Starting phenix.real_space_refine on Sun Feb 18 22:10:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpy_30435/02_2024/7cpy_30435_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpy_30435/02_2024/7cpy_30435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpy_30435/02_2024/7cpy_30435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpy_30435/02_2024/7cpy_30435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpy_30435/02_2024/7cpy_30435_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cpy_30435/02_2024/7cpy_30435_trim_updated.pdb" } resolution = 3.6 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 204 5.16 5 C 25872 2.51 5 N 7096 2.21 5 O 7706 1.98 5 H 34672 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 22": "OE1" <-> "OE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 288": "OE1" <-> "OE2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C GLU 304": "OE1" <-> "OE2" Residue "C ARG 305": "NH1" <-> "NH2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 337": "OD1" <-> "OD2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 288": "OE1" <-> "OE2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D ARG 305": "NH1" <-> "NH2" Residue "D PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 337": "OD1" <-> "OD2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1583": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 2337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 2418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1583": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1673": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 2337": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 2418": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 75556 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2742 Classifications: {'peptide': 357} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 325} Chain breaks: 1 Chain: "D" Number of atoms: 2742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2742 Classifications: {'peptide': 357} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 28, 'TRANS': 325} Chain breaks: 1 Chain: "A" Number of atoms: 34988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2262, 34988 Classifications: {'peptide': 2262} Link IDs: {'PCIS': 2, 'PTRANS': 124, 'TRANS': 2135} Chain breaks: 12 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 34988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2262, 34988 Classifications: {'peptide': 2262} Link IDs: {'PCIS': 2, 'PTRANS': 124, 'TRANS': 2135} Chain breaks: 12 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1B NAP A3500 " occ=0.00 ... (46 atoms not shown) pdb=" PN NAP A3500 " occ=0.00 residue: pdb=" C1B NAP B3500 " occ=0.00 ... (46 atoms not shown) pdb=" PN NAP B3500 " occ=0.00 Time building chain proxies: 25.83, per 1000 atoms: 0.34 Number of scatterers: 75556 At special positions: 0 Unit cell: (268, 127, 227, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 204 16.00 P 6 15.00 O 7706 8.00 N 7096 7.00 C 25872 6.00 H 34672 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 49.45 Conformation dependent library (CDL) restraints added in 6.1 seconds 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 197 helices and 34 sheets defined 35.7% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 15.22 Creating SS restraints... Processing helix chain 'C' and resid 50 through 54 Processing helix chain 'C' and resid 57 through 59 No H-bonds generated for 'chain 'C' and resid 57 through 59' Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 134 through 147 Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.652A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN C 183 " --> pdb=" O THR C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 207 removed outlier: 4.976A pdb=" N ASP C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS C 205 " --> pdb=" O ASP C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 227 Processing helix chain 'C' and resid 242 through 251 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 302 through 320 Processing helix chain 'C' and resid 336 through 347 Processing helix chain 'D' and resid 50 through 54 Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 134 through 147 Processing helix chain 'D' and resid 176 through 187 removed outlier: 3.652A pdb=" N VAL D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN D 183 " --> pdb=" O THR D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 207 removed outlier: 4.975A pdb=" N ASP D 202 " --> pdb=" O HIS D 199 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 227 Processing helix chain 'D' and resid 242 through 251 Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'D' and resid 302 through 320 Processing helix chain 'D' and resid 336 through 347 Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 51 through 53 No H-bonds generated for 'chain 'A' and resid 51 through 53' Processing helix chain 'A' and resid 82 through 85 No H-bonds generated for 'chain 'A' and resid 82 through 85' Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 97 through 112 Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 157 through 168 removed outlier: 4.657A pdb=" N ARG A 163 " --> pdb=" O ALA A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 197 removed outlier: 4.625A pdb=" N SER A 184 " --> pdb=" O CYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 223 removed outlier: 3.857A pdb=" N LEU A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 262 Processing helix chain 'A' and resid 289 through 302 Processing helix chain 'A' and resid 327 through 339 Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 369 through 386 removed outlier: 4.330A pdb=" N GLY A 373 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS A 386 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Proline residue: A 404 - end of helix No H-bonds generated for 'chain 'A' and resid 400 through 405' Processing helix chain 'A' and resid 482 through 498 Processing helix chain 'A' and resid 504 through 512 Processing helix chain 'A' and resid 529 through 542 Processing helix chain 'A' and resid 575 through 580 Processing helix chain 'A' and resid 582 through 596 Processing helix chain 'A' and resid 608 through 611 No H-bonds generated for 'chain 'A' and resid 608 through 611' Processing helix chain 'A' and resid 624 through 644 Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 657 through 665 Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 765 through 768 No H-bonds generated for 'chain 'A' and resid 765 through 768' Processing helix chain 'A' and resid 770 through 780 removed outlier: 4.080A pdb=" N TYR A 774 " --> pdb=" O CYS A 770 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU A 780 " --> pdb=" O GLN A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 813 No H-bonds generated for 'chain 'A' and resid 811 through 813' Processing helix chain 'A' and resid 815 through 822 removed outlier: 4.027A pdb=" N LEU A 822 " --> pdb=" O TRP A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 838 Processing helix chain 'A' and resid 855 through 865 Processing helix chain 'A' and resid 883 through 898 Processing helix chain 'A' and resid 900 through 902 No H-bonds generated for 'chain 'A' and resid 900 through 902' Processing helix chain 'A' and resid 905 through 911 Processing helix chain 'A' and resid 941 through 947 Processing helix chain 'A' and resid 995 through 1012 removed outlier: 3.623A pdb=" N ILE A 999 " --> pdb=" O ALA A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1127 Processing helix chain 'A' and resid 1133 through 1135 No H-bonds generated for 'chain 'A' and resid 1133 through 1135' Processing helix chain 'A' and resid 1170 through 1184 removed outlier: 3.720A pdb=" N VAL A1180 " --> pdb=" O ALA A1176 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A1181 " --> pdb=" O PHE A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1217 Processing helix chain 'A' and resid 1266 through 1268 No H-bonds generated for 'chain 'A' and resid 1266 through 1268' Processing helix chain 'A' and resid 1290 through 1292 No H-bonds generated for 'chain 'A' and resid 1290 through 1292' Processing helix chain 'A' and resid 1296 through 1307 Proline residue: A1303 - end of helix Processing helix chain 'A' and resid 1310 through 1325 removed outlier: 3.586A pdb=" N ILE A1313 " --> pdb=" O TYR A1310 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ARG A1314 " --> pdb=" O PHE A1311 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A1317 " --> pdb=" O ARG A1314 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER A1318 " --> pdb=" O SER A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1333 No H-bonds generated for 'chain 'A' and resid 1330 through 1333' Processing helix chain 'A' and resid 1339 through 1354 removed outlier: 3.764A pdb=" N LYS A1347 " --> pdb=" O LEU A1343 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP A1353 " --> pdb=" O GLY A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1370 removed outlier: 3.664A pdb=" N ILE A1366 " --> pdb=" O GLU A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1376 through 1387 removed outlier: 3.829A pdb=" N LEU A1381 " --> pdb=" O PRO A1377 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1393 No H-bonds generated for 'chain 'A' and resid 1390 through 1393' Processing helix chain 'A' and resid 1409 through 1414 Processing helix chain 'A' and resid 1420 through 1436 Processing helix chain 'A' and resid 1451 through 1458 Processing helix chain 'A' and resid 1477 through 1483 Processing helix chain 'A' and resid 1485 through 1487 No H-bonds generated for 'chain 'A' and resid 1485 through 1487' Processing helix chain 'A' and resid 1503 through 1505 No H-bonds generated for 'chain 'A' and resid 1503 through 1505' Processing helix chain 'A' and resid 1521 through 1523 No H-bonds generated for 'chain 'A' and resid 1521 through 1523' Processing helix chain 'A' and resid 1527 through 1537 Processing helix chain 'A' and resid 1554 through 1563 removed outlier: 3.656A pdb=" N GLY A1558 " --> pdb=" O HIS A1554 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE A1559 " --> pdb=" O THR A1555 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE A1560 " --> pdb=" O ARG A1556 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU A1563 " --> pdb=" O PHE A1559 " (cutoff:3.500A) Processing helix chain 'A' and resid 1571 through 1573 No H-bonds generated for 'chain 'A' and resid 1571 through 1573' Processing helix chain 'A' and resid 1583 through 1593 Processing helix chain 'A' and resid 1652 through 1664 Processing helix chain 'A' and resid 1676 through 1680 Processing helix chain 'A' and resid 1709 through 1719 Processing helix chain 'A' and resid 1735 through 1750 removed outlier: 3.789A pdb=" N ARG A1749 " --> pdb=" O ARG A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1776 through 1784 removed outlier: 3.724A pdb=" N ASP A1784 " --> pdb=" O GLU A1780 " (cutoff:3.500A) Processing helix chain 'A' and resid 1814 through 1823 removed outlier: 3.903A pdb=" N SER A1823 " --> pdb=" O ARG A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1920 through 1922 No H-bonds generated for 'chain 'A' and resid 1920 through 1922' Processing helix chain 'A' and resid 1935 through 1953 removed outlier: 3.526A pdb=" N ILE A1953 " --> pdb=" O ALA A1949 " (cutoff:3.500A) Processing helix chain 'A' and resid 1974 through 1985 Processing helix chain 'A' and resid 2018 through 2024 Processing helix chain 'A' and resid 2039 through 2049 removed outlier: 3.801A pdb=" N GLY A2043 " --> pdb=" O SER A2040 " (cutoff:3.500A) Processing helix chain 'A' and resid 2061 through 2063 No H-bonds generated for 'chain 'A' and resid 2061 through 2063' Processing helix chain 'A' and resid 2086 through 2101 removed outlier: 3.590A pdb=" N GLN A2097 " --> pdb=" O SER A2093 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A2098 " --> pdb=" O LEU A2094 " (cutoff:3.500A) Proline residue: A2100 - end of helix Processing helix chain 'A' and resid 2111 through 2117 Processing helix chain 'A' and resid 2135 through 2138 No H-bonds generated for 'chain 'A' and resid 2135 through 2138' Processing helix chain 'A' and resid 2167 through 2179 Processing helix chain 'A' and resid 2195 through 2204 Processing helix chain 'A' and resid 2218 through 2230 removed outlier: 3.644A pdb=" N LYS A2229 " --> pdb=" O LEU A2225 " (cutoff:3.500A) Processing helix chain 'A' and resid 2256 through 2276 Proline residue: A2265 - end of helix Processing helix chain 'A' and resid 2295 through 2299 Processing helix chain 'A' and resid 2305 through 2323 Processing helix chain 'A' and resid 2341 through 2345 Processing helix chain 'A' and resid 2348 through 2354 removed outlier: 3.806A pdb=" N ILE A2354 " --> pdb=" O ASP A2350 " (cutoff:3.500A) Processing helix chain 'A' and resid 2363 through 2385 Processing helix chain 'A' and resid 2394 through 2396 No H-bonds generated for 'chain 'A' and resid 2394 through 2396' Processing helix chain 'A' and resid 2410 through 2412 No H-bonds generated for 'chain 'A' and resid 2410 through 2412' Processing helix chain 'A' and resid 2422 through 2427 removed outlier: 5.316A pdb=" N ASN A2426 " --> pdb=" O ARG A2423 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 35 Processing helix chain 'B' and resid 51 through 53 No H-bonds generated for 'chain 'B' and resid 51 through 