Starting phenix.real_space_refine on Mon Mar 18 07:28:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3j_0134/03_2024/6h3j_0134.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3j_0134/03_2024/6h3j_0134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3j_0134/03_2024/6h3j_0134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3j_0134/03_2024/6h3j_0134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3j_0134/03_2024/6h3j_0134.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3j_0134/03_2024/6h3j_0134.pdb" } resolution = 3.7 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= 0.002 sd= 0.013 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: 5 Type Number sf(0) Gaussians S 47 5.16 5 C 12715 2.51 5 N 3389 2.21 5 O 3938 1.98 5 H 212 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 164": "NH1" <-> "NH2" Residue "A PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 782": "NH1" <-> "NH2" Residue "A ARG 1099": "NH1" <-> "NH2" Residue "A ARG 1266": "NH1" <-> "NH2" Residue "A PHE 1393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1646": "NH1" <-> "NH2" Residue "A TYR 1766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1988": "NH1" <-> "NH2" Residue "A TYR 2045": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 116": "NH1" <-> "NH2" Residue "C TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20301 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 15853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1988, 15853 Classifications: {'peptide': 1988} Link IDs: {'PTRANS': 90, 'TRANS': 1897} Chain breaks: 17 Chain: "B" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1185 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 1 Chain: "C" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 397, 3263 Classifications: {'peptide': 397} Link IDs: {'PTRANS': 12, 'TRANS': 384} Time building chain proxies: 9.80, per 1000 atoms: 0.48 Number of scatterers: 20301 At special positions: 0 Unit cell: (124.64, 132.84, 136.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 47 16.00 O 3938 8.00 N 3389 7.00 C 12715 6.00 H 212 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: 7.22 Conformation dependent library (CDL) restraints added in 3.4 seconds 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4694 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 47 sheets defined 10.0% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.601A pdb=" N GLN A 202 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 4.105A pdb=" N LYS A 307 " --> pdb=" O VAL A 304 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASN A 308 " --> pdb=" O SER A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 308' Processing helix chain 'A' and resid 359 through 363 Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.055A pdb=" N ASN A 386 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 removed outlier: 3.926A pdb=" N ILE A 393 " --> pdb=" O PRO A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 414 removed outlier: 3.857A pdb=" N ALA A 410 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N LYS A 411 " --> pdb=" O VAL A 408 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 413 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A 414 " --> pdb=" O LYS A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 removed outlier: 4.054A pdb=" N ASN A 521 " --> pdb=" O ASN A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 583 Processing helix chain 'A' and resid 623 through 634 removed outlier: 4.890A pdb=" N ILE A 629 " --> pdb=" O PHE A 625 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 630 " --> pdb=" O GLY A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.580A pdb=" N THR A 646 " --> pdb=" O ASP A 643 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 647 " --> pdb=" O PRO A 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 643 through 647' Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.858A pdb=" N MET A 659 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 810 through 819 removed outlier: 3.804A pdb=" N THR A 814 " --> pdb=" O VAL A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 944 Processing helix chain 'A' and resid 982 through 986 Processing helix chain 'A' and resid 998 through 1003 Processing helix chain 'A' and resid 1081 through 1089 removed outlier: 4.414A pdb=" N ASN A1087 " --> pdb=" O ASP A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1103 Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 3.777A pdb=" N TYR A1132 " --> pdb=" O VAL A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1412 through 1417 Processing helix chain 'A' and resid 1427 through 1438 removed outlier: 3.503A pdb=" N THR A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A1432 " --> pdb=" O ASP A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1613 removed outlier: 3.541A pdb=" N LEU A1611 " --> pdb=" O LYS A1607 " (cutoff:3.500A) Processing helix chain 'A' and resid 1619 through 1624 removed outlier: 3.884A pdb=" N ASN A1623 " --> pdb=" O ALA A1619 " (cutoff:3.500A) Processing helix chain 'A' and resid 1856 through 1861 removed outlier: 3.726A pdb=" N SER A1860 " --> pdb=" O SER A1856 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU A1861 " --> pdb=" O THR A1857 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1856 through 1861' Processing helix chain 'A' and resid 1989 through 1995 Processing helix chain 'A' and resid 2072 through 2076 removed outlier: 3.604A pdb=" N ALA A2075 " --> pdb=" O ILE A2072 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE A2076 " --> pdb=" O LYS A2073 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2072 through 2076' Processing helix chain 'A' and resid 2084 through 2104 removed outlier: 3.967A pdb=" N ARG A2094 " --> pdb=" O PHE A2090 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU A2095 " --> pdb=" O ARG A2091 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE A2096 " --> pdb=" O SER A2092 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA A2098 " --> pdb=" O ARG A2094 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A2104 " --> pdb=" O ARG A2100 " (cutoff:3.500A) Processing helix chain 'A' and resid 2129 through 2135 removed outlier: 3.822A pdb=" N TYR A2133 " --> pdb=" O ASN A2129 " (cutoff:3.500A) Processing helix chain 'A' and resid 2151 through 2159 Processing helix chain 'A' and resid 2185 through 2189 removed outlier: 4.139A pdb=" N