Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 01:51:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xja_22204/04_2023/6xja_22204.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xja_22204/04_2023/6xja_22204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xja_22204/04_2023/6xja_22204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xja_22204/04_2023/6xja_22204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xja_22204/04_2023/6xja_22204.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xja_22204/04_2023/6xja_22204.pdb" } resolution = 4.0 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= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 10337 2.51 5 N 2810 2.21 5 O 3244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P GLU 670": "OE1" <-> "OE2" Residue "P GLU 681": "OE1" <-> "OE2" Residue "P GLU 810": "OE1" <-> "OE2" Residue "P ARG 816": "NH1" <-> "NH2" Residue "P ARG 826": "NH1" <-> "NH2" Residue "P GLU 847": "OE1" <-> "OE2" Residue "P GLU 895": "OE1" <-> "OE2" Residue "P ARG 896": "NH1" <-> "NH2" Residue "P GLU 1010": "OE1" <-> "OE2" Residue "P GLU 1070": "OE1" <-> "OE2" Residue "P GLU 1087": "OE1" <-> "OE2" Residue "P TYR 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 1247": "NH1" <-> "NH2" Residue "P ARG 1296": "NH1" <-> "NH2" Residue "P GLU 1416": "OE1" <-> "OE2" Residue "P GLU 1423": "OE1" <-> "OE2" Residue "P ARG 1442": "NH1" <-> "NH2" Residue "P ARG 1463": "NH1" <-> "NH2" Residue "P PHE 1466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 1524": "NH1" <-> "NH2" Residue "P ARG 1621": "NH1" <-> "NH2" Residue "P ARG 1622": "NH1" <-> "NH2" Residue "P GLU 1698": "OE1" <-> "OE2" Residue "P ARG 1716": "NH1" <-> "NH2" Residue "P GLU 1743": "OE1" <-> "OE2" Residue "P ARG 1773": "NH1" <-> "NH2" Residue "P ARG 1875": "NH1" <-> "NH2" Residue "P GLU 1931": "OE1" <-> "OE2" Residue "P ARG 1955": "NH1" <-> "NH2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B VAL 307": "CG1" <-> "CG2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L ARG 113": "NH1" <-> "NH2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H GLU 162": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 16441 Number of models: 1 Model: "" Number of chains: 5 Chain: "P" Number of atoms: 10159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1286, 10159 Classifications: {'peptide': 1286} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 32, 'TRANS': 1253} Chain breaks: 3 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1598 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 17, 'TRANS': 191} Chain: "B" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1604 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 17, 'TRANS': 192} Chain: "L" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1541 Classifications: {'peptide': 219} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 209} Chain: "H" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1539 Classifications: {'peptide': 232} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 213} Residues with excluded nonbonded symmetry interactions: 25 residue: pdb=" N SER L 7 " occ=0.40 ... (4 atoms not shown) pdb=" OG SER L 7 " occ=0.40 residue: pdb=" N SER L 61 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER L 61 " occ=0.70 residue: pdb=" N SER L 68 " occ=0.60 ... (4 atoms not shown) pdb=" OG SER L 68 " occ=0.60 residue: pdb=" N LYS L 112 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS L 112 " occ=0.50 residue: pdb=" N SER L 119 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER L 119 " occ=0.70 residue: pdb=" N ASP L 127 " occ=0.60 ... (6 atoms not shown) pdb=" OD2 ASP L 127 " occ=0.60 residue: pdb=" N LYS L 154 " occ=0.70 ... (7 atoms not shown) pdb=" NZ LYS L 154 " occ=0.70 residue: pdb=" N LYS L 188 " occ=0.70 ... (7 atoms not shown) pdb=" NZ LYS L 188 " occ=0.70 residue: pdb=" N GLU L 192 " occ=0.60 ... (7 atoms not shown) pdb=" OE2 GLU L 192 " occ=0.60 residue: pdb=" N CYS L 199 " occ=0.60 ... (4 atoms not shown) pdb=" SG CYS L 199 " occ=0.60 residue: pdb=" N SER L 208 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER L 208 " occ=0.70 residue: pdb=" N SER L 213 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER L 213 " occ=0.70 ... (remaining 13 not shown) Time building chain proxies: 8.65, per 1000 atoms: 0.53 Number of scatterers: 16441 At special positions: 0 Unit cell: (96.99, 131.97, 192.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 3244 8.00 N 2810 7.00 C 10337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.01 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 196 " - pdb=" SG CYS H 220 " distance=2.04 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: 6.84 Conformation dependent library (CDL) restraints added in 2.4 seconds 4268 Ramachandran restraints generated. 