53' Processing helix chain 'B' and resid 82 through 85 No H-bonds generated for 'chain 'B' and resid 82 through 85' Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 97 through 112 Processing helix chain 'B' and resid 117 through 120 No H-bonds generated for 'chain 'B' and resid 117 through 120' Processing helix chain 'B' and resid 135 through 139 Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 157 through 168 removed outlier: 4.658A pdb=" N ARG B 163 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 197 removed outlier: 4.624A pdb=" N SER B 184 " --> pdb=" O CYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 223 removed outlier: 3.857A pdb=" N LEU B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 262 Processing helix chain 'B' and resid 289 through 302 Processing helix chain 'B' and resid 327 through 339 Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 369 through 386 removed outlier: 4.329A pdb=" N GLY B 373 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N HIS B 386 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Proline residue: B 404 - end of helix No H-bonds generated for 'chain 'B' and resid 400 through 405' Processing helix chain 'B' and resid 482 through 498 Processing helix chain 'B' and resid 504 through 512 Processing helix chain 'B' and resid 529 through 542 Processing helix chain 'B' and resid 575 through 580 Processing helix chain 'B' and resid 582 through 596 Processing helix chain 'B' and resid 608 through 611 No H-bonds generated for 'chain 'B' and resid 608 through 611' Processing helix chain 'B' and resid 624 through 644 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 657 through 665 Processing helix chain 'B' and resid 671 through 681 Processing helix chain 'B' and resid 765 through 768 No H-bonds generated for 'chain 'B' and resid 765 through 768' Processing helix chain 'B' and resid 772 through 777 Processing helix chain 'B' and resid 811 through 813 No H-bonds generated for 'chain 'B' and resid 811 through 813' Processing helix chain 'B' and resid 815 through 822 removed outlier: 4.028A pdb=" N LEU B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 838 Processing helix chain 'B' and resid 855 through 865 Processing helix chain 'B' and resid 883 through 898 Processing helix chain 'B' and resid 900 through 902 No H-bonds generated for 'chain 'B' and resid 900 through 902' Processing helix chain 'B' and resid 905 through 911 Processing helix chain 'B' and resid 941 through 947 Processing helix chain 'B' and resid 995 through 1012 removed outlier: 3.623A pdb=" N ILE B 999 " --> pdb=" O ALA B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1117 through 1127 Processing helix chain 'B' and resid 1170 through 1184 removed outlier: 3.720A pdb=" N VAL B1180 " --> pdb=" O ALA B1176 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE B1181 " --> pdb=" O PHE B1177 " (cutoff:3.500A) Processing helix chain 'B' and resid 1208 through 1217 Processing helix chain 'B' and resid 1266 through 1268 No H-bonds generated for 'chain 'B' and resid 1266 through 1268' Processing helix chain 'B' and resid 1290 through 1292 No H-bonds generated for 'chain 'B' and resid 1290 through 1292' Processing helix chain 'B' and resid 1296 through 1307 Proline residue: B1303 - end of helix Processing helix chain 'B' and resid 1310 through 1325 removed outlier: 3.586A pdb=" N ILE B1313 " --> pdb=" O TYR B1310 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ARG B1314 " --> pdb=" O PHE B1311 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B1317 " --> pdb=" O ARG B1314 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N SER B1318 " --> pdb=" O SER B1315 " (cutoff:3.500A) Processing helix chain 'B' and resid 1330 through 1333 No H-bonds generated for 'chain 'B' and resid 1330 through 1333' Processing helix chain 'B' and resid 1339 through 1354 removed outlier: 3.764A pdb=" N LYS B1347 " --> pdb=" O LEU B1343 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP B1353 " --> pdb=" O GLY B1349 " (cutoff:3.500A) Processing helix chain 'B' and resid 1359 through 1370 removed outlier: 3.664A pdb=" N ILE B1366 " --> pdb=" O GLU B1363 " (cutoff:3.500A) Processing helix chain 'B' and resid 1376 through 1387 removed outlier: 3.829A pdb=" N LEU B1381 " --> pdb=" O PRO B1377 " (cutoff:3.500A) Processing helix chain 'B' and resid 1390 through 1393 No H-bonds generated for 'chain 'B' and resid 1390 through 1393' Processing helix chain 'B' and resid 1409 through 1414 Processing helix chain 'B' and resid 1420 through 1436 Processing helix chain 'B' and resid 1451 through 1458 Processing helix chain 'B' and resid 1477 through 1483 Processing helix chain 'B' and resid 1485 through 1487 No H-bonds generated for 'chain 'B' and resid 1485 through 1487' Processing helix chain 'B' and resid 1503 through 1505 No H-bonds generated for 'chain 'B' and resid 1503 through 1505' Processing helix chain 'B' and resid 1521 through 1523 No H-bonds generated for 'chain 'B' and resid 1521 through 1523' Processing helix chain 'B' and resid 1527 through 1537 Processing helix chain 'B' and resid 1554 through 1563 removed outlier: 3.655A pdb=" N GLY B1558 " --> pdb=" O HIS B1554 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N PHE B1559 " --> pdb=" O THR B1555 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ILE B1560 " --> pdb=" O ARG B1556 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU B1563 " --> pdb=" O PHE B1559 " (cutoff:3.500A) Processing helix chain 'B' and resid 1571 through 1573 No H-bonds generated for 'chain 'B' and resid 1571 through 1573' Processing helix chain 'B' and resid 1583 through 1593 Processing helix chain 'B' and resid 1652 through 1664 Processing helix chain 'B' and resid 1676 through 1680 Processing helix chain 'B' and resid 1709 through 1719 Processing helix chain 'B' and resid 1735 through 1750 removed outlier: 3.789A pdb=" N ARG B1749 " --> pdb=" O ARG B1745 " (cutoff:3.500A) Processing helix chain 'B' and resid 1776 through 1784 removed outlier: 3.723A pdb=" N ASP B1784 " --> pdb=" O GLU B1780 " (cutoff:3.500A) Processing helix chain 'B' and resid 1814 through 1823 removed outlier: 3.904A pdb=" N SER B1823 " --> pdb=" O ARG B1819 " (cutoff:3.500A) Processing helix chain 'B' and resid 1920 through 1922 No H-bonds generated for 'chain 'B' and resid 1920 through 1922' Processing helix chain 'B' and resid 1935 through 1953 removed outlier: 3.526A pdb=" N ILE B1953 " --> pdb=" O ALA B1949 " (cutoff:3.500A) Processing helix chain 'B' and resid 1974 through 1985 Processing helix chain 'B' and resid 2018 through 2024 Processing helix chain 'B' and resid 2039 through 2049 removed outlier: 3.801A pdb=" N GLY B2043 " --> pdb=" O SER B2040 " (cutoff:3.500A) Processing helix chain 'B' and resid 2061 through 2063 No H-bonds generated for 'chain 'B' and resid 2061 through 2063' Processing helix chain 'B' and resid 2086 through 2101 removed outlier: 3.590A pdb=" N GLN B2097 " --> pdb=" O SER B2093 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B2098 " --> pdb=" O LEU B2094 " (cutoff:3.500A) Proline residue: B2100 - end of helix Processing helix chain 'B' and resid 2111 through 2117 Processing helix chain 'B' and resid 2135 through 2138 No H-bonds generated for 'chain 'B' and resid 2135 through 2138' Processing helix chain 'B' and resid 2167 through 2179 Processing helix chain 'B' and resid 2195 through 2204 Processing helix chain 'B' and resid 2218 through 2230 removed outlier: 3.643A pdb=" N LYS B2229 " --> pdb=" O LEU B2225 " (cutoff:3.500A) Processing helix chain 'B' and resid 2256 through 2276 Proline residue: B2265 - end of helix Processing helix chain 'B' and resid 2295 through 2299 Processing helix chain 'B' and resid 2305 through 2323 Processing helix chain 'B' and resid 2341 through 2345 Processing helix chain 'B' and resid 2348 through 2354 removed outlier: 3.806A pdb=" N ILE B2354 " --> pdb=" O ASP B2350 " (cutoff:3.500A) Processing helix chain 'B' and resid 2363 through 2385 Processing helix chain 'B' and resid 2394 through 2396 No H-bonds generated for 'chain 'B' and resid 2394 through 2396' Processing helix chain 'B' and resid 2410 through 2412 No H-bonds generated for 'chain 'B' and resid 2410 through 2412' Processing helix chain 'B' and resid 2422 through 2427 removed outlier: 5.316A pdb=" N ASN B2426 " --> pdb=" O ARG B2423 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 14 through 17 Processing sheet with id= B, first strand: chain 'C' and resid 110 through 112 removed outlier: 3.675A pdb=" N ALA C 76 " --> pdb=" O TYR C 40 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N ARG C 42 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL C 74 " --> pdb=" O ARG C 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 69 through 71 removed outlier: 4.334A pdb=" N ASP C 69 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 275 through 279 removed outlier: 6.566A pdb=" N GLY C 257 " --> pdb=" O THR C 276 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N ASP C 278 " --> pdb=" O GLY C 257 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR C 259 " --> pdb=" O ASP C 278 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR C 167 " --> pdb=" O TYR C 234 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LEU C 236 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 169 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE C 191 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL C 170 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C 193 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU C 211 " --> pdb=" O ALA C 194 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS C 196 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N PHE C 213 " --> pdb=" O CYS C 196 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 14 through 17 Processing sheet with id= F, first strand: chain 'D' and resid 110 through 112 removed outlier: 3.675A pdb=" N ALA D 76 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG D 42 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N VAL D 74 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 69 through 71 removed outlier: 4.335A pdb=" N ASP D 69 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 275 through 279 removed outlier: 6.565A pdb=" N GLY D 257 " --> pdb=" O THR D 276 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ASP D 278 " --> pdb=" O GLY D 257 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR D 259 " --> pdb=" O ASP D 278 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N TYR D 167 " --> pdb=" O TYR D 234 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N LEU D 236 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU D 169 " --> pdb=" O LEU D 236 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE D 191 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL D 170 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE D 193 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU D 211 " --> pdb=" O ALA D 194 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS D 196 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N PHE D 213 " --> pdb=" O CYS D 196 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 174 through 177 removed outlier: 6.393A pdb=" N VAL A 127 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE A 177 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL A 129 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY A 15 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LYS A 254 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL A 13 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS A 268 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 444 " --> pdb=" O ARG A 271 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR A 273 " --> pdb=" O HIS A 442 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N HIS A 442 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL A 275 " --> pdb=" O ASN A 440 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN A 440 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE A 316 " --> pdb=" O SER A 430 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ASN A 432 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU A 318 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE A 434 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 475 through 479 Processing sheet with id= K, first strand: chain 'A' and resid 872 through 875 removed outlier: 6.083A pdb=" N LEU A 560 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL A 848 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE A 562 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE A 563 " --> pdb=" O VAL A 652 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'A' and resid 967 through 974 removed outlier: 6.624A pdb=" N THR A1059 " --> pdb=" O SER A1049 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ASN A1051 " --> pdb=" O SER A1057 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER A1057 " --> pdb=" O ASN A1051 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N SER A1066 " --> pdb=" O LEU A1076 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU A1076 " --> pdb=" O SER A1066 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU A1087 " --> pdb=" O VAL A1017 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL A1017 " --> pdb=" O GLU A1087 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A1242 " --> pdb=" O LEU