Starting phenix.real_space_refine (version: dev) on Sat May 14 03:17:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xja_22204/05_2022/6xja_22204.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xja_22204/05_2022/6xja_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_22204/05_2022/6xja_22204.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xja_22204/05_2022/6xja_22204.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xja_22204/05_2022/6xja_22204.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xja_22204/05_2022/6xja_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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "P TYR 1223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 1466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B VAL 307": "CG1" <-> "CG2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 8, 'TRANS': 209, 'PCIS': 1} Chain: "H" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1539 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 16, 'TRANS': 213, 'PCIS': 2} 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: 9.62, per 1000 atoms: 0.59 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: 6.66 Conformation dependent library (CDL) restraints added in 2.6 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: 1.12 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: 6.89 Time building geometry restraints manager: 7.18 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: 9292 26.92 - 53.84: 691 53.84 - 80.76: 124 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 - 0.437: 2552 0.437 - 0.874: 12 0.874 - 1.311: 2 1.311 - 1.748: 0 1.748 - 2.184: 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 -2.18 2.00e-01 2.50e+01 1.19e+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 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. 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: 0.630 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: 4.210 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.150 Process input model: 46.750 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5351 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= 1.606 Angle : 1.934 76.622 22780 Z= 1.415 Chirality : 0.110 2.184 2567 Planarity : 0.012 0.271 2961 Dihedral : 18.021 134.597 6059 Min Nonbonded Distance : 0.468 Molprobity Statistics. All-atom Clashscore : 73.82 Ramachandran Plot: Outliers : 1.73 % Allowed : 6.09 % Favored : 92.17 % Rotamer Outliers : 18.37 % 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 703 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 383 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 320 outliers final: 118 residues processed: 656 average time/residue: 0.3114 time to fit residues: 295.6467 Evaluate side-chains 342 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 224 time to evaluate : 1.892 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: 118 outliers final: 9 residues processed: 118 average time/residue: 0.1994 time to fit residues: 41.0743 ------------------------------------------------------------------------------- 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 P1089 ASN P1114 HIS ** P1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1166 GLN P1379 GLN P1380 HIS P1399 ASN ** P1654 HIS ** 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 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 129 GLN L 194 HIS ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 ASN ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.126 16776 Z= 0.397 Angle : 0.939 16.551 22780 Z= 0.491 Chirality : 0.052 0.381 2567 Planarity : 0.008 0.131 2961 Dihedral : 5.948 84.114 2315 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 29.49 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.68 % Favored : 92.85 % Rotamer Outliers : 6.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.10 % 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: -2.10 (0.17), residues: 2140 helix: -0.50 (0.23), residues: 444 sheet: -0.82 (0.26), residues: 412 loop : -1.99 (0.15), residues: 1284 *********************** 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 343 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 230 time to evaluate : 1.900 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 outliers start: 113 outliers final: 58 residues processed: 330 average time/residue: 0.2811 time to fit residues: 139.1505 Evaluate side-chains 223 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 165 time to evaluate : 1.863 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.1560 time to fit residues: 19.3941 ------------------------------------------------------------------------------- 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: 4.9990 chunk 60 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 193 optimal weight: 20.0000 chunk 209 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 192 optimal weight: 40.0000 chunk 66 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 791 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 942 ASN P1324 ASN P1511 HIS P1563 ASN ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1758 HIS ** P1825 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1961 ASN A 402 GLN ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS ** 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 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.6406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.124 16776 Z= 0.438 Angle : 0.943 17.270 22780 Z= 0.493 Chirality : 0.052 0.272 2567 Planarity : 0.009 0.112 2961 Dihedral : 6.386 67.337 2315 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 34.07 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.11 % Favored : 90.56 % Rotamer Outliers : 6.49 % 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: -2.43 (0.17), residues: 2140 helix: -1.09 (0.23), residues: 428 sheet: -0.90 (0.27), residues: 361 loop : -2.09 (0.15), residues: 1351 *********************** 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 303 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 190 time to evaluate : 1.874 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: 113 outliers final: 63 residues processed: 288 average time/residue: 0.2852 time to fit residues: 123.9866 Evaluate side-chains 218 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 155 time to evaluate : 2.328 Switching outliers to nearest non-outliers outliers start: 63 outliers final: 0 residues processed: 63 average time/residue: 0.2019 time to fit residues: 24.7584 ------------------------------------------------------------------------------- 