2134 Oldfield, 0 Emsley, 2134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4028 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 28 sheets defined 22.4% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'P' and resid 782 through 793 removed outlier: 4.011A pdb=" N LYS P 788 " --> pdb=" O SER P 784 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN P 791 " --> pdb=" O VAL P 787 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN P 792 " --> pdb=" O LYS P 788 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN P 793 " --> pdb=" O ALA P 789 " (cutoff:3.500A) Processing helix chain 'P' and resid 1010 through 1015 removed outlier: 4.579A pdb=" N GLY P1015 " --> pdb=" O GLU P1011 " (cutoff:3.500A) Processing helix chain 'P' and resid 1075 through 1083 removed outlier: 3.530A pdb=" N SER P1079 " --> pdb=" O MET P1075 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE P1081 " --> pdb=" O ASP P1077 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL P1082 " --> pdb=" O ALA P1078 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER P1083 " --> pdb=" O SER P1079 " (cutoff:3.500A) Processing helix chain 'P' and resid 1119 through 1128 removed outlier: 3.582A pdb=" N LYS P1128 " --> pdb=" O LYS P1124 " (cutoff:3.500A) Processing helix chain 'P' and resid 1134 through 1144 removed outlier: 3.780A pdb=" N LEU P1144 " --> pdb=" O LYS P1140 " (cutoff:3.500A) Processing helix chain 'P' and resid 1169 through 1174 removed outlier: 3.544A pdb=" N SER P1173 " --> pdb=" O THR P1169 " (cutoff:3.500A) Processing helix chain 'P' and resid 1211 through 1213 No H-bonds generated for 'chain 'P' and resid 1211 through 1213' Processing helix chain 'P' and resid 1225 through 1238 removed outlier: 3.996A pdb=" N GLU P1231 " --> pdb=" O SER P1227 " (cutoff:3.500A) Proline residue: P1234 - end of helix removed outlier: 3.679A pdb=" N LYS P1238 " --> pdb=" O PRO P1234 " (cutoff:3.500A) Processing helix chain 'P' and resid 1243 through 1250 removed outlier: 3.719A pdb=" N ARG P1247 " --> pdb=" O SER P1243 " (cutoff:3.500A) Processing helix chain 'P' and resid 1263 through 1273 Processing helix chain 'P' and resid 1273 through 1286 removed outlier: 4.147A pdb=" N SER P1277 " --> pdb=" O ASN P1273 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA P1286 " --> pdb=" O LEU P1282 " (cutoff:3.500A) Processing helix chain 'P' and resid 1292 through 1306 removed outlier: 4.630A pdb=" N ARG P1296 " --> pdb=" O ASN P1292 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN P1306 " --> pdb=" O LYS P1302 " (cutoff:3.500A) Processing helix chain 'P' and resid 1306 through 1320 Processing helix chain 'P' and resid 1347 through 1357 removed outlier: 3.562A pdb=" N LEU P1352 " --> pdb=" O PRO P1348 " (cutoff:3.500A) Processing helix chain 'P' and resid 1367 through 1375 removed outlier: 3.757A pdb=" N TYR P1372 " --> pdb=" O ASN P1368 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY P1373 " --> pdb=" O VAL P1369 " (cutoff:3.500A) Processing helix chain 'P' and resid 1384 through 1396 Processing helix chain 'P' and resid 1401 through 1410 Processing helix chain 'P' and resid 1421 through 1430 removed outlier: 3.709A pdb=" N GLY P1429 " --> pdb=" O LYS P1425 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU P1430 " --> pdb=" O THR P1426 " (cutoff:3.500A) Processing helix chain 'P' and resid 1438 through 1444 Processing helix chain 'P' and resid 1450 through 1452 No H-bonds generated for 'chain 'P' and resid 1450 through 1452' Processing helix chain 'P' and resid 1453 through 1459 removed outlier: 3.618A pdb=" N LEU P1457 " --> pdb=" O MET P1453 " (cutoff:3.500A) Processing helix chain 'P' and resid 1480 through 1482 No H-bonds generated for 'chain 'P' and resid 1480 through 1482' Processing helix chain 'P' and resid 1490 through 1519 Processing helix chain 'P' and resid 1523 through 1527 Processing helix chain 'P' and resid 1558 through 1564 Processing helix chain 'P' and resid 1595 through 1610 removed outlier: 3.964A pdb=" N ALA P1599 " --> pdb=" O ASP P1595 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE P1600 " --> pdb=" O LYS P1596 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR P1601 " --> pdb=" O ASP P1597 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS P1604 " --> pdb=" O ILE P1600 " (cutoff:3.500A) Processing helix chain 'P' and resid 1658 through 1662 Processing helix chain 'P' and resid 1669 through 1674 Processing helix chain 'P' and resid 1676 through 1705 Processing helix chain 