A1250 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN A1252 " --> pdb=" O ILE A1240 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE A1240 " --> pdb=" O GLN A1252 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLU A1254 " --> pdb=" O GLY A1238 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLY A1238 " --> pdb=" O GLU A1254 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ASP A1239 " --> pdb=" O ASN A1228 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASN A1228 " --> pdb=" O ASP A1239 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL A1241 " --> pdb=" O THR A1226 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR A1226 " --> pdb=" O VAL A1241 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N PHE A1243 " --> pdb=" O PHE A1224 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE A1224 " --> pdb=" O PHE A1243 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 1235 through 1238 removed outlier: 5.555A pdb=" N LYS A1259 " --> pdb=" O PRO A1198 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 1275 through 1280 removed outlier: 6.772A pdb=" N SER A1689 " --> pdb=" O SER A1721 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR A1723 " --> pdb=" O SER A1689 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N PHE A1691 " --> pdb=" O THR A1723 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP A1725 " --> pdb=" O PHE A1691 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N MET A1693 " --> pdb=" O TRP A1725 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR A1727 " --> pdb=" O MET A1693 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 1614 through 1618 removed outlier: 3.693A pdb=" N LEU A1514 " --> pdb=" O ASP A1441 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE A1442 " --> pdb=" O ASN A1465 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR A1467 " --> pdb=" O ILE A1442 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLU A1444 " --> pdb=" O TYR A1467 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR A1469 " --> pdb=" O GLU A1444 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 1828 through 1832 Processing sheet with id= Q, first strand: chain 'A' and resid 1838 through 1842 Processing sheet with id= R, first strand: chain 'A' and resid 1915 through 1918 removed outlier: 7.794A pdb=" N THR A1870 " --> pdb=" O GLN A1897 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLN A1897 " --> pdb=" O THR A1870 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLN A1893 " --> pdb=" O HIS A1874 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER A1876 " --> pdb=" O LEU A1891 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU A1891 " --> pdb=" O SER A1876 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 1875 through 1877 Processing sheet with id= T, first strand: chain 'A' and resid 1988 through 1992 removed outlier: 4.060A pdb=" N ALA A2031 " --> pdb=" O SER A1964 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA A2057 " --> pdb=" O LEU A2032 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASP A2034 " --> pdb=" O ALA A2057 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TYR A2059 " --> pdb=" O ASP A2034 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 2207 through 2210 removed outlier: 6.340A pdb=" N TYR A2159 " --> pdb=" O VAL A2185 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR A2187 " --> pdb=" O TYR A2159 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A2161 " --> pdb=" O THR A2187 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU A2160 " --> pdb=" O GLY A2237 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE A2239 " --> pdb=" O LEU A2160 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL A2162 " --> pdb=" O ILE A2239 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE A2241 " --> pdb=" O VAL A2162 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE A2288 " --> pdb=" O ILE A2239 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE A2241 " --> pdb=" O PHE A2288 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL A2290 " --> pdb=" O PHE A2241 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER A2329 " --> pdb=" O MET A2291 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N SER A2293 " --> pdb=" O SER A2329 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE A2331 " --> pdb=" O SER A2293 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 174 through 177 removed outlier: 6.394A pdb=" N VAL B 127 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE B 177 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL B 129 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B 15 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LYS B 254 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N VAL B 13 " --> pdb=" O LYS B 254 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS B 268 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 444 " --> pdb=" O ARG B 271 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N THR B 273 " --> pdb=" O HIS B 442 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N HIS B 442 " --> pdb=" O THR B 273 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N VAL B 275 " --> pdb=" O ASN B 440 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ASN B 440 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N PHE B 316 " --> pdb=" O SER B 430 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ASN B 432 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N GLU B 318 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N PHE B 434 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 475 through 479 Processing sheet with id= X, first strand: chain 'B' and resid 872 through 875 removed outlier: 6.084A pdb=" N LEU B 560 " --> pdb=" O ILE B 846 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL B 848 " --> pdb=" O LEU B 560 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ILE B 562 " --> pdb=" O VAL B 848 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 563 " --> pdb=" O VAL B 652 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 967 through 974 removed outlier: 6.623A pdb=" N THR B1059 " --> pdb=" O SER B1049 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ASN B1051 " --> pdb=" O SER B1057 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N SER B1057 " --> pdb=" O ASN B1051 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N SER B1066 " --> pdb=" O LEU B1076 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU B1076 " --> pdb=" O SER B1066 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU B1087 " --> pdb=" O VAL B1017 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N VAL B1017 " --> pdb=" O GLU B1087 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL B1242 " --> pdb=" O LEU B1250 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLN B1252 " --> pdb=" O ILE B1240 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ILE B1240 " --> pdb=" O GLN B1252 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU B1254 " --> pdb=" O GLY B1238 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLY B1238 " --> pdb=" O GLU B1254 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP B1239 " --> pdb=" O ASN B1228 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN B1228 " --> pdb=" O ASP B1239 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B1241 " --> pdb=" O THR B1226 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR B1226 " --> pdb=" O VAL B1241 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N PHE B1243 " --> pdb=" O PHE B1224 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N PHE B1224 " --> pdb=" O PHE B1243 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 1235 through 1238 removed outlier: 5.555A pdb=" N LYS B1259 " --> pdb=" O PRO B1198 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'B' and resid 1275 through 1280 removed outlier: 6.772A pdb=" N SER B1689 " --> pdb=" O SER B1721 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N THR B1723 " --> pdb=" O SER B1689 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N PHE B1691 " --> pdb=" O THR B1723 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N TRP B1725 " --> pdb=" O PHE B1691 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N MET B1693 " --> pdb=" O TRP B1725 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR B1727 " --> pdb=" O MET B1693 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 1614 through 1618 removed outlier: 3.693A pdb=" N LEU B1514 " --> pdb=" O ASP B1441 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE B1442 " --> pdb=" O ASN B1465 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR B1467 " --> pdb=" O ILE B1442 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N GLU B1444 " --> pdb=" O TYR B1467 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N TYR B1469 " --> pdb=" O GLU B1444 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 1828 through 1832 Processing sheet with id= AD, first strand: chain 'B' and resid 1838 through 1842 Processing sheet with id= AE, first strand: chain 'B' and resid 1915 through 1918 removed outlier: 7.795A pdb=" N THR B1870 " --> pdb=" O GLN B1897 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLN B1897 " --> pdb=" O THR B1870 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLN B1893 " --> pdb=" O HIS B1874 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER B1876 " --> pdb=" O LEU B1891 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU B1891 " --> pdb=" O SER B1876 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 1875 through 1877 Processing sheet with id= AG, first strand: chain 'B' and resid 1988 through 1992 removed outlier: 4.060A pdb=" N ALA B2031 " --> pdb=" O SER B1964 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ALA B2057 " --> pdb=" O LEU B2032 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ASP B2034 " --> pdb=" O ALA B2057 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TYR B2059 " --> pdb=" O ASP B2034 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'B' and resid 2207 through 2210 removed outlier: 6.341A pdb=" N TYR B2159 " --> pdb=" O VAL B2185 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR B2187 " --> pdb=" O TYR B2159 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N LEU B2161 " --> pdb=" O THR B2187 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU B2160 " --> pdb=" O GLY B2237 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ILE B2239 " --> pdb=" O LEU B2160 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B2162 " --> pdb=" O ILE B2239 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE B2241 " --> pdb=" O VAL B2162 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B2288 " --> pdb=" O ILE B2239 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N PHE B2241 " --> pdb=" O PHE B2288 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B2290 " --> pdb=" O PHE B2241 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N SER B2329 " --> pdb=" O MET B2291 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N SER B2293 " --> pdb=" O SER B2329 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ILE B2331 " --> pdb=" O SER B2293 " (cutoff:3.500A) 1455 hydrogen bonds defined for protein. 3825 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: 34.20 Time building geometry restraints manager: 51.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 34614 1.04 - 1.24: 5443 1.24 - 1.45: 12784 1.45 - 1.65: 23364 1.65 - 1.85: 343 Bond restraints: 76548 Sorted by residual: bond pdb=" C5A NAP A3500 " pdb=" N7A NAP A3500 " ideal model delta sigma weight residual 1.370 1.519 -0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" C5A NAP B3500 " pdb=" N7A NAP B3500 " ideal model delta sigma weight residual 1.370 1.519 -0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" C1B NAP A3500 " pdb=" O4B NAP A3500 " ideal model delta sigma weight residual 1.400 1.528 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C1B NAP B3500 " pdb=" O4B NAP B3500 " ideal model delta sigma weight residual 1.400 1.528 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C6A NAP B3500 " pdb=" N6A NAP B3500 " ideal model delta sigma weight residual 1.335 1.451 -0.116 2.00e-02 2.50e+03 3.35e+01 ... (remaining 76543 not shown) Histogram of bond angle deviations from ideal: 57.59 - 73.44: 39 73.44 - 89.28: 87 89.28 - 105.13: 1091 105.13 - 120.97: 116098 120.97 - 136.81: 18377 Bond angle restraints: 135692 Sorted by residual: angle pdb=" C PRO B 773 " pdb=" N TYR B 774 " pdb=" H TYR B 774 " ideal model delta sigma weight residual 124.93 67.85 57.08 3.00e+00 1.11e-01 3.62e+02 angle pdb=" CA TYR B 774 " pdb=" N TYR B 774 " pdb=" H TYR B 774 " ideal model delta sigma weight residual 114.63 57.59 57.04 3.00e+00 1.11e-01 3.61e+02 angle pdb=" C ILE B1308 " pdb=" N VAL B1309 " pdb=" H VAL B1309 " ideal model delta sigma weight residual 124.30 67.34 56.95 3.00e+00 1.11e-01 3.60e+02 angle pdb=" C TYR B 136 " pdb=" N GLU B 137 " pdb=" H GLU B 137 " ideal model delta sigma weight residual 125.01 68.08 56.93 3.00e+00 1.11e-01 3.60e+02 angle pdb=" C LEU B 778 " pdb=" N GLU B 779 " pdb=" H GLU B 779 " ideal model delta sigma weight residual 125.01 68.13 56.88 3.00e+00 1.11e-01 3.59e+02 ... (remaining 135687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 34424 17.39 - 34.78: 1696 34.78 - 52.18: 689 52.18 - 69.57: 209 69.57 - 86.96: 86 Dihedral angle restraints: 37104 sinusoidal: 