328 (m100) REVERT: K 91 MET cc_start: 0.8481 (mtp) cc_final: 0.8181 (mtp) REVERT: K 259 THR cc_start: 0.7401 (p) cc_final: 0.7039 (t) REVERT: K 407 TYR cc_start: 0.8370 (p90) cc_final: 0.8150 (p90) REVERT: K 411 GLU cc_start: 0.6905 (pm20) cc_final: 0.6638 (pm20) REVERT: K 447 LYS cc_start: 0.7380 (ttmm) cc_final: 0.7080 (ttmt) REVERT: K 537 PHE cc_start: 0.7885 (m-80) cc_final: 0.7621 (m-80) REVERT: K 918 TYR cc_start: 0.6609 (t80) cc_final: 0.6070 (t80) REVERT: K 925 THR cc_start: 0.7423 (p) cc_final: 0.7182 (p) REVERT: K 958 ARG cc_start: 0.6634 (mtp180) cc_final: 0.6334 (mmm-85) REVERT: K 993 ARG cc_start: 0.7661 (tpp80) cc_final: 0.7082 (mmm160) REVERT: K 1043 GLU cc_start: 0.6638 (tp30) cc_final: 0.6201 (tp30) REVERT: K 1150 MET cc_start: 0.7231 (ptm) cc_final: 0.6574 (tmm) REVERT: K 1184 ASN cc_start: 0.8230 (m110) cc_final: 0.7921 (m110) REVERT: K 1206 ASP cc_start: 0.7894 (t0) cc_final: 0.7335 (t70) REVERT: K 1284 GLU cc_start: 0.6797 (tm-30) cc_final: 0.6539 (mt-10) REVERT: L 64 VAL cc_start: 0.6093 (p) cc_final: 0.5572 (p) REVERT: L 140 ARG cc_start: 0.6588 (mmt180) cc_final: 0.6191 (mmt90) REVERT: L 141 GLU cc_start: 0.6274 (tm-30) cc_final: 0.5946 (tm-30) REVERT: L 241 LYS cc_start: 0.8390 (tptt) cc_final: 0.7963 (tptt) REVERT: L 268 LYS cc_start: 0.7402 (mmtp) cc_final: 0.6908 (ttpt) REVERT: L 302 TYR cc_start: 0.7951 (m-80) cc_final: 0.7507 (m-80) REVERT: L 382 LYS cc_start: 0.7439 (mtpp) cc_final: 0.7014 (ttpt) REVERT: L 802 LEU cc_start: 0.6933 (mt) cc_final: 0.6726 (mt) REVERT: L 1006 MET cc_start: 0.7790 (mmt) cc_final: 0.6792 (mmt) REVERT: L 1080 ASN cc_start: 0.7523 (t0) cc_final: 0.7183 (t0) REVERT: L 1092 SER cc_start: 0.8656 (m) cc_final: 0.8260 (t) REVERT: L 1106 MET cc_start: 0.7413 (mtp) cc_final: 0.7055 (mtt) REVERT: L 1175 ILE cc_start: 0.8258 (pt) cc_final: 0.7828 (mt) REVERT: L 1308 GLU cc_start: 0.7168 (pm20) cc_final: 0.6334 (pm20) REVERT: L 1330 LEU cc_start: 0.8037 (mt) cc_final: 0.7792 (mp) REVERT: M 320 SER cc_start: 0.7396 (t) cc_final: 0.7162 (m) REVERT: M 467 ARG cc_start: 0.7683 (mtp85) cc_final: 0.6829 (ttt180) REVERT: M 500 ARG cc_start: 0.5771 (mmm160) cc_final: 0.5406 (mmt-90) REVERT: M 512 MET cc_start: 0.8156 (mtm) cc_final: 0.7795 (mtp) REVERT: M 650 SER cc_start: 0.7895 (t) cc_final: 0.7660 (m) REVERT: M 675 ARG cc_start: 0.6356 (ptm160) cc_final: 0.6067 (ptm160) REVERT: M 863 ASP cc_start: 0.6905 (p0) cc_final: 0.5631 (m-30) REVERT: M 1022 LEU cc_start: 0.7464 (mt) cc_final: 0.7135 (mp) REVERT: M 1106 MET cc_start: 0.7653 (mtm) cc_final: 0.7411 (mtm) REVERT: M 1223 GLN cc_start: 0.5743 (OUTLIER) cc_final: 0.3983 (mm110) REVERT: M 1308 GLU cc_start: 0.6687 (pt0) cc_final: 0.6156 (mm-30) REVERT: N 30 THR cc_start: 0.6744 (p) cc_final: 0.6513 (p) REVERT: N 61 LYS cc_start: 0.7777 (mttt) cc_final: 0.7365 (mttt) REVERT: O 62 LEU cc_start: 0.7892 (tp) cc_final: 0.7685 (tp) REVERT: Q 14 ARG cc_start: 0.3321 (mtp180) cc_final: 0.3100 (ttt-90) REVERT: Q 22 VAL cc_start: 0.6687 (t) cc_final: 0.6371 (t) REVERT: Q 60 PHE cc_start: 0.7023 (m-80) cc_final: 0.6580 (m-80) REVERT: R 19 ARG cc_start: 0.5556 (ptp-110) cc_final: 0.4904 (mtt180) REVERT: S 54 PHE cc_start: 0.5581 (m-10) cc_final: 0.4745 (m-10) REVERT: U 58 TYR cc_start: 0.8061 (t80) cc_final: 0.7779 (t80) REVERT: U 80 GLN cc_start: 0.5307 (tt0) cc_final: 0.4754 (mm-40) REVERT: U 131 GLU cc_start: 0.6997 (tt0) cc_final: 0.6368 (mt-10) REVERT: U 153 MET cc_start: 0.7413 (tpp) cc_final: 0.7046 (tpp) REVERT: U 197 MET cc_start: 0.7455 (mtm) cc_final: 0.6570 (ttm) REVERT: U 204 MET cc_start: 0.7759 (mtm) cc_final: 0.7482 (mtm) REVERT: U 298 LYS cc_start: 0.7621 (mmpt) cc_final: 0.6977 (mmtt) REVERT: V 244 GLU cc_start: 0.5686 (mm-30) cc_final: 0.4438 (mt-10) REVERT: V 264 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6963 (tm-30) REVERT: V 299 SER cc_start: 0.6583 (m) cc_final: 0.6194 (p) REVERT: W 70 MET cc_start: 0.6891 (ppp) cc_final: 0.6621 (ptt) REVERT: W 166 MET cc_start: 0.7481 (mmm) cc_final: 0.7219 (mmm) REVERT: W 268 GLU cc_start: 0.6184 (mp0) cc_final: 0.5801 (mp0) REVERT: X 91 LEU cc_start: 0.8612 (tp) cc_final: 0.8293 (mp) REVERT: X 206 MET cc_start: 0.6944 (mmm) cc_final: 0.6592 (mmm) REVERT: X 273 VAL cc_start: 0.7844 (t) cc_final: 0.7615 (t) REVERT: Y 9 PHE cc_start: 0.7080 (m-80) cc_final: 0.6822 (m-10) REVERT: Y 131 GLU cc_start: 0.6331 (tt0) cc_final: 0.6095 (tt0) REVERT: Y 153 MET cc_start: 0.8428 (ptp) cc_final: 0.7907 (ptp) REVERT: Y 217 THR cc_start: 0.6952 (m) cc_final: 0.6730 (p) REVERT: Y 230 LEU cc_start: 0.7895 (pp) cc_final: 0.7227 (tp) REVERT: Z 40 LYS cc_start: 0.4879 (tppp) cc_final: 0.4047 (mmtm) REVERT: Z 84 CYS cc_start: 0.5695 (m) cc_final: 0.5466 (m) REVERT: Z 151 THR cc_start: 0.6425 (p) cc_final: 0.6116 (t) REVERT: Z 272 ILE cc_start: 0.7255 (mm) cc_final: 0.6896 (mm) outliers start: 5 outliers final: 1 residues processed: 2231 average time/residue: 0.8843 time to fit residues: 3369.0127 Evaluate side-chains 1767 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1765 time to evaluate : 8.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1206 random chunks: chunk 970 optimal weight: 7.9990 chunk 661 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 867 optimal weight: 20.0000 chunk 480 optimal weight: 4.9990 chunk 994 optimal weight: 20.0000 chunk 805 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 595 optimal weight: 8.9990 chunk 1046 optimal weight: 0.7980 chunk 294 optimal weight: 3.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1779 GLN A2014 HIS A2045 GLN ** A2047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2233 GLN A2234 HIS E 93 GLN E 243 GLN ** E 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 321 GLN H 643 GLN H 740 ASN ** H 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1000 ASN H1027 HIS I 96 GLN I 231 ASN I 331 HIS ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 731 GLN ** I 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 985 ASN J 231 ASN J 311 ASN ** J 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 534 HIS J 676 ASN ** J 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 874 GLN ** J 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 965 HIS ** J1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1082 ASN J1133 HIS K 94 HIS ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 969 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1080 ASN K1133 HIS K1166 HIS L 194 GLN L 541 HIS L 560 ASN ** L1082 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1166 HIS L1223 GLN ** L1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 211 GLN ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1060 ASN M1133 HIS N 20 HIS ** Q 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 HIS ** W 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 GLN Y 173 GLN Z 120 HIS Z 150 GLN Z 256 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 98950 Z= 0.234 Angle : 0.627 14.393 134608 Z= 0.317 Chirality : 0.043 0.375 15519 Planarity : 0.005 0.073 17313 Dihedral : 5.316 82.159 13396 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 0.06 % Allowed : 3.07 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.35 (0.08), residues: 12037 helix: 0.57 (0.07), residues: 4790 sheet: -0.27 (0.12), residues: 1709 loop : -0.86 (0.08), residues: 5538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 986 HIS 0.015 0.001 HIS W 43 PHE 0.027 0.002 PHE A2075 TYR 0.021 0.002 TYR W 155 ARG 0.013 0.000 ARG H1101 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2176 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2170 time to evaluate : 8.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 PHE cc_start: 0.2458 (p90) cc_final: 0.2205 (p90) REVERT: A 1473 ARG cc_start: 0.5094 (tmt170) cc_final: 0.3828 (mmm160) REVERT: A 1493 ARG cc_start: 0.2256 (mmm160) cc_final: 0.1563 (tpm170) REVERT: A 1641 VAL cc_start: 0.4336 (t) cc_final: 0.4043 (p) REVERT: A 1707 ARG cc_start: 0.5342 (mtm-85) cc_final: 0.4111 (ttp-110) REVERT: A 1802 LYS cc_start: 0.3545 (tptt) cc_final: 0.2835 (mmmt) REVERT: A 1804 PHE cc_start: 0.0903 (p90) cc_final: 0.0431 (p90) REVERT: A 1827 GLN cc_start: 0.3527 (tp40) cc_final: 0.2887 (tp40) REVERT: A 1841 LEU cc_start: 0.4702 (mt) cc_final: 0.4336 (tt) REVERT: A 1894 MET cc_start: 0.3454 (pmm) cc_final: 0.2910 (mmp) REVERT: A 1913 MET cc_start: 0.4324 (tmm) cc_final: 0.3212 (tmm) REVERT: A 1915 ARG cc_start: 0.4328 (tpt90) cc_final: 0.3647 (ttp-170) REVERT: A 1992 GLN cc_start: 0.6190 (mm-40) cc_final: 0.3909 (pt0) REVERT: A 2234 HIS cc_start: 0.7032 (OUTLIER) cc_final: 0.6814 (t70) REVERT: E 60 TYR cc_start: 0.8200 (m-80) cc_final: 0.7974 (m-80) REVERT: E 207 MET cc_start: 0.4224 (mmm) cc_final: 0.2992 (tmm) REVERT: E 247 PHE cc_start: 0.4011 (m-80) cc_final: 0.3697 (t80) REVERT: E 349 MET cc_start: 0.1503 (mtt) cc_final: 0.0845 (ppp) REVERT: E 364 ARG cc_start: 0.5535 (ttm110) cc_final: 0.5286 (ttm110) REVERT: E 409 ARG cc_start: 0.4062 (mtt180) cc_final: 0.2126 (tmt-80) REVERT: F 42 MET cc_start: 0.2519 (mmt) cc_final: 0.2190 (ppp) REVERT: G 321 GLN cc_start: 0.6802 (OUTLIER) cc_final: 0.6450 (mm-40) REVERT: G 364 GLU cc_start: 0.7026 (pm20) cc_final: 0.6630 (pm20) REVERT: G 373 ASP cc_start: 0.6294 (m-30) cc_final: 0.5832 (m-30) REVERT: G 374 GLU cc_start: 0.5504 (mm-30) cc_final: 0.5207 (mm-30) REVERT: G 389 ARG cc_start: 0.6475 (mmt-90) cc_final: 0.6189 (mmt180) REVERT: G 447 ARG cc_start: 0.5658 (tmt-80) cc_final: 0.5348 (tmt-80) REVERT: G 484 GLN cc_start: 0.7157 (tp-100) cc_final: 0.6945 (tp-100) REVERT: G 507 ARG cc_start: 0.7269 (ptm160) cc_final: 0.6741 (ptm-80) REVERT: G 513 ARG cc_start: 0.5561 (mtp-110) cc_final: 0.5294 (ttt90) REVERT: G 543 SER cc_start: 0.7535 (t) cc_final: 0.7216 (m) REVERT: G 577 GLN cc_start: 0.5794 (tt0) cc_final: 0.5104 (pp30) REVERT: H 81 HIS cc_start: 0.7480 (t-170) cc_final: 0.5789 (m-70) REVERT: H 90 LYS cc_start: 0.7383 (mttm) cc_final: 0.6732 (pttp) REVERT: H 91 MET cc_start: 0.7558 (tpp) cc_final: 0.6804 (tpt) REVERT: H 110 ARG cc_start: 0.5546 (tmt170) cc_final: 0.3902 (mmp-170) REVERT: H 359 VAL cc_start: 0.8420 (t) cc_final: 0.8141 (m) REVERT: H 589 ASP cc_start: 0.7937 (t0) cc_final: 0.7636 (t0) REVERT: H 598 LYS cc_start: 0.7793 (tmtt) cc_final: 0.6768 (ttpp) REVERT: H 745 GLU cc_start: 0.7276 (tp30) cc_final: 0.7002 (tp30) REVERT: H 844 ASP cc_start: 0.5652 (p0) cc_final: 0.4934 (m-30) REVERT: H 849 GLN cc_start: 0.6962 (pt0) cc_final: 0.6603 (pt0) REVERT: H 900 ASP cc_start: 0.6724 (p0) cc_final: 0.6269 (m-30) REVERT: H 919 ASN cc_start: 0.6778 (t0) cc_final: 0.6575 (m-40) REVERT: H 1072 SER cc_start: 0.7452 (t) cc_final: 0.7220 (t) REVERT: H 1156 MET cc_start: 0.6902 (mmm) cc_final: 0.5949 (mmm) REVERT: H 1254 TYR cc_start: 0.6968 (p90) cc_final: 0.6691 (p90) REVERT: H 1320 GLU cc_start: 0.5998 (mt-10) cc_final: 0.5661 (mt-10) REVERT: H 1362 LEU cc_start: 0.7447 (tp) cc_final: 0.6978 (tp) REVERT: I 1 MET