'P' and resid 1707 through 1714 removed outlier: 3.603A pdb=" N ALA P1713 " --> pdb=" O TYR P1709 " (cutoff:3.500A) Processing helix chain 'P' and resid 1742 through 1748 removed outlier: 3.901A pdb=" N ASN P1748 " --> pdb=" O ALA P1744 " (cutoff:3.500A) Processing helix chain 'P' and resid 1751 through 1758 removed outlier: 3.766A pdb=" N ILE P1756 " --> pdb=" O PHE P1752 " (cutoff:3.500A) Processing helix chain 'P' and resid 1798 through 1812 removed outlier: 3.762A pdb=" N ARG P1803 " --> pdb=" O LEU P1799 " (cutoff:3.500A) Processing helix chain 'P' and resid 1817 through 1823 Processing helix chain 'P' and resid 1826 through 1834 Processing helix chain 'P' and resid 1848 through 1857 Processing helix chain 'P' and resid 1863 through 1880 Processing helix chain 'P' and resid 1904 through 1921 removed outlier: 3.716A pdb=" N LEU P1908 " --> pdb=" O ASN P1904 " (cutoff:3.500A) Processing helix chain 'P' and resid 1930 through 1933 Processing helix chain 'P' and resid 1934 through 1951 removed outlier: 3.683A pdb=" N THR P1951 " --> pdb=" O TYR P1947 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.754A pdb=" N LYS A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 259 removed outlier: 3.632A pdb=" N LEU B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 318 removed outlier: 3.832A pdb=" N HIS B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY B 318 " --> pdb=" O PRO B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 427 removed outlier: 3.540A pdb=" N GLY B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 194 removed outlier: 3.694A pdb=" N HIS L 194 " --> pdb=" O ASP L 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing sheet with id=AA1, first strand: chain 'P' and resid 699 through 700 removed outlier: 3.874A pdb=" N ARG P 699 " --> pdb=" O SER P 692 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER P 732 " --> pdb=" O THR P 747 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N PHE P 765 " --> pdb=" O ALA P 748 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 699 through 700 removed outlier: 3.874A pdb=" N ARG P 699 " --> pdb=" O SER P 692 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'P' and resid 755 through 757 Processing sheet with id=AA4, first strand: chain 'P' and resid 797 through 799 removed outlier: 6.168A pdb=" N TYR P 798 " --> pdb=" O GLY P 829 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE P 828 " --> pdb=" O GLU P 855 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'P' and resid 804 through 805 removed outlier: 6.630A pdb=" N LEU P 804 " --> pdb=" O TYR P 839 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'P' and resid 858 through 866 removed outlier: 3.666A pdb=" N ASN P 861 " --> pdb=" O ASP P 889 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL P 891 " --> pdb=" O ASN P 861 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA P 863 " --> pdb=" O VAL P 891 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA P 893 " --> pdb=" O ALA P 863 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER P 865 " --> pdb=" O ALA P 893 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 858 through 866 removed outlier: 3.666A pdb=" N ASN P 861 " --> pdb=" O ASP P 889 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL P 891 " --> pdb=" O ASN P 861 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA P 863 " --> pdb=" O VAL P 891 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA P 893 " --> pdb=" O ALA P 863 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER P 865 " --> pdb=" O ALA P 893 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL P 920 " --> pdb=" O GLY P 890 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU P 892 " --> pdb=" O VAL P 920 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE P 919 " --> pdb=" O SER P 955 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'P' and resid 870 through 871 removed outlier: 6.176A pdb=" N ILE P 870 " --> pdb=" O GLY P 899 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'P' and resid 874 through 877 removed outlier: 6.933A pdb=" N ASN P 875 " --> pdb=" O LEU P 902 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 883 through 884 removed outlier: 6.583A pdb=" N ILE P 883 " --> pdb=" O ALA P 911 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE P 945 " --> pdb=" O GLN P 979 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 930 through 931 Processing sheet with id=AB3, first strand: chain 'P' and resid 1020 through 1021 removed outlier: 6.397A pdb=" N VAL P1020 " --> pdb=" O PHE P1046 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'P' and resid 1159 through 1161 removed outlier: 