19550 harmonic: 17554 Sorted by residual: dihedral pdb=" C ASP C 321 " pdb=" N ASP C 321 " pdb=" CA ASP C 321 " pdb=" CB ASP C 321 " ideal model delta harmonic sigma weight residual -122.60 -136.62 14.02 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" C ASP D 321 " pdb=" N ASP D 321 " pdb=" CA ASP D 321 " pdb=" CB ASP D 321 " ideal model delta harmonic sigma weight residual -122.60 -136.57 13.97 0 2.50e+00 1.60e-01 3.12e+01 dihedral pdb=" N ASP C 321 " pdb=" C ASP C 321 " pdb=" CA ASP C 321 " pdb=" CB ASP C 321 " ideal model delta harmonic sigma weight residual 122.80 136.40 -13.60 0 2.50e+00 1.60e-01 2.96e+01 ... (remaining 37101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 6265 0.186 - 0.372: 89 0.372 - 0.558: 19 0.558 - 0.744: 7 0.744 - 0.930: 2 Chirality restraints: 6382 Sorted by residual: chirality pdb=" CG LEU C 147 " pdb=" CB LEU C 147 " pdb=" CD1 LEU C 147 " pdb=" CD2 LEU C 147 " both_signs ideal model delta sigma weight residual False -2.59 -1.66 -0.93 2.00e-01 2.50e+01 2.16e+01 chirality pdb=" CG LEU D 147 " pdb=" CB LEU D 147 " pdb=" CD1 LEU D 147 " pdb=" CD2 LEU D 147 " both_signs ideal model delta sigma weight residual False -2.59 -1.66 -0.93 2.00e-01 2.50e+01 2.16e+01 chirality pdb=" CG LEU B2251 " pdb=" CB LEU B2251 " pdb=" CD1 LEU B2251 " pdb=" CD2 LEU B2251 " both_signs ideal model delta sigma weight residual False -2.59 -1.87 -0.72 2.00e-01 2.50e+01 1.28e+01 ... (remaining 6379 not shown) Planarity restraints: 11670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 70 " -0.035 2.00e-02 2.50e+03 2.04e-02 8.29e+00 pdb=" CG TYR D 70 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 70 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR D 70 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR D 70 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 70 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR D 70 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR D 70 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 70 " -0.035 2.00e-02 2.50e+03 2.03e-02 8.28e+00 pdb=" CG TYR C 70 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR C 70 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR C 70 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR C 70 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 70 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR C 70 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR C 70 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 190 " -0.033 2.00e-02 2.50e+03 1.90e-02 7.24e+00 pdb=" CG TYR C 190 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR C 190 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR C 190 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 190 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 190 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 190 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR C 190 " -0.005 2.00e-02 2.50e+03 ... (remaining 11667 not shown) Histogram of nonbonded interaction distances: 1.09 - 1.79: 383 1.79 - 2.50: 54388 2.50 - 3.20: 240019 3.20 - 3.90: 323120 3.90 - 4.60: 515259 Nonbonded interactions: 1133169 Sorted by model distance: nonbonded pdb=" H ASN B1900 " pdb=" HA ASN B1900 " model vdw 1.093 1.816 nonbonded pdb=" H VAL B1309 " pdb=" HA VAL B1309 " model vdw 1.358 1.816 nonbonded pdb=" H ASP B1566 " pdb=" HA ASP B1566 " model vdw 1.371 1.816 nonbonded pdb=" H GLU B 780 " pdb=" HA GLU B 780 " model vdw 1.412 1.816 nonbonded pdb=" H GLN B1461 " pdb=" HA GLN B1461 " model vdw 1.474 1.816 ... (remaining 1133164 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.890 Extract box with map and model: 10.980 Check model and map are aligned: 0.820 Set scattering table: 0.510 Process input model: 199.200 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 219.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 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 : 0.007 0.149 41876 Z= 0.478 Angle : 0.834 21.210 57018 Z= 0.463 Chirality : 0.067 0.930 6382 Planarity : 0.004 0.038 7424 Dihedral : 11.839 86.818 15294 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.88 % Favored : 96.04 % Rotamer: Outliers : 3.10 % Allowed : 5.03 % Favored : 91.87 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.12), residues: 5178 helix: 0.87 (0.12), residues: 1940 sheet: -0.43 (0.19), residues: 750 loop : -0.27 (0.13), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 63 HIS 0.007 0.001 HIS D 326 PHE 0.027 0.002 PHE C 265 TYR 0.038 0.002 TYR D 190 ARG 0.008 0.001 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 1271 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1135 time to evaluate : 4.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 146 LEU cc_start: 0.1683 (OUTLIER) cc_final: 0.1156 (mt) REVERT: D 274 MET cc_start: 0.1380 (mtt) cc_final: 0.0879 (tpp) REVERT: D 361 GLU cc_start: 0.3542 (OUTLIER) cc_final: 0.2114 (mt-10) REVERT: A 292 GLN cc_start: 0.7767 (mt0) cc_final: 0.7563 (mt0) REVERT: A 1234 ASP cc_start: 0.7484 (p0) cc_final: 0.6871 (p0) REVERT: A 1250 LEU cc_start: 0.8614 (mt) cc_final: 0.8398 (mp) REVERT: A 1368 HIS cc_start: 0.4363 (m170) cc_final: 0.3994 (m170) REVERT: A 1376 HIS cc_start: 0.6445 (t70) cc_final: 0.5788 (t-170) REVERT: A 1515 ILE cc_start: 0.8967 (mt) cc_final: 0.8675 (mt) REVERT: A 1546 ILE cc_start: 0.8335 (mt) cc_final: 0.7930 (mm) REVERT: A 1605 ARG cc_start: 0.4460 (OUTLIER) cc_final: 0.3618 (ptt-90) REVERT: A 1722 ASN cc_start: 0.7276 (m-40) cc_final: 0.6910 (t0) REVERT: A 1761 VAL cc_start: 0.8443 (t) cc_final: 0.7916 (m) REVERT: A 1775 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.5929 (tm-30) REVERT: A 1820 MET cc_start: 0.8312 (ttp) cc_final: 0.8020 (ttp) REVERT: A 1850 PHE cc_start: 0.7994 (p90) cc_final: 0.7720 (p90) REVERT: A 2178 GLN cc_start: 0.8291 (mt0) cc_final: 0.8043 (mt0) REVERT: A 2254 MET cc_start: 0.8246 (ttm) cc_final: 0.7583 (ttm) REVERT: A 2418 PHE cc_start: 0.7358 (p90) cc_final: 0.7105 (p90) REVERT: A 2419 PHE cc_start: 0.8330 (t80) cc_final: 0.8075 (t80) REVERT: B 30 LEU cc_start: 0.9189 (tp) cc_final: 0.8889 (tt) REVERT: B 179 THR cc_start: 0.8316 (p) cc_final: 0.8063 (p) REVERT: B 307 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7900 (mp) REVERT: B 318 GLU cc_start: 0.7515 (tm-30) cc_final: 0.6846 (tm-30) REVERT: B 360 SER cc_start: 0.8420 (t) cc_final: 0.8021 (t) REVERT: B 394 LEU cc_start: 0.8349 (mm) cc_final: 0.8119 (mm) REVERT: B 767 MET cc_start: 0.3674 (mtt) cc_final: 0.3459 (mtt) REVERT: B 893 TYR cc_start: 0.7578 (t80) cc_final: 0.6913 (t80) REVERT: B 963 SER cc_start: 0.8814 (m) cc_final: 0.8553 (p) REVERT: B 1032 ILE cc_start: 0.8716 (mm) cc_final: 0.8472 (tp) REVERT: B 1044 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8676 (tt) REVERT: B 1281 LEU cc_start: 0.7941 (tt) cc_final: 0.7109 (tt) REVERT: B 1404 ASP cc_start: 0.7339 (m-30) cc_final: 0.7083 (m-30) REVERT: B 1429 LEU cc_start: 0.8872 (tp) cc_final: 0.8453 (mt) REVERT: B 1762 ASP cc_start: 0.6406 (p0) cc_final: 0.6183 (t70) REVERT: B 1777 LEU cc_start: 0.8403 (mm) cc_final: 0.7913 (tp) REVERT: B 1872 TYR cc_start: 0.7586 (m-80) cc_final: 0.7323 (m-80) REVERT: B 1938 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6934 (tt) REVERT: B 2330 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8198 (p) REVERT: B 2331 ILE cc_start: 0.8619 (pt) cc_final: 0.8364 (pt) REVERT: B 2400 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7204 (mt-10) outliers start: 136 outliers final: 41 residues processed: 1224 average time/residue: 1.1467 time to fit residues: 2198.3493 Evaluate side-chains 716 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 667 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 762 TYR Chi-restraints excluded: chain A residue 884 LEU Chi-restraints excluded: chain A residue 937 TRP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1070 LYS Chi-restraints excluded: chain A residue 1384 ARG Chi-restraints excluded: chain A residue 1464 PHE Chi-restraints excluded: chain A residue 1559 PHE Chi-restraints excluded: chain A residue 1601 ARG Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1775 GLN Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 2088 TRP Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2426 ASN Chi-restraints excluded: chain A residue 2431 GLU Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1464 PHE Chi-restraints excluded: chain B residue 1544 MET Chi-restraints excluded: chain B residue 1559 PHE Chi-restraints excluded: chain B residue 1567 TRP Chi-restraints excluded: chain B residue 1605 ARG Chi-restraints excluded: chain B residue 1725 TRP Chi-restraints excluded: chain B residue 1807 ILE Chi-restraints excluded: chain B residue 1938 LEU Chi-restraints excluded: chain B residue 2330 THR Chi-restraints excluded: chain B residue 2362 GLU Chi-restraints excluded: chain B residue 2387 GLN Chi-restraints excluded: chain B residue 2431 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 440 optimal weight: 8.9990 chunk 395 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 135 optimal weight: 9.9990 chunk 266 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 chunk 409 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 248 optimal weight: 7.9990 chunk 304 optimal weight: 3.9990 chunk 474 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 27 ASN C 129 GLN C 183 GLN C 199 HIS C 222 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 HIS C 338 HIS D 58 GLN D 129 GLN D 158 GLN D 183 GLN D 199 HIS D 222 GLN D 230 ASN D 231 ASN D 327 HIS D 338 HIS D 341 GLN ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 ASN ** A1255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 HIS A1483 GLN B 25 ASN B 41 GLN ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1331 HIS ** B1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1378 HIS B1794 GLN B2117 HIS ** B2387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2426 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 41876 Z= 0.428 Angle : 0.715 24.682 57018 Z= 0.378 Chirality : 0.065 1.533 6382 Planarity : 0.005 0.084 7424 Dihedral : 8.079 84.997 5906 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.39 % Favored : 94.57 % Rotamer: Outliers : 3.37 % Allowed : 10.91 % Favored : 85.72 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.56 % 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: -0.37 (0.12), residues: 5178 helix: 0.43 (0.12), residues: 1946 sheet: -0.81 (0.18), residues: 784 loop : -0.48 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 312 HIS 0.010 0.001 HIS A 505 PHE 0.022 0.002 PHE A1135 TYR 0.028 0.002 TYR A1235 ARG 0.012 0.001 ARG A1380 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 811 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 663 time to evaluate : 4.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 345 LEU cc_start: 0.1805 (OUTLIER) cc_final: 0.1469 (tp) REVERT: D 182 MET cc_start: -0.1216 (mmm) cc_final: -0.1783 (ttm) REVERT: D 274 MET cc_start: 0.1589 (mtt) cc_final: 0.0792 (tpp) REVERT: D 361 GLU cc_start: 0.3445 (OUTLIER) cc_final: 0.1819 (mt-10) REVERT: A 566 GLN cc_start: 0.6138 (tt0) cc_final: 0.5929 (tt0) REVERT: A 1127 MET cc_start: 0.8073 (mmm) cc_final: 0.7737 (mmm) REVERT: A 1546 ILE cc_start: 0.8547 (mt) cc_final: 0.8061 (mm) REVERT: A 1605 ARG cc_start: 0.4761 (OUTLIER) cc_final: 0.3949 (ptt-90) REVERT: A 1722 ASN cc_start: 0.7493 (m-40) cc_final: 0.7027 (m-40) REVERT: A 1758 VAL cc_start: 0.8466 (m) cc_final: 0.8150 (t) REVERT: A 1759 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7863 (tt) REVERT: A 1775 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.6432 (tm-30) REVERT: A 1850 PHE cc_start: 0.8380 (p90) cc_final: 0.8136 (p90) REVERT: A 2178 GLN cc_start: 0.8591 (mt0) cc_final: 0.8258 (mt0) REVERT: A 2254 MET cc_start: 0.8174 (ttm) cc_final: 0.7972 (ttm) REVERT: A 2418 PHE cc_start: 0.7422 (p90) cc_final: 0.7185 (p90) REVERT: A 2424 ILE cc_start: 0.8965 (pt) cc_final: 0.8673 (pt) REVERT: B 169 ASP cc_start: 0.8001 (t0) cc_final: 0.7448 (t70) REVERT: B 202 MET cc_start: 0.8365 (ttp) cc_final: 0.8089 (ttp) REVERT: B 215 MET cc_start: 0.8295 (tmm) cc_final: 0.8055 (tmm) REVERT: B 276 ASN cc_start: 0.8872 (OUTLIER) cc_final: 0.8635 (p0) REVERT: B 307 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8081 (mp) REVERT: B 318 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7065 (tm-30) REVERT: B 524 ILE cc_start: 0.8697 (mm) cc_final: 0.8359 (mm) REVERT: B 893 TYR cc_start: 0.7554 (t80) cc_final: 0.7049 (t80) REVERT: B 1032 ILE cc_start: 0.8789 (mm) cc_final: 0.8502 (tp) REVERT: B 1429 LEU cc_start: 0.8887 (tp) cc_final: 0.8440 (mt) REVERT: B 1531 MET cc_start: 0.7720 (ttm) cc_final: 0.7336 (ttm) REVERT: B 1777 LEU cc_start: 0.8504 (mm) cc_final: 0.8010 (tp) REVERT: B 1849 TYR cc_start: 0.8214 (m-80) cc_final: 0.7936 (m-80) REVERT: B 2372 GLU cc_start: 0.8334 (tp30) cc_final: 0.7910 (tp30) outliers start: 148 outliers final: 97 residues processed: 771 average time/residue: 1.0104 time to fit residues: 1254.9692 Evaluate side-chains 654 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 550 time to evaluate : 4.