MET A2188 " --> pdb=" O ASN A2185 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A2189 " --> pdb=" O GLY A2186 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2185 through 2189' Processing helix chain 'B' and resid 28 through 42 Processing helix chain 'B' and resid 126 through 133 removed outlier: 3.668A pdb=" N LYS B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.715A pdb=" N ILE C 172 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ASN C 173 " --> pdb=" O SER C 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 169 through 173' Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 298 through 303 Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.684A pdb=" N LYS C 339 " --> pdb=" O PRO C 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 204 through 208 removed outlier: 3.878A pdb=" N ALA A 208 " --> pdb=" O GLU A 188 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU A 144 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET A 180 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AA3, first strand: chain 'A' and resid 219 through 222 removed outlier: 3.764A pdb=" N LYS A 219 " --> pdb=" O GLN A 246 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 252 through 253 removed outlier: 3.842A pdb=" N THR A 253 " --> pdb=" O GLU A 763 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 292 through 293 Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 344 removed outlier: 4.898A pdb=" N ARG A 342 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 430 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS A 471 " --> pdb=" O VAL A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 342 through 344 removed outlier: 4.898A pdb=" N ARG A 342 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 430 " --> pdb=" O ARG A 342 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 318 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR A 467 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 527 through 528 Processing sheet with id=AA9, first strand: chain 'A' and resid 544 through 545 removed outlier: 3.725A pdb=" N ASN A 544 " --> pdb=" O ARG A 679 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 771 through 772 Processing sheet with id=AB2, first strand: chain 'A' and resid 831 through 832 Processing sheet with id=AB3, first strand: chain 'A' and resid 866 through 869 removed outlier: 3.553A pdb=" N LEU A1259 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A1009 " --> pdb=" O PHE A1216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 990 through 991 removed outlier: 3.706A pdb=" N ILE A 990 " --> pdb=" O MET A1241 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY A1034 " --> pdb=" O ARG A1237 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1201 through 1202 removed outlier: 3.758A pdb=" N VAL A1201 " --> pdb=" O THR A1209 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A1209 " --> pdb=" O VAL A1201 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1286 through 1290 removed outlier: 3.734A pdb=" N ALA A1288 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A1329 " --> pdb=" O ALA A1288 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1363 through 1364 Processing sheet with id=AB8, first strand: chain 'A' and resid 1383 through 1386 removed outlier: 4.875A pdb=" N GLY A1386 " --> pdb=" O ASN A1485 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN A1485 " --> pdb=" O GLY A1386 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1540 through 1541 Processing sheet with id=AC1, first strand: chain 'A' and resid 1559 through 1560 Processing sheet with id=AC2, first strand: chain 'A' and resid 1565 through 1569 removed outlier: 3.872A pdb=" N ASN A1638 " --> pdb=" O ASN A1587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 1565 through 1569 Processing sheet with id=AC4, first strand: chain 'A' and resid 1663 through 1664 removed outlier: 3.856A pdb=" N SER A1663 " --> pdb=" O ALA A1687 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A1732 " --> pdb=" O GLN A1767 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 1787 through 1789 removed outlier: 6.321A pdb=" N ASN A1787 " --> pdb=" O ASN A1817 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1822 through 1824 Processing sheet with id=AC7, first strand: chain 'A' and resid 1851 through 1852 removed outlier: 4.169A pdb=" N MET A1851 " --> pdb=" O GLN A1877 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1882 through 1883 removed outlier: 3.529A pdb=" N TYR A2037 " --> pdb=" O LYS A2013 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER A2066 " --> pdb=" O SER A2036 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A2038 " --> pdb=" O MET A2064 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A2063 " --> pdb=" O PHE A2215 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE A2065 " --> pdb=" O ASN A2213 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASN A2213 " --> pdb=" O PHE A2065 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 1948 through 1949 Processing sheet with id=AD1, first strand: chain 'A' and resid 2007 through 2008 removed outlier: 6.789A pdb=" N SER A2042 " --> pdb=" O PRO A2059 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A2044 " --> pdb=" O LEU A2057 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 2199 through 2200 removed outlier: 3.554A pdb=" N ARG A2199 " --> pdb=" O GLU A2258 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'A' and resid 2248 through 2249 Processing sheet with id=AD4, first strand: chain 'A' and resid 2293 through 2297 Processing sheet with id=AD5, first strand: chain 'A' and resid 2300 through 2301 removed outlier: 3.558A pdb=" N ASP A2320 " --> pdb=" O SER A2362 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 2332 through 2333 removed outlier: 3.827A pdb=" N GLN A2350 " --> pdb=" O ASN A2332 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 2353 through 2354 removed outlier: 3.847A pdb=" N TRP A2353 " --> pdb=" O PHE A2377 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 2370 through 2371 removed outlier: 3.636A pdb=" N THR A2396 " --> pdb=" O ILE A2370 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 47 through 48 removed outlier: 3.805A pdb=" N GLN B 47 " --> pdb=" O TYR B 55 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 55 " --> pdb=" O GLN B 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'B' and resid 102 through 