3.855A pdb=" N LYS P1196 " --> pdb=" O ASN P1208 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LEU P1214 " --> pdb=" O LEU P1209 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'P' and resid 1324 through 1325 Processing sheet with id=AB6, first strand: chain 'P' and resid 1413 through 1417 removed outlier: 3.858A pdb=" N GLU P1417 " --> pdb=" O SER P1469 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU P1474 " --> pdb=" O LEU P1533 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU P1532 " --> pdb=" O VAL P1586 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N TYR P1588 " --> pdb=" O LEU P1532 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR P1534 " --> pdb=" O TYR P1588 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 1734 through 1739 Processing sheet with id=AB8, first strand: chain 'P' and resid 1836 through 1839 Processing sheet with id=AB9, first strand: chain 'A' and resid 245 through 246 removed outlier: 4.151A pdb=" N CYS A 266 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER A 306 " --> pdb=" O CYS A 266 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 322 through 325 removed outlier: 4.405A pdb=" N ALA A 325 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU A 334 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 401 through 402 removed outlier: 3.728A pdb=" N ARG B 401 " --> pdb=" O ALA B 412 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 412 " --> pdb=" O ARG B 401 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'L' and resid 20 through 21 Processing sheet with id=AC4, first strand: chain 'L' and resid 58 through 59 removed outlier: 4.155A pdb=" N ALA L 58 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR L 54 " --> pdb=" O ALA L 58 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.530A pdb=" N SER L 119 " --> pdb=" O ASN L 142 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS L 139 " --> pdb=" O SER L 182 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU L 141 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 158 through 160 removed outlier: 4.076A pdb=" N TRP L 153 " --> pdb=" O GLN L 160 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS L 150 " --> pdb=" O THR L 202 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU L 200 " --> pdb=" O GLN L 152 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.572A pdb=" N ALA H 82 " --> pdb=" O SER H 73 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 95 through 96 removed outlier: 3.577A pdb=" N TYR H 96 " --> pdb=" O THR H 113 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 126 through 130 removed outlier: 3.783A pdb=" N LYS H 126 " --> pdb=" O GLN H 148 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA H 144 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR H 185 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY H 149 " --> pdb=" O TYR H 183 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N TYR H 183 " --> pdb=" O GLY H 149 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER H 186 " --> pdb=" O PHE H 172 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE H 172 " --> pdb=" O SER H 186 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.529A pdb=" N SER H 157 " --> pdb=" O LYS H 207 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL H 202 " --> pdb=" O VAL H 218 " (cutoff:3.500A) 399 hydrogen bonds defined for protein. 1101 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: 6.41 Time building geometry restraints manager: 7.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.47: 8299 1.47 - 1.83: 8471 1.83 - 2.18: 3 2.18 - 2.53: 2 2.53 - 2.88: 1 Bond restraints: 16776 Sorted by residual: bond pdb=" C GLN P 673 " pdb=" N THR P 674 " ideal model delta sigma weight residual 1.333 2.878 -1.545 1.29e-02 6.01e+03 1.43e+04 bond pdb=" C LEU P1091 " pdb=" N THR P1092 " ideal model delta sigma weight residual 1.332 2.386 -1.053 1.40e-02 5.10e+03 5.66e+03 bond pdb=" CA HIS B 243 " pdb=" CB HIS B 243 " ideal model delta sigma weight residual 1.530 2.514 -0.984 1.58e-02 4.01e+03 3.88e+03 bond pdb=" C ILE P1958 " pdb=" N PHE P1959 " ideal model delta sigma weight residual 1.331 2.007 -0.676 1.40e-02 5.10e+03 2.33e+03 bond pdb=" CA VAL B 307 " pdb=" CB VAL B 307 " ideal model delta sigma weight residual 1.543 2.093 -0.550 1.32e-02 5.74e+03 1.73e+03 ... (remaining 16771 not shown) Histogram of bond angle deviations from ideal: 46.01 - 70.25: 4 70.25 - 94.49: 2 94.49 - 118.73: 14767 118.73 - 142.97: 8000 142.97 - 167.21: 7 Bond angle restraints: 22780 Sorted by residual: angle pdb=" C GLN P 673 " pdb=" N THR P 674 " pdb=" CA THR P 674 " ideal model delta sigma weight residual 