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 361 GLU Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 762 TYR Chi-restraints excluded: chain A residue 850 CYS Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 937 TRP Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1209 SER Chi-restraints excluded: chain A residue 1262 SER Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1464 PHE Chi-restraints excluded: chain A residue 1559 PHE Chi-restraints excluded: chain A residue 1567 TRP Chi-restraints excluded: chain A residue 1601 ARG Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1615 PHE Chi-restraints excluded: chain A residue 1718 THR Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1775 GLN Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1906 VAL Chi-restraints excluded: chain A residue 1910 GLU Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 2088 TRP Chi-restraints excluded: chain A residue 2107 GLU Chi-restraints excluded: chain A residue 2119 ASP Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2261 MET Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2293 SER Chi-restraints excluded: chain A residue 2426 ASN Chi-restraints excluded: chain A residue 2431 GLU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 966 LEU Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1037 ASP Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1246 GLU Chi-restraints excluded: chain B residue 1262 SER Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1384 ARG Chi-restraints excluded: chain B residue 1464 PHE Chi-restraints excluded: chain B residue 1526 ASP Chi-restraints excluded: chain B residue 1544 MET Chi-restraints excluded: chain B residue 1559 PHE Chi-restraints excluded: chain B residue 1567 TRP Chi-restraints excluded: chain B residue 1605 ARG Chi-restraints excluded: chain B residue 1614 VAL Chi-restraints excluded: chain B residue 1701 LEU Chi-restraints excluded: chain B residue 1725 TRP Chi-restraints excluded: chain B residue 1780 GLU Chi-restraints excluded: chain B residue 1807 ILE Chi-restraints excluded: chain B residue 1822 SER Chi-restraints excluded: chain B residue 1841 GLN Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1963 ASP Chi-restraints excluded: chain B residue 2136 ASP Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2368 THR Chi-restraints excluded: chain B residue 2387 GLN Chi-restraints excluded: chain B residue 2424 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 263 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 394 optimal weight: 2.9990 chunk 322 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 474 optimal weight: 2.9990 chunk 513 optimal weight: 4.9990 chunk 422 optimal weight: 10.0000 chunk 470 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 380 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 ASN ** B 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1378 HIS B2030 GLN ** B2387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 41876 Z= 0.271 Angle : 0.655 27.487 57018 Z= 0.340 Chirality : 0.066 1.667 6382 Planarity : 0.004 0.052 7424 Dihedral : 7.584 87.839 5883 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 2.96 % Allowed : 12.23 % Favored : 84.81 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.41 (0.12), residues: 5178 helix: 0.34 (0.12), residues: 1930 sheet: -0.86 (0.18), residues: 768 loop : -0.45 (0.13), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 63 HIS 0.007 0.001 HIS B 62 PHE 0.022 0.002 PHE B1595 TYR 0.020 0.001 TYR A1235 ARG 0.011 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 715 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 585 time to evaluate : 4.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 343 MET cc_start: -0.0549 (OUTLIER) cc_final: -0.0920 (ttp) REVERT: C 345 LEU cc_start: 0.1949 (OUTLIER) cc_final: 0.1560 (tp) REVERT: D 274 MET cc_start: 0.1774 (mtt) cc_final: 0.0875 (tpp) REVERT: A 318 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6777 (tm-30) REVERT: A 489 MET cc_start: 0.8500 (mtm) cc_final: 0.8272 (mmm) REVERT: A 774 TYR cc_start: 0.3821 (t80) cc_final: 0.3519 (t80) REVERT: A 1127 MET cc_start: 0.8041 (mmm) cc_final: 0.7661 (mmm) REVERT: A 1491 MET cc_start: 0.7024 (ttm) cc_final: 0.6216 (ttm) REVERT: A 1605 ARG cc_start: 0.4608 (OUTLIER) cc_final: 0.3750 (ptt-90) REVERT: A 1722 ASN cc_start: 0.7406 (m-40) cc_final: 0.7106 (t0) REVERT: A 1775 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.6372 (tm-30) REVERT: A 1850 PHE cc_start: 0.8317 (p90) cc_final: 0.8036 (p90) REVERT: A 2254 MET cc_start: 0.8147 (ttm) cc_final: 0.7816 (ttm) REVERT: B 30 LEU cc_start: 0.9288 (tp) cc_final: 0.9060 (tt) REVERT: B 169 ASP cc_start: 0.7991 (t0) cc_final: 0.7545 (t0) REVERT: B 215 MET cc_start: 0.8285 (tmm) cc_final: 0.8059 (tmm) REVERT: B 276 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8602 (p0) REVERT: B 307 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8107 (mp) REVERT: B 318 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7099 (tm-30) REVERT: B 524 ILE cc_start: 0.8663 (mm) cc_final: 0.8330 (mm) REVERT: B 563 PHE cc_start: 0.6685 (m-80) cc_final: 0.6197 (m-80) REVERT: B 1032 ILE cc_start: 0.8783 (mm) cc_final: 0.8499 (tp) REVERT: B 1429 LEU cc_start: 0.8881 (tp) cc_final: 0.8453 (mt) REVERT: B 1849 TYR cc_start: 0.8241 (m-80) cc_final: 0.7962 (m-80) REVERT: B 1943 LEU cc_start: 0.7782 (mm) cc_final: 0.6986 (mm) REVERT: B 2142 THR cc_start: 0.9090 (m) cc_final: 0.8727 (p) REVERT: B 2174 ARG cc_start: 0.8314 (ptm-80) cc_final: 0.7821 (ttp-170) outliers start: 130 outliers final: 100 residues processed: 677 average time/residue: 0.9960 time to fit residues: 1089.4258 Evaluate side-chains 642 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 536 time to evaluate : 4.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 762 TYR Chi-restraints excluded: chain A residue 830 HIS Chi-restraints excluded: chain A residue 850 CYS Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 937 TRP Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1209 SER Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1262 SER Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1464 PHE Chi-restraints excluded: chain A residue 1559 PHE Chi-restraints excluded: chain A residue 1601 ARG Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1615 PHE Chi-restraints excluded: chain A residue 1618 HIS Chi-restraints excluded: chain A residue 1718 THR Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1775 GLN Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 1810 LEU Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 2107 GLU Chi-restraints excluded: chain A residue 2119 ASP Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2261 MET Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2278 SER Chi-restraints excluded: chain A residue 2293 SER Chi-restraints excluded: chain A residue 2426 ASN Chi-restraints excluded: chain A residue 2431 GLU Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain B residue 833 GLN Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1384 ARG Chi-restraints excluded: chain B residue 1476 PHE Chi-restraints excluded: chain B residue 1526 ASP Chi-restraints excluded: chain B residue 1544 MET Chi-restraints excluded: chain B residue 1545 VAL Chi-restraints excluded: chain B residue 1559 PHE Chi-restraints excluded: chain B residue 1567 TRP Chi-restraints excluded: chain B residue 1605 ARG Chi-restraints excluded: chain B residue 1608 ASN Chi-restraints excluded: chain B residue 1614 VAL Chi-restraints excluded: chain B residue 1725 TRP Chi-restraints excluded: chain B residue 1780 GLU Chi-restraints excluded: chain B residue 1789 SER Chi-restraints excluded: chain B residue 1807 ILE Chi-restraints excluded: chain B residue 1822 SER Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1881 LEU Chi-restraints excluded: chain B residue 1938 LEU Chi-restraints excluded: chain B residue 1963 ASP Chi-restraints excluded: chain B residue 2293 SER Chi-restraints excluded: chain B residue 2368 THR Chi-restraints excluded: chain B residue 2387 GLN Chi-restraints excluded: chain B residue 2426 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 469 optimal weight: 0.0980 chunk 357 optimal weight: 10.0000 chunk 246 optimal weight: 8.9990 chunk 52 optimal weight: 30.0000 chunk 226 optimal weight: 5.9990 chunk 318 optimal weight: 1.9990 chunk 476 optimal weight: 7.9990 chunk 504 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 451 optimal weight: 10.0000 chunk 135 optimal weight: 0.0770 overall best weight: 1.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN D 104 GLN ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1162 ASN A1378 HIS A1734 HIS ** A1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1378 HIS B2030 GLN ** B2387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 41876 Z= 0.283 Angle : 0.652 30.547 57018 Z= 0.337 Chirality : 0.066 1.691 6382 Planarity : 0.004 0.057 7424 Dihedral : 7.403 89.773 5874 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.83 % Favored : 94.13 % Rotamer: Outliers : 3.19 % Allowed : 12.57 % Favored : 84.24 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.12), residues: 5178 helix: 0.27 (0.12), residues: 1908 sheet: -0.92 (0.18), residues: 768 loop : -0.47 (0.13), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 279 HIS 0.019 0.001 HIS A1895 PHE 0.025 0.001 PHE A1507 TYR 0.020 0.001 TYR A1235 ARG 0.009 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 708 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 568 time to evaluate : 4.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 343 MET cc_start: 0.0177 (OUTLIER) cc_final: -0.0324 (ttp) REVERT: C 345 LEU cc_start: 0.1969 (OUTLIER) cc_final: 0.1598 (tp) REVERT: D 55 MET cc_start: 0.2914 (mmt) cc_final: 0.2565 (mmt) REVERT: D 274 MET cc_start: 0.2189 (mtt) cc_final: 0.1187 (tpp) REVERT: D 343 MET cc_start: 0.2436 (mtt) cc_final: 0.0081 (mmt) REVERT: A 1127 MET cc_start: 0.8021 (mmm) cc_final: 0.7638 (mmm) REVERT: A 1507 PHE cc_start: 0.7168 (m-10) cc_final: 0.6614 (m-10) REVERT: A 1605 ARG cc_start: 0.4613 (OUTLIER) cc_final: 0.3755 (ptt-90) REVERT: A 1710 PHE cc_start: 0.7114 (t80) cc_final: 0.6774 (t80) REVERT: A 1722 ASN cc_start: 0.7362 (m-40) cc_final: 0.7073 (t0) REVERT: A 1759 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7774 (tt) REVERT: A 1775 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.6443 (tm-30) REVERT: A 1850 PHE cc_start: 0.8316 (p90) cc_final: 0.8113 (p90) REVERT: A 2254 MET cc_start: 0.8205 (ttm) cc_final: 0.7836 (ttm) REVERT: B 30 LEU cc_start: 0.9291 (tp) cc_final: 0.9059 (tt) REVERT: B 169 ASP cc_start: 0.7976 (t0) cc_final: 0.7435 (t0) REVERT: B 276 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8645 (p0) REVERT: B 318 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7153 (tm-30) REVERT: B 524 ILE cc_start: 0.8670 (mm) cc_final: 0.8349 (mm) REVERT: B 563 PHE cc_start: 0.6848 (m-80) cc_final: 0.6351 (m-80) REVERT: B 1032 ILE cc_start: 0.8812 (mm) cc_final: 0.8514 (tp) REVERT: B 1412 PHE cc_start: 0.7201 (t80) cc_final: 0.6810 (t80) REVERT: B 1429 LEU cc_start: 0.8892 (tp) cc_final: 0.8375 (mt) REVERT: B 1777 LEU cc_start: 0.8498 (mm) cc_final: 0.7818 (tp) REVERT: B 1849 TYR cc_start: 0.8297 (m-80) cc_final: 0.8040 (m-80) REVERT: B 2142 THR cc_start: 0.9104 (m) cc_final: 0.8752 (p) REVERT: B 2337 TYR cc_start: 0.6627 (m-80) cc_final: 0.6414 (m-80) outliers start: 140 outliers final: 106 residues processed: 666 average time/residue: 1.0254 time to fit residues: 1119.1812 Evaluate side-chains 643 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 531 time to evaluate : 4.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 33 MET Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 762 TYR Chi-restraints excluded: chain A residue 830 HIS Chi-restraints excluded: chain A residue 937 TRP Chi-restraints excluded: chain A residue 963 SER Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1147 ARG Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1209 SER Chi-restraints excluded: chain A residue 1262 SER Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1464 PHE Chi-restraints excluded: chain A residue 1559 PHE Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1615 PHE Chi-restraints excluded: chain A residue 1618 HIS Chi-restraints excluded: chain A residue 1718 THR Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1739 SER Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1775 GLN Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 2107 GLU Chi-restraints excluded: chain A residue 2119 ASP Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2278 SER Chi-restraints excluded: chain A residue 2293 SER Chi-restraints excluded: chain A residue 2369 LEU Chi-restraints excluded: chain A residue 2426 ASN Chi-restraints excluded: chain A residue 2431 GLU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 121 GLN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 220 GLU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 276 ASN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 982 LEU Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain B residue 1037 ASP Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1262 SER Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1384 ARG Chi-restraints excluded: chain B residue 1443 LEU Chi-restraints excluded: chain B residue 1476 PHE Chi-restraints excluded: chain B residue 1526 ASP Chi-restraints excluded: chain B residue 1544 MET Chi-restraints excluded: chain B residue 1545 VAL Chi-restraints excluded: chain B residue 1559 PHE Chi-restraints excluded: chain B residue 1567 TRP Chi-restraints excluded: chain B residue 1605 ARG Chi-restraints excluded: chain B residue 1614 VAL Chi-restraints excluded: chain B residue 1725 TRP Chi-restraints excluded: chain B residue 1780 GLU Chi-restraints excluded: chain B residue 1789 SER Chi-restraints excluded: chain B residue 1807 ILE Chi-restraints excluded: chain B residue 1822 SER Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1881 LEU Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 1963 ASP Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2368 THR Chi-restraints excluded: chain B residue 2387 GLN Chi-restraints excluded: chain B residue 2426 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 420 optimal weight: 9.9990 chunk 286 optimal weight: 3.9990 chunk 7 optimal weight: 40.0000 chunk 375 optimal weight: 9.9990 chunk 208 optimal weight: 0.6980 chunk 430 optimal weight: 7.9990 chunk 348 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 257 optimal weight: 4.9990 chunk 452 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 HIS C 222 GLN ** C 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 GLN A 635 GLN ** A 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1118 ASN A1162 ASN A1365 GLN A1378 HIS ** A1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2284 ASN ** B 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 GLN ** B1081 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1378 HIS ** B1618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.084 41876 Z= 0.623 Angle : 0.823 31.616 57018 Z= 0.440 Chirality : 0.070 1.642 6382 Planarity : 0.006 0.117 7424 Dihedral : 7.930 86.580 5866 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 30.