104 removed outlier: 6.675A pdb=" N GLY B 103 " --> pdb=" O PHE B 111 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 142 through 146 Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 50 removed outlier: 3.976A pdb=" N ASN C 132 " --> pdb=" O CYS C 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS C 76 " --> pdb=" O ASN C 132 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 59 through 61 Processing sheet with id=AE5, first strand: chain 'C' and resid 159 through 164 Processing sheet with id=AE6, first strand: chain 'C' and resid 159 through 164 Processing sheet with id=AE7, first strand: chain 'C' and resid 198 through 201 removed outlier: 6.427A pdb=" N ILE C 392 " --> pdb=" O LYS C 409 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LYS C 409 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL C 394 " --> pdb=" O ILE C 407 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 198 through 201 Processing sheet with id=AE9, first strand: chain 'C' and resid 240 through 244 removed outlier: 4.266A pdb=" N ASN C 244 " --> pdb=" O GLY C 358 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 358 " --> pdb=" O ASN C 244 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 257 through 258 Processing sheet with id=AF2, first strand: chain 'C' and resid 257 through 258 removed outlier: 3.540A pdb=" N ILE C 355 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 351 " --> pdb=" O PHE C 310 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 789 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: 9.43 Time building geometry restraints manager: 7.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 212 1.03 - 1.23: 36 1.23 - 1.42: 8923 1.42 - 1.61: 11472 1.61 - 1.81: 90 Bond restraints: 20733 Sorted by residual: bond pdb=" CG1 ILE A1876 " pdb=" CD1 ILE A1876 " ideal model delta sigma weight residual 1.513 1.438 0.075 3.90e-02 6.57e+02 3.72e+00 bond pdb=" CB PHE A1242 " pdb=" CG PHE A1242 " ideal model delta sigma weight residual 1.502 1.458 0.044 2.30e-02 1.89e+03 3.66e+00 bond pdb=" CB TYR A1048 " pdb=" CG TYR A1048 " ideal model delta sigma weight residual 1.512 1.471 0.041 2.20e-02 2.07e+03 3.39e+00 bond pdb=" CB TYR A 309 " pdb=" CG TYR A 309 " ideal model delta sigma weight residual 1.512 1.474 0.038 2.20e-02 2.07e+03 2.98e+00 bond pdb=" C SER A1097 " pdb=" N SER A1098 " ideal model delta sigma weight residual 1.333 1.309 0.025 1.49e-02 4.50e+03 2.73e+00 ... (remaining 20728 not shown) Histogram of bond angle deviations from ideal: 97.30 - 104.66: 346 104.66 - 112.03: 9495 112.03 - 119.39: 6949 119.39 - 126.76: 11250 126.76 - 134.12: 187 Bond angle restraints: 28227 Sorted by residual: angle pdb=" N ILE C 415 " pdb=" CA ILE C 415 " pdb=" C ILE C 415 " ideal model delta sigma weight residual 112.29 106.80 5.49 9.40e-01 1.13e+00 3.41e+01 angle pdb=" N ILE A 216 " pdb=" CA ILE A 216 " pdb=" C ILE A 216 " ideal model delta sigma weight residual 113.71 108.23 5.48 9.50e-01 1.11e+00 3.32e+01 angle pdb=" N SER A2250 " pdb=" CA SER A2250 " pdb=" C SER A2250 " ideal model delta sigma weight residual 109.41 101.33 8.08 1.53e+00 4.27e-01 2.79e+01 angle pdb=" N ASN A 650 " pdb=" CA ASN A 650 " pdb=" C ASN A 650 " ideal model delta sigma weight residual 112.68 106.77 5.91 1.33e+00 5.65e-01 1.98e+01 angle pdb=" N THR A2160 " pdb=" CA THR A2160 " pdb=" C THR A2160 " ideal model delta sigma weight residual 114.64 107.93 6.71 1.52e+00 4.33e-01 1.95e+01 ... (remaining 28222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.94: 11593 14.94 - 29.88: 615 29.88 - 44.82: 141 44.82 - 59.76: 20 59.76 - 74.70: 9 Dihedral angle restraints: 12378 sinusoidal: 5039 harmonic: 7339 Sorted by residual: dihedral pdb=" CA SER A 563 " pdb=" C SER A 563 " pdb=" N PHE A 564 " pdb=" CA PHE A 564 " ideal model delta harmonic sigma weight residual -180.00 -140.01 -39.99 0 5.00e+00 4.00e-02 6.40e+01 dihedral pdb=" CA GLY A 394 " pdb=" C GLY A 394 " pdb=" N GLN A 395 " pdb=" CA GLN A 395 " ideal model delta harmonic sigma weight residual -180.00 -143.28 -36.72 0 5.00e+00 4.00e-02 5.39e+01 dihedral pdb=" CA SER A2250 " pdb=" C SER A2250 " pdb=" N PRO A2251 " pdb=" CA PRO A2251 " ideal model delta harmonic sigma weight residual -180.00 -144.64 -35.36 0 5.00e+00 4.00e-02 5.00e+01 ... (remaining 12375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 2048 0.044 - 0.088: 681 0.088 - 0.133: 258 0.133 - 0.177: 34 0.177 - 0.221: 5 Chirality restraints: 3026 Sorted by residual: chirality pdb=" CA PHE C 119 " pdb=" N PHE C 119 " pdb=" C PHE C 119 " pdb=" CB PHE C 119 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ASN A 998 " pdb=" N ASN A 998 " pdb=" C ASN A 998 " pdb=" CB ASN A 998 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA PRO A2178 " pdb=" N PRO A2178 " pdb=" C PRO A2178 " pdb=" CB PRO A2178 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.85e-01 ... (remaining 3023 not shown) Planarity restraints: 3795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 564 " -0.052 5.00e-02 4.00e+02 7.84e-02 9.84e+00 pdb=" N PRO A 565 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A2250 " -0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO A2251 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A2251 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A2251 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1996 " 0.020 2.00e-02 2.50e+03 1.69e-02 7.12e+00 pdb=" CG TRP A1996 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A1996 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A1996 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1996 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A1996 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1996 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1996 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1996 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A1996 " 0.002 2.00e-02 2.50e+03 ... (remaining 3792 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.30: 103 2.30 - 2.87: 8671 2.87 - 3.45: 24767 3.45 - 4.02: 37434 4.02 - 4.60: 56237 Nonbonded interactions: 127212 Sorted by model distance: nonbonded pdb=" O THR B 98 " pdb=" H VAL B 173 " model vdw 1.719 1.850 nonbonded pdb=" O TYR B 54 " pdb=" H PHE B 145 " model vdw 1.733 1.850 nonbonded pdb=" O LEU B 93 " pdb="HH11 ARG B 123 " model vdw 1.791 1.850 nonbonded pdb=" O TYR B 27 " pdb="HD21 ASN B 31 " model vdw 1.796 1.850 nonbonded pdb=" HG SER B 51 " pdb=" OE1 GLU B 131 " model vdw 1.842 1.850 ... (remaining 127207 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 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: 1.540 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: 0.480 Extract box with map and model: 6.850 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 52.390 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 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 0.075 20521 Z= 0.456 Angle : 0.874 8.492 27849 Z= 0.495 Chirality : 0.051 0.221 3026 Planarity : 0.005 0.078 3678 Dihedral : 10.174 74.698 7511 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 43.