Starting phenix.real_space_refine (version: dev) on Sat May 14 17:12:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3j_0134/05_2022/6h3j_0134.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3j_0134/05_2022/6h3j_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_0134/05_2022/6h3j_0134.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3j_0134/05_2022/6h3j_0134.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3j_0134/05_2022/6h3j_0134.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h3j_0134/05_2022/6h3j_0134.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 11.47, per 1000 atoms: 0.56 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: 8.22 Conformation dependent library (CDL) restraints added in 2.5 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: 1.68 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: 9.87 Time building geometry restraints manager: 8.89 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: 11488 14.94 - 29.88: 611 29.88 - 44.82: 137 44.82 - 59.76: 16 59.76 - 74.70: 9 Dihedral angle restraints: 12261 sinusoidal: 4922 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 12258 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 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. 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: 1.160 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: 0.520 Extract box with map and model: 7.370 Check model and map are aligned: 0.300 Convert atoms to be neutral: 0.160 Process input model: 54.560 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 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 : 43.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 23.77 % Favored : 76.18 % Rotamer Outliers : 0.05 % 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 *********************** 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 : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.3783 time to fit residues: 145.4402 Evaluate side-chains 108 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.393 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1640 ------------------------------------------------------------------------------- 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 A1210 ASN A1224 GLN ** 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 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 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: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 20521 Z= 0.360 Angle : 0.655 6.794 27849 Z= 0.353 Chirality : 0.045 0.172 3026 Planarity : 0.004 0.078 3678 Dihedral : 6.333 38.497 2753 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 57.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 23.69 % Favored : 76.27 % Rotamer Outliers : 1.58 % 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: -6.32 (0.14), residues: 2469 helix: -3.25 (0.27), residues: 235 sheet: -4.72 (0.13), residues: 841 loop : -4.11 (0.14), residues: 1393 *********************** 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 153 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 118 time to evaluate : 2.609 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 22 residues processed: 144 average time/residue: 0.3161 time to fit residues: 74.8287 Evaluate side-chains 125 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 103 time to evaluate : 2.391 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1979 time to fit residues: 11.1219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 125 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 62 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 GLN ** 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 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** A1224 GLN ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1672 HIS ** 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** ** A2083 GLN ** 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** ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 20521 Z= 0.281 Angle : 0.588 7.851 27849 Z= 0.314 Chirality : 0.043 0.153 3026 Planarity : 0.004 0.067 3678 Dihedral : 5.846 33.965 2753 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 56.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.24 % Favored : 77.76 % Rotamer Outliers : 1.31 % 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: -5.89 (0.14), residues: 2469 helix: -2.84 (0.29), residues: 224 sheet: -4.46 (0.14), residues: 827 loop : -3.83 (0.15), residues: 1418 *********************** 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 150 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 2.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 144 average time/residue: 0.3065 time to fit residues: 72.9756 Evaluate side-chains 119 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 2.499 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1905 time to fit residues: 8.6153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 223 optimal weight: 9.9990 chunk 170 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 215 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 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 317 GLN ** 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 ** 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** ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 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** ** 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** A2400 ASN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 20521 Z= 0.355 Angle : 0.619 6.806 27849 Z= 0.331 Chirality : 0.044 0.159 3026 Planarity : 0.004 0.064 3678 Dihedral : 5.833 32.469 2753 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 57.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.54 % Favored : 75.46 % Rotamer Outliers : 1.62 % 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: -5.81 (0.14), residues: 2469 helix: -2.70 (0.30), residues: 224 sheet: -4.37 (0.14), residues: 839 loop : -3.80 (0.15), residues: 1406 *********************** 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 140 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 2.464 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 22 residues processed: 134 average time/residue: 0.3028 time to fit residues: 67.3349 Evaluate side-chains 118 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 2.469 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2087 time to fit residues: 11.5886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 200 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 166 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 9.9990 chunk 216 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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 ** 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** A1668 GLN 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** ** B 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 20521 Z= 0.402 Angle : 0.646 6.897 27849 Z= 0.344 Chirality : 0.045 0.192 3026 Planarity : 0.004 0.062 3678 Dihedral : 5.951 31.111 2753 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 57.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.31 % Favored : 74.69 % Rotamer Outliers : 1.67 % 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: -5.76 (0.15), residues: 2469 helix: -2.65 (0.31), residues: 219 sheet: -4.32 (0.14), residues: 829 loop : -3.80 (0.15), residues: 1421 *********************** 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 137 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 100 time to evaluate : 2.398 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 18 residues processed: 130 average time/residue: 0.3455 time to fit residues: 73.1552 Evaluate side-chains 114 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 2.293 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2267 time to fit residues: 10.5930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 80 optimal weight: 0.3980 chunk 216 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 141 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 240 optimal weight: 8.9990 chunk 199 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 overall best weight: 2.8184 ------------------------------------------------------------------------------- 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** A1668 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 ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** 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: 0.8610 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 20521 Z= 0.241 Angle : 0.547 5.823 27849 Z= 0.292 Chirality : 0.043 0.149 3026 Planarity : 0.003 0.054 3678 Dihedral : 5.517 30.009 2753 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 55.