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.01 % Favored : 91.93 % Rotamer: Outliers : 4.03 % Allowed : 13.32 % Favored : 82.65 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.11), residues: 5178 helix: -0.63 (0.11), residues: 1936 sheet: -1.43 (0.17), residues: 812 loop : -1.17 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 63 HIS 0.011 0.002 HIS B1013 PHE 0.042 0.003 PHE A1507 TYR 0.031 0.003 TYR A1235 ARG 0.012 0.001 ARG A1601 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 720 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 543 time to evaluate : 4.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 343 MET cc_start: 0.0826 (OUTLIER) cc_final: 0.0292 (ttp) REVERT: C 345 LEU cc_start: 0.1985 (OUTLIER) cc_final: 0.1586 (tp) REVERT: D 274 MET cc_start: 0.2692 (mtt) cc_final: 0.1305 (tmm) REVERT: D 343 MET cc_start: 0.2593 (mtt) cc_final: 0.0133 (tpp) REVERT: A 1127 MET cc_start: 0.8121 (mmm) cc_final: 0.7898 (mmt) REVERT: A 1147 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7627 (ttm170) REVERT: A 1191 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7835 (ttt90) REVERT: A 1722 ASN cc_start: 0.7709 (m-40) cc_final: 0.7458 (t0) REVERT: A 1759 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.8059 (tt) REVERT: A 1850 PHE cc_start: 0.8570 (p90) cc_final: 0.8217 (p90) REVERT: A 2094 LEU cc_start: 0.7707 (mt) cc_final: 0.7505 (mt) REVERT: A 2320 GLN cc_start: 0.8571 (OUTLIER) cc_final: 0.8162 (pp30) REVERT: A 2364 HIS cc_start: 0.8295 (m-70) cc_final: 0.8071 (m-70) REVERT: B 169 ASP cc_start: 0.8319 (t0) cc_final: 0.7853 (t70) REVERT: B 369 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7386 (mm-30) REVERT: B 524 ILE cc_start: 0.8796 (mm) cc_final: 0.8424 (mm) REVERT: B 573 MET cc_start: 0.3150 (mmp) cc_final: 0.2902 (mmp) REVERT: B 1024 ASP cc_start: 0.8327 (t70) cc_final: 0.8053 (t0) REVERT: B 1032 ILE cc_start: 0.8867 (mm) cc_final: 0.8503 (tp) REVERT: B 1429 LEU cc_start: 0.8897 (tp) cc_final: 0.8457 (mt) REVERT: B 1557 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7265 (pp) REVERT: B 1600 SER cc_start: 0.6445 (t) cc_final: 0.6037 (t) REVERT: B 1977 MET cc_start: 0.8843 (tpp) cc_final: 0.8600 (tpt) REVERT: B 2362 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.6440 (mp0) REVERT: B 2372 GLU cc_start: 0.8482 (tp30) cc_final: 0.8222 (tp30) outliers start: 177 outliers final: 122 residues processed: 668 average time/residue: 0.9603 time to fit residues: 1049.5426 Evaluate side-chains 628 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 498 time to evaluate : 4.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 343 MET Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 188 SER Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 762 TYR Chi-restraints excluded: chain A residue 830 HIS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 937 TRP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1036 GLU Chi-restraints excluded: chain A residue 1048 VAL Chi-restraints excluded: chain A residue 1058 MET Chi-restraints excluded: chain A residue 1147 ARG Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1162 ASN Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1191 ARG Chi-restraints excluded: chain A residue 1209 SER Chi-restraints excluded: chain A residue 1262 SER Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1464 PHE Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1559 PHE Chi-restraints excluded: chain A residue 1584 ASP Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1615 PHE Chi-restraints excluded: chain A residue 1618 HIS Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1759 LEU Chi-restraints excluded: chain A residue 1775 GLN Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 1906 VAL Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 2044 LEU Chi-restraints excluded: chain A residue 2107 GLU Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ASP Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2259 MET Chi-restraints excluded: chain A residue 2261 MET Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2278 SER Chi-restraints excluded: chain A residue 2287 ASP Chi-restraints excluded: chain A residue 2293 SER Chi-restraints excluded: chain A residue 2320 GLN Chi-restraints excluded: chain A residue 2332 ASP Chi-restraints excluded: chain A residue 2341 PHE Chi-restraints excluded: chain A residue 2362 GLU Chi-restraints excluded: chain A residue 2426 ASN Chi-restraints excluded: chain A residue 2431 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain B residue 762 TYR Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1037 ASP Chi-restraints excluded: chain B residue 1159 ASP Chi-restraints excluded: chain B residue 1197 VAL Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1262 SER Chi-restraints excluded: chain B residue 1265 ASP Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1443 LEU Chi-restraints excluded: chain B residue 1476 PHE Chi-restraints excluded: chain B residue 1526 ASP Chi-restraints excluded: chain B residue 1544 MET Chi-restraints excluded: chain B residue 1557 LEU Chi-restraints excluded: chain B residue 1559 PHE Chi-restraints excluded: chain B residue 1567 TRP Chi-restraints excluded: chain B residue 1605 ARG Chi-restraints excluded: chain B residue 1608 ASN Chi-restraints excluded: chain B residue 1614 VAL Chi-restraints excluded: chain B residue 1725 TRP Chi-restraints excluded: chain B residue 1727 THR Chi-restraints excluded: chain B residue 1780 GLU Chi-restraints excluded: chain B residue 1807 ILE Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1881 LEU Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 1963 ASP Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2215 VAL Chi-restraints excluded: chain B residue 2287 ASP Chi-restraints excluded: chain B residue 2293 SER Chi-restraints excluded: chain B residue 2362 GLU Chi-restraints excluded: chain B residue 2387 GLN Chi-restraints excluded: chain B residue 2424 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 169 optimal weight: 0.9980 chunk 454 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 296 optimal weight: 0.6980 chunk 124 optimal weight: 5.9990 chunk 505 optimal weight: 2.9990 chunk 419 optimal weight: 9.9990 chunk 233 optimal weight: 7.9990 chunk 41 optimal weight: 20.0000 chunk 167 optimal weight: 0.5980 chunk 265 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 11 GLN D 258 HIS ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 HIS ** A1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2311 ASN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1378 HIS ** B1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2090 HIS ** B2387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 41876 Z= 0.218 Angle : 0.651 20.155 57018 Z= 0.342 Chirality : 0.066 1.704 6382 Planarity : 0.005 0.064 7424 Dihedral : 7.333 86.741 5859 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.81 % Favored : 94.15 % Rotamer: Outliers : 2.76 % Allowed : 14.91 % Favored : 82.33 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.12), residues: 5178 helix: -0.13 (0.12), residues: 1912 sheet: -1.25 (0.17), residues: 802 loop : -0.79 (0.13), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 279 HIS 0.013 0.001 HIS B1533 PHE 0.022 0.002 PHE A1507 TYR 0.018 0.001 TYR A1235 ARG 0.013 0.000 ARG A1816 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 667 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 546 time to evaluate : 4.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: C 345 LEU cc_start: 0.1830 (OUTLIER) cc_final: 0.1484 (tp) REVERT: D 274 MET cc_start: 0.2550 (mtt) cc_final: 0.1244 (tmm) REVERT: D 343 MET cc_start: 0.2614 (mtt) cc_final: 0.0076 (tpp) REVERT: A 1127 MET cc_start: 0.7984 (mmm) cc_final: 0.7637 (mmt) REVERT: A 1147 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7377 (ttm170) REVERT: A 1605 ARG cc_start: 0.4768 (OUTLIER) cc_final: 0.3706 (ptt-90) REVERT: A 1722 ASN cc_start: 0.7501 (m-40) cc_final: 0.7260 (t0) REVERT: A 1850 PHE cc_start: 0.8365 (p90) cc_final: 0.7960 (p90) REVERT: A 1977 MET cc_start: 0.8170 (tpp) cc_final: 0.7707 (tpp) REVERT: B 169 ASP cc_start: 0.8140 (t0) cc_final: 0.7736 (t70) REVERT: B 369 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6706 (mm-30) REVERT: B 524 ILE cc_start: 0.8718 (mm) cc_final: 0.8331 (mm) REVERT: B 937 TRP cc_start: 0.7253 (OUTLIER) cc_final: 0.7022 (t60) REVERT: B 948 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.7069 (mmt90) REVERT: B 1024 ASP cc_start: 0.8058 (t70) cc_final: 0.7788 (t0) REVERT: B 1032 ILE cc_start: 0.8815 (mm) cc_final: 0.8459 (tp) REVERT: B 1380 ARG cc_start: 0.7432 (tpt170) cc_final: 0.7136 (tpm170) REVERT: B 1429 LEU cc_start: 0.8910 (tp) cc_final: 0.8418 (mt) REVERT: B 1600 SER cc_start: 0.6287 (t) cc_final: 0.5902 (t) REVERT: B 2142 THR cc_start: 0.9150 (m) cc_final: 0.8821 (p) outliers start: 121 outliers final: 100 residues processed: 629 average time/residue: 1.0223 time to fit residues: 1057.6987 Evaluate side-chains 620 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 515 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain D residue 261 SER Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 762 TYR Chi-restraints excluded: chain A residue 830 HIS Chi-restraints excluded: chain A residue 937 TRP Chi-restraints excluded: chain A residue 948 ARG Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1147 ARG Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1262 SER Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1464 PHE Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1559 PHE Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1615 PHE Chi-restraints excluded: chain A residue 1618 HIS Chi-restraints excluded: chain A residue 1650 GLN Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 2107 GLU Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ASP Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2259 MET Chi-restraints excluded: chain A residue 2261 MET Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2278 SER Chi-restraints excluded: chain A residue 2293 SER Chi-restraints excluded: chain A residue 2426 ASN Chi-restraints excluded: chain A residue 2431 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain B residue 937 TRP Chi-restraints excluded: chain B residue 948 ARG Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1037 ASP Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1281 LEU Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1443 LEU Chi-restraints excluded: chain B residue 1476 PHE Chi-restraints excluded: chain B residue 1496 LEU Chi-restraints excluded: chain B residue 1526 ASP Chi-restraints excluded: chain B residue 1544 MET Chi-restraints excluded: chain B residue 1557 LEU Chi-restraints excluded: chain B residue 1559 PHE Chi-restraints excluded: chain B residue 1567 TRP Chi-restraints excluded: chain B residue 1605 ARG Chi-restraints excluded: chain B residue 1608 ASN Chi-restraints excluded: chain B residue 1614 VAL Chi-restraints excluded: chain B residue 1716 LEU Chi-restraints excluded: chain B residue 1725 TRP Chi-restraints excluded: chain B residue 1807 ILE Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1881 LEU Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 1963 ASP Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2167 ASP Chi-restraints excluded: chain B residue 2293 SER Chi-restraints excluded: chain B residue 2387 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 486 optimal weight: 3.9990 chunk 56 optimal weight: 20.0000 chunk 287 optimal weight: 5.9990 chunk 368 optimal weight: 9.9990 chunk 285 optimal weight: 6.9990 chunk 425 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 chunk 503 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1378 HIS ** A1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2311 ASN A2319 GLN ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 GLN ** B1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1378 HIS ** B1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 41876 Z= 0.457 Angle : 0.712 19.699 57018 Z= 0.379 Chirality : 0.068 1.657 6382 Planarity : 0.005 0.070 7424 Dihedral : 7.270 69.122 5856 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 27.