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 23.77 % Favored : 76.18 % Rotamer: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.87 % Twisted General : 0.17 % 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: -6.63 (0.13), residues: 2469 helix: -3.98 (0.22), residues: 205 sheet: -4.89 (0.12), residues: 830 loop : -4.29 (0.13), residues: 1434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A1996 HIS 0.005 0.001 HIS C 75 PHE 0.039 0.003 PHE C 119 TYR 0.030 0.002 TYR A 528 ARG 0.010 0.001 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 259 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 43 ASN cc_start: 0.8618 (p0) cc_final: 0.8406 (m-40) REVERT: C 158 THR cc_start: 0.8846 (m) cc_final: 0.8510 (p) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.3807 time to fit residues: 145.2585 Evaluate side-chains 109 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 210 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 195 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 118 optimal weight: 0.0970 chunk 145 optimal weight: 10.0000 chunk 226 optimal weight: 8.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 ASN ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN A 584 ASN ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 805 ASN ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 ASN ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 GLN A1018 ASN ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1084 ASN A1087 ASN ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1210 ASN ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1562 GLN ** A1587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1603 ASN A1604 GLN ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1623 ASN ** A1667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 GLN A1740 ASN A1767 GLN A1787 ASN A1805 ASN ** A1819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1874 ASN ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1889 ASN ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2052 ASN ** A2083 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2213 ASN A2214 GLN ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2375 HIS A2400 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN C 44 ASN C 104 ASN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN C 232 GLN C 261 ASN C 271 ASN C 295 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 20521 Z= 0.362 Angle : 0.653 6.871 27849 Z= 0.352 Chirality : 0.045 0.168 3026 Planarity : 0.004 0.079 3678 Dihedral : 6.304 38.517 2753 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 57.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.69 % Favored : 76.31 % Rotamer: Outliers : 1.71 % Allowed : 8.78 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -6.29 (0.14), residues: 2469 helix: -3.24 (0.27), residues: 235 sheet: -4.71 (0.13), residues: 833 loop : -4.10 (0.14), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1996 HIS 0.003 0.001 HIS C 75 PHE 0.025 0.002 PHE A 564 TYR 0.017 0.002 TYR A1120 ARG 0.005 0.001 ARG A2392 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 119 time to evaluate : 2.484 Fit side-chains revert: symmetry clash REVERT: A 341 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9255 (pp) REVERT: A 762 ILE cc_start: 0.9489 (OUTLIER) cc_final: 0.9071 (pt) REVERT: A 1425 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8877 (tm) REVERT: A 1508 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8799 (tt) REVERT: A 2210 TYR cc_start: 0.8288 (t80) cc_final: 0.8062 (t80) REVERT: C 158 THR cc_start: 0.8836 (m) cc_final: 0.8548 (p) outliers start: 38 outliers final: 22 residues processed: 147 average time/residue: 0.3007 time to fit residues: 72.5979 Evaluate side-chains 131 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1394 TYR Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1997 LEU Chi-restraints excluded: chain A residue 2334 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 354 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 244 optimal weight: 8.9990 chunk 201 optimal weight: 8.9990 chunk 224 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 GLN ** A1667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1672 HIS A1740 ASN ** A1819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1853 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 20521 Z= 0.486 Angle : 0.723 7.696 27849 Z= 0.386 Chirality : 0.046 0.203 3026 Planarity : 0.005 0.075 3678 Dihedral : 6.441 36.229 2753 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 59.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.57 % Favored : 73.43 % Rotamer: Outliers : 2.75 % Allowed : 10.45 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -6.13 (0.14), residues: 2469 helix: -3.02 (0.29), residues: 224 sheet: -4.60 (0.13), residues: 834 loop : -4.01 (0.14), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1996 HIS 0.003 0.001 HIS C 75 PHE 0.028 0.002 PHE A 564 TYR 0.019 0.002 TYR A1120 ARG 0.006 0.001 ARG A1234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 105 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 341 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9285 (pp) REVERT: A 350 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8694 (tm) REVERT: A 523 MET cc_start: 0.8544 (ttt) cc_final: 0.8186 (ttt) REVERT: A 762 ILE cc_start: 0.9533 (OUTLIER) cc_final: 0.9124 (pt) REVERT: A 1425 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8959 (tm) REVERT: A 1508 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8749 (tt) REVERT: C 158 THR cc_start: 0.8870 (m) cc_final: 0.8534 (p) REVERT: C 227 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.7445 (p90) outliers start: 61 outliers final: 37 residues processed: 155 average time/residue: 0.2743 time to fit residues: 71.2090 Evaluate side-chains 138 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 95 time to evaluate : 2.