122.63 46.01 76.62 1.44e+00 4.82e-01 2.83e+03 angle pdb=" O CYS B 242 " pdb=" C CYS B 242 " pdb=" N HIS B 243 " ideal model delta sigma weight residual 122.28 60.26 62.02 1.30e+00 5.92e-01 2.28e+03 angle pdb=" O GLN P 673 " pdb=" C GLN P 673 " pdb=" N THR P 674 " ideal model delta sigma weight residual 122.13 51.58 70.55 1.50e+00 4.44e-01 2.21e+03 angle pdb=" CA HIS B 243 " pdb=" CB HIS B 243 " pdb=" CG HIS B 243 " ideal model delta sigma weight residual 113.80 152.90 -39.10 1.00e+00 1.00e+00 1.53e+03 angle pdb=" O ILE P1958 " pdb=" C ILE P1958 " pdb=" N PHE P1959 " ideal model delta sigma weight residual 123.18 83.88 39.30 1.04e+00 9.25e-01 1.43e+03 ... (remaining 22775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.92: 9291 26.92 - 53.84: 691 53.84 - 80.76: 125 80.76 - 107.68: 6 107.68 - 134.60: 1 Dihedral angle restraints: 10114 sinusoidal: 3845 harmonic: 6269 Sorted by residual: dihedral pdb=" CA TYR L 145 " pdb=" C TYR L 145 " pdb=" N PRO L 146 " pdb=" CA PRO L 146 " ideal model delta harmonic sigma weight residual 180.00 45.40 134.60 0 5.00e+00 4.00e-02 7.25e+02 dihedral pdb=" C VAL B 307 " pdb=" N VAL B 307 " pdb=" CA VAL B 307 " pdb=" CB VAL B 307 " ideal model delta harmonic sigma weight residual -122.00 -166.14 44.14 0 2.50e+00 1.60e-01 3.12e+02 dihedral pdb=" CA ALA H 85 " pdb=" C ALA H 85 " pdb=" N ALA H 86 " pdb=" CA ALA H 86 " ideal model delta harmonic sigma weight residual 180.00 -92.22 -87.78 0 5.00e+00 4.00e-02 3.08e+02 ... (remaining 10111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.615: 2562 0.615 - 1.230: 4 1.230 - 1.844: 0 1.844 - 2.459: 0 2.459 - 3.074: 1 Chirality restraints: 2567 Sorted by residual: chirality pdb=" CB VAL B 307 " pdb=" CA VAL B 307 " pdb=" CG1 VAL B 307 " pdb=" CG2 VAL B 307 " both_signs ideal model delta sigma weight residual False -2.63 0.44 -3.07 2.00e-01 2.50e+01 2.36e+02 chirality pdb=" CA ALA H 86 " pdb=" N ALA H 86 " pdb=" C ALA H 86 " pdb=" CB ALA H 86 " both_signs ideal model delta sigma weight residual False 2.48 1.30 1.18 2.00e-01 2.50e+01 3.48e+01 chirality pdb=" CA VAL B 307 " pdb=" N VAL B 307 " pdb=" C VAL B 307 " pdb=" CB VAL B 307 " both_signs ideal model delta sigma weight residual False 2.44 1.35 1.09 2.00e-01 2.50e+01 2.99e+01 ... (remaining 2564 not shown) Planarity restraints: 2961 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN P 673 " -0.185 2.00e-02 2.50e+03 2.71e-01 7.35e+02 pdb=" C GLN P 673 " 0.440 2.00e-02 2.50e+03 pdb=" O GLN P 673 " -0.257 2.00e-02 2.50e+03 pdb=" N THR P 674 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE P1958 " -0.178 2.00e-02 2.50e+03 2.67e-01 7.15e+02 pdb=" C ILE P1958 " 0.444 2.00e-02 2.50e+03 pdb=" O ILE P1958 " -0.237 2.00e-02 2.50e+03 pdb=" N PHE P1959 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU P1091 " -0.156 2.00e-02 2.50e+03 2.48e-01 6.14e+02 pdb=" C LEU P1091 " 0.419 2.00e-02 2.50e+03 pdb=" O LEU P1091 " -0.206 2.00e-02 2.50e+03 pdb=" N THR P1092 " -0.056 2.00e-02 2.50e+03 ... (remaining 2958 not shown) Histogram of nonbonded interaction distances: 0.47 - 1.35: 27 1.35 - 2.24: 234 2.24 - 3.13: 13716 3.13 - 4.01: 43048 4.01 - 4.90: 75031 Warning: very small nonbonded interaction distances. Nonbonded interactions: 132056 Sorted by model distance: nonbonded pdb=" O CYS A 299 " pdb=" SG CYS B 241 " model vdw 0.468 3.400 nonbonded pdb=" ND2 ASN P 779 " pdb=" CA LEU P 786 " model vdw 0.597 3.550 nonbonded pdb=" ND2 ASN P 684 " pdb=" N ASP P1106 " model vdw 0.682 3.200 nonbonded pdb=" CG GLU P 924 " pdb=" OD1 ASN P1361 " model vdw 0.697 3.440 nonbonded pdb=" CZ ARG B 250 " pdb=" OG1 THR B 267 " model vdw 0.767 3.270 ... (remaining 132051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 242 through 450) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 max=1.00 mean=0.99 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: 0.700 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: 0.010 Extract box with map and model: 4.080 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 44.610 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5396 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 : 0.023 1.545 16776 Z= 1.607 Angle : 1.934 76.622 22780 Z= 1.415 Chirality : 0.118 3.074 2567 Planarity : 0.012 0.271 2961 Dihedral : 18.035 134.597 6059 Min Nonbonded Distance : 0.468 Molprobity Statistics. All-atom Clashscore : 73.73 Ramachandran Plot: Outliers : 1.73 % Allowed : 6.09 % Favored : 92.17 % Rotamer Outliers : 18.43 % Cbeta Deviations : 1.54 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 5.38 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.17), residues: 2134 helix: -0.64 (0.23), residues: 438 sheet: -0.34 (0.27), residues: 405 loop : -1.91 (0.15), residues: 1291 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4268 Ramachandran restraints generated. 