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.11 % Favored : 91.81 % Rotamer: Outliers : 3.07 % Allowed : 15.05 % Favored : 81.88 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.11), residues: 5178 helix: -0.39 (0.11), residues: 1950 sheet: -1.48 (0.17), residues: 824 loop : -1.04 (0.13), residues: 2404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 63 HIS 0.013 0.001 HIS C 327 PHE 0.023 0.002 PHE A1507 TYR 0.025 0.002 TYR A1235 ARG 0.009 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 651 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 516 time to evaluate : 4.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 345 LEU cc_start: 0.2021 (OUTLIER) cc_final: 0.1641 (tp) REVERT: D 274 MET cc_start: 0.2586 (mtt) cc_final: 0.1362 (tmm) REVERT: D 343 MET cc_start: 0.2711 (mtt) cc_final: 0.0206 (tpp) REVERT: A 286 MET cc_start: 0.8039 (tpp) cc_final: 0.7434 (tpp) REVERT: A 488 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8225 (mmm) REVERT: A 1127 MET cc_start: 0.7971 (mmm) cc_final: 0.7768 (mmt) REVERT: A 1147 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7445 (ttm170) REVERT: A 1722 ASN cc_start: 0.7651 (m-40) cc_final: 0.7427 (t0) REVERT: A 1760 ASP cc_start: 0.6816 (t0) cc_final: 0.5198 (p0) REVERT: A 1775 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.6545 (tm-30) REVERT: A 1850 PHE cc_start: 0.8487 (p90) cc_final: 0.8092 (p90) REVERT: B 169 ASP cc_start: 0.8249 (t0) cc_final: 0.7740 (t70) REVERT: B 369 GLU cc_start: 0.7496 (mm-30) cc_final: 0.6886 (mm-30) REVERT: B 524 ILE cc_start: 0.8720 (mm) cc_final: 0.8319 (mm) REVERT: B 649 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7244 (m-80) REVERT: B 937 TRP cc_start: 0.7347 (OUTLIER) cc_final: 0.7034 (t60) REVERT: B 948 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.7234 (mmt90) REVERT: B 1024 ASP cc_start: 0.8136 (t70) cc_final: 0.7890 (t0) REVERT: B 1032 ILE cc_start: 0.8862 (mm) cc_final: 0.8595 (tp) REVERT: B 1429 LEU cc_start: 0.8959 (tp) cc_final: 0.8469 (mt) REVERT: B 2142 THR cc_start: 0.9157 (m) cc_final: 0.8844 (p) REVERT: B 2372 GLU cc_start: 0.8489 (tp30) cc_final: 0.8176 (tp30) outliers start: 135 outliers final: 108 residues processed: 614 average time/residue: 0.9512 time to fit residues: 961.0079 Evaluate side-chains 610 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 495 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain D residue 267 GLU Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 762 TYR Chi-restraints excluded: chain A residue 830 HIS Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 937 TRP Chi-restraints excluded: chain A residue 948 ARG Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1147 ARG Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1209 SER Chi-restraints excluded: chain A residue 1262 SER Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain A residue 1445 ILE Chi-restraints excluded: chain A residue 1464 PHE Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1559 PHE Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1615 PHE Chi-restraints excluded: chain A residue 1618 HIS Chi-restraints excluded: chain A residue 1701 LEU Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1775 GLN Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 2107 GLU Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ASP Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2259 MET Chi-restraints excluded: chain A residue 2261 MET Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2278 SER Chi-restraints excluded: chain A residue 2293 SER Chi-restraints excluded: chain A residue 2319 GLN Chi-restraints excluded: chain A residue 2362 GLU Chi-restraints excluded: chain A residue 2426 ASN Chi-restraints excluded: chain A residue 2431 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain B residue 649 PHE Chi-restraints excluded: chain B residue 762 TYR Chi-restraints excluded: chain B residue 937 TRP Chi-restraints excluded: chain B residue 948 ARG Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1037 ASP Chi-restraints excluded: chain B residue 1047 ASP Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1262 SER Chi-restraints excluded: chain B residue 1281 LEU Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1443 LEU Chi-restraints excluded: chain B residue 1470 THR Chi-restraints excluded: chain B residue 1476 PHE Chi-restraints excluded: chain B residue 1526 ASP Chi-restraints excluded: chain B residue 1544 MET Chi-restraints excluded: chain B residue 1559 PHE Chi-restraints excluded: chain B residue 1567 TRP Chi-restraints excluded: chain B residue 1605 ARG Chi-restraints excluded: chain B residue 1608 ASN Chi-restraints excluded: chain B residue 1614 VAL Chi-restraints excluded: chain B residue 1725 TRP Chi-restraints excluded: chain B residue 1780 GLU Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1881 LEU Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 1963 ASP Chi-restraints excluded: chain B residue 2041 CYS Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2287 ASP Chi-restraints excluded: chain B residue 2293 SER Chi-restraints excluded: chain B residue 2362 GLU Chi-restraints excluded: chain B residue 2387 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 311 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 300 optimal weight: 0.6980 chunk 151 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 319 optimal weight: 5.9990 chunk 342 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 46 optimal weight: 20.0000 chunk 395 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 GLN ** B1270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1378 HIS ** B1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41876 Z= 0.214 Angle : 0.642 20.169 57018 Z= 0.337 Chirality : 0.067 1.701 6382 Planarity : 0.005 0.054 7424 Dihedral : 6.914 65.511 5854 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 24.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.79 % Favored : 94.15 % Rotamer: Outliers : 2.39 % Allowed : 15.80 % Favored : 81.81 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.12), residues: 5178 helix: -0.08 (0.12), residues: 1936 sheet: -1.36 (0.17), residues: 798 loop : -0.79 (0.13), residues: 2444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 63 HIS 0.009 0.001 HIS B1378 PHE 0.022 0.001 PHE B1610 TYR 0.017 0.001 TYR A1235 ARG 0.009 0.000 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 640 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 535 time to evaluate : 4.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 343 MET cc_start: 0.0994 (mtp) cc_final: -0.0057 (tmm) REVERT: C 345 LEU cc_start: 0.1828 (OUTLIER) cc_final: 0.1542 (tp) REVERT: D 274 MET cc_start: 0.2434 (mtt) cc_final: 0.1279 (tmm) REVERT: D 343 MET cc_start: 0.2592 (mtt) cc_final: 0.0145 (tpp) REVERT: A 998 TYR cc_start: 0.8866 (m-80) cc_final: 0.8349 (m-80) REVERT: A 1028 ASP cc_start: 0.7492 (m-30) cc_final: 0.7269 (m-30) REVERT: A 1147 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7396 (ttm170) REVERT: A 1605 ARG cc_start: 0.4794 (OUTLIER) cc_final: 0.3706 (ptt-90) REVERT: A 1687 MET cc_start: 0.8042 (tpt) cc_final: 0.7783 (tpp) REVERT: A 1722 ASN cc_start: 0.7510 (m-40) cc_final: 0.7297 (t0) REVERT: A 1760 ASP cc_start: 0.6729 (t0) cc_final: 0.5187 (p0) REVERT: A 1775 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.6602 (tm-30) REVERT: A 1850 PHE cc_start: 0.8342 (p90) cc_final: 0.7879 (p90) REVERT: B 169 ASP cc_start: 0.8097 (t0) cc_final: 0.7609 (t70) REVERT: B 524 ILE cc_start: 0.8647 (mm) cc_final: 0.8254 (mm) REVERT: B 937 TRP cc_start: 0.7287 (OUTLIER) cc_final: 0.7015 (t60) REVERT: B 948 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7126 (mmt90) REVERT: B 1024 ASP cc_start: 0.8035 (t70) cc_final: 0.7760 (t0) REVERT: B 1032 ILE cc_start: 0.8793 (mm) cc_final: 0.8550 (tp) REVERT: B 1236 LEU cc_start: 0.9159 (mp) cc_final: 0.8955 (mp) REVERT: B 1380 ARG cc_start: 0.8335 (tpt-90) cc_final: 0.7464 (tpm170) REVERT: B 1429 LEU cc_start: 0.8920 (tp) cc_final: 0.8428 (mt) REVERT: B 1544 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.7409 (tpt) REVERT: B 2142 THR cc_start: 0.9144 (m) cc_final: 0.8849 (p) outliers start: 105 outliers final: 88 residues processed: 606 average time/residue: 0.9700 time to fit residues: 959.6285 Evaluate side-chains 600 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 505 time to evaluate : 4.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain C residue 274 MET Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 762 TYR Chi-restraints excluded: chain A residue 830 HIS Chi-restraints excluded: chain A residue 937 TRP Chi-restraints excluded: chain A residue 948 ARG Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1147 ARG Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1262 SER Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1464 PHE Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1559 PHE Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1615 PHE Chi-restraints excluded: chain A residue 1618 HIS Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1775 GLN Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 2107 GLU Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ASP Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2259 MET Chi-restraints excluded: chain A residue 2261 MET Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2278 SER Chi-restraints excluded: chain A residue 2293 SER Chi-restraints excluded: chain A residue 2362 GLU Chi-restraints excluded: chain A residue 2426 ASN Chi-restraints excluded: chain A residue 2431 GLU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain B residue 937 TRP Chi-restraints excluded: chain B residue 948 ARG Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1037 ASP Chi-restraints excluded: chain B residue 1047 ASP Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1281 LEU Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1443 LEU Chi-restraints excluded: chain B residue 1470 THR Chi-restraints excluded: chain B residue 1476 PHE Chi-restraints excluded: chain B residue 1526 ASP Chi-restraints excluded: chain B residue 1544 MET Chi-restraints excluded: chain B residue 1559 PHE Chi-restraints excluded: chain B residue 1567 TRP Chi-restraints excluded: chain B residue 1605 ARG Chi-restraints excluded: chain B residue 1608 ASN Chi-restraints excluded: chain B residue 1614 VAL Chi-restraints excluded: chain B residue 1725 TRP Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1881 LEU Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 2041 CYS Chi-restraints excluded: chain B residue 2088 TRP Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2287 ASP Chi-restraints excluded: chain B residue 2387 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 457 optimal weight: 3.9990 chunk 482 optimal weight: 0.3980 chunk 439 optimal weight: 9.9990 chunk 468 optimal weight: 6.9990 chunk 481 optimal weight: 2.9990 chunk 282 optimal weight: 3.9990 chunk 204 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 chunk 143 optimal weight: 8.9990 chunk 423 optimal weight: 0.9980 chunk 443 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 98 GLN ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 GLN ** B1270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1378 HIS ** B1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 41876 Z= 0.359 Angle : 0.669 19.887 57018 Z= 0.355 Chirality : 0.067 1.667 6382 Planarity : 0.005 0.074 7424 Dihedral : 6.817 64.264 5851 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 26.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.69 % Favored : 92.26 % Rotamer: Outliers : 2.73 % Allowed : 15.85 % Favored : 81.42 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.12), residues: 5178 helix: -0.14 (0.12), residues: 1936 sheet: -1.43 (0.17), residues: 792 loop : -0.90 (0.13), residues: 2450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 63 HIS 0.008 0.001 HIS B1378 PHE 0.023 0.002 PHE B2419 TYR 0.028 0.002 TYR B2307 ARG 0.010 0.001 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 620 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 500 time to evaluate : 4.