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: 9.9990 chunk 145 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 130 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 101 optimal weight: 0.8980 chunk 184 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 P 879 ASN ** P 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1025 ASN P1272 GLN ** P1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P1774 ASN ** 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** H 153 GLN ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6298 moved from start: 0.6621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.125 16776 Z= 0.253 Angle : 0.761 16.745 22780 Z= 0.390 Chirality : 0.045 0.267 2567 Planarity : 0.007 0.112 2961 Dihedral : 5.818 67.185 2315 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 24.82 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.96 % Favored : 92.80 % Rotamer Outliers : 2.30 % 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: -2.22 (0.17), residues: 2140 helix: -0.60 (0.23), residues: 441 sheet: -0.88 (0.27), residues: 388 loop : -2.06 (0.16), residues: 1311 *********************** 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 221 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 1.971 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: 40 outliers final: 20 residues processed: 216 average time/residue: 0.2638 time to fit residues: 89.2341 Evaluate side-chains 173 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 153 time to evaluate : 1.921 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1602 time to fit residues: 8.5513 ------------------------------------------------------------------------------- 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: 0.9990 chunk 116 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 153 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 175 optimal weight: 9.9990 chunk 142 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 chunk 184 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 921 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1878 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 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.7358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.123 16776 Z= 0.359 Angle : 0.819 11.583 22780 Z= 0.429 Chirality : 0.047 0.296 2567 Planarity : 0.007 0.116 2961 Dihedral : 5.995 59.130 2315 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 31.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.44 % Favored : 90.28 % Rotamer Outliers : 4.31 % 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: -2.45 (0.17), residues: 2140 helix: -1.06 (0.22), residues: 436 sheet: -1.00 (0.27), residues: 364 loop : -2.11 (0.16), residues: 1340 *********************** 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 241 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 166 time to evaluate : 1.944 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: 75 outliers final: 42 residues processed: 227 average time/residue: 0.2741 time to fit residues: 97.5512 Evaluate side-chains 191 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 149 time to evaluate : 2.090 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 0 residues processed: 42 average time/residue: 0.1854 time to fit residues: 17.0571 ------------------------------------------------------------------------------- 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: 2.9990 chunk 185 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 206 optimal weight: 0.9990 chunk 171 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 921 ASN ** P1306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1748 ASN P1838 ASN ** P1878 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 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.7523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.195 16776 Z= 0.328 Angle : 0.782 13.758 22780 Z= 0.408 Chirality : 0.044 0.216 2567 Planarity : 0.007 0.123 2961 Dihedral : 5.881 58.539 2315 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 27.74 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.55 % Favored : 91.21 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.05 % 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: -2.38 (0.17), residues: 2140 helix: -0.79 (0.23), residues: 437 sheet: -0.99 (0.27), residues: 380 loop : -2.14 (0.16), residues: 1323 *********************** 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 210 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 175 time to evaluate : 1.921 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: 35 outliers final: 18 residues processed: 205 average time/residue: 0.2780 time to fit residues: 89.0195 Evaluate side-chains 166 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1606 time to fit residues: 7.8691 ------------------------------------------------------------------------------- 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: 6.9990 chunk 23 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 116 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 205 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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** ** P1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1748 ASN ** P1878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P1903 ASN ** 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 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6490 moved from start: 0.7560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.745 16776 Z= 0.777 Angle : 1.177 106.100 22780 Z= 0.546 Chirality : 0.048 0.672 2567 Planarity : 0.008 0.187 2961 Dihedral : 5.956 59.104 2315 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 33.52 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.69 % Favored : 91.03 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 2.15 % 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: -2.38 (0.17), residues: 2140 helix: -0.79 (0.23), residues: 437 sheet: -0.99 (0.27), residues: 380 loop : -2.14 (0.16), residues: 1323 *********************** 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 163 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 150 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 159 average time/residue: 0.2835 time to fit residues: 71.8002 Evaluate side-chains 153 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 1.963 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1593 time to fit residues: 4.9069 ------------------------------------------------------------------------------- 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: 1.9990 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 139 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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** ** P1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1748 ASN P1838 ASN ** 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 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.7918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.248 16776 Z= 0.368 Angle : 0.831 19.047 22780 Z= 0.439 Chirality : 0.046 0.233 2567 Planarity : 0.007 0.128 2961 Dihedral : 5.997 55.452 2315 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 30.41 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.09 % Favored : 89.67 % Rotamer Outliers : 1.55 % 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: -2.60 (0.17), residues: 2140 helix: -0.96 (0.23), residues: 436 sheet: -1.25 (0.26), residues: 391 loop : -2.24 (0.16), residues: 1313 *********************** 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 186 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 2.200 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: 27 outliers final: 16 residues processed: 176 average time/residue: 0.3131 time to fit residues: 85.8407 Evaluate side-chains 164 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 148 time to evaluate : 2.324 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1684 time to fit residues: 8.0120 ------------------------------------------------------------------------------- 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: 6.9990 chunk 196 optimal weight: 30.0000 chunk 179 optimal weight: 30.0000 chunk 191 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 83 optimal weight: 2.9990 chunk 150 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 180 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- 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** ** P1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1748 ASN ** 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 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.7958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.990 16776 Z= 0.767 Angle : 1.159 106.098 22780 Z= 0.545 Chirality : 0.047 0.231 2567 Planarity : 0.008 0.126 2961 Dihedral : 6.029 54.636 2315 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 31.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.91 % Favored : 89.86 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.05 % 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: -2.62 (0.17), residues: 2140 helix: -0.96 (0.23), residues: 435 sheet: -1.33 (0.26), residues: 391 loop : -2.24 (0.16), residues: 1314 *********************** 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 166 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 1.938 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: 13 outliers final: 4 residues processed: 164 average time/residue: 0.2844 time to fit residues: 73.4306 Evaluate side-chains 155 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 2.002 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1609 time to fit residues: 3.7872 ------------------------------------------------------------------------------- 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: 4.9990 chunk 202 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 140 optimal weight: 9.9990 chunk 212 optimal weight: 8.9990 chunk 195 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1748 ASN P1838 ASN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.7978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.990 16776 Z= 0.818 Angle : 1.173 106.098 22780 Z= 0.560 Chirality : 0.047 0.231 2567 Planarity : 0.008 0.167 2961 Dihedral : 6.029 54.636 2315 Min Nonbonded Distance : 1.514 Molprobity Statistics. All-atom Clashscore : 34.16 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.91 % Favored : 89.86 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.05 % 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: -2.62 (0.17), residues: 2140 helix: -0.96 (0.23), residues: 435 sheet: -1.33 (0.26), residues: 391 loop : -2.24 (0.16), residues: 1314 ********************** 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 154 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 1.728 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: 1 outliers final: 1 residues processed: 153 average time/residue: 0.2811 time to fit residues: 67.2354 Evaluate side-chains 151 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.971 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1547 time to fit residues: 2.9942 ------------------------------------------------------------------------------- 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: 3.9990 chunk 180 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 169 optimal weight: 8.9990 chunk 70 optimal weight: 0.3980 chunk 173 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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** ** P1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1654 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P1748 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.122306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.100382 restraints weight = 63621.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.102082 restraints weight = 37649.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.103193 restraints weight = 25588.998| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4368 r_free = 0.4368 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4351 r_free = 0.4351 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.4351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.7978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.990 16776 Z= 0.818 Angle : 1.173 106.098 22780 Z= 0.560 Chirality : 0.047 0.231 2567 Planarity : 0.008 0.167 2961 Dihedral : 6.029 54.636 2315 Min Nonbonded Distance : 1.514 Molprobity Statistics. All-atom Clashscore : 34.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.91 % Favored : 89.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.05 % 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: -2.62 (0.17), residues: 2140 helix: -0.96 (0.23), residues: 435 sheet: -1.33 (0.26), residues: 391 loop : -2.24 (0.16), residues: 1314 =============================================================================== Job complete usr+sys time: 3193.64 seconds wall clock time: 59 minutes 46.11 seconds (3586.11 seconds total)