2134 Oldfield, 0 Emsley, 2134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4268 Ramachandran restraints generated. 2134 Oldfield, 0 Emsley, 2134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 321 poor density : 383 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 321 outliers final: 119 residues processed: 657 average time/residue: 0.3308 time to fit residues: 311.7806 Evaluate side-chains 349 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 230 time to evaluate : 1.891 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 119 outliers final: 9 residues processed: 119 average time/residue: 0.2058 time to fit residues: 43.2059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 193 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 673 GLN ** P 779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 835 ASN P 840 ASN P 868 ASN P1089 ASN P1114 HIS P1166 GLN P1324 ASN P1379 GLN P1380 HIS P1399 ASN ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1903 ASN ** P1961 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 249 HIS A 291 GLN ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 129 GLN L 194 HIS H 140 ASN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.117 16776 Z= 0.395 Angle : 0.951 15.738 22780 Z= 0.496 Chirality : 0.053 0.414 2567 Planarity : 0.007 0.095 2961 Dihedral : 6.131 80.518 2315 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 27.74 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.45 % Favored : 93.08 % Rotamer Outliers : 6.72 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.17), residues: 2140 helix: -0.62 (0.23), residues: 446 sheet: -0.70 (0.26), residues: 404 loop : -2.01 (0.15), residues: 1290 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 231 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 56 residues processed: 335 average time/residue: 0.2936 time to fit residues: 146.5431 Evaluate side-chains 227 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 171 time to evaluate : 1.862 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.1521 time to fit residues: 18.2983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 160 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 193 optimal weight: 20.0000 chunk 209 optimal weight: 0.2980 chunk 172 optimal weight: 50.0000 chunk 192 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 921 ASN ** P 942 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1143 ASN ** P1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1758 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6036 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.075 16776 Z= 0.224 Angle : 0.744 13.339 22780 Z= 0.382 Chirality : 0.045 0.283 2567 Planarity : 0.006 0.103 2961 Dihedral : 5.485 70.274 2315 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 23.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.54 % Favored : 93.27 % Rotamer Outliers : 3.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.17), residues: 2140 helix: -0.24 (0.24), residues: 448 sheet: -0.70 (0.27), residues: 359 loop : -2.00 (0.15), residues: 1333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 192 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 25 residues processed: 243 average time/residue: 0.3068 time to fit residues: 112.3421 Evaluate side-chains 179 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 2.117 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.2000 time to fit residues: 11.4552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 0.4980 chunk 145 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 194 optimal weight: 0.4980 chunk 205 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 184 optimal weight: 0.0870 chunk 55 optimal weight: 0.9980 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 673 GLN ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 942 ASN P1511 HIS ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1748 ASN P1758 HIS P1774 ASN ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.5890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 16776 Z= 0.202 Angle : 0.702 12.699 22780 Z= 0.356 Chirality : 0.044 0.247 2567 Planarity : 0.005 0.091 2961 Dihedral : 5.204 64.628 2315 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.36 % Favored : 93.41 % Rotamer Outliers : 2.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.17), residues: 2140 helix: -0.08 (0.24), residues: 447 sheet: -0.81 (0.25), residues: 401 loop : -2.04 (0.16), residues: 1292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 168 time to evaluate : 2.