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 345 LEU cc_start: 0.1982 (OUTLIER) cc_final: 0.1615 (tp) REVERT: D 274 MET cc_start: 0.2733 (mtt) cc_final: 0.1533 (tmm) REVERT: D 343 MET cc_start: 0.2623 (mtt) cc_final: 0.0369 (tpp) REVERT: A 286 MET cc_start: 0.7996 (tpp) cc_final: 0.7408 (tpp) REVERT: A 488 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8188 (mmm) REVERT: A 506 ASP cc_start: 0.7956 (m-30) cc_final: 0.7665 (m-30) REVERT: A 998 TYR cc_start: 0.8955 (m-80) cc_final: 0.8387 (m-80) REVERT: A 1028 ASP cc_start: 0.7553 (m-30) cc_final: 0.7346 (m-30) REVERT: A 1147 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7468 (ttm170) REVERT: A 1526 ASP cc_start: 0.8380 (m-30) cc_final: 0.8102 (m-30) REVERT: A 1687 MET cc_start: 0.8006 (tpt) cc_final: 0.7757 (tpp) REVERT: A 1722 ASN cc_start: 0.7560 (m-40) cc_final: 0.7349 (t0) REVERT: A 1760 ASP cc_start: 0.6804 (t0) cc_final: 0.5255 (p0) REVERT: A 1775 GLN cc_start: 0.8029 (OUTLIER) cc_final: 0.6526 (tm-30) REVERT: A 1850 PHE cc_start: 0.8436 (p90) cc_final: 0.8005 (p90) REVERT: B 169 ASP cc_start: 0.8147 (t0) cc_final: 0.7631 (t70) REVERT: B 524 ILE cc_start: 0.8659 (mm) cc_final: 0.8248 (mm) REVERT: B 649 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7106 (m-80) REVERT: B 937 TRP cc_start: 0.7366 (OUTLIER) cc_final: 0.6980 (t60) REVERT: B 948 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7235 (mmt90) REVERT: B 1024 ASP cc_start: 0.8106 (t70) cc_final: 0.7827 (t0) REVERT: B 1032 ILE cc_start: 0.8846 (mm) cc_final: 0.8569 (tp) REVERT: B 1236 LEU cc_start: 0.9161 (mp) cc_final: 0.8908 (mt) REVERT: B 1380 ARG cc_start: 0.8330 (tpt-90) cc_final: 0.7419 (tpm170) REVERT: B 1429 LEU cc_start: 0.8949 (tp) cc_final: 0.8489 (mt) REVERT: B 2142 THR cc_start: 0.9174 (m) cc_final: 0.8863 (p) REVERT: B 2362 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.5663 (mp0) REVERT: B 2372 GLU cc_start: 0.8423 (tp30) cc_final: 0.8118 (tp30) outliers start: 120 outliers final: 101 residues processed: 584 average time/residue: 0.9621 time to fit residues: 922.9190 Evaluate side-chains 599 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 490 time to evaluate : 4.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 265 PHE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain C residue 331 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 762 TYR Chi-restraints excluded: chain A residue 830 HIS Chi-restraints excluded: chain A residue 937 TRP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1147 ARG Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1209 SER Chi-restraints excluded: chain A residue 1262 SER Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain A residue 1464 PHE Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1559 PHE Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1615 PHE Chi-restraints excluded: chain A residue 1618 HIS Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1775 GLN Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 1968 LEU Chi-restraints excluded: chain A residue 2107 GLU Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ASP Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2259 MET Chi-restraints excluded: chain A residue 2261 MET Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2278 SER Chi-restraints excluded: chain A residue 2293 SER Chi-restraints excluded: chain A residue 2343 THR Chi-restraints excluded: chain A residue 2362 GLU Chi-restraints excluded: chain A residue 2426 ASN Chi-restraints excluded: chain A residue 2431 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain B residue 649 PHE Chi-restraints excluded: chain B residue 937 TRP Chi-restraints excluded: chain B residue 948 ARG Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1037 ASP Chi-restraints excluded: chain B residue 1047 ASP Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1256 ILE Chi-restraints excluded: chain B residue 1281 LEU Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1470 THR Chi-restraints excluded: chain B residue 1476 PHE Chi-restraints excluded: chain B residue 1526 ASP Chi-restraints excluded: chain B residue 1544 MET Chi-restraints excluded: chain B residue 1559 PHE Chi-restraints excluded: chain B residue 1567 TRP Chi-restraints excluded: chain B residue 1605 ARG Chi-restraints excluded: chain B residue 1608 ASN Chi-restraints excluded: chain B residue 1725 TRP Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1881 LEU Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 2041 CYS Chi-restraints excluded: chain B residue 2088 TRP Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2287 ASP Chi-restraints excluded: chain B residue 2362 GLU Chi-restraints excluded: chain B residue 2387 GLN Chi-restraints excluded: chain B residue 2396 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 467 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 495 optimal weight: 2.9990 chunk 302 optimal weight: 0.7980 chunk 235 optimal weight: 6.9990 chunk 344 optimal weight: 1.9990 chunk 520 optimal weight: 1.9990 chunk 478 optimal weight: 0.0270 chunk 414 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 319 optimal weight: 6.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2090 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 GLN B1378 HIS ** B1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41876 Z= 0.217 Angle : 0.635 20.182 57018 Z= 0.333 Chirality : 0.067 1.698 6382 Planarity : 0.005 0.062 7424 Dihedral : 6.591 61.823 5851 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 24.17 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.03 % Favored : 93.92 % Rotamer: Outliers : 2.41 % Allowed : 16.10 % Favored : 81.49 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.12), residues: 5178 helix: 0.03 (0.12), residues: 1930 sheet: -1.34 (0.18), residues: 776 loop : -0.76 (0.13), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 63 HIS 0.009 0.001 HIS B1378 PHE 0.024 0.001 PHE B1610 TYR 0.032 0.001 TYR B2307 ARG 0.009 0.000 ARG A 231 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10356 Ramachandran restraints generated. 5178 Oldfield, 0 Emsley, 5178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 1834 is missing expected H atoms. Skipping. Residue SER 1834 is missing expected H atoms. Skipping. Evaluate side-chains 628 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 522 time to evaluate : 4.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 345 LEU cc_start: 0.1902 (OUTLIER) cc_final: 0.1563 (tp) REVERT: D 55 MET cc_start: 0.2548 (mmt) cc_final: 0.2214 (mmt) REVERT: D 274 MET cc_start: 0.2798 (mtt) cc_final: 0.1601 (tmm) REVERT: A 506 ASP cc_start: 0.7845 (m-30) cc_final: 0.7581 (m-30) REVERT: A 573 MET cc_start: 0.5767 (mmm) cc_final: 0.5322 (mmt) REVERT: A 998 TYR cc_start: 0.8872 (m-80) cc_final: 0.8237 (m-80) REVERT: A 1028 ASP cc_start: 0.7511 (m-30) cc_final: 0.7293 (m-30) REVERT: A 1375 TYR cc_start: 0.5363 (m-80) cc_final: 0.5141 (m-80) REVERT: A 1526 ASP cc_start: 0.8375 (m-30) cc_final: 0.8034 (m-30) REVERT: A 1605 ARG cc_start: 0.4786 (OUTLIER) cc_final: 0.3661 (ptt-90) REVERT: A 1687 MET cc_start: 0.8061 (tpt) cc_final: 0.7822 (tpp) REVERT: A 1760 ASP cc_start: 0.6747 (t0) cc_final: 0.5223 (p0) REVERT: A 1775 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.6464 (tm-30) REVERT: A 1850 PHE cc_start: 0.8328 (p90) cc_final: 0.7917 (p90) REVERT: B 169 ASP cc_start: 0.8059 (t0) cc_final: 0.7580 (t70) REVERT: B 524 ILE cc_start: 0.8624 (mm) cc_final: 0.8190 (mm) REVERT: B 613 MET cc_start: 0.3887 (mtt) cc_final: 0.3552 (mtt) REVERT: B 937 TRP cc_start: 0.7336 (OUTLIER) cc_final: 0.6945 (t60) REVERT: B 1024 ASP cc_start: 0.7987 (t70) cc_final: 0.7716 (t0) REVERT: B 1032 ILE cc_start: 0.8807 (mm) cc_final: 0.8543 (tp) REVERT: B 1168 LEU cc_start: 0.8814 (mt) cc_final: 0.8607 (mt) REVERT: B 1236 LEU cc_start: 0.9143 (mp) cc_final: 0.8917 (mt) REVERT: B 1380 ARG cc_start: 0.8325 (tpt-90) cc_final: 0.7412 (tpm170) REVERT: B 1429 LEU cc_start: 0.8928 (tp) cc_final: 0.8399 (mt) REVERT: B 1544 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7595 (tpt) REVERT: B 2142 THR cc_start: 0.9110 (m) cc_final: 0.8840 (p) REVERT: B 2339 VAL cc_start: 0.8447 (m) cc_final: 0.8244 (m) REVERT: B 2362 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.5720 (mp0) outliers start: 106 outliers final: 93 residues processed: 591 average time/residue: 0.9637 time to fit residues: 938.2784 Evaluate side-chains 599 residues out of total 4396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 500 time to evaluate : 4.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 291 THR Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 265 PHE Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 222 LYS Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 623 TYR Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain A residue 681 ARG Chi-restraints excluded: chain A residue 762 TYR Chi-restraints excluded: chain A residue 830 HIS Chi-restraints excluded: chain A residue 937 TRP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1155 ILE Chi-restraints excluded: chain A residue 1164 CYS Chi-restraints excluded: chain A residue 1262 SER Chi-restraints excluded: chain A residue 1304 ILE Chi-restraints excluded: chain A residue 1318 SER Chi-restraints excluded: chain A residue 1464 PHE Chi-restraints excluded: chain A residue 1524 THR Chi-restraints excluded: chain A residue 1559 PHE Chi-restraints excluded: chain A residue 1605 ARG Chi-restraints excluded: chain A residue 1614 VAL Chi-restraints excluded: chain A residue 1615 PHE Chi-restraints excluded: chain A residue 1618 HIS Chi-restraints excluded: chain A residue 1725 TRP Chi-restraints excluded: chain A residue 1775 GLN Chi-restraints excluded: chain A residue 1777 LEU Chi-restraints excluded: chain A residue 1807 ILE Chi-restraints excluded: chain A residue 1925 THR Chi-restraints excluded: chain A residue 2107 GLU Chi-restraints excluded: chain A residue 2109 MET Chi-restraints excluded: chain A residue 2119 ASP Chi-restraints excluded: chain A residue 2198 LEU Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain A residue 2256 LEU Chi-restraints excluded: chain A residue 2259 MET Chi-restraints excluded: chain A residue 2263 LEU Chi-restraints excluded: chain A residue 2278 SER Chi-restraints excluded: chain A residue 2293 SER Chi-restraints excluded: chain A residue 2343 THR Chi-restraints excluded: chain A residue 2362 GLU Chi-restraints excluded: chain A residue 2426 ASN Chi-restraints excluded: chain A residue 2431 GLU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 307 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain B residue 623 TYR Chi-restraints excluded: chain B residue 937 TRP Chi-restraints excluded: chain B residue 948 ARG Chi-restraints excluded: chain B residue 964 THR Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1037 ASP Chi-restraints excluded: chain B residue 1047 ASP Chi-restraints excluded: chain B residue 1226 THR Chi-restraints excluded: chain B residue 1281 LEU Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1470 THR Chi-restraints excluded: chain B residue 1476 PHE Chi-restraints excluded: chain B residue 1526 ASP Chi-restraints excluded: chain B residue 1544 MET Chi-restraints excluded: chain B residue 1559 PHE Chi-restraints excluded: chain B residue 1567 TRP Chi-restraints excluded: chain B residue 1605 ARG Chi-restraints excluded: chain B residue 1608 ASN Chi-restraints excluded: chain B residue 1614 VAL Chi-restraints excluded: chain B residue 1725 TRP Chi-restraints excluded: chain B residue 1870 THR Chi-restraints excluded: chain B residue 1881 LEU Chi-restraints excluded: chain B residue 1939 MET Chi-restraints excluded: chain B residue 2041 CYS Chi-restraints excluded: chain B residue 2088 TRP Chi-restraints excluded: chain B residue 2158 THR Chi-restraints excluded: chain B residue 2287 ASP Chi-restraints excluded: chain B residue 2293 SER Chi-restraints excluded: chain B residue 2362 GLU Chi-restraints excluded: chain B residue 2387 GLN Chi-restraints excluded: chain B residue 2396 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 522 random chunks: chunk 253 optimal weight: 6.9990 chunk 328 optimal weight: 0.6980 chunk 441 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 381 optimal weight: 0.6980 chunk 61 optimal weight: 0.0060 chunk 115 optimal weight: 2.9990 chunk 414 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 425 optimal weight: 8.9990 chunk 52 optimal weight: 40.0000 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2311 ASN B 199 GLN ** B 635 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 GLN B1378 HIS ** B1895 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.137370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.107878 restraints weight = 268113.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.108529 restraints weight = 141901.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.108824 restraints weight = 93713.744| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3680 r_free = 0.3680 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 96 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 104 | |-----------------------------------------------------------------------------| r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.5105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 41876 Z= 0.201 Angle : 0.629 20.270 57018 Z= 0.329 Chirality : 0.066 1.690 6382 Planarity : 0.004 0.059 7424 Dihedral : 6.427 58.489 5851 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.18 % Favored : 93.78 % Rotamer: Outliers : 2.21 % Allowed : 16.39 % Favored : 81.40 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.12), residues: 5178 helix: 0.14 (0.12), residues: 1940 sheet: -1.28 (0.18), residues: 776 loop : -0.68 (0.13), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 279 HIS 0.009 0.001 HIS B1378 PHE 0.023 0.001 PHE B1610 TYR 0.027 0.001 TYR B2307 ARG 0.009 0.000 ARG A 231 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17809.21 seconds wall clock time: 309 minutes 52.56 seconds (18592.56 seconds total)