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 511 ASN Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1997 LEU Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2067 ILE Chi-restraints excluded: chain A residue 2231 ASN Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 240 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 ASN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1150 ASN ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1603 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN A1767 GLN ** A1819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2400 ASN ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 ASN ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20521 Z= 0.351 Angle : 0.625 6.533 27849 Z= 0.335 Chirality : 0.044 0.172 3026 Planarity : 0.004 0.066 3678 Dihedral : 6.044 33.932 2753 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 57.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.46 % Favored : 75.54 % Rotamer: Outliers : 3.15 % Allowed : 11.53 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -5.94 (0.14), residues: 2469 helix: -2.83 (0.30), residues: 225 sheet: -4.46 (0.14), residues: 836 loop : -3.89 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1996 HIS 0.002 0.001 HIS A1364 PHE 0.022 0.002 PHE A 564 TYR 0.014 0.001 TYR A1120 ARG 0.004 0.000 ARG A2100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 105 time to evaluate : 2.197 Fit side-chains revert: symmetry clash REVERT: A 341 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9244 (pp) REVERT: A 350 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8621 (tm) REVERT: A 523 MET cc_start: 0.8533 (ttt) cc_final: 0.8193 (ttt) REVERT: A 762 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9119 (pt) REVERT: A 1425 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8947 (tm) REVERT: A 1508 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8727 (tt) REVERT: C 158 THR cc_start: 0.8848 (m) cc_final: 0.8510 (p) REVERT: C 227 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.7478 (p90) outliers start: 70 outliers final: 46 residues processed: 167 average time/residue: 0.2889 time to fit residues: 79.6414 Evaluate side-chains 147 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 95 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1171 ILE Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1638 ASN Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1997 LEU Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2067 ILE Chi-restraints excluded: chain A residue 2253 ILE Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 99 optimal weight: 0.0030 chunk 205 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 8.9990 chunk 216 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 865 GLN ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN ** A1819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1826 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 20521 Z= 0.394 Angle : 0.644 7.037 27849 Z= 0.344 Chirality : 0.044 0.178 3026 Planarity : 0.004 0.063 3678 Dihedral : 6.021 33.384 2753 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 58.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.80 % Favored : 74.20 % Rotamer: Outliers : 4.01 % Allowed : 11.94 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.84 (0.15), residues: 2469 helix: -2.65 (0.31), residues: 211 sheet: -4.37 (0.14), residues: 848 loop : -3.84 (0.15), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1996 HIS 0.002 0.001 HIS C 75 PHE 0.023 0.002 PHE A 564 TYR 0.014 0.002 TYR A1120 ARG 0.005 0.001 ARG A2100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 96 time to evaluate : 2.464 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8034 (ptt180) REVERT: A 341 LEU cc_start: 0.9464 (OUTLIER) cc_final: 0.9252 (pp) REVERT: A 350 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8674 (tm) REVERT: A 372 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8059 (p90) REVERT: A 523 MET cc_start: 0.8586 (ttt) cc_final: 0.8246 (ttt) REVERT: A 762 ILE cc_start: 0.9534 (OUTLIER) cc_final: 0.9134 (pt) REVERT: A 1425 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8949 (tm) REVERT: A 1508 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8693 (tt) REVERT: C 158 THR cc_start: 0.8883 (m) cc_final: 0.8534 (p) REVERT: C 227 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.7522 (p90) REVERT: C 387 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7111 (tm-30) outliers start: 89 outliers final: 59 residues processed: 176 average time/residue: 0.3057 time to fit residues: 87.9593 Evaluate side-chains 160 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 92 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 TYR Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1772 PHE Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1997 LEU Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2067 ILE Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain A residue 2231 ASN Chi-restraints excluded: chain A residue 2253 ILE Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 10.0000 chunk 216 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 chunk 199 optimal weight: 8.9990 chunk 111 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN ** A1819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1826 ASN ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2375 HIS ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20521 Z= 0.319 Angle : 0.595 6.146 27849 Z= 0.319 Chirality : 0.044 0.157 3026 Planarity : 0.004 0.060 3678 Dihedral : 5.801 32.300 2753 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 57.