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 24 residues processed: 209 average time/residue: 0.2873 time to fit residues: 93.1752 Evaluate side-chains 182 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 1.958 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1928 time to fit residues: 10.7239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 142 optimal weight: 0.0040 chunk 0 optimal weight: 30.0000 chunk 105 optimal weight: 0.3980 chunk 184 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 673 GLN ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1563 ASN ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6200 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 16776 Z= 0.220 Angle : 0.690 12.341 22780 Z= 0.352 Chirality : 0.043 0.275 2567 Planarity : 0.005 0.067 2961 Dihedral : 5.095 62.519 2315 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 21.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.15 % Favored : 92.66 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.17), residues: 2140 helix: 0.07 (0.25), residues: 436 sheet: -0.80 (0.26), residues: 382 loop : -1.97 (0.16), residues: 1322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 172 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 19 residues processed: 203 average time/residue: 0.2941 time to fit residues: 91.9304 Evaluate side-chains 164 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.992 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2050 time to fit residues: 9.1904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 5.9990 chunk 185 optimal weight: 0.0000 chunk 40 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 206 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 overall best weight: 1.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1748 ASN ** P1825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1838 ASN P1903 ASN ** A 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 16776 Z= 0.224 Angle : 0.677 11.395 22780 Z= 0.345 Chirality : 0.043 0.268 2567 Planarity : 0.005 0.080 2961 Dihedral : 5.089 53.491 2315 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.24 % Favored : 92.62 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.17), residues: 2140 helix: 0.03 (0.25), residues: 435 sheet: -0.81 (0.26), residues: 387 loop : -2.01 (0.16), residues: 1318 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 163 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 25 residues processed: 198 average time/residue: 0.3006 time to fit residues: 91.9746 Evaluate side-chains 173 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 2.070 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1723 time to fit residues: 10.7152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 150 optimal weight: 30.0000 chunk 116 optimal weight: 0.5980 chunk 173 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 205 optimal weight: 9.9990 chunk 128 optimal weight: 0.0050 chunk 125 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1730 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1774 ASN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.7139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 16776 Z= 0.230 Angle : 0.693 17.225 22780 Z= 0.351 Chirality : 0.043 0.253 2567 Planarity : 0.005 0.071 2961 Dihedral : 5.113 51.878 2315 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.85 % Favored : 92.01 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 2140 helix: -0.03 (0.25), residues: 429 sheet: -0.82 (0.26), residues: 380 loop : -2.00 (0.16), residues: 1331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 1.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 15 residues processed: 192 average time/residue: 0.2823 time to fit residues: 85.0004 Evaluate side-chains 164 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 2.025 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1574 time to fit residues: 6.9656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 122 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 161 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 792 GLN ** P1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1838 ASN ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 205 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.8035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 16776 Z= 0.413 Angle : 0.867 16.614 22780 Z= 0.448 Chirality : 0.049 0.274 2567 Planarity : 0.006 0.071 2961 Dihedral : 5.999 46.041 2315 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 32.72 