cc_start: 0.6868 (mtm) cc_final: 0.6221 (mtt) REVERT: I 30 GLU cc_start: 0.6478 (tp30) cc_final: 0.6209 (tp30) REVERT: I 31 MET cc_start: 0.7503 (tpp) cc_final: 0.7249 (ttt) REVERT: I 60 ARG cc_start: 0.6270 (mtp180) cc_final: 0.5933 (ptp-110) REVERT: I 130 GLU cc_start: 0.6266 (pt0) cc_final: 0.5778 (pt0) REVERT: I 169 ASP cc_start: 0.8470 (t70) cc_final: 0.8137 (t0) REVERT: I 291 ILE cc_start: 0.7920 (mt) cc_final: 0.7683 (mt) REVERT: I 467 ARG cc_start: 0.7401 (mtp85) cc_final: 0.6470 (mtp-110) REVERT: I 514 GLN cc_start: 0.7317 (tp40) cc_final: 0.6301 (tp40) REVERT: I 866 THR cc_start: 0.7963 (p) cc_final: 0.7734 (p) REVERT: I 1098 TYR cc_start: 0.6627 (t80) cc_final: 0.6381 (t80) REVERT: I 1115 ARG cc_start: 0.5911 (mpt-90) cc_final: 0.5467 (mpt-90) REVERT: I 1150 MET cc_start: 0.5493 (mtp) cc_final: 0.5210 (mtp) REVERT: I 1250 GLU cc_start: 0.6618 (mt-10) cc_final: 0.6331 (mt-10) REVERT: I 1259 TYR cc_start: 0.6553 (t80) cc_final: 0.5765 (t80) REVERT: I 1265 TYR cc_start: 0.8137 (m-80) cc_final: 0.7785 (m-80) REVERT: I 1282 ILE cc_start: 0.8050 (pt) cc_final: 0.7814 (pt) REVERT: I 1287 LEU cc_start: 0.6085 (mm) cc_final: 0.5722 (mm) REVERT: I 1294 ARG cc_start: 0.6835 (mmm-85) cc_final: 0.6023 (tpp-160) REVERT: I 1365 SER cc_start: 0.7406 (p) cc_final: 0.7013 (m) REVERT: J 126 THR cc_start: 0.5237 (t) cc_final: 0.4926 (t) REVERT: J 185 ARG cc_start: 0.6986 (ptp-170) cc_final: 0.6024 (ptp-110) REVERT: J 193 VAL cc_start: 0.9134 (m) cc_final: 0.8628 (p) REVERT: J 293 LYS cc_start: 0.7246 (tptp) cc_final: 0.6963 (mmtt) REVERT: J 475 MET cc_start: 0.7403 (mmm) cc_final: 0.6874 (mtt) REVERT: J 488 MET cc_start: 0.5749 (mmt) cc_final: 0.5365 (tpp) REVERT: J 628 ARG cc_start: 0.7321 (mtp85) cc_final: 0.6946 (mtp85) REVERT: J 638 MET cc_start: 0.6773 (mmp) cc_final: 0.6269 (mmm) REVERT: J 659 GLU cc_start: 0.6051 (pt0) cc_final: 0.5646 (pt0) REVERT: J 669 GLN cc_start: 0.6306 (mp10) cc_final: 0.5216 (mt0) REVERT: J 693 LEU cc_start: 0.8213 (mp) cc_final: 0.7961 (mt) REVERT: J 694 ASN cc_start: 0.8140 (p0) cc_final: 0.7833 (p0) REVERT: J 697 GLN cc_start: 0.6785 (mm110) cc_final: 0.5302 (mp10) REVERT: J 706 TYR cc_start: 0.8030 (m-80) cc_final: 0.7579 (m-80) REVERT: J 731 GLN cc_start: 0.7785 (pt0) cc_final: 0.6960 (pt0) REVERT: J 880 PHE cc_start: 0.7533 (t80) cc_final: 0.7264 (t80) REVERT: J 962 GLU cc_start: 0.5558 (tp30) cc_final: 0.5042 (tp30) REVERT: J 963 PHE cc_start: 0.5777 (m-80) cc_final: 0.5433 (m-80) REVERT: J 1270 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6872 (mt-10) REVERT: J 1348 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6594 (mt-10) REVERT: K 61 LEU cc_start: 0.7429 (mp) cc_final: 0.7131 (tp) REVERT: K 91 MET cc_start: 0.8494 (mtp) cc_final: 0.8238 (mtp) REVERT: K 240 LEU cc_start: 0.7911 (tp) cc_final: 0.7520 (tp) REVERT: K 259 THR cc_start: 0.7483 (p) cc_final: 0.7107 (t) REVERT: K 407 TYR cc_start: 0.8264 (p90) cc_final: 0.8052 (p90) REVERT: K 411 GLU cc_start: 0.6908 (pm20) cc_final: 0.6670 (pm20) REVERT: K 447 LYS cc_start: 0.7447 (ttmm) cc_final: 0.7043 (ttmt) REVERT: K 537 PHE cc_start: 0.7820 (m-80) cc_final: 0.7465 (m-80) REVERT: K 958 ARG cc_start: 0.6613 (mtp180) cc_final: 0.6286 (mmm-85) REVERT: K 966 TYR cc_start: 0.7079 (m-80) cc_final: 0.6700 (m-10) REVERT: K 1150 MET cc_start: 0.7224 (ptm) cc_final: 0.6320 (tmm) REVERT: K 1184 ASN cc_start: 0.8226 (m110) cc_final: 0.7902 (m110) REVERT: K 1206 ASP cc_start: 0.8014 (t0) cc_final: 0.7487 (t70) REVERT: K 1284 GLU cc_start: 0.6753 (tm-30) cc_final: 0.6543 (mt-10) REVERT: L 64 VAL cc_start: 0.5997 (p) cc_final: 0.5613 (p) REVERT: L 140 ARG cc_start: 0.6602 (mmt180) cc_final: 0.6195 (mmt90) REVERT: L 141 GLU cc_start: 0.6073 (tm-30) cc_final: 0.5798 (tm-30) REVERT: L 241 LYS cc_start: 0.8600 (tptt) cc_final: 0.8008 (tptt) REVERT: L 268 LYS cc_start: 0.7579 (mmtp) cc_final: 0.6955 (ttpt) REVERT: L 302 TYR cc_start: 0.7833 (m-80) cc_final: 0.7424 (m-80) REVERT: L 382 LYS cc_start: 0.7441 (mtpp) cc_final: 0.6975 (ttpt) REVERT: L 475 MET cc_start: 0.5599 (mmp) cc_final: 0.3833 (tmm) REVERT: L 479 LEU cc_start: 0.7511 (mt) cc_final: 0.7065 (mt) REVERT: L 512 MET cc_start: 0.8339 (mtp) cc_final: 0.7933 (mtp) REVERT: L 656 LEU cc_start: 0.8053 (mp) cc_final: 0.7807 (mt) REVERT: L 866 THR cc_start: 0.5411 (p) cc_final: 0.5164 (p) REVERT: L 1006 MET cc_start: 0.7772 (mmt) cc_final: 0.6822 (mmt) REVERT: L 1080 ASN cc_start: 0.7544 (t0) cc_final: 0.7338 (t0) REVERT: L 1092 SER cc_start: 0.8559 (m) cc_final: 0.8187 (t) REVERT: L 1106 MET cc_start: 0.7493 (mtp) cc_final: 0.7083 (mtt) REVERT: L 1219 GLU cc_start: 0.6420 (mp0) cc_final: 0.6050 (mp0) REVERT: L 1330 LEU cc_start: 0.8102 (mt) cc_final: 0.7796 (mp) REVERT: M 223 MET cc_start: 0.7041 (ttp) cc_final: 0.6831 (ttp) REVERT: M 296 VAL cc_start: 0.7998 (m) cc_final: 0.7060 (p) REVERT: M 320 SER cc_start: 0.7338 (t) cc_final: 0.7128 (m) REVERT: M 467 ARG cc_start: 0.7633 (mtp85) cc_final: 0.6796 (ttt180) REVERT: M 500 ARG cc_start: 0.5710 (mmm160) cc_final: 0.5203 (mmt180) REVERT: M 512 MET cc_start: 0.8178 (mtm) cc_final: 0.7862 (mtp) REVERT: M 675 ARG cc_start: 0.6288 (ptm160) cc_final: 0.5906 (ptm160) REVERT: M 732 VAL cc_start: 0.8562 (t) cc_final: 0.8121 (p) REVERT: M 803 ASN cc_start: 0.6723 (t0) cc_final: 0.6274 (t0) REVERT: M 863 ASP cc_start: 0.6890 (p0) cc_final: 0.5616 (m-30) REVERT: M 1022 LEU cc_start: 0.7628 (mt) cc_final: 0.7304 (mp) REVERT: M 1106 MET cc_start: 0.7596 (mtm) cc_final: 0.7341 (mtm) REVERT: M 1308 GLU cc_start: 0.6796 (pt0) cc_final: 0.6147 (mm-30) REVERT: N 61 LYS cc_start: 0.7787 (mttt) cc_final: 0.7469 (mttt) REVERT: O 62 LEU cc_start: 0.7930 (tp) cc_final: 0.7703 (tp) REVERT: Q 22 VAL cc_start: 0.6691 (t) cc_final: 0.6327 (t) REVERT: R 19 ARG cc_start: 0.5652 (ptp-110) cc_final: 0.4974 (mtt180) REVERT: R 42 THR cc_start: 0.7120 (t) cc_final: 0.6740 (m) REVERT: S 54 PHE cc_start: 0.5708 (m-10) cc_final: 0.4819 (m-10) REVERT: T 181 ARG cc_start: 0.5899 (ttp80) cc_final: 0.5030 (mtp-110) REVERT: U 58 TYR cc_start: 0.8069 (t80) cc_final: 0.7725 (t80) REVERT: U 80 GLN cc_start: 0.5288 (tt0) cc_final: 0.4715 (mm-40) REVERT: U 92 TYR cc_start: 0.6649 (m-10) cc_final: 0.6416 (m-80) REVERT: U 131 GLU cc_start: 0.6988 (tt0) cc_final: 0.6422 (mt-10) REVERT: U 153 MET cc_start: 0.7482 (tpp) cc_final: 0.7084 (tpp) REVERT: U 197 MET cc_start: 0.7428 (mtm) cc_final: 0.6578 (ttm) REVERT: U 298 LYS cc_start: 0.7609 (mmpt) cc_final: 0.6943 (mmmt) REVERT: W 21 VAL cc_start: 0.8089 (m) cc_final: 0.7806 (p) REVERT: X 91 LEU cc_start: 0.8634 (tp) cc_final: 0.8315 (mp) REVERT: X 145 GLU cc_start: 0.6730 (mt-10) cc_final: 0.6483 (mt-10) REVERT: X 206 MET cc_start: 0.6814 (mmm) cc_final: 0.6522 (mmm) REVERT: X 273 VAL cc_start: 0.7808 (t) cc_final: 0.7582 (t) REVERT: Y 131 GLU cc_start: 0.6130 (tt0) cc_final: 0.5863 (tt0) REVERT: Y 153 MET cc_start: 0.8487 (ptp) cc_final: 0.8261 (ptp) REVERT: Y 230 LEU cc_start: 0.7644 (pp) cc_final: 0.7034 (tp) REVERT: Z 40 LYS cc_start: 0.4440 (tppp) cc_final: 0.4052 (mmtm) REVERT: Z 151 THR cc_start: 0.6410 (p) cc_final: 0.6103 (t) REVERT: Z 178 MET cc_start: 0.8012 (ptt) cc_final: 0.7751 (ptm) REVERT: Z 270 LEU cc_start: 0.8209 (tp) cc_final: 0.7971 (tp) outliers start: 6 outliers final: 0 residues processed: 2175 average time/residue: 0.8903 time to fit residues: 3313.2459 Evaluate side-chains 1766 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1764 time to evaluate : 8.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1206 random chunks: chunk 392 optimal weight: 0.7980 chunk 1049 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 684 optimal weight: 30.0000 chunk 287 optimal weight: 10.0000 chunk 1166 optimal weight: 7.9990 chunk 968 optimal weight: 0.8980 chunk 540 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 385 optimal weight: 8.9990 chunk 612 optimal weight: 20.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1612 ASN A1886 GLN A1890 GLN A2045 GLN ** A2047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 622 ASN F 22 ASN G 333 ASN H 643 GLN H 740 ASN ** H 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H1027 HIS I 22 HIS ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 637 ASN ** I 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 985 ASN I1000 ASN I1133 HIS I1300 GLN J 581 HIS J 676 ASN ** J 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 874 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1080 ASN K1133 HIS L 194 GLN L 541 HIS L1223 GLN ** L1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1060 ASN ** Q 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 HIS U 36 GLN ** U 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 88 HIS ** W 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 173 GLN Z 256 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 98950 Z= 0.229 Angle : 0.623 14.700 134608 Z= 0.315 Chirality : 0.043 0.475 15519 Planarity : 0.005 0.068 17313 Dihedral : 5.268 79.101 13396 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.88 % Favored : 95.07 % Rotamer: Outliers : 0.04 % Allowed : 2.77 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.36 (0.08), residues: 12037 helix: 0.59 (0.07), residues: 4760 sheet: -0.32 (0.12), residues: 1694 loop : -0.88 (0.08), residues: 5583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP G 514 HIS 0.018 0.001 HIS W 43 PHE 0.036 0.002 PHE K 672 TYR 0.021 0.002 TYR L1254 ARG 0.016 0.000 ARG U 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2212 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 2208 time to evaluate : 8.