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.06 % Favored : 75.94 % Rotamer: Outliers : 3.96 % Allowed : 12.43 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.64 (0.15), residues: 2469 helix: -2.54 (0.32), residues: 211 sheet: -4.21 (0.15), residues: 816 loop : -3.75 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1264 HIS 0.003 0.001 HIS A2375 PHE 0.021 0.001 PHE A 564 TYR 0.012 0.001 TYR C 227 ARG 0.004 0.000 ARG A2100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 188 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 100 time to evaluate : 2.209 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8005 (ptt180) REVERT: A 350 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8627 (tm) REVERT: A 523 MET cc_start: 0.8567 (ttt) cc_final: 0.8224 (ttt) REVERT: A 762 ILE cc_start: 0.9520 (OUTLIER) cc_final: 0.9117 (pt) REVERT: A 1425 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8975 (tm) REVERT: A 1508 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8666 (tt) REVERT: C 158 THR cc_start: 0.8866 (m) cc_final: 0.8513 (p) REVERT: C 227 TYR cc_start: 0.8764 (OUTLIER) cc_final: 0.7577 (p90) REVERT: C 387 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7109 (tm-30) outliers start: 88 outliers final: 66 residues processed: 179 average time/residue: 0.3003 time to fit residues: 88.6387 Evaluate side-chains 170 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 97 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 TYR Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1605 ASP Chi-restraints excluded: chain A residue 1638 ASN Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1772 PHE Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1997 LEU Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2067 ILE Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain A residue 2231 ASN Chi-restraints excluded: chain A residue 2253 ILE Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain A residue 2375 HIS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 175 optimal weight: 3.9990 chunk 136 optimal weight: 8.9990 chunk 202 optimal weight: 9.9990 chunk 134 optimal weight: 1.9990 chunk 239 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1395 GLN ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN ** A1819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2375 HIS ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 20521 Z= 0.333 Angle : 0.598 6.350 27849 Z= 0.320 Chirality : 0.044 0.158 3026 Planarity : 0.004 0.057 3678 Dihedral : 5.750 32.341 2753 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 57.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.71 % Favored : 75.29 % Rotamer: Outliers : 4.32 % Allowed : 12.75 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.57 (0.15), residues: 2469 helix: -2.50 (0.32), residues: 211 sheet: -4.15 (0.15), residues: 813 loop : -3.72 (0.15), residues: 1445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1264 HIS 0.014 0.001 HIS A2375 PHE 0.022 0.001 PHE A 564 TYR 0.016 0.001 TYR A2373 ARG 0.004 0.000 ARG A2100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 98 time to evaluate : 2.388 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8019 (ptt180) REVERT: A 341 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9243 (pp) REVERT: A 350 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8667 (tm) REVERT: A 523 MET cc_start: 0.8571 (ttt) cc_final: 0.8237 (ttt) REVERT: A 762 ILE cc_start: 0.9526 (OUTLIER) cc_final: 0.9123 (pt) REVERT: A 1425 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8977 (tm) REVERT: A 1508 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8652 (tt) REVERT: C 158 THR cc_start: 0.8876 (m) cc_final: 0.8514 (p) REVERT: C 227 TYR cc_start: 0.8765 (OUTLIER) cc_final: 0.7580 (p90) REVERT: C 387 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7133 (tm-30) outliers start: 96 outliers final: 73 residues processed: 181 average time/residue: 0.2953 time to fit residues: 88.0893 Evaluate side-chains 176 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 95 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 498 ILE Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 TYR Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1366 GLU Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1563 GLN Chi-restraints excluded: chain A residue 1605 ASP Chi-restraints excluded: chain A residue 1638 ASN Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1772 PHE Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 1997 LEU Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2067 ILE Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain A residue 2231 ASN Chi-restraints excluded: chain A residue 2253 ILE Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain A residue 2390 ASN Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 72 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 188 optimal weight: 0.0060 overall best weight: 3.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN ** A1819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2205 ASN ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2375 HIS ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20521 Z= 0.251 Angle : 0.555 9.893 27849 Z= 0.295 Chirality : 0.043 0.151 3026 Planarity : 0.003 0.055 3678 Dihedral : 5.499 30.974 2753 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 56.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.52 % Favored : 77.48 % Rotamer: Outliers : 3.69 % Allowed : 13.65 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.43 (0.15), residues: 2469 helix: -2.37 (0.33), residues: 211 sheet: -4.06 (0.16), residues: 802 loop : -3.62 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1264 HIS 0.002 0.001 HIS A2375 PHE 0.019 0.001 PHE A 564 TYR 0.014 0.001 TYR A1963 ARG 0.004 0.000 ARG A2100 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 103 time to evaluate : 2.514 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7940 (ptt180) REVERT: A 341 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9248 (pp) REVERT: A 350 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8638 (tm) REVERT: A 523 MET cc_start: 0.8561 (ttt) cc_final: 0.8219 (ttt) REVERT: A 762 ILE cc_start: 0.9518 (OUTLIER) cc_final: 0.9121 (pt) REVERT: A 1394 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7877 (m-10) REVERT: A 1425 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8966 (tm) REVERT: A 1876 ILE cc_start: 0.9275 (OUTLIER) cc_final: 0.9010 (pt) REVERT: C 158 THR cc_start: 0.8858 (m) cc_final: 0.8490 (p) REVERT: C 227 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.7585 (p90) REVERT: C 387 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7104 (tm-30) outliers start: 82 outliers final: 60 residues processed: 175 average time/residue: 0.3100 time to fit residues: 88.0331 Evaluate side-chains 168 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 99 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 TYR Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1266 ARG Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1366 GLU Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1394 TYR Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1605 ASP Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1772 PHE Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain A residue 1876 ILE Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2067 ILE Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain A residue 2253 ILE Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain A residue 2375 HIS Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 10.0000 chunk 229 optimal weight: 0.0570 chunk 209 optimal weight: 9.9990 chunk 223 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 175 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 211 optimal weight: 10.0000 chunk 222 optimal weight: 8.9990 overall best weight: 4.