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.72 % Favored : 90.05 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.17), residues: 2140 helix: -1.01 (0.23), residues: 441 sheet: -1.29 (0.25), residues: 423 loop : -2.22 (0.16), residues: 1276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 160 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 24 residues processed: 190 average time/residue: 0.2884 time to fit residues: 85.2041 Evaluate side-chains 166 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.941 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1542 time to fit residues: 9.2942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 0.2980 chunk 196 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 150 optimal weight: 0.0470 chunk 58 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 180 optimal weight: 4.9990 chunk 190 optimal weight: 20.0000 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 moved from start: 0.8103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 16776 Z= 0.243 Angle : 0.746 16.328 22780 Z= 0.376 Chirality : 0.045 0.249 2567 Planarity : 0.005 0.067 2961 Dihedral : 5.603 48.846 2315 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 25.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.18 % Favored : 91.64 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.17), residues: 2140 helix: -0.50 (0.24), residues: 434 sheet: -1.21 (0.25), residues: 415 loop : -2.14 (0.16), residues: 1291 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 164 average time/residue: 0.2989 time to fit residues: 76.5952 Evaluate side-chains 149 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1742 time to fit residues: 3.8331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 0.9980 chunk 202 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 140 optimal weight: 8.9990 chunk 212 optimal weight: 3.9990 chunk 195 optimal weight: 8.9990 chunk 168 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 957 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 989 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 402 GLN ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.8212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 16776 Z= 0.228 Angle : 0.720 14.174 22780 Z= 0.362 Chirality : 0.044 0.227 2567 Planarity : 0.005 0.072 2961 Dihedral : 5.374 46.844 2315 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 24.64 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.60 % Favored : 91.21 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.17), residues: 2140 helix: -0.25 (0.25), residues: 421 sheet: -1.17 (0.25), residues: 414 loop : -2.12 (0.16), residues: 1305 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 158 time to evaluate : 2.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 164 average time/residue: 0.3140 time to fit residues: 78.9974 Evaluate side-chains 159 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 152 time to evaluate : 1.929 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1802 time to fit residues: 5.0295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 10.0000 chunk 180 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 169 optimal weight: 0.0570 chunk 70 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 700 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1379 GLN ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** 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 = 0.4347 r_free = 0.4347 target = 0.121464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.099036 restraints weight = 63856.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.100945 restraints weight = 38331.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.102173 restraints weight = 25973.119| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3992 r_free = 0.3992 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3975 r_free = 0.3975 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.8581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 16776 Z= 0.382 Angle : 0.819 11.637 22780 Z= 0.422 Chirality : 0.048 0.293 2567 Planarity : 0.006 0.073 2961 Dihedral : 5.857 46.132 2315 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 31.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.61 % Favored : 89.21 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.17), residues: 2140 helix: -0.67 (0.24), residues: 414 sheet: -1.32 (0.25), residues: 407 loop : -2.18 (0.16), residues: 1319 =============================================================================== Job complete usr+sys time: 3254.91 seconds wall clock time: 60 minutes 50.66 seconds (3650.66 seconds total)