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1455 GLU cc_start: 0.5025 (pt0) cc_final: 0.2908 (tp30) REVERT: A 1472 PHE cc_start: 0.2211 (p90) cc_final: 0.1878 (p90) REVERT: A 1473 ARG cc_start: 0.5203 (tmt170) cc_final: 0.3698 (mmm160) REVERT: A 1493 ARG cc_start: 0.2209 (mmm160) cc_final: 0.1545 (tpm170) REVERT: A 1550 GLU cc_start: 0.6240 (mm-30) cc_final: 0.5701 (mm-30) REVERT: A 1616 LYS cc_start: 0.3631 (pttp) cc_final: 0.3034 (pttp) REVERT: A 1707 ARG cc_start: 0.5334 (mtm-85) cc_final: 0.4041 (ttm-80) REVERT: A 1802 LYS cc_start: 0.3893 (tptt) cc_final: 0.3010 (mmmt) REVERT: A 1804 PHE cc_start: 0.1569 (p90) cc_final: 0.0862 (p90) REVERT: A 1827 GLN cc_start: 0.2896 (tp40) cc_final: 0.2495 (tp40) REVERT: A 1841 LEU cc_start: 0.4698 (mt) cc_final: 0.4366 (tt) REVERT: A 1894 MET cc_start: 0.3498 (pmm) cc_final: 0.2918 (mmp) REVERT: A 1913 MET cc_start: 0.4344 (tmm) cc_final: 0.3252 (tmm) REVERT: A 1915 ARG cc_start: 0.4489 (tpt90) cc_final: 0.3773 (ttp-170) REVERT: A 1940 GLN cc_start: 0.5234 (mm-40) cc_final: 0.4968 (mm-40) REVERT: A 1992 GLN cc_start: 0.6187 (mm-40) cc_final: 0.3916 (pt0) REVERT: E 207 MET cc_start: 0.3850 (mmm) cc_final: 0.2840 (tmm) REVERT: E 349 MET cc_start: 0.1594 (mtt) cc_final: 0.0725 (ppp) REVERT: E 364 ARG cc_start: 0.5466 (ttm110) cc_final: 0.5200 (ttm110) REVERT: E 409 ARG cc_start: 0.4119 (mtt180) cc_final: 0.2150 (tmt-80) REVERT: E 570 MET cc_start: 0.4716 (mtt) cc_final: 0.4102 (mmm) REVERT: F 42 MET cc_start: 0.2461 (mmt) cc_final: 0.2062 (ppp) REVERT: G 364 GLU cc_start: 0.7013 (pm20) cc_final: 0.6617 (pm20) REVERT: G 373 ASP cc_start: 0.6171 (m-30) cc_final: 0.5594 (m-30) REVERT: G 374 GLU cc_start: 0.5514 (mm-30) cc_final: 0.5191 (mm-30) REVERT: G 447 ARG cc_start: 0.5562 (tmt-80) cc_final: 0.5202 (tmt-80) REVERT: G 507 ARG cc_start: 0.7187 (ptm160) cc_final: 0.6751 (ptm-80) REVERT: G 556 ARG cc_start: 0.6334 (tpp-160) cc_final: 0.5750 (mmt-90) REVERT: G 577 GLN cc_start: 0.5835 (tt0) cc_final: 0.5123 (pp30) REVERT: H 81 HIS cc_start: 0.7461 (t-170) cc_final: 0.5849 (m-70) REVERT: H 86 LEU cc_start: 0.6968 (mt) cc_final: 0.6578 (mt) REVERT: H 90 LYS cc_start: 0.7379 (mttm) cc_final: 0.6758 (pttp) REVERT: H 91 MET cc_start: 0.7598 (tpp) cc_final: 0.7283 (tpp) REVERT: H 110 ARG cc_start: 0.5586 (tmt170) cc_final: 0.3958 (mmp-170) REVERT: H 359 VAL cc_start: 0.8494 (t) cc_final: 0.8190 (m) REVERT: H 467 ARG cc_start: 0.7381 (mmm-85) cc_final: 0.7037 (mmm160) REVERT: H 589 ASP cc_start: 0.7951 (t0) cc_final: 0.7606 (t0) REVERT: H 598 LYS cc_start: 0.7724 (tmtt) cc_final: 0.6732 (ttpp) REVERT: H 745 GLU cc_start: 0.7327 (tp30) cc_final: 0.7062 (tp30) REVERT: H 844 ASP cc_start: 0.5689 (p0) cc_final: 0.4888 (m-30) REVERT: H 849 GLN cc_start: 0.6975 (pt0) cc_final: 0.6614 (pt0) REVERT: H 900 ASP cc_start: 0.6785 (p0) cc_final: 0.6318 (m-30) REVERT: H 1156 MET cc_start: 0.6956 (mmm) cc_final: 0.6024 (mmm) REVERT: H 1320 GLU cc_start: 0.6008 (mt-10) cc_final: 0.5558 (mt-10) REVERT: H 1362 LEU cc_start: 0.7417 (tp) cc_final: 0.6915 (tp) REVERT: I 1 MET cc_start: 0.6883 (mtm) cc_final: 0.6210 (mtt) REVERT: I 30 GLU cc_start: 0.6382 (tp30) cc_final: 0.6099 (tp30) REVERT: I 130 GLU cc_start: 0.6300 (pt0) cc_final: 0.5761 (pt0) REVERT: I 149 ASP cc_start: 0.6800 (t70) cc_final: 0.6455 (t0) REVERT: I 169 ASP cc_start: 0.8489 (t70) cc_final: 0.8169 (t0) REVERT: I 328 TYR cc_start: 0.7436 (m-80) cc_final: 0.7236 (m-80) REVERT: I 467 ARG cc_start: 0.7413 (mtp85) cc_final: 0.6452 (mtp-110) REVERT: I 514 GLN cc_start: 0.7338 (tp40) cc_final: 0.6301 (tp40) REVERT: I 1025 LYS cc_start: 0.7034 (mmmm) cc_final: 0.6831 (mmmm) REVERT: I 1115 ARG cc_start: 0.6424 (mpt-90) cc_final: 0.5930 (mpt-90) REVERT: I 1150 MET cc_start: 0.5645 (mtp) cc_final: 0.5436 (mtp) REVERT: I 1250 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6292 (mt-10) REVERT: I 1294 ARG cc_start: 0.6574 (mmm-85) cc_final: 0.5848 (tpp-160) REVERT: I 1365 SER cc_start: 0.7433 (p) cc_final: 0.7053 (m) REVERT: J 126 THR cc_start: 0.5232 (t) cc_final: 0.4910 (t) REVERT: J 185 ARG cc_start: 0.6954 (ptp-170) cc_final: 0.6313 (ptp-110) REVERT: J 193 VAL cc_start: 0.9119 (m) cc_final: 0.8657 (p) REVERT: J 293 LYS cc_start: 0.7336 (tptp) cc_final: 0.6982 (mmtt) REVERT: J 475 MET cc_start: 0.7416 (mmm) cc_final: 0.6965 (mtt) REVERT: J 488 MET cc_start: 0.5855 (mmt) cc_final: 0.5490 (tpp) REVERT: J 507 ARG cc_start: 0.7709 (mtp-110) cc_final: 0.6972 (mtp-110) REVERT: J 628 ARG cc_start: 0.7430 (mtp85) cc_final: 0.7110 (mtp85) REVERT: J 638 MET cc_start: 0.6747 (mmp) cc_final: 0.6224 (mmm) REVERT: J 659 GLU cc_start: 0.6009 (pt0) cc_final: 0.5608 (pt0) REVERT: J 669 GLN cc_start: 0.6269 (mp10) cc_final: 0.5210 (mt0) REVERT: J 693 LEU cc_start: 0.8281 (mp) cc_final: 0.8050 (mt) REVERT: J 694 ASN cc_start: 0.8089 (p0) cc_final: 0.7791 (p0) REVERT: J 697 GLN cc_start: 0.6834 (mm110) cc_final: 0.5237 (mp10) REVERT: J 706 TYR cc_start: 0.7964 (m-80) cc_final: 0.7511 (m-80) REVERT: J 731 GLN cc_start: 0.7933 (pt0) cc_final: 0.7000 (pt0) REVERT: J 789 MET cc_start: 0.8233 (mmt) cc_final: 0.8032 (mmt) REVERT: J 880 PHE cc_start: 0.7516 (t80) cc_final: 0.7238 (t80) REVERT: J 962 GLU cc_start: 0.5762 (tp30) cc_final: 0.5137 (tp30) REVERT: J 963 PHE cc_start: 0.5646 (m-80) cc_final: 0.5312 (m-80) REVERT: J 1270 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6877 (mt-10) REVERT: J 1288 ARG cc_start: 0.6237 (mtp-110) cc_final: 0.6016 (mtp-110) REVERT: J 1348 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6647 (mt-10) REVERT: K 61 LEU cc_start: 0.7341 (mp) cc_final: 0.7103 (tp) REVERT: K 91 MET cc_start: 0.8552 (mtp) cc_final: 0.8271 (mtp) REVERT: K 115 MET cc_start: 0.7785 (mtt) cc_final: 0.7466 (mtt) REVERT: K 162 ARG cc_start: 0.5202 (mtm110) cc_final: 0.4998 (tpt-90) REVERT: K 240 LEU cc_start: 0.7932 (tp) cc_final: 0.7563 (tp) REVERT: K 259 THR cc_start: 0.7316 (p) cc_final: 0.7083 (t) REVERT: K 447 LYS cc_start: 0.7429 (ttmm) cc_final: 0.7026 (ttmt) REVERT: K 537 PHE cc_start: 0.7830 (m-80) cc_final: 0.7469 (m-80) REVERT: K 591 GLU cc_start: 0.6390 (tp30) cc_final: 0.6178 (tp30) REVERT: K 958 ARG cc_start: 0.6620 (mtp180) cc_final: 0.6296 (mmm-85) REVERT: K 966 TYR cc_start: 0.7009 (m-80) cc_final: 0.6655 (m-10) REVERT: K 993 ARG cc_start: 0.7676 (tpp80) cc_final: 0.7396 (mmm160) REVERT: K 1006 MET cc_start: 0.8015 (mtp) cc_final: 0.7763 (mtp) REVERT: K 1150 MET cc_start: 0.7210 (ptm) cc_final: 0.6275 (tmm) REVERT: K 1184 ASN cc_start: 0.8216 (m110) cc_final: 0.7914 (m110) REVERT: K 1206 ASP cc_start: 0.8004 (t0) cc_final: 0.7498 (t70) REVERT: L 64 VAL cc_start: 0.6038 (p) cc_final: 0.5453 (p) REVERT: L 140 ARG cc_start: 0.6595 (mmt180) cc_final: 0.6109 (mmt90) REVERT: L 141 GLU cc_start: 0.5936 (tm-30) cc_final: 0.5637 (tm-30) REVERT: L 241 LYS cc_start: 0.8360 (tptt) cc_final: 0.7917 (tptt) REVERT: L 268 LYS cc_start: 0.7580 (mmtp) cc_final: 0.7101 (ttpt) REVERT: L 302 TYR cc_start: 0.7848 (m-80) cc_final: 0.7422 (m-80) REVERT: L 382 LYS cc_start: 0.7395 (mtpp) cc_final: 0.7055 (ttpt) REVERT: L 475 MET cc_start: 0.5667 (mmp) cc_final: 0.3954 (tmm) REVERT: L 582 MET cc_start: 0.8220 (mmt) cc_final: 0.7942 (mmm) REVERT: L 656 LEU cc_start: 0.8072 (mp) cc_final: 0.7853 (mt) REVERT: L 1006 MET cc_start: 0.7751 (mmt) cc_final: 0.6695 (mmt) REVERT: L 1080 ASN cc_start: 0.7691 (t0) cc_final: 0.7387 (t0) REVERT: L 1092 SER cc_start: 0.8563 (m) cc_final: 0.8175 (t) REVERT: L 1106 MET cc_start: 0.7547 (mtp) cc_final: 0.7164 (mtt) REVERT: L 1150 MET cc_start: 0.4763 (tpp) cc_final: 0.3866 (tpp) REVERT: L 1219 GLU cc_start: 0.6499 (mp0) cc_final: 0.6232 (mp0) REVERT: L 1330 LEU cc_start: 0.8108 (mt) cc_final: 0.7764 (mp) REVERT: M 182 THR cc_start: 0.8839 (p) cc_final: 0.8467 (m) REVERT: M 183 LEU cc_start: 0.8818 (mt) cc_final: 0.8414 (mm) REVERT: M 223 MET cc_start: 0.7072 (ttp) cc_final: 0.6842 (ttp) REVERT: M 467 ARG cc_start: 0.7581 (mtp85) cc_final: 0.6794 (ttt180) REVERT: M 500 ARG cc_start: 0.5697 (mmm160) cc_final: 0.5207 (mmt180) REVERT: M 512 MET cc_start: 0.8212 (mtm) cc_final: 0.7776 (mtp) REVERT: M 675 ARG cc_start: 0.6278 (ptm160) cc_final: 0.5892 (ptm160) REVERT: M 732 VAL cc_start: 0.8577 (t) cc_final: 0.8132 (p) REVERT: M 803 ASN cc_start: 0.6633 (t0) cc_final: 0.6087 (t0) REVERT: M 863 ASP cc_start: 0.6853 (p0) cc_final: 0.5662 (m-30) REVERT: M 1022 LEU cc_start: 0.7614 (mt) cc_final: 0.7297 (mp) REVERT: M 1106 MET cc_start: 0.7566 (mtm) cc_final: 0.7299 (mtm) REVERT: M 1308 GLU cc_start: 0.6742 (pt0) cc_final: 0.6136 (mm-30) REVERT: N 61 LYS cc_start: 0.7805 (mttt) cc_final: 0.7395 (mttt) REVERT: O 62 LEU cc_start: 0.7976 (tp) cc_final: 0.7766 (tp) REVERT: Q 22 VAL cc_start: 0.6573 (t) cc_final: 0.6248 (t) REVERT: Q 43 MET cc_start: 0.4493 (mmm) cc_final: 0.4021 (mmp) REVERT: R 19 ARG cc_start: 0.5692 (ptp-110) cc_final: 0.4946 (mtt180) REVERT: R 73 THR cc_start: 0.4814 (p) cc_final: 0.4335 (m) REVERT: T 181 ARG cc_start: 0.6014 (ttp80) cc_final: 0.5426 (mtp-110) REVERT: U 55 THR cc_start: 0.7520 (m) cc_final: 0.7291 (m) REVERT: U 58 TYR cc_start: 0.8085 (t80) cc_final: 0.7704 (t80) REVERT: U 80 GLN cc_start: 0.5318 (tt0) cc_final: 0.4588 (mm-40) REVERT: U 131 GLU cc_start: 0.6802 (tt0) cc_final: 0.6404 (mt-10) REVERT: U 140 MET cc_start: 0.6921 (tpt) cc_final: 0.6399 (tpp) REVERT: U 148 GLN cc_start: 0.8290 (tt0) cc_final: 0.7768 (tt0) REVERT: U 153 MET cc_start: 0.7428 (tpp) cc_final: 0.7136 (tpp) REVERT: U 197 MET cc_start: 0.7411 (mtm) cc_final: 0.6779 (ttm) REVERT: U 234 CYS cc_start: 0.6491 (m) cc_final: 0.6115 (m) REVERT: U 279 ASP cc_start: 0.6590 (t0) cc_final: 0.6323 (t70) REVERT: U 298 LYS cc_start: 0.7569 (mmpt) cc_final: 0.6736 (mmmt) REVERT: V 244 GLU cc_start: 0.5738 (mm-30) cc_final: 0.4722 (mt-10) REVERT: X 91 LEU cc_start: 0.8719 (tp) cc_final: 0.8371 (mp) REVERT: X 145 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6577 (mm-30) REVERT: X 206 MET cc_start: 0.6936 (mmm) cc_final: 0.6483 (mmm) REVERT: Y 68 MET cc_start: 0.8041 (ptp) cc_final: 0.7605 (ptp) REVERT: Y 131 GLU cc_start: 0.6071 (tt0) cc_final: 0.5779 (tt0) REVERT: Y 153 MET cc_start: 0.8429 (ptp) cc_final: 0.8113 (ptp) REVERT: Y 186 ASP cc_start: 0.6277 (t70) cc_final: 0.6062 (t0) REVERT: Y 230 LEU cc_start: 0.7826 (pp) cc_final: 0.7135 (tp) REVERT: Z 40 LYS cc_start: 0.4504 (tppp) cc_final: 0.4060 (mmtm) REVERT: Z 63 TYR cc_start: 0.6427 (t80) cc_final: 0.5799 (t80) REVERT: Z 79 GLU cc_start: 0.5733 (tp30) cc_final: 0.5385 (tp30) REVERT: Z 90 ARG cc_start: 0.8196 (mmm160) cc_final: 0.7849 (mmm160) REVERT: Z 151 THR cc_start: 0.6399 (p) cc_final: 0.6104 (t) REVERT: Z 178 MET cc_start: 0.7982 (ptt) cc_final: 0.7733 (ptm) REVERT: Z 182 LYS cc_start: 0.6389 (mmtt) cc_final: 0.6135 (mmtt) outliers start: 4 outliers final: 0 residues processed: 2210 average time/residue: 0.9571 time to fit residues: 3640.5877 Evaluate side-chains 1774 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1774 time to evaluate : 8.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1206 random chunks: chunk 1124 optimal weight: 20.0000 chunk 131 optimal weight: 7.9990 chunk 664 optimal weight: 8.9990 chunk 852 optimal weight: 10.0000 chunk 660 optimal weight: 7.9990 chunk 982 optimal weight: 3.9990 chunk 651 optimal weight: 0.7980 chunk 1162 optimal weight: 0.6980 chunk 727 optimal weight: 5.9990 chunk 708 optimal weight: 20.0000 chunk 536 optimal weight: 0.0770 overall best weight: 2.