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1166 ASN ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN ** A1819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2375 HIS ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20521 Z= 0.332 Angle : 0.595 9.571 27849 Z= 0.315 Chirality : 0.043 0.158 3026 Planarity : 0.004 0.056 3678 Dihedral : 5.574 31.505 2753 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 56.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.63 % Favored : 75.37 % Rotamer: Outliers : 4.05 % Allowed : 13.47 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.43 (0.15), residues: 2469 helix: -2.37 (0.33), residues: 211 sheet: -4.06 (0.16), residues: 815 loop : -3.62 (0.15), residues: 1443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1264 HIS 0.002 0.001 HIS A2375 PHE 0.021 0.001 PHE A 564 TYR 0.015 0.001 TYR A1963 ARG 0.004 0.000 ARG A2100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 187 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 97 time to evaluate : 2.384 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.8577 (OUTLIER) cc_final: 0.8008 (ptt180) REVERT: A 341 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9253 (pp) REVERT: A 350 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8664 (tm) REVERT: A 523 MET cc_start: 0.8567 (ttt) cc_final: 0.8226 (ttt) REVERT: A 762 ILE cc_start: 0.9532 (OUTLIER) cc_final: 0.9134 (pt) REVERT: A 1363 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8869 (mp) REVERT: A 1394 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7882 (m-10) REVERT: A 1425 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8943 (tm) REVERT: C 158 THR cc_start: 0.8864 (m) cc_final: 0.8513 (p) REVERT: C 227 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.7607 (p90) REVERT: C 387 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7255 (tm-30) outliers start: 90 outliers final: 69 residues processed: 177 average time/residue: 0.2998 time to fit residues: 87.0022 Evaluate side-chains 175 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 97 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 TYR Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1325 GLU Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1361 MET Chi-restraints excluded: chain A residue 1363 LEU Chi-restraints excluded: chain A residue 1366 GLU Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1394 TYR Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1605 ASP Chi-restraints excluded: chain A residue 1638 ASN Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1645 ASP Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1676 VAL Chi-restraints excluded: chain A residue 1693 THR Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1772 PHE Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2067 ILE Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain A residue 2231 ASN Chi-restraints excluded: chain A residue 2253 ILE Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 0.9990 chunk 236 optimal weight: 0.6980 chunk 144 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 164 optimal weight: 0.9980 chunk 248 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN ** A1819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20521 Z= 0.285 Angle : 0.572 9.442 27849 Z= 0.303 Chirality : 0.043 0.153 3026 Planarity : 0.003 0.055 3678 Dihedral : 5.509 30.904 2753 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 57.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.37 % Favored : 76.63 % Rotamer: Outliers : 3.83 % Allowed : 13.74 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.35 (0.15), residues: 2469 helix: -2.29 (0.33), residues: 211 sheet: -3.96 (0.16), residues: 825 loop : -3.59 (0.15), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1264 HIS 0.002 0.001 HIS C 75 PHE 0.020 0.001 PHE A 564 TYR 0.016 0.001 TYR A1963 ARG 0.004 0.000 ARG A2100 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4938 Ramachandran restraints generated. 2469 Oldfield, 0 Emsley, 2469 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 24 is missing expected H atoms. Skipping. Residue THR 28 is missing expected H atoms. Skipping. Residue ALA 29 is missing expected H atoms. Skipping. Residue ILE 35 is missing expected H atoms. Skipping. Residue VAL 36 is missing expected H atoms. Skipping. Residue LEU 39 is missing expected H atoms. Skipping. Residue ALA 40 is missing expected H atoms. Skipping. Residue LEU 44 is missing expected H atoms. Skipping. Residue THR 45 is missing expected H atoms. Skipping. Residue ALA 46 is missing expected H atoms. Skipping. Residue THR 49 is missing expected H atoms. Skipping. Residue LEU 53 is missing expected H atoms. Skipping. Residue ILE 56 is missing expected H atoms. Skipping. Residue ILE 57 is missing expected H atoms. Skipping. Residue THR 58 is missing expected H atoms. Skipping. Residue THR 92 is missing expected H atoms. Skipping. Residue LEU 93 is missing expected H atoms. Skipping. Residue ILE 97 is missing expected H atoms. Skipping. Residue THR 98 is missing expected H atoms. Skipping. Residue VAL 99 is missing expected H atoms. Skipping. Residue ILE 100 is missing expected H atoms. Skipping. Residue THR 106 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue THR 115 is missing expected H atoms. Skipping. Residue VAL 118 is missing expected H atoms. Skipping. Residue LEU 122 is missing expected H atoms. Skipping. Residue THR 124 is missing expected H