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.36 % Favored : 77.64 % Rotamer Outliers : 1.22 % 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: -5.53 (0.15), residues: 2469 helix: -2.46 (0.31), residues: 223 sheet: -4.11 (0.15), residues: 809 loop : -3.70 (0.15), residues: 1437 *********************** 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 132 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 2.476 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 124 average time/residue: 0.3150 time to fit residues: 63.7141 Evaluate side-chains 114 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 2.374 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2108 time to fit residues: 9.0300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 232 optimal weight: 8.9990 chunk 27 optimal weight: 0.6980 chunk 137 optimal weight: 7.9990 chunk 175 optimal weight: 0.2980 chunk 136 optimal weight: 7.9990 chunk 202 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- 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** A1395 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** ** B 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 20521 Z= 0.322 Angle : 0.587 6.213 27849 Z= 0.312 Chirality : 0.043 0.158 3026 Planarity : 0.004 0.056 3678 Dihedral : 5.569 30.657 2753 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 56.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.22 % Favored : 75.78 % Rotamer Outliers : 1.13 % 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: -5.45 (0.15), residues: 2469 helix: -2.38 (0.32), residues: 217 sheet: -4.05 (0.15), residues: 828 loop : -3.64 (0.15), residues: 1424 *********************** 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 127 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 2.483 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 11 residues processed: 122 average time/residue: 0.3231 time to fit residues: 64.7894 Evaluate side-chains 109 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 2.490 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2459 time to fit residues: 7.7756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 148 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 152 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 188 optimal weight: 0.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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** ** 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** A2375 HIS ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 20521 Z= 0.286 Angle : 0.567 5.864 27849 Z= 0.303 Chirality : 0.043 0.154 3026 Planarity : 0.003 0.053 3678 Dihedral : 5.486 29.702 2753 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 56.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.21 % Favored : 76.79 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.33 (0.15), residues: 2469 helix: -2.26 (0.32), residues: 217 sheet: -3.95 (0.16), residues: 807 loop : -3.60 (0.15), residues: 1445 *********************** 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 123 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 2.454 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 119 average time/residue: 0.3186 time to fit residues: 62.9087 Evaluate side-chains 108 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 2.618 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2295 time to fit residues: 7.5011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 218 optimal weight: 0.6980 chunk 229 optimal weight: 0.3980 chunk 209 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 202 optimal weight: 9.9990 chunk 211 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 650 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 ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1819 HIS A1821 GLN 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** ** A2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2282 ASN A2345 GLN ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 20521 Z= 0.133 Angle : 0.486 5.185 27849 Z= 0.259 Chirality : 0.042 0.144 3026 Planarity : 0.003 0.054 3678 Dihedral : 4.912 28.106 2753 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 55.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.39 % Favored : 81.61 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.06 (0.16), residues: 2469 helix: -1.94 (0.34), residues: 222 sheet: -3.79 (0.16), residues: 793 loop : -3.43 (0.15), residues: 1454 *********************** 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 128 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 2.600 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 127 average time/residue: 0.3077 time to fit residues: 64.5414 Evaluate side-chains 106 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 103 time to evaluate : 2.610 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2253 time to fit residues: 4.6275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 146 optimal weight: 0.7980 chunk 236 optimal weight: 10.0000 chunk 144 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 248 optimal weight: 0.0870 chunk 228 optimal weight: 0.0170 chunk 197 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 152 optimal weight: 0.0870 chunk 121 optimal weight: 5.9990 overall best weight: 0.7976 ------------------------------------------------------------------------------- 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 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 650 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** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 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** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 20521 Z= 0.113 Angle : 0.463 4.796 27849 Z= 0.245 Chirality : 0.041 0.141 3026 Planarity : 0.003 0.047 3678 Dihedral : 4.529 26.191 2753 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 55.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.05 % Favored : 82.95 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (0.16), residues: 2469 helix: -1.57 (0.36), residues: 203 sheet: -3.67 (0.16), residues: 800 loop : -3.23 (0.15), residues: 1466 ********************** 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 126 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 121 average time/residue: 0.3309 time to fit residues: 66.7755 Evaluate side-chains 108 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 2.913 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2708 time to fit residues: 6.9117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 249 random chunks: chunk 156 optimal weight: 10.0000 chunk 210 optimal weight: 0.0060 chunk 60 optimal weight: 5.9990 chunk 182 optimal weight: 0.0370 chunk 29 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 overall best weight: 3.8080 ------------------------------------------------------------------------------- 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 650 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** ** A1295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1506 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** ** A2136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 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 = 0.3158 r_free = 0.3158 target = 0.065820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.055903 restraints weight = 65139.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057429 restraints weight = 35968.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.058462 restraints weight = 24042.831| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 20521 Z= 0.306 Angle : 0.565 6.324 27849 Z= 0.300 Chirality : 0.043 0.154 3026 Planarity : 0.004 0.059 3678 Dihedral : 5.050 28.256 2753 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 56.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.39 % Favored : 78.61 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.95 (0.16), residues: 2469 helix: -1.74 (0.34), residues: 216 sheet: -3.73 (0.16), residues: 835 loop : -3.32 (0.15), residues: 1418 =============================================================================== Job complete usr+sys time: 2992.17 seconds wall clock time: 56 minutes 55.66 seconds (3415.66 seconds total)