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1599 GLN A1605 HIS ** A1688 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1886 GLN A1890 GLN ** A2045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2234 HIS C2234 HIS E 93 GLN E 243 GLN E 356 HIS E 622 ASN G 321 GLN H 484 GLN ** H 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 919 ASN H1000 ASN H1027 HIS H1133 HIS ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 637 ASN I 731 GLN I 748 HIS I 795 ASN ** I 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 985 ASN I1133 HIS ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 874 GLN ** J 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1120 ASN J1353 ASN K 526 ASN K1080 ASN K1133 HIS L 541 HIS L1023 GLN ** L1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 640 HIS M 915 HIS M1060 ASN M1133 HIS ** Q 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 HIS ** U 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 84 HIS ** W 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 96 ASN Y 173 GLN Z 34 HIS Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 98950 Z= 0.180 Angle : 0.600 14.731 134608 Z= 0.302 Chirality : 0.042 0.405 15519 Planarity : 0.005 0.069 17313 Dihedral : 5.110 80.126 13396 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.55 % Favored : 95.41 % Rotamer: Outliers : 0.07 % Allowed : 1.64 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.08), residues: 12037 helix: 0.66 (0.07), residues: 4809 sheet: -0.28 (0.12), residues: 1695 loop : -0.88 (0.08), residues: 5533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP G 514 HIS 0.017 0.001 HIS M 618 PHE 0.025 0.002 PHE X 272 TYR 0.021 0.001 TYR K1254 ARG 0.017 0.000 ARG G 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2210 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2203 time to evaluate : 8.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 PHE cc_start: 0.2425 (p90) cc_final: 0.2146 (p90) REVERT: A 1473 ARG cc_start: 0.5107 (tmt170) cc_final: 0.3729 (mmm160) REVERT: A 1493 ARG cc_start: 0.1907 (mmm160) cc_final: 0.1137 (tpm170) REVERT: A 1550 GLU cc_start: 0.6246 (mm-30) cc_final: 0.5631 (mm-30) REVERT: A 1707 ARG cc_start: 0.5324 (mtm-85) cc_final: 0.4034 (ttp-110) REVERT: A 1802 LYS cc_start: 0.3940 (tptt) cc_final: 0.3000 (mmmt) REVERT: A 1804 PHE cc_start: 0.1525 (p90) cc_final: 0.0856 (p90) REVERT: A 1827 GLN cc_start: 0.2235 (tp40) cc_final: 0.1923 (tp40) REVERT: A 1841 LEU cc_start: 0.4567 (mt) cc_final: 0.4162 (tt) REVERT: A 1894 MET cc_start: 0.3492 (pmm) cc_final: 0.2913 (mmp) REVERT: A 1913 MET cc_start: 0.4089 (tmm) cc_final: 0.3184 (tmm) REVERT: A 1915 ARG cc_start: 0.4351 (tpt90) cc_final: 0.3678 (ttm170) REVERT: A 1940 GLN cc_start: 0.5034 (mm-40) cc_final: 0.4779 (mm-40) REVERT: A 1981 TYR cc_start: 0.2990 (t80) cc_final: 0.2491 (t80) REVERT: A 1992 GLN cc_start: 0.6261 (mm-40) cc_final: 0.3936 (pt0) REVERT: C 2237 PHE cc_start: 0.4052 (m-10) cc_final: 0.3754 (m-80) REVERT: E 207 MET cc_start: 0.3817 (mmm) cc_final: 0.2892 (tmm) REVERT: E 349 MET cc_start: 0.1586 (mtt) cc_final: 0.0700 (ppp) REVERT: E 364 ARG cc_start: 0.5285 (ttm110) cc_final: 0.5060 (ttm110) REVERT: E 496 ARG cc_start: 0.5500 (ptp-170) cc_final: 0.5214 (ptt180) REVERT: E 630 PHE cc_start: 0.2055 (t80) cc_final: 0.1817 (t80) REVERT: F 42 MET cc_start: 0.2532 (mmt) cc_final: 0.2106 (ppp) REVERT: G 364 GLU cc_start: 0.6984 (pm20) cc_final: 0.6603 (pm20) REVERT: G 373 ASP cc_start: 0.6622 (m-30) cc_final: 0.6063 (m-30) REVERT: G 374 GLU cc_start: 0.5395 (mm-30) cc_final: 0.5068 (mm-30) REVERT: G 484 GLN cc_start: 0.7144 (tp-100) cc_final: 0.6909 (tp-100) REVERT: G 507 ARG cc_start: 0.7123 (ptm160) cc_final: 0.6794 (ptm-80) REVERT: G 543 SER cc_start: 0.7267 (m) cc_final: 0.7060 (m) REVERT: G 556 ARG cc_start: 0.6134 (tpp-160) cc_final: 0.5896 (mmt-90) REVERT: G 577 GLN cc_start: 0.5616 (tt0) cc_final: 0.5038 (pp30) REVERT: H 81 HIS cc_start: 0.7540 (t-170) cc_final: 0.6048 (m-70) REVERT: H 90 LYS cc_start: 0.7392 (mttm) cc_final: 0.6824 (pttp) REVERT: H 91 MET cc_start: 0.7616 (tpp) cc_final: 0.7348 (tpp) REVERT: H 110 ARG cc_start: 0.5622 (tmt170) cc_final: 0.4039 (mmp-170) REVERT: H 467 ARG cc_start: 0.7369 (mmm-85) cc_final: 0.7065 (mmm160) REVERT: H 844 ASP cc_start: 0.5418 (p0) cc_final: 0.4620 (m-30) REVERT: H 849 GLN cc_start: 0.6944 (pt0) cc_final: 0.6558 (pt0) REVERT: H 900 ASP cc_start: 0.6675 (p0) cc_final: 0.6196 (m-30) REVERT: H 1156 MET cc_start: 0.6915 (mmm) cc_final: 0.6091 (mmm) REVERT: H 1174 LEU cc_start: 0.8115 (mt) cc_final: 0.7612 (mt) REVERT: H 1320 GLU cc_start: 0.5916 (mt-10) cc_final: 0.5571 (mt-10) REVERT: H 1362 LEU cc_start: 0.7325 (tp) cc_final: 0.6844 (tp) REVERT: I 1 MET cc_start: 0.6866 (mtm) cc_final: 0.6197 (mtt) REVERT: I 30 GLU cc_start: 0.6303 (tp30) cc_final: 0.6088 (tp30) REVERT: I 130 GLU cc_start: 0.6250 (pt0) cc_final: 0.5717 (pt0) REVERT: I 169 ASP cc_start: 0.8481 (t70) cc_final: 0.8157 (t0) REVERT: I 467 ARG cc_start: 0.7392 (mtp85) cc_final: 0.6469 (mtp-110) REVERT: I 514 GLN cc_start: 0.7379 (tp40) cc_final: 0.6373 (tp40) REVERT: I 1115 ARG cc_start: 0.6392 (mpt-90) cc_final: 0.5950 (mpt-90) REVERT: I 1250 GLU cc_start: 0.6772 (mt-10) cc_final: 0.6500 (mt-10) REVERT: I 1265 TYR cc_start: 0.8131 (m-80) cc_final: 0.7838 (m-80) REVERT: I 1268 THR cc_start: 0.7201 (m) cc_final: 0.6930 (p) REVERT: I 1269 GLU cc_start: 0.7607 (tp30) cc_final: 0.7405 (tp30) REVERT: I 1282 ILE cc_start: 0.8081 (pt) cc_final: 0.7798 (pt) REVERT: I 1294 ARG cc_start: 0.6803 (mmm-85) cc_final: 0.6032 (tpp-160) REVERT: I 1365 SER cc_start: 0.7536 (p) cc_final: 0.7105 (m) REVERT: J 60 ARG cc_start: 0.5182 (mpt180) cc_final: 0.4659 (mpt180) REVERT: J 126 THR cc_start: 0.5154 (t) cc_final: 0.4847 (t) REVERT: J 185 ARG cc_start: 0.7008 (ptp-170) cc_final: 0.6391 (ptp-110) REVERT: J 193 VAL cc_start: 0.9109 (m) cc_final: 0.8642 (p) REVERT: J 293 LYS cc_start: 0.7199 (tptp) cc_final: 0.6910 (mmtt) REVERT: J 475 MET cc_start: 0.7310 (mmm) cc_final: 0.6788 (mtt) REVERT: J 488 MET cc_start: 0.5963 (mmt) cc_final: 0.5530 (tpp) REVERT: J 507 ARG cc_start: 0.7547 (mtp-110) cc_final: 0.6794 (mtp-110) REVERT: J 628 ARG cc_start: 0.7269 (mtp85) cc_final: 0.6919 (mtp85) REVERT: J 669 GLN cc_start: 0.5914 (mp10) cc_final: 0.5371 (mt0) REVERT: J 693 LEU cc_start: 0.8251 (mp) cc_final: 0.8026 (mt) REVERT: J 694 ASN cc_start: 0.8057 (p0) cc_final: 0.7775 (p0) REVERT: J 697 GLN cc_start: 0.6762 (mm110) cc_final: 0.5242 (mp10) REVERT: J 731 GLN cc_start: 0.7839 (pt0) cc_final: 0.6904 (pt0) REVERT: J 962 GLU cc_start: 0.5775 (tp30) cc_final: 0.5073 (tp30) REVERT: J 963 PHE cc_start: 0.5654 (m-80) cc_final: 0.5447 (m-80) REVERT: J 1066 LYS cc_start: 0.6661 (tttt) cc_final: 0.6437 (mttt) REVERT: J 1123 ARG cc_start: 0.6428 (tpp-160) cc_final: 0.5825 (tpp80) REVERT: J 1270 GLU cc_start: 0.7328 (mt-10) cc_final: 0.6928 (mt-10) REVERT: J 1348 GLU cc_start: 0.6900 (mt-10) cc_final: 0.6692 (mt-10) REVERT: K 61 LEU cc_start: 0.7324 (mp) cc_final: 0.7110 (tp) REVERT: K 91 MET cc_start: 0.8462 (mtp) cc_final: 0.8261 (mtp) REVERT: K 240 LEU cc_start: 0.7704 (tp) cc_final: 0.7283 (tp) REVERT: K 259 THR cc_start: 0.7217 (p) cc_final: 0.6998 (t) REVERT: K 447 LYS cc_start: 0.7383 (ttmm) cc_final: 0.6929 (ttmt) REVERT: K 537 PHE cc_start: 0.7822 (m-80) cc_final: 0.7479 (m-80) REVERT: K 578 ILE cc_start: 0.8338 (mm) cc_final: 0.8127 (mm) REVERT: K 591 GLU cc_start: 0.6511 (tp30) cc_final: 0.6266 (tp30) REVERT: K 918 TYR cc_start: 0.6746 (t80) cc_final: 0.6413 (t80) REVERT: K 958 ARG cc_start: 0.6514 (mtp180) cc_final: 0.6172 (mmm-85) REVERT: K 966 TYR cc_start: 0.6969 (m-80) cc_final: 0.6578 (m-10) REVERT: K 993 ARG cc_start: 0.7681 (tpp80) cc_final: 0.7377 (mmm160) REVERT: K 1006 MET cc_start: 0.8055 (mtp) cc_final: 0.7709 (mtp) REVERT: K 1043 GLU cc_start: 0.6674 (tp30) cc_final: 0.6194 (tp30) REVERT: K 1150 MET cc_start: 0.7038 (ptm) cc_final: 0.6793 (tmm) REVERT: K 1184 ASN cc_start: 0.8209 (m110) cc_final: 0.7932 (m110) REVERT: K 1206 ASP cc_start: 0.7970 (t0) cc_final: 0.7452 (t70) REVERT: L 64 VAL cc_start: 0.6022 (p) cc_final: 0.5354 (p) REVERT: L 140 ARG cc_start: 0.6607 (mmt180) cc_final: 0.6116 (mmt90) REVERT: L 141 GLU cc_start: 0.5897 (tm-30) cc_final: 0.5632 (tm-30) REVERT: L 241 LYS cc_start: 0.8394 (tptt) cc_final: 0.7879 (tptt) REVERT: L 268 LYS cc_start: 0.7787 (mmtp) cc_final: 0.7095 (ttpt) REVERT: L 302 TYR cc_start: 0.7855 (m-80) cc_final: 0.7430 (m-80) REVERT: L 382 LYS cc_start: 0.7379 (mtpp) cc_final: 0.7061 (ttpt) REVERT: L 475 MET cc_start: 0.5861 (mmp) cc_final: 0.3926 (tmm) REVERT: L 479 LEU cc_start: 0.7276 (mt) cc_final: 0.6794 (mt) REVERT: L 484 GLN cc_start: 0.7007 (mm110) cc_final: 0.6501 (mm110) REVERT: L 866 THR cc_start: 0.5391 (p) cc_final: 0.5126 (p) REVERT: L 892 VAL cc_start: 0.8350 (t) cc_final: 0.7826 (m) REVERT: L 930 LEU cc_start: 0.8026 (mt) cc_final: 0.7800 (mp) REVERT: L 1006 MET cc_start: 0.7815 (mmt) cc_final: 0.6695 (mmt) REVERT: L 1035 THR cc_start: 0.7097 (p) cc_final: 0.6823 (p) REVERT: L 1106 MET cc_start: 0.7492 (mtp) cc_final: 0.7179 (mtt) REVERT: L 1150 MET cc_start: 0.4769 (tpp) cc_final: 0.3854 (tpp) REVERT: L 1175 ILE cc_start: 0.8234 (pt) cc_final: 0.7709 (mt) REVERT: L 1219 GLU cc_start: 0.6495 (mp0) cc_final: 0.6259 (mp0) REVERT: L 1330 LEU cc_start: 0.8139 (mt) cc_final: 0.7541 (mp) REVERT: M 183 LEU cc_start: 0.8769 (mt) cc_final: 0.8504 (mm) REVERT: M 223 MET cc_start: 0.7037 (ttp) cc_final: 0.6819 (ttp) REVERT: M 296 VAL cc_start: 0.8009 (m) cc_final: 0.7036 (p) REVERT: M 324 ASP cc_start: 0.7383 (t0) cc_final: 0.7077 (t0) REVERT: M 467 ARG cc_start: 0.7642 (mtp85) cc_final: 0.6829 (ttt180) REVERT: M 500 ARG cc_start: 0.5629 (mmm160) cc_final: 0.5208 (mmt180) REVERT: M 512 MET cc_start: 0.8211 (mtm) cc_final: 0.7860 (mtp) REVERT: M 532 GLU cc_start: 0.7153 (tp30) cc_final: 0.6587 (tp30) REVERT: M 640 HIS cc_start: 0.6402 (OUTLIER) cc_final: 0.6159 (t-90) REVERT: M 675 ARG cc_start: 0.6227 (ptm160) cc_final: 0.5838 (ptm160) REVERT: M 803 ASN cc_start: 0.6535 (t0) cc_final: 0.6064 (t0) REVERT: M 863 ASP cc_start: 0.6831 (p0) cc_final: 0.5727 (m-30) REVERT: M 1022 LEU cc_start: 0.7606 (mt) cc_final: 0.7287 (mp) REVERT: M 1308 GLU cc_start: 0.6595 (pt0) cc_final: 0.6213 (mm-30) REVERT: N 31 GLU cc_start: 0.7454 (mp0) cc_final: 0.7246 (mp0) REVERT: N 61 LYS cc_start: 0.7780 (mttt) cc_final: 0.7287 (mttt) REVERT: O 62 LEU cc_start: 0.8085 (tp) cc_final: 0.7806 (tp) REVERT: Q 22 VAL cc_start: 0.6507 (t) cc_final: 0.6182 (t) REVERT: Q 43 MET cc_start: 0.4539 (mmm) cc_final: 0.4256 (mmp) REVERT: Q 46 LYS cc_start: 0.7146 (ptpt) cc_final: 0.6766 (ptmm) REVERT: R 19 ARG cc_start: 0.5653 (ptp-110) cc_final: 0.4959 (mtt180) REVERT: S 15 ASP cc_start: 0.5771 (t70) cc_final: 0.5391 (t70) REVERT: S 50 MET cc_start: 0.6637 (mtp) cc_final: 0.6374 (mtp) REVERT: S 54 PHE cc_start: 0.5618 (m-10) cc_final: 0.4782 (m-10) REVERT: T 181 ARG cc_start: 0.6014 (ttp80) cc_final: 0.5397 (mtp-110) REVERT: U 58 TYR cc_start: 0.8112 (t80) cc_final: 0.7752 (t80) REVERT: U 131 GLU cc_start: 0.6746 (tt0) cc_final: 0.6420 (mt-10) REVERT: U 140 MET cc_start: 0.6872 (tpt) cc_final: 0.6399 (tpp) REVERT: U 148 GLN cc_start: 0.8263 (tt0) cc_final: 0.7599 (tt0) REVERT: U 153 MET cc_start: 0.7403 (tpp) cc_final: 0.7157 (tpp) REVERT: U 197 MET cc_start: 0.7427 (mtm) cc_final: 0.6494 (ttm) REVERT: U 204 MET cc_start: 0.7710 (mtm) cc_final: 0.7437 (mtm) REVERT: U 235 GLN cc_start: 0.5845 (tp40) cc_final: 0.5294 (mm110) REVERT: U 279 ASP cc_start: 0.6736 (t0) cc_final: 0.6394 (t70) REVERT: U 298 LYS cc_start: 0.7396 (mmpt) cc_final: 0.6863 (mmmt) REVERT: W 21 VAL cc_start: 0.8125 (m) cc_final: 0.7773 (p) REVERT: W 166 MET cc_start: 0.7655 (mmm) cc_final: 0.7168 (mmm) REVERT: X 91 LEU cc_start: 0.8638 (tp) cc_final: 0.8300 (mp) REVERT: X 104 LYS cc_start: 0.6955 (mmpt) cc_final: 0.6338 (ttpp) REVERT: X 164 GLU cc_start: 0.6437 (mm-30) cc_final: 0.6019 (mm-30) REVERT: X 206 MET cc_start: 0.6953 (mmm) cc_final: 0.6612 (mmm) REVERT: X 273 VAL cc_start: 0.7612 (t) cc_final: 0.7411 (t) REVERT: Y 68 MET cc_start: 0.8105 (ptp) cc_final: 0.7529 (ptp) REVERT: Y 131 GLU cc_start: 0.6112 (tt0) cc_final: 0.5844 (tt0) REVERT: Y 153 MET cc_start: 0.8306 (ptp) cc_final: 0.7981 (ptp) REVERT: Y 186 ASP cc_start: 0.6231 (t70) cc_final: 0.6020 (t0) REVERT: Y 230 LEU cc_start: 0.7987 (pp) cc_final: 0.7166 (tp) REVERT: Y 239 MET cc_start: 0.7381 (mmm) cc_final: 0.6972 (mmm) REVERT: Z 40 LYS cc_start: 0.4385 (tppp) cc_final: 0.3933 (mmtm) REVERT: Z 63 TYR cc_start: 0.6290 (t80) cc_final: 0.5688 (t80) REVERT: Z 79 GLU cc_start: 0.5476 (tp30) cc_final: 0.5218 (tp30) REVERT: Z 151 THR cc_start: 0.6361 (p) cc_final: 0.6068 (t) REVERT: Z 272 ILE cc_start: 0.7271 (mm) cc_final: 0.6917 (mm) outliers start: 7 outliers final: 0 residues processed: 2206 average time/residue: 0.9013 time to fit residues: 3404.2076 Evaluate side-chains 1807 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1806 time to evaluate : 8.