atoms. Skipping. Residue LEU 125 is missing expected H atoms. Skipping. Residue ILE 126 is missing expected H atoms. Skipping. Residue ILE 133 is missing expected H atoms. Skipping. Residue LEU 135 is missing expected H atoms. Skipping. Residue LEU 136 is missing expected H atoms. Skipping. Residue ILE 142 is missing expected H atoms. Skipping. Residue LEU 144 is missing expected H atoms. Skipping. Residue VAL 146 is missing expected H atoms. Skipping. Residue ALA 148 is missing expected H atoms. Skipping. Residue LEU 150 is missing expected H atoms. Skipping. Residue THR 159 is missing expected H atoms. Skipping. Residue VAL 160 is missing expected H atoms. Skipping. Residue ALA 164 is missing expected H atoms. Skipping. Residue VAL 165 is missing expected H atoms. Skipping. Residue LEU 166 is missing expected H atoms. Skipping. Residue ILE 167 is missing expected H atoms. Skipping. Residue ILE 170 is missing expected H atoms. Skipping. Residue THR 171 is missing expected H atoms. Skipping. Residue LEU 172 is missing expected H atoms. Skipping. Residue VAL 173 is missing expected H atoms. Skipping. Residue VAL 175 is missing expected H atoms. Skipping. Evaluate side-chains 184 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 99 time to evaluate : 2.173 Fit side-chains revert: symmetry clash REVERT: A 290 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7996 (ptt180) REVERT: A 341 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9248 (pp) REVERT: A 350 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8648 (tm) REVERT: A 523 MET cc_start: 0.8569 (ttt) cc_final: 0.8233 (ttt) REVERT: A 762 ILE cc_start: 0.9526 (OUTLIER) cc_final: 0.9132 (pt) REVERT: A 1394 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7783 (m-10) REVERT: A 1425 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8955 (tm) REVERT: C 158 THR cc_start: 0.8866 (m) cc_final: 0.8496 (p) REVERT: C 227 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.7599 (p90) REVERT: C 387 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7236 (tm-30) outliers start: 85 outliers final: 72 residues processed: 173 average time/residue: 0.3062 time to fit residues: 85.8019 Evaluate side-chains 178 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 98 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 164 ARG Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 614 ASN Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 768 ASP Chi-restraints excluded: chain A residue 799 ILE Chi-restraints excluded: chain A residue 908 LEU Chi-restraints excluded: chain A residue 943 LEU Chi-restraints excluded: chain A residue 972 TYR Chi-restraints excluded: chain A residue 1047 GLN Chi-restraints excluded: chain A residue 1055 ASP Chi-restraints excluded: chain A residue 1168 MET Chi-restraints excluded: chain A residue 1175 TYR Chi-restraints excluded: chain A residue 1221 SER Chi-restraints excluded: chain A residue 1226 THR Chi-restraints excluded: chain A residue 1244 THR Chi-restraints excluded: chain A residue 1266 ARG Chi-restraints excluded: chain A residue 1325 GLU Chi-restraints excluded: chain A residue 1328 LEU Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1361 MET Chi-restraints excluded: chain A residue 1366 GLU Chi-restraints excluded: chain A residue 1368 LEU Chi-restraints excluded: chain A residue 1394 TYR Chi-restraints excluded: chain A residue 1419 ASP Chi-restraints excluded: chain A residue 1425 LEU Chi-restraints excluded: chain A residue 1441 ASP Chi-restraints excluded: chain A residue 1605 ASP Chi-restraints excluded: chain A residue 1638 ASN Chi-restraints excluded: chain A residue 1642 VAL Chi-restraints excluded: chain A residue 1666 TYR Chi-restraints excluded: chain A residue 1676 VAL Chi-restraints excluded: chain A residue 1740 ASN Chi-restraints excluded: chain A residue 1765 ASN Chi-restraints excluded: chain A residue 1772 PHE Chi-restraints excluded: chain A residue 1788 ASN Chi-restraints excluded: chain A residue 1840 VAL Chi-restraints excluded: chain A residue 1970 LEU Chi-restraints excluded: chain A residue 2027 LEU Chi-restraints excluded: chain A residue 2030 ASP Chi-restraints excluded: chain A residue 2067 ILE Chi-restraints excluded: chain A residue 2070 VAL Chi-restraints excluded: chain A residue 2231 ASN Chi-restraints excluded: chain A residue 2253 ILE Chi-restraints excluded: chain A residue 2272 ASP Chi-restraints excluded: chain A residue 2340 ASP Chi-restraints excluded: chain A residue 2372 TYR Chi-restraints excluded: chain B residue 24 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 GLN Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 179 ASP Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 227 TYR Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 354 MET Chi-restraints excluded: chain C residue 370 LYS Chi-restraints excluded: chain C residue 387 GLU Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 418 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 3.9990 chunk 210 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1667 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1740 ASN ** A1819 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1984 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2020 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.064990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.055023 restraints weight = 65355.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.056568 restraints weight = 36289.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.057619 restraints weight = 24193.411| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 20521 Z= 0.285 Angle : 0.570 9.316 27849 Z= 0.302 Chirality : 0.043 0.153 3026 Planarity : 0.003 0.054 3678 Dihedral : 5.468 30.818 2753 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 56.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.14 % Favored : 75.86 % Rotamer: Outliers : 3.92 % Allowed : 13.78 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.32 (0.15), residues: 2469 helix: -2.28 (0.32), residues: 216 sheet: -3.95 (0.16), residues: 832 loop : -3.55 (0.15), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1264 HIS 0.002 0.001 HIS C 75 PHE 0.020 0.001 PHE A 564 TYR 0.015 0.001 TYR A1963 ARG 0.004 0.000 ARG A2100 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3307.28 seconds wall clock time: 62 minutes 4.68 seconds (3724.68 seconds total)