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1206 random chunks: chunk 719 optimal weight: 0.0770 chunk 464 optimal weight: 9.9990 chunk 694 optimal weight: 2.9990 chunk 350 optimal weight: 0.6980 chunk 228 optimal weight: 0.8980 chunk 225 optimal weight: 9.9990 chunk 739 optimal weight: 6.9990 chunk 791 optimal weight: 4.9990 chunk 574 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 913 optimal weight: 0.6980 overall best weight: 1.0740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1688 HIS ** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2234 HIS E 93 GLN E 243 GLN E 622 ASN F 22 ASN H 388 ASN ** H 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 643 GLN H 903 GLN H1027 HIS I 96 GLN ** I 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 637 ASN I 722 HIS I 748 HIS ** I 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1133 HIS ** J 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 311 ASN ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 581 HIS ** J 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 874 GLN ** J 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 919 ASN ** J1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1120 ASN ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 914 GLN K1133 HIS L 199 ASN L 422 ASN L 541 HIS L1080 ASN ** L1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1060 ASN M1133 HIS M1230 ASN ** Q 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 HIS ** T 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 173 GLN Y 297 ASN ** Z 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 165 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 98950 Z= 0.157 Angle : 0.587 15.029 134608 Z= 0.293 Chirality : 0.041 0.370 15519 Planarity : 0.004 0.068 17313 Dihedral : 4.937 80.666 13396 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 0.08 % Allowed : 1.14 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.08), residues: 12037 helix: 0.80 (0.08), residues: 4808 sheet: -0.26 (0.12), residues: 1701 loop : -0.81 (0.08), residues: 5528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.001 TRP G 514 HIS 0.016 0.001 HIS M 618 PHE 0.030 0.001 PHE K 672 TYR 0.029 0.001 TYR J 918 ARG 0.013 0.000 ARG S 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2253 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 2245 time to evaluate : 8.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 PHE cc_start: 0.2467 (p90) cc_final: 0.2229 (p90) REVERT: A 1473 ARG cc_start: 0.5087 (tmt170) cc_final: 0.3808 (mmm160) REVERT: A 1493 ARG cc_start: 0.2001 (mmm160) cc_final: 0.1102 (tpm170) REVERT: A 1503 LEU cc_start: 0.3686 (mt) cc_final: 0.3311 (mt) REVERT: A 1568 MET cc_start: 0.3726 (ptt) cc_final: 0.3075 (mmm) REVERT: A 1707 ARG cc_start: 0.5157 (mtm-85) cc_final: 0.4160 (ttp-110) REVERT: A 1802 LYS cc_start: 0.3779 (tptt) cc_final: 0.2884 (mmmt) REVERT: A 1804 PHE cc_start: 0.1437 (p90) cc_final: 0.0752 (p90) REVERT: A 1827 GLN cc_start: 0.2343 (tp40) cc_final: 0.2086 (tp40) REVERT: A 1841 LEU cc_start: 0.4544 (mt) cc_final: 0.4139 (tt) REVERT: A 1894 MET cc_start: 0.3495 (pmm) cc_final: 0.2957 (mmp) REVERT: A 1913 MET cc_start: 0.4157 (tmm) cc_final: 0.3103 (tmm) REVERT: A 1915 ARG cc_start: 0.4357 (tpt90) cc_final: 0.3688 (ttm110) REVERT: A 1940 GLN cc_start: 0.4879 (mm-40) cc_final: 0.4585 (mm-40) REVERT: A 1981 TYR cc_start: 0.2890 (t80) cc_final: 0.1978 (t80) REVERT: A 1992 GLN cc_start: 0.6268 (mm-40) cc_final: 0.3945 (pt0) REVERT: A 2234 HIS cc_start: 0.6853 (OUTLIER) cc_final: 0.5735 (t-90) REVERT: E 42 MET cc_start: 0.4016 (mtt) cc_final: 0.3744 (mtt) REVERT: E 207 MET cc_start: 0.3778 (mmm) cc_final: 0.2914 (tmm) REVERT: E 349 MET cc_start: 0.1475 (mtt) cc_final: 0.0674 (ppp) REVERT: E 364 ARG cc_start: 0.5291 (ttm110) cc_final: 0.5086 (ttm110) REVERT: E 496 ARG cc_start: 0.5339 (ptp-170) cc_final: 0.5084 (ptt180) REVERT: E 570 MET cc_start: 0.4843 (mtt) cc_final: 0.4408 (mmm) REVERT: F 42 MET cc_start: 0.2393 (mmt) cc_final: 0.2056 (ppp) REVERT: G 8 ASP cc_start: 0.7801 (t70) cc_final: 0.7570 (t70) REVERT: G 364 GLU cc_start: 0.6848 (pm20) cc_final: 0.6501 (pm20) REVERT: G 373 ASP cc_start: 0.6295 (m-30) cc_final: 0.5794 (m-30) REVERT: G 374 GLU cc_start: 0.5307 (mm-30) cc_final: 0.5036 (mm-30) REVERT: G 507 ARG cc_start: 0.7299 (ptm160) cc_final: 0.7061 (ptm-80) REVERT: G 543 SER cc_start: 0.7139 (m) cc_final: 0.6917 (m) REVERT: G 577 GLN cc_start: 0.5561 (tt0) cc_final: 0.5037 (pp30) REVERT: H 81 HIS cc_start: 0.7497 (t-170) cc_final: 0.6064 (m-70) REVERT: H 90 LYS cc_start: 0.7408 (mttm) cc_final: 0.6784 (pttp) REVERT: H 91 MET cc_start: 0.7678 (tpp) cc_final: 0.7324 (tpp) REVERT: H 110 ARG cc_start: 0.5502 (tmt170) cc_final: 0.3989 (mmp-170) REVERT: H 467 ARG cc_start: 0.7327 (mmm-85) cc_final: 0.7049 (mmm160) REVERT: H 844 ASP cc_start: 0.5313 (p0) cc_final: 0.4577 (m-30) REVERT: H 849 GLN cc_start: 0.6883 (pt0) cc_final: 0.6537 (pt0) REVERT: H 1106 MET cc_start: 0.7621 (mtp) cc_final: 0.7269 (mtm) REVERT: H 1156 MET cc_start: 0.6909 (mmm) cc_final: 0.6108 (mmm) REVERT: H 1320 GLU cc_start: 0.5924 (mt-10) cc_final: 0.5549 (mt-10) REVERT: H 1362 LEU cc_start: 0.7277 (tp) cc_final: 0.6801 (tp) REVERT: I 1 MET cc_start: 0.6845 (mtm) cc_final: 0.6545 (mtt) REVERT: I 30 GLU cc_start: 0.6114 (tp30) cc_final: 0.5847 (tm-30) REVERT: I 130 GLU cc_start: 0.6214 (pt0) cc_final: 0.5636 (pt0) REVERT: I 169 ASP cc_start: 0.8474 (t70) cc_final: 0.8114 (t0) REVERT: I 467 ARG cc_start: 0.7325 (mtp85) cc_final: 0.6381 (mtp-110) REVERT: I 514 GLN cc_start: 0.7357 (tp40) cc_final: 0.6336 (tp40) REVERT: I 970 ASP cc_start: 0.8531 (p0) cc_final: 0.8314 (p0) REVERT: I 1115 ARG cc_start: 0.6370 (mpt-90) cc_final: 0.5940 (mpt-90) REVERT: I 1250 GLU cc_start: 0.6767 (mt-10) cc_final: 0.6495 (mt-10) REVERT: I 1265 TYR cc_start: 0.8105 (m-80) cc_final: 0.7844 (m-80) REVERT: I 1269 GLU cc_start: 0.7581 (tp30) cc_final: 0.7360 (tp30) REVERT: I 1282 ILE cc_start: 0.8108 (pt) cc_final: 0.7787 (pt) REVERT: I 1294 ARG cc_start: 0.6781 (mmm-85) cc_final: 0.6044 (tpp-160) REVERT: I 1365 SER cc_start: 0.7554 (p) cc_final: 0.7104 (m) REVERT: J 185 ARG cc_start: 0.7003 (ptp-170) cc_final: 0.6393 (ptp-110) REVERT: J 193 VAL cc_start: 0.9074 (m) cc_final: 0.8614 (p) REVERT: J 293 LYS cc_start: 0.7179 (tptp) cc_final: 0.6836 (mmmt) REVERT: J 358 ASP cc_start: 0.7388 (t70) cc_final: 0.6775 (p0) REVERT: J 407 TYR cc_start: 0.7683 (p90) cc_final: 0.7403 (p90) REVERT: J 475 MET cc_start: 0.7259 (mmm) cc_final: 0.6672 (mtt) REVERT: J 488 MET cc_start: 0.5959 (mmt) cc_final: 0.5582 (tpp) REVERT: J 507 ARG cc_start: 0.7503 (mtp-110) cc_final: 0.6696 (mtp-110) REVERT: J 614 ASP cc_start: 0.6614 (t0) cc_final: 0.6347 (t0) REVERT: J 628 ARG cc_start: 0.7524 (mtp85) cc_final: 0.7112 (mtp85) REVERT: J 669 GLN cc_start: 0.5950 (mp10) cc_final: 0.5365 (mt0) REVERT: J 694 ASN cc_start: 0.7842 (p0) cc_final: 0.7506 (p0) REVERT: J 697 GLN cc_start: 0.6525 (mm110) cc_final: 0.4957 (mp10) REVERT: J 918 TYR cc_start: 0.6755 (t80) cc_final: 0.6548 (t80) REVERT: J 962 GLU cc_start: 0.5804 (tp30) cc_final: 0.5094 (tp30) REVERT: J 963 PHE cc_start: 0.5635 (m-80) cc_final: 0.5361 (m-80) REVERT: J 1066 LYS cc_start: 0.6667 (tttt) cc_final: 0.6435 (mttt) REVERT: J 1270 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6878 (mt-10) REVERT: K 63 TRP cc_start: 0.6887 (m100) cc_final: 0.6415 (m100) REVERT: K 240 LEU cc_start: 0.7630 (tp) cc_final: 0.7274 (tp) REVERT: K 382 LYS cc_start: 0.6336 (tptt) cc_final: 0.6068 (tptt) REVERT: K 447 LYS cc_start: 0.7648 (ttmm) cc_final: 0.7360 (tppp) REVERT: K 537 PHE cc_start: 0.7781 (m-80) cc_final: 0.7448 (m-80) REVERT: K 958 ARG cc_start: 0.6529 (mtp180) cc_final: 0.6157 (mmm-85) REVERT: K 966 TYR cc_start: 0.7006 (m-80) cc_final: 0.6545 (m-10) REVERT: K 993 ARG cc_start: 0.7635 (tpp80) cc_final: 0.7364 (mmm160) REVERT: K 1006 MET cc_start: 0.8015 (mtp) cc_final: 0.7699 (mtp) REVERT: K 1043 GLU cc_start: 0.6645 (tp30) cc_final: 0.6183 (tp30) REVERT: K 1150 MET cc_start: 0.7354 (ptm) cc_final: 0.7002 (tmm) REVERT: K 1184 ASN cc_start: 0.8228 (m110) cc_final: 0.7959 (m110) REVERT: K 1206 ASP cc_start: 0.8078 (t0) cc_final: 0.7667 (t70) REVERT: L 64 VAL cc_start: 0.6026 (p) cc_final: 0.5348 (p) REVERT: L 241 LYS cc_start: 0.8298 (tptt) cc_final: 0.7886 (tptt) REVERT: L 268 LYS cc_start: 0.7583 (mmtp) cc_final: 0.7029 (ttpt) REVERT: L 285 SER cc_start: 0.7590 (p) cc_final: 0.7230 (t) REVERT: L 302 TYR cc_start: 0.7805 (m-80) cc_final: 0.7367 (m-80) REVERT: L 475 MET cc_start: 0.5823 (mmp) cc_final: 0.3812 (tmm) REVERT: L 479 LEU cc_start: 0.7283 (mt) cc_final: 0.6774 (mt) REVERT: L 484 GLN cc_start: 0.6868 (mm110) cc_final: 0.6402 (mm110) REVERT: L 506 PRO cc_start: 0.8191 (Cg_exo) cc_final: 0.7947 (Cg_endo) REVERT: L 878 GLU cc_start: 0.7268 (tp30) cc_final: 0.7000 (tp30) REVERT: L 881 LEU cc_start: 0.6820 (mt) cc_final: 0.6587 (mp) REVERT: L 918 TYR cc_start: 0.6548 (t80) cc_final: 0.5467 (t80) REVERT: L 1006 MET cc_start: 0.7846 (mmt) cc_final: 0.6781 (mmt) REVERT: L 1035 THR cc_start: 0.6976 (p) cc_final: 0.6740 (p) REVERT: L 1106 MET cc_start: 0.7674 (mtp) cc_final: 0.7290 (mtt) REVERT: L 1129 ARG cc_start: 0.7405 (mmm160) cc_final: 0.6929 (mtp85) REVERT: L 1175 ILE cc_start: 0.8207 (pt) cc_final: 0.7697 (mt) REVERT: L 1330 LEU cc_start: 0.8137 (mt) cc_final: 0.7550 (mp) REVERT: L 1338 LYS cc_start: 0.7255 (mtmm) cc_final: 0.7033 (mtmm) REVERT: M 139 LEU cc_start: 0.6663 (tp) cc_final: 0.6444 (tt) REVERT: M 172 GLU cc_start: 0.7232 (tp30) cc_final: 0.7018 (tp30) REVERT: M 296 VAL cc_start: 0.7773 (m) cc_final: 0.7090 (p) REVERT: M 467 ARG cc_start: 0.7580 (mtp85) cc_final: 0.6822 (ttt180) REVERT: M 500 ARG cc_start: 0.5713 (mmm160) cc_final: 0.5237 (mmt180) REVERT: M 512 MET cc_start: 0.8254 (mtm) cc_final: 0.7831 (mtp) REVERT: M 638 MET cc_start: 0.7706 (mmm) cc_final: 0.7420 (mmm) REVERT: M 675 ARG cc_start: 0.6058 (ptm160) cc_final: 0.5752 (ptm160) REVERT: M 786 LEU cc_start: 0.7138 (mm) cc_final: 0.6864 (mt) REVERT: M 803 ASN cc_start: 0.6513 (t0) cc_final: 0.6037 (t0) REVERT: M 863 ASP cc_start: 0.6809 (p0) cc_final: 0.5788 (m-30) REVERT: M 1133 HIS cc_start: 0.4235 (OUTLIER) cc_final: 0.3984 (t70) REVERT: M 1308 GLU cc_start: 0.6313 (pt0) cc_final: 0.6061 (mm-30) REVERT: N 43 MET cc_start: 0.6550 (mmm) cc_final: 0.6213 (mmm) REVERT: N 65 LEU cc_start: 0.7949 (mt) cc_final: 0.7656 (mt) REVERT: Q 22 VAL cc_start: 0.6516 (t) cc_final: 0.6134 (t) REVERT: Q 43 MET cc_start: 0.4502 (mmm) cc_final: 0.4225 (mmp) REVERT: Q 46 LYS cc_start: 0.7026 (ptpt) cc_final: 0.6659 (ptmm) REVERT: R 19 ARG cc_start: 0.5236 (ptp-110) cc_final: 0.5018 (mtt180) REVERT: S 15 ASP cc_start: 0.5669 (t70) cc_final: 0.5215 (t70) REVERT: S 50 MET cc_start: 0.6687 (mtp) cc_final: 0.6483 (mtm) REVERT: S 54 PHE cc_start: 0.5634 (m-10) cc_final: 0.4792 (m-10) REVERT: T 137 THR cc_start: 0.7201 (p) cc_final: 0.6751 (t) REVERT: T 177 GLU cc_start: 0.5704 (pt0) cc_final: 0.5468 (pt0) REVERT: T 181 ARG cc_start: 0.5995 (ttp80) cc_final: 0.5389 (mtp-110) REVERT: U 55 THR cc_start: 0.7294 (m) cc_final: 0.7076 (m) REVERT: U 58 TYR cc_start: 0.8126 (t80) cc_final: 0.7712 (t80) REVERT: U 131 GLU cc_start: 0.6693 (tt0) cc_final: 0.6374 (mt-10) REVERT: U 140 MET cc_start: 0.6809 (tpt) cc_final: 0.6289 (tpp) REVERT: U 148 GLN cc_start: 0.8220 (tt0) cc_final: 0.7590 (tt0) REVERT: U 153 MET cc_start: 0.7419 (tpp) cc_final: 0.7141 (tpp) REVERT: U 197 MET cc_start: 0.7321 (mtm) cc_final: 0.6504 (ttm) REVERT: U 235 GLN cc_start: 0.5877 (tp40) cc_final: 0.5102 (mm-40) REVERT: U 298 LYS cc_start: 0.7396 (mmpt) cc_final: 0.6859 (mmmt) REVERT: V 136 TRP cc_start: 0.6366 (m-10) cc_final: 0.5706 (m-10) REVERT: V 242 ASP cc_start: 0.6689 (m-30) cc_final: 0.6025 (m-30) REVERT: V 267 ARG cc_start: 0.6848 (mtt-85) cc_final: 0.6240 (tpp80) REVERT: W 87 LEU cc_start: 0.7476 (tp) cc_final: 0.7152 (tp) REVERT: W 166 MET cc_start: 0.7236 (mmm) cc_final: 0.6642 (mmm) REVERT: W 197 GLU cc_start: 0.6825 (tt0) cc_final: 0.5799 (pp20) REVERT: W 268 GLU cc_start: 0.6079 (mp0) cc_final: 0.5632 (mp0) REVERT: X 46 LEU cc_start: 0.8254 (tp) cc_final: 0.8044 (tp) REVERT: X 91 LEU cc_start: 0.8588 (tp) cc_final: 0.8342 (mp) REVERT: X 101 THR cc_start: 0.6446 (m) cc_final: 0.5978 (m) REVERT: X 132 LEU cc_start: 0.7551 (tp) cc_final: 0.6908 (tt) REVERT: X 164 GLU cc_start: 0.6348 (mm-30) cc_final: 0.5878 (mm-30) REVERT: X 206 MET cc_start: 0.6914 (mmm) cc_final: 0.6497 (mmm) REVERT: X 273 VAL cc_start: 0.7669 (t) cc_final: 0.7469 (t) REVERT: Y 68 MET cc_start: 0.7933 (ptp) cc_final: 0.7338 (ptp) REVERT: Y 131 GLU cc_start: 0.6448 (tt0) cc_final: 0.6166 (tt0) REVERT: Y 230 LEU cc_start: 0.7844 (pp) cc_final: 0.7203 (tp) REVERT: Y 267 ARG cc_start: 0.5936 (ttm170) cc_final: 0.5482 (mtm180) REVERT: Z 23 LEU cc_start: 0.6799 (pp) cc_final: 0.6487 (pt) REVERT: Z 40 LYS cc_start: 0.4473 (tppp) cc_final: 0.4081 (mmtm) REVERT: Z 63 TYR cc_start: 0.5988 (t80) cc_final: 0.5563 (t80) REVERT: Z 79 GLU cc_start: 0.5553 (tp30) cc_final: 0.5278 (tp30) REVERT: Z 90 ARG cc_start: 0.7971 (mmm160) cc_final: 0.7681 (mmm160) REVERT: Z 178 MET cc_start: 0.7430 (ptm) cc_final: 0.7156 (ptm) REVERT: Z 182 LYS cc_start: 0.6144 (mmtt) cc_final: 0.5867 (mmtt) REVERT: Z 272 ILE cc_start: 0.7244 (mm) cc_final: 0.6923 (mm) REVERT: Z 282 PHE cc_start: 0.5467 (m-80) cc_final: 0.5216 (m-80) outliers start: 8 outliers final: 1 residues processed: 2249 average time/residue: 0.9161 time to fit residues: 3532.4477 Evaluate side-chains 1818 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1815 time to evaluate : 8.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1206 random chunks: chunk 1057 optimal weight: 3.9990 chunk 1113 optimal weight: 5.9990 chunk 1016 optimal weight: 8.9990 chunk 1083 optimal weight: 5.9990 chunk 651 optimal weight: 2.9990 chunk 471 optimal weight: 20.0000 chunk 850 optimal weight: 0.0040 chunk 332 optimal weight: 4.9990 chunk 978 optimal weight: 20.0000 chunk 1024 optimal weight: 20.0000 chunk 1079 optimal weight: 20.0000 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1464 GLN ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1856 GLN A1886 GLN A1890 GLN ** A1903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 243 GLN E 356 HIS G 321 GLN ** H 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1027 HIS I 637 ASN I 748 HIS ** I 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1027 HIS I1133 HIS ** J 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 676 ASN ** J 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 874 GLN ** J 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 969 HIS ** J1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1120 ASN K 94 HIS ** K 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1133 HIS L 199 ASN L 541 HIS L 618 HIS ** L 981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1080 ASN L1223 GLN ** L1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1230 ASN ** Q 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 HIS T 79 HIS ** T 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 173 GLN ** W 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 7 ASN Y 297 ASN Z 150 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 98950 Z= 0.208 Angle : 0.621 14.442 134608 Z= 0.310 Chirality : 0.043 0.456 15519 Planarity : 0.005 0.097 17313 Dihedral : 4.999 79.096 13396 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.75 % Favored : 95.21 % Rotamer: Outliers : 0.06 % Allowed : 0.63 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.08), residues: 12037 helix: 0.74 (0.08), residues: 4817 sheet: -0.31 (0.12), residues: 1686 loop : -0.83 (0.08), residues: 5534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP G 514 HIS 0.015 0.001 HIS M 618 PHE 0.040 0.002 PHE E 247 TYR 0.023 0.001 TYR L1265 ARG 0.012 0.000 ARG W 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2130 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2124 time to evaluate : 8.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 PHE cc_start: 0.2364 (p90) cc_final: 0.2075 (p90) REVERT: A 1473 ARG cc_start: 0.4945 (tmt170) cc_final: 0.3682 (mmm160) REVERT: A 1503 LEU cc_start: 0.3515 (mt) cc_final: 0.3146 (mt) REVERT: A 1550 GLU cc_start: 0.6498 (mm-30) cc_final: 0.6235 (mm-30) REVERT: A 1568 MET cc_start: 0.3866 (ptt) cc_final: 0.3058 (mmm) REVERT: A 1707 ARG cc_start: 0.4982 (mtm-85) cc_final: 0.3970 (ttp-110) REVERT: A 1802 LYS cc_start: 0.3598 (tptt) cc_final: 0.2582 (mmmt) REVERT: A 1804 PHE cc_start: 0.1515 (p90) cc_final: 0.0805 (p90) REVERT: A 1827 GLN cc_start: 0.2084 (tp40) cc_final: 0.1852 (tp40) REVERT: A 1841 LEU cc_start: 0.4562 (mt) cc_final: 0.4158 (tt) REVERT: A 1894 MET cc_start: 0.3651 (pmm) cc_final: 0.3037 (mmp) REVERT: A 1913 MET cc_start: 0.3851 (tmm) cc_final: 0.3236 (tmm) REVERT: A 1915 ARG cc_start: 0.4349 (tpt90) cc_final: 0.3656 (ttm110) REVERT: A 1940 GLN cc_start: 0.4886 (mm-40) cc_final: 0.4580 (mm-40) REVERT: A 1981 TYR cc_start: 0.2995 (t80) cc_final: 0.2476 (t80) REVERT: A 1992 GLN cc_start: 0.6272 (mm-40) cc_final: 0.3963 (pt0) REVERT: C 2237 PHE cc_start: 0.4006 (m-10) cc_final: 0.3593 (m-80) REVERT: E 35 LEU cc_start: 0.6987 (mt) cc_final: 0.6493 (mt) REVERT: E 207 MET cc_start: 0.3828 (mmm) cc_final: 0.2964 (tmm) REVERT: E 349 MET cc_start: 0.1460 (mtt) cc_final: 0.0605 (ppp) REVERT: E 364 ARG cc_start: 0.5287 (ttm110) cc_final: 0.5075 (ttm110) REVERT: F 42 MET cc_start: 0.2201 (mmt) cc_final: 0.1817 (ppp) REVERT: G 124 MET cc_start: 0.5965 (pmm) cc_final: 0.5458 (pmm) REVERT: G 364 GLU cc_start: 0.6828 (pm20) cc_final: 0.6505 (pm20) REVERT: G 373 ASP cc_start: 0.6229 (m-30) cc_final: 0.5560 (m-30) REVERT: G 374 GLU cc_start: 0.5374 (mm-30) cc_final: 0.5116 (mm-30) REVERT: G 389 ARG cc_start: 0.6563 (mpt90) cc_final: 0.5844 (mmt180) REVERT: G 507 ARG cc_start: 0.7319 (ptm160) cc_final: 0.7104 (ptm-80) REVERT: G 543 SER cc_start: 0.7234 (m) cc_final: 0.7024 (m) REVERT: G 577 GLN cc_start: 0.5613 (tt0) cc_final: 0.5053 (pp30) REVERT: H 8 GLU cc_start: 0.7677 (mp0) cc_final: 0.7390 (mp0) REVERT: H 81 HIS cc_start: 0.7533 (t-170) cc_final: 0.5993 (m-70) REVERT: H 90 LYS cc_start: 0.7385 (mttm) cc_final: 0.6756 (pttp) REVERT: H 91 MET cc_start: 0.7673 (tpp) cc_final: 0.7262 (tpp) REVERT: H 110 ARG cc_start: 0.5221 (tmt170) cc_final: 0.3719 (mmp-170) REVERT: H 467 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.7038 (mmm160) REVERT: H 792 MET cc_start: 0.8307 (tpp) cc_final: 0.8047 (tpp) REVERT: H 844 ASP cc_start: 0.5537 (p0) cc_final: 0.4805 (m-30) REVERT: H 849 GLN cc_start: 0.6893 (pt0) cc_final: 0.6559 (pt0) REVERT: H 1106 MET cc_start: 0.7816 (mtp) cc_final: 0.7477 (mtm) REVERT: H 1156 MET cc_start: 0.6578 (mmm) cc_final: 0.5822 (mmm) REVERT: H 1291 ASP cc_start: 0.5790 (m-30) cc_final: 0.5585 (m-30) REVERT: H 1320 GLU cc_start: 0.6025 (mt-10) cc_final: 0.5663 (mt-10) REVERT: H 1362 LEU cc_start: 0.7345 (tp) cc_final: 0.6848 (tp) REVERT: I 1 MET cc_start: 0.6850 (mtm) cc_final: 0.6525 (mtt) REVERT: I 30 GLU cc_start: 0.6135 (tp30) cc_final: 0.5854 (tm-30) REVERT: I 169 ASP cc_start: 0.8480 (t70) cc_final: 0.8142 (t0) REVERT: I 467 ARG cc_start: 0.7379 (mtp85) cc_final: 0.6478 (mtp-110) REVERT: I 514 GLN cc_start: 0.7377 (tp40) cc_final: 0.6389 (tp40) REVERT: I 760 MET cc_start: 0.8537 (mmt) cc_final: 0.8109 (mmm) REVERT: I 970 ASP cc_start: 0.8506 (p0) cc_final: 0.8289 (p0) REVERT: I 1250 GLU cc_start: 0.6599 (mt-10) cc_final: 0.6332 (mt-10) REVERT: I 1265 TYR cc_start: 0.8175 (m-80) cc_final: 0.7963 (m-80) REVERT: I 1294 ARG cc_start: 0.6754 (mmm-85) cc_final: 0.6014 (tpp-160) REVERT: I 1365 SER cc_start: 0.7578 (p) cc_final: 0.7084 (m) REVERT: J 185 ARG cc_start: 0.6984 (ptp-170) cc_final: 0.6365 (ptp-110) REVERT: J 193 VAL cc_start: 0.9091 (m) cc_final: 0.8644 (p) REVERT: J 358 ASP cc_start: 0.7378 (t70) cc_final: 0.6755 (p0) REVERT: J 475 MET cc_start: 0.7315 (mmm) cc_final: 0.6871 (mtt) REVERT: J 488 MET cc_start: 0.5927 (mmt) cc_final: 0.5484 (tpp) REVERT: J 507 ARG cc_start: 0.7477 (mtp-110) cc_final: 0.6657 (mtp-110) REVERT: J 614 ASP cc_start: 0.6707 (t0) cc_final: 0.6507 (t0) REVERT: J 628 ARG cc_start: 0.7390 (mtp85) cc_final: 0.6962 (mtp85) REVERT: J 669 GLN cc_start: 0.5913 (mp10) cc_final: 0.5412 (mt0) REVERT: J 694 ASN cc_start: 0.7834 (p0) cc_final: 0.7525 (p0) REVERT: J 697 GLN cc_start: 0.6677 (mm110) cc_final: 0.5093 (mp10) REVERT: J 962 GLU cc_start: 0.5642 (tp30) cc_final: 0.4835 (tp30) REVERT: J 963 PHE cc_start: 0.5540 (m-80) cc_final: 0.5015 (m-80) REVERT: J 1066 LYS cc_start: 0.6749 (tttt) cc_final: 0.6462 (mttt) REVERT: J 1270 GLU cc_start: 0.7279 (mt-10) cc_final: 0.6875 (mt-10) REVERT: J 1324 ILE cc_start: 0.8628 (tp) cc_final: 0.8418 (tt) REVERT: K 240 LEU cc_start: 0.7667 (tp) cc_final: 0.7266 (tp) REVERT: K 382 LYS cc_start: 0.6796 (tptt) cc_final: 0.6498 (tptt) REVERT: K 447 LYS cc_start: 0.7215 (ttmm) cc_final: 0.6858 (tttm) REVERT: K 537 PHE cc_start: 0.7838 (m-80) cc_final: 0.7575 (m-80) REVERT: K 820 MET cc_start: 0.5868 (mtm) cc_final: 0.5562 (mtm) REVERT: K 958 ARG cc_start: 0.6632 (mtp180) cc_final: 0.6283 (mmm-85) REVERT: K 966 TYR cc_start: 0.7004 (m-80) cc_final: 0.6629 (m-10) REVERT: K 993 ARG cc_start: 0.7686 (tpp80) cc_final: 0.7365 (mmm160) REVERT: K 1006 MET cc_start: 0.8136 (mtp) cc_final: 0.7824 (mtp) REVERT: K 1150 MET cc_start: 0.7309 (ptm) cc_final: 0.6910 (tmm) REVERT: K 1184 ASN cc_start: 0.8229 (m110) cc_final: 0.7913 (m110) REVERT: K 1206 ASP cc_start: 0.8083 (t0) cc_final: 0.7685 (t70) REVERT: K 1348 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7351 (mm-30) REVERT: L 64 VAL cc_start: 0.6029 (p) cc_final: 0.5344 (p) REVERT: L 241 LYS cc_start: 0.8679 (tptt) cc_final: 0.8047 (tptt) REVERT: L 268 LYS cc_start: 0.7612 (mmtp) cc_final: 0.7030 (ttpt) REVERT: L 302 TYR cc_start: 0.7821 (m-80) cc_final: 0.7379 (m-80) REVERT: L 484 GLN cc_start: 0.6883 (mm110) cc_final: 0.6438 (mm110) REVERT: L 537 PHE cc_start: 0.7358 (m-80) cc_final: 0.6819 (m-80) REVERT: L 622 ASP cc_start: 0.5972 (p0) cc_final: 0.5751 (p0) REVERT: L 878 GLU cc_start: 0.7225 (tp30) cc_final: 0.6901 (tp30) REVERT: L 881 LEU cc_start: 0.6891 (mt) cc_final: 0.6609 (mp) REVERT: L 892 VAL cc_start: 0.8332 (t) cc_final: 0.7772 (m) REVERT: L 918 TYR cc_start: 0.6654 (t80) cc_final: 0.5556 (t80) REVERT: L 945 ASN cc_start: 0.7303 (t0) cc_final: 0.6974 (t0) REVERT: L 1006 MET cc_start: 0.7861 (mmt) cc_final: 0.6728 (mmt) REVERT: L 1106 MET cc_start: 0.7755 (mtp) cc_final: 0.7506 (mtt) REVERT: L 1330 LEU cc_start: 0.8163 (mt) cc_final: 0.7600 (mp) REVERT: M 46 TYR cc_start: 0.5306 (t80) cc_final: 0.5079 (t80) REVERT: M 172 GLU cc_start: 0.7252 (tp30) cc_final: 0.7020 (tp30) REVERT: M 467 ARG cc_start: 0.7587 (mtp85) cc_final: 0.6758 (ttt180) REVERT: M 500 ARG cc_start: 0.5708 (mmm160) cc_final: 0.5181 (mmt180) REVERT: M 512 MET cc_start: 0.8312 (mtm) cc_final: 0.7832 (mtp) REVERT: M 532 GLU cc_start: 0.7409 (tp30) cc_final: 0.6732 (tp30) REVERT: M 675 ARG cc_start: 0.6092 (ptm160) cc_final: 0.5802 (ptm160) REVERT: M 786 LEU cc_start: 0.7008 (mm) cc_final: 0.6735 (mt) REVERT: M 863 ASP cc_start: 0.6720 (p0) cc_final: 0.5753 (m-30) REVERT: M 1022 LEU cc_start: 0.7588 (mt) cc_final: 0.7290 (mp) REVERT: M 1288 ARG cc_start: 0.6732 (ptp90) cc_final: 0.5679 (ptp-170) REVERT: M 1308 GLU cc_start: 0.6491 (pt0) cc_final: 0.6105 (mm-30) REVERT: N 43 MET cc_start: 0.6907 (mmm) cc_final: 0.6692 (mmm) REVERT: N 65 LEU cc_start: 0.7925 (mt) cc_final: 0.7706 (mt) REVERT: O 63 ASP cc_start: 0.5904 (t0) cc_final: 0.5663 (t0) REVERT: Q 22 VAL cc_start: 0.6561 (t) cc_final: 0.6230 (t) REVERT: R 19 ARG cc_start: 0.5331 (ptp-110) cc_final: 0.4882 (mtt180) REVERT: S 15 ASP cc_start: 0.5666 (t70) cc_final: 0.5225 (t70) REVERT: S 54 PHE cc_start: 0.5629 (m-10) cc_final: 0.4782 (m-10) REVERT: T 181 ARG cc_start: 0.5982 (ttp80) cc_final: 0.5374 (mtp-110) REVERT: U 58 TYR cc_start: 0.8118 (t80) cc_final: 0.7724 (t80) REVERT: U 131 GLU cc_start: 0.6701 (tt0) cc_final: 0.6401 (mt-10) REVERT: U 140 MET cc_start: 0.6923 (tpt) cc_final: 0.6447 (tpp) REVERT: U 148 GLN cc_start: 0.8220 (tt0) cc_final: 0.7643 (tt0) REVERT: U 197 MET cc_start: 0.7490 (mtm) cc_final: 0.6563 (ttm) REVERT: U 235 GLN cc_start: 0.5925 (tp40) cc_final: 0.5097 (mm-40) REVERT: U 296 ASP cc_start: 0.8355 (p0) cc_final: 0.8146 (p0) REVERT: U 298 LYS cc_start: 0.7428 (mmpt) cc_final: 0.7076 (mmmm) REVERT: V 136 TRP cc_start: 0.6364 (m-10) cc_final: 0.5829 (m-10) REVERT: V 274 MET cc_start: 0.6744 (mtp) cc_final: 0.6476 (mtp) REVERT: W 21 VAL cc_start: 0.8030 (m) cc_final: 0.7726 (p) REVERT: W 87 LEU cc_start: 0.7472 (tp) cc_final: 0.7219 (tp) REVERT: W 166 MET cc_start: 0.7566 (mmm) cc_final: 0.6945 (mmm) REVERT: X 46 LEU cc_start: 0.8268 (tp) cc_final: 0.8061 (tp) REVERT: X 91 LEU cc_start: 0.8607 (tp) cc_final: 0.8296 (mp) REVERT: X 132 LEU cc_start: 0.7553 (tp) cc_final: 0.7054 (tt) REVERT: X 164 GLU cc_start: 0.6375 (mm-30) cc_final: 0.5850 (mm-30) REVERT: X 206 MET cc_start: 0.7070 (mmm) cc_final: 0.6547 (mmm) REVERT: Y 9 PHE cc_start: 0.7491 (m-80) cc_final: 0.6980 (m-10) REVERT: Y 68 MET cc_start: 0.7914 (ptp) cc_final: 0.7343 (ptp) REVERT: Y 131 GLU cc_start: 0.6515 (tt0) cc_final: 0.6218 (tt0) REVERT: Y 230 LEU cc_start: 0.7813 (pp) cc_final: 0.7142 (tp) REVERT: Y 267 ARG cc_start: 0.5936 (ttm170) cc_final: 0.5722 (mtp85) REVERT: Z 40 LYS cc_start: 0.4499 (tppp) cc_final: 0.4082 (mmtm) REVERT: Z 63 TYR cc_start: 0.6006 (t80) cc_final: 0.5589 (t80) REVERT: Z 79 GLU cc_start: 0.5612 (tp30) cc_final: 0.5312 (tp30) REVERT: Z 151 THR cc_start: 0.6452 (p) cc_final: 0.6187 (t) REVERT: Z 182 LYS cc_start: 0.6261 (mmtt) cc_final: 0.6010 (mmtt) REVERT: Z 272 ILE cc_start: 0.7267 (mm) cc_final: 0.6942 (mm) REVERT: Z 282 PHE cc_start: 0.5456 (m-80) cc_final: 0.5220 (m-80) outliers start: 6 outliers final: 0 residues processed: 2126 average time/residue: 0.9468 time to fit residues: 3428.6756 Evaluate side-chains 1755 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1755 time to evaluate : 8.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1206 random chunks: chunk 711 optimal weight: 6.9990 chunk 1145 optimal weight: 0.6980 chunk 699 optimal weight: 0.5980 chunk 543 optimal weight: 5.9990 chunk 796 optimal weight: 0.0030 chunk 1201 optimal weight: 9.9990 chunk 1105 optimal weight: 4.9990 chunk 956 optimal weight: 5.9990 chunk 99 optimal weight: 0.4980 chunk 739 optimal weight: 8.9990 chunk 586 optimal weight: 6.9990 overall best weight: 1.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1886 GLN A1890 GLN ** A1903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2234 HIS E 93 GLN E 243 GLN G 34 ASN ** H 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1027 HIS ** I 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 637 ASN I 731 GLN I 748 HIS ** I 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1133 HIS ** I1319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 311 ASN J 350 HIS ** J 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 581 HIS J 676 ASN ** J 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 874 GLN ** J 903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1120 ASN K 497 HIS ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 795 ASN K1133 HIS L 199 ASN L 541 HIS L 618 HIS ** L 981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1080 ASN L1217 HIS L1223 GLN ** L1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1350 HIS ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1061 ASN M1223 GLN M1230 ASN ** Q 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 HIS T 79 HIS ** T 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 173 GLN Y 297 ASN ** Z 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 98950 Z= 0.160 Angle : 0.595 14.850 134608 Z= 0.296 Chirality : 0.041 0.425 15519 Planarity : 0.004 0.089 17313 Dihedral : 4.829 80.132 13396 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.74 % Rotamer: Outliers : 0.06 % Allowed : 0.39 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.08), residues: 12037 helix: 0.85 (0.08), residues: 4826 sheet: -0.29 (0.12), residues: 1658 loop : -0.80 (0.08), residues: 5553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A2007 HIS 0.014 0.001 HIS Q 37 PHE 0.026 0.001 PHE K 672 TYR 0.022 0.001 TYR J 918 ARG 0.011 0.000 ARG M 583 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24074 Ramachandran restraints generated. 12037 Oldfield, 0 Emsley, 12037 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2173 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 2167 time to evaluate : 8.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1472 PHE cc_start: 0.2237 (p90) cc_final: 0.2024 (p90) REVERT: A 1473 ARG cc_start: 0.4992 (tmt170) cc_final: 0.3695 (mmm160) REVERT: A 1493 ARG cc_start: 0.2020 (mmm160) cc_final: 0.1206 (tpp-160) REVERT: A 1503 LEU cc_start: 0.3699 (mt) cc_final: 0.3312 (mt) REVERT: A 1549 LEU cc_start: 0.2961 (mm) cc_final: 0.1943 (pp) REVERT: A 1707 ARG cc_start: 0.5188 (mtm-85) cc_final: 0.4491 (ttp-110) REVERT: A 1802 LYS cc_start: 0.3726 (tptt) cc_final: 0.2599 (mmmt) REVERT: A 1804 PHE cc_start: 0.1360 (p90) cc_final: 0.0721 (p90) REVERT: A 1827 GLN cc_start: 0.2357 (tp40) cc_final: 0.2088 (tp40) REVERT: A 1894 MET cc_start: 0.3601 (pmm) cc_final: 0.2917 (mmp) REVERT: A 1913 MET cc_start: 0.4136 (tmm) cc_final: 0.3121 (tmm) REVERT: A 1915 ARG cc_start: 0.4347 (tpt90) cc_final: 0.3591 (ttm110) REVERT: A 1940 GLN cc_start: 0.4989 (mm-40) cc_final: 0.4721 (mm-40) REVERT: A 1981 TYR cc_start: 0.2996 (t80) cc_final: 0.2480 (t80) REVERT: A 1992 GLN cc_start: 0.6254 (mm-40) cc_final: 0.4013 (pt0) REVERT: C 2237 PHE cc_start: 0.3984 (m-10) cc_final: 0.3713 (m-80) REVERT: E 207 MET cc_start: 0.3781 (mmm) cc_final: 0.2935 (tmm) REVERT: E 349 MET cc_start: 0.1388 (mtt) cc_final: 0.0588 (ppp) REVERT: E 496 ARG cc_start: 0.5663 (ptp-170) cc_final: 0.5365 (ptt180) REVERT: E 570 MET cc_start: 0.4375 (mtt) cc_final: 0.3871 (mmm) REVERT: G 8 ASP cc_start: 0.7815 (t70) cc_final: 0.7603 (t70) REVERT: G 124 MET cc_start: 0.5971 (pmm) cc_final: 0.5577 (pmm) REVERT: G 364 GLU cc_start: 0.6742 (pm20) cc_final: 0.6480 (pm20) REVERT: G 373 ASP cc_start: 0.6212 (m-30) cc_final: 0.5657 (m-30) REVERT: G 374 GLU cc_start: 0.5361 (mm-30) cc_final: 0.5148 (mm-30) REVERT: G 389 ARG cc_start: 0.6534 (mpt90) cc_final: 0.6000 (mmt180) REVERT: G 507 ARG cc_start: 0.7263 (ptm160) cc_final: 0.7035 (ptm-80) REVERT: G 577 GLN cc_start: 0.5597 (tt0) cc_final: 0.5031 (pp30) REVERT: H 81 HIS cc_start: 0.7507 (t-170) cc_final: 0.5995 (m-70) REVERT: H 90 LYS cc_start: 0.7280 (mttm) cc_final: 0.6665 (pttp) REVERT: H 91 MET cc_start: 0.7696 (tpp) cc_final: 0.7295 (tpp) REVERT: H 110 ARG cc_start: 0.5196 (tmt170) cc_final: 0.3809 (mmp-170) REVERT: H 403 GLU cc_start: 0.6347 (tp30) cc_final: 0.5578 (tp30) REVERT: H 467 ARG cc_start: 0.7135 (mmm-85) cc_final: 0.6871 (mmm160) REVERT: H 792 MET cc_start: 0.8191 (tpp) cc_final: 0.7945 (tpp) REVERT: H 818 LEU cc_start: 0.6901 (mm) cc_final: 0.6435 (mm) REVERT: H 844 ASP cc_start: 0.5325 (p0) cc_final: 0.4539 (m-30) REVERT: H 849 GLN cc_start: 0.6861 (pt0) cc_final: 0.6522 (pt0) REVERT: H 1106 MET cc_start: 0.7759 (mtp) cc_final: 0.7423 (mtm) REVERT: H 1156 MET cc_start: 0.6884 (mmm) cc_final: 0.6215 (mmm) REVERT: H 1157 SER cc_start: 0.8846 (m) cc_final: 0.8640 (m) REVERT: H 1291 ASP cc_start: 0.5598 (m-30) cc_final: 0.5356 (m-30) REVERT: H 1320 GLU cc_start: 0.6039 (mt-10) cc_final: 0.5632 (mt-10) REVERT: H 1362 LEU cc_start: 0.7280 (tp) cc_final: 0.6787 (tp) REVERT: I 1 MET cc_start: 0.6841 (mtm) cc_final: 0.6554 (mtt) REVERT: I 30 GLU cc_start: 0.6269 (tp30) cc_final: 0.6001 (tm-30) REVERT: I 169 ASP cc_start: 0.8393 (t70) cc_final: 0.8038 (t0) REVERT: I 467 ARG cc_start: 0.7331 (mtp85) cc_final: 0.6395 (mtp-110) REVERT: I 514 GLN cc_start: 0.7351 (tp40) cc_final: 0.6327 (tp40) REVERT: I 970 ASP cc_start: 0.8524 (p0) cc_final: 0.8316 (p0) REVERT: I 1250 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6371 (mt-10) REVERT: I 1265 TYR cc_start: 0.8099 (m-80) cc_final: 0.7725 (m-80) REVERT: I 1282 ILE cc_start: 0.8114 (pt) cc_final: 0.7813 (pt) REVERT: I 1294 ARG cc_start: 0.6727 (mmm-85) cc_final: 0.6091 (tpp-160) REVERT: I 1365 SER cc_start: 0.7516 (p) cc_final: 0.7100 (m) REVERT: J 185 ARG cc_start: 0.6953 (ptp-170) cc_final: 0.6346 (ptp-110) REVERT: J 193 VAL cc_start: 0.9004 (m) cc_final: 0.8603 (p) REVERT: J 407 TYR cc_start: 0.7588 (p90) cc_final: 0.7351 (p90) REVERT: J 475 MET cc_start: 0.7304 (mmm) cc_final: 0.6836 (mtt) REVERT: J 488 MET cc_start: 0.5782 (mmt) cc_final: 0.5394 (tpp) REVERT: J 507 ARG cc_start: 0.7442 (mtp-110) cc_final: 0.6667 (mtp-110) REVERT: J 542 CYS cc_start: 0.7484 (m) cc_final: 0.7088 (t) REVERT: J 614 ASP cc_start: 0.6663 (t0) cc_final: 0.6373 (t0) REVERT: J 628 ARG cc_start: 0.7552 (mtp85) cc_final: 0.7240 (mtp85) REVERT: J 669 GLN cc_start: 0.5916 (mp10) cc_final: 0.5374 (mt0) REVERT: J 693 LEU cc_start: 0.8542 (mt) cc_final: 0.8324 (mt) REVERT: J 694 ASN cc_start: 0.7768 (p0) cc_final: 0.7466 (p0) REVERT: J 697 GLN cc_start: 0.6482 (mm110) cc_final: 0.4864 (mp10) REVERT: J 962 GLU cc_start: 0.5974 (tp30) cc_final: 0.5119 (tp30) REVERT: J 963 PHE cc_start: 0.5485 (m-80) cc_final: 0.4968 (m-80) REVERT: J 1061 ASN cc_start: 0.7476 (m-40) cc_final: 0.7167 (m-40) REVERT: J 1066 LYS cc_start: 0.6728 (tttt) cc_final: 0.6465 (mttt) REVERT: J 1115 ARG cc_start: 0.7015 (mmm-85) cc_final: 0.6255 (mmm-85) REVERT: J 1270 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6828 (mt-10) REVERT: J 1324 ILE cc_start: 0.8664 (tp) cc_final: 0.8435 (tt) REVERT: K 240 LEU cc_start: 0.7676 (tp) cc_final: 0.7313 (tp) REVERT: K 255 LEU cc_start: 0.7068 (pt) cc_final: 0.6732 (pt) REVERT: K 270 SER cc_start: 0.8156 (m) cc_final: 0.7918 (t) REVERT: K 447 LYS cc_start: 0.7398 (ttmm) cc_final: 0.7017 (tttm) REVERT: K 475 MET cc_start: 0.7717 (mmm) cc_final: 0.6216 (mtt) REVERT: K 497 HIS cc_start: 0.6406 (m90) cc_final: 0.5937 (m-70) REVERT: K 537 PHE cc_start: 0.7850 (m-80) cc_final: 0.7428 (m-80) REVERT: K 647 PHE cc_start: 0.6964 (m-80) cc_final: 0.6693 (m-80) REVERT: K 721 THR cc_start: 0.8143 (m) cc_final: 0.7936 (m) REVERT: K 820 MET cc_start: 0.5678 (mtm) cc_final: 0.5430 (mtm) REVERT: K 918 TYR cc_start: 0.6688 (t80) cc_final: 0.6206 (t80) REVERT: K 958 ARG cc_start: 0.6614 (mtp180) cc_final: 0.6261 (mmm-85) REVERT: K 966 TYR cc_start: 0.6961 (m-80) cc_final: 0.6581 (m-10) REVERT: K 993 ARG cc_start: 0.7649 (tpp80) cc_final: 0.7348 (mmm160) REVERT: K 1006 MET cc_start: 0.8091 (mtp) cc_final: 0.7774 (mtp) REVERT: K 1150 MET cc_start: 0.7286 (ptm) cc_final: 0.6915 (tmm) REVERT: K 1184 ASN cc_start: 0.8220 (m110) cc_final: 0.7924 (m110) REVERT: K 1206 ASP cc_start: 0.8069 (t0) cc_final: 0.7851 (t70) REVERT: L 64 VAL cc_start: 0.6007 (p) cc_final: 0.5352 (p) REVERT: L 141 GLU cc_start: 0.6485 (pp20) cc_final: 0.6174 (tm-30) REVERT: L 241 LYS cc_start: 0.8659 (tptt) cc_final: 0.8028 (tptt) REVERT: L 268 LYS cc_start: 0.7601 (mmtp) cc_final: 0.7020 (ttpt) REVERT: L 294 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6344 (mm-30) REVERT: L 302 TYR cc_start: 0.7811 (m-80) cc_final: 0.7371 (m-80) REVERT: L 475 MET cc_start: 0.4753 (mmp) cc_final: 0.3549 (tmm) REVERT: L 537 PHE cc_start: 0.7319 (m-80) cc_final: 0.6808 (m-80) REVERT: L 635 ILE cc_start: 0.7327 (pt) cc_final: 0.7085 (mt) REVERT: L 878 GLU cc_start: 0.7198 (tp30) cc_final: 0.6922 (tp30) REVERT: L 881 LEU cc_start: 0.6835 (mt) cc_final: 0.6595 (mp) REVERT: L 918 TYR cc_start: 0.6556 (t80) cc_final: 0.5435 (t80) REVERT: L 1006 MET cc_start: 0.7880 (mmt) cc_final: 0.6791 (mmt) REVERT: L 1071 ILE cc_start: 0.8472 (tt) cc_final: 0.8207 (tt) REVERT: L 1106 MET cc_start: 0.7544 (mtp) cc_final: 0.7292 (mtt) REVERT: L 1129 ARG cc_start: 0.7314 (mmm160) cc_final: 0.6915 (mtp85) REVERT: L 1285 TYR cc_start: 0.8006 (t80) cc_final: 0.7439 (t80) REVERT: L 1330 LEU cc_start: 0.8130 (mt) cc_final: 0.7565 (mp) REVERT: M 467 ARG cc_start: 0.7564 (mtp85) cc_final: 0.6796 (ttt180) REVERT: M 500 ARG cc_start: 0.5636 (mmm160) cc_final: 0.5216 (mmt180) REVERT: M 512 MET cc_start: 0.8313 (mtm) cc_final: 0.7886 (mtp) REVERT: M 532 GLU cc_start: 0.7043 (tp30) cc_final: 0.6672 (tp30) REVERT: M 675 ARG cc_start: 0.6020 (ptm160) cc_final: 0.5762 (ptm160) REVERT: M 786 LEU cc_start: 0.7053 (mm) cc_final: 0.6753 (mt) REVERT: M 856 MET cc_start: 0.7399 (mmm) cc_final: 0.6893 (mmm) REVERT: M 863 ASP cc_start: 0.6644 (p0) cc_final: 0.5732 (m-30) REVERT: M 1288 ARG cc_start: 0.6795 (ptp90) cc_final: 0.5736 (ptp-170) REVERT: Q 22 VAL cc_start: 0.6387 (t) cc_final: 0.6039 (t) REVERT: Q 66 ARG cc_start: 0.6587 (ptm-80) cc_final: 0.6201 (mtm110) REVERT: R 19 ARG cc_start: 0.5285 (ptp-110) cc_final: 0.4860 (mtt180) REVERT: S 15 ASP cc_start: 0.5586 (t70) cc_final: 0.5156 (t70) REVERT: S 54 PHE cc_start: 0.5594 (m-10) cc_final: 0.4732 (m-10) REVERT: T 60 GLU cc_start: 0.6000 (pp20) cc_final: 0.4880 (mp0) REVERT: T 181 ARG cc_start: 0.5943 (ttp80) cc_final: 0.5347 (mtp-110) REVERT: T 186 TYR cc_start: 0.7157 (m-80) cc_final: 0.6948 (m-80) REVERT: U 58 TYR cc_start: 0.8067 (t80) cc_final: 0.7732 (t80) REVERT: U 131 GLU cc_start: 0.6652 (tt0) cc_final: 0.6363 (mt-10) REVERT: U 140 MET cc_start: 0.6867 (tpt) cc_final: 0.6368 (tpp) REVERT: U 148 GLN cc_start: 0.8132 (tt0) cc_final: 0.7581 (tt0) REVERT: U 197 MET cc_start: 0.7450 (mtm) cc_final: 0.6398 (ttm) REVERT: U 204 MET cc_start: 0.7795 (mtm) cc_final: 0.7498 (mtm) REVERT: U 235 GLN cc_start: 0.5943 (tp40) cc_final: 0.5123 (mm-40) REVERT: U 268 LEU cc_start: 0.8040 (tp) cc_final: 0.7829 (mt) REVERT: U 298 LYS cc_start: 0.7284 (mmpt) cc_final: 0.6962 (mmtt) REVERT: V 136 TRP cc_start: 0.6358 (m-10) cc_final: 0.5864 (m-10) REVERT: V 274 MET cc_start: 0.6693 (mtp) cc_final: 0.6229 (mtp) REVERT: V 299 SER cc_start: 0.6558 (m) cc_final: 0.6206 (p) REVERT: V 305 LYS cc_start: 0.5741 (mmtt) cc_final: 0.5432 (mptt) REVERT: W 87 LEU cc_start: 0.7384 (tp) cc_final: 0.7043 (tp) REVERT: W 268 GLU cc_start: 0.5864 (mp0) cc_final: 0.5554 (mp0) REVERT: X 37 ARG cc_start: 0.6829 (mtp180) cc_final: 0.6444 (ttm170) REVERT: X 46 LEU cc_start: 0.8339 (tp) cc_final: 0.8052 (tp) REVERT: X 91 LEU cc_start: 0.8622 (tp) cc_final: 0.8380 (mp) REVERT: X 132 LEU cc_start: 0.7578 (tp) cc_final: 0.7041 (tt) REVERT: X 164 GLU cc_start: 0.6349 (mm-30) cc_final: 0.5855 (mm-30) REVERT: X 206 MET cc_start: 0.7164 (mmm) cc_final: 0.6570 (mmm) REVERT: X 292 ASP cc_start: 0.6963 (t70) cc_final: 0.6259 (m-30) REVERT: Y 68 MET cc_start: 0.8156 (ptp) cc_final: 0.7403 (ptp) REVERT: Y 131 GLU cc_start: 0.6721 (tt0) cc_final: 0.6435 (tt0) REVERT: Y 230 LEU cc_start: 0.7917 (pp) cc_final: 0.7200 (tp) REVERT: Y 267 ARG cc_start: 0.5816 (ttm170) cc_final: 0.5529 (mtm180) REVERT: Z 40 LYS cc_start: 0.4635 (tppp) cc_final: 0.4136 (mmtm) REVERT: Z 63 TYR cc_start: 0.6047 (t80) cc_final: 0.5578 (t80) REVERT: Z 65 GLU cc_start: 0.7250 (pt0) cc_final: 0.6908 (pt0) REVERT: Z 79 GLU cc_start: 0.5519 (tp30) cc_final: 0.5228 (tp30) REVERT: Z 90 ARG cc_start: 0.8211 (mmm160) cc_final: 0.7859 (mmm160) REVERT: Z 182 LYS cc_start: 0.6315 (mmtt) cc_final: 0.6102 (mmtt) REVERT: Z 211 MET cc_start: 0.6730 (mtp) cc_final: 0.6517 (mtm) REVERT: Z 272 ILE cc_start: 0.7185 (mm) cc_final: 0.6877 (mm) REVERT: Z 282 PHE cc_start: 0.5418 (m-80) cc_final: 0.5173 (m-80) outliers start: 6 outliers final: 0 residues processed: 2169 average time/residue: 0.9098 time to fit residues: 3397.0783 Evaluate side-chains 1797 residues out of total 10637 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1797 time to evaluate : 8.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1206 random chunks: chunk 759 optimal weight: 0.3980 chunk 1019 optimal weight: 20.0000 chunk 293 optimal weight: 0.9980 chunk 882 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 265 optimal weight: 8.9990 chunk 958 optimal weight: 3.9990 chunk 401 optimal weight: 4.9990 chunk 983 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 176 optimal weight: 9.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1886 GLN A1890 GLN ** A1903 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2045 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 243 GLN G 34 ASN G 321 GLN ** H 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1027 HIS I 158 HIS I 637 ASN I 713 HIS I 748 HIS ** I 849 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 985 ASN I1133 HIS ** J 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 350 HIS J 534 HIS J 676 ASN ** J 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 903 GLN ** J1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1120 ASN ** K 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 749 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1133 HIS L 199 ASN L 541 HIS L 618 HIS ** L 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 981 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L1023 GLN L1080 ASN ** L1309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 618 HIS M1061 ASN M1133 HIS M1309 GLN ** Q 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 HIS T 79 HIS ** T 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 297 ASN ** Z 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 248 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.152354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.135766 restraints weight = 167604.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.135239 restraints weight = 221775.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.136361 restraints weight = 132574.675| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.3488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 98950 Z= 0.201 Angle : 0.617 14.326 134608 Z= 0.308 Chirality : 0.043 0.437 15519 Planarity : 0.005 0.094 17313 Dihedral : 4.885 78.985 13396 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.57 % Favored : 95.39 % Rotamer: Outliers : 0.07 % Allowed : 0.41 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.08), residues: 12037 helix: 0.79 (0.08), residues: 4807 sheet: -0.32 (0.12), residues: 1665 loop : -0.82 (0.08), residues: 5565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.002 TRP G 514 HIS 0.013 0.001 HIS Q 37 PHE 0.025 0.002 PHE E 208 TYR 0.030 0.001 TYR V 218 ARG 0.015 0.000 ARG I 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42592.62 seconds wall clock time: 734 minutes 21.43 seconds (44061.43 seconds total)