Starting phenix.real_space_refine (version: dev) on Mon Feb 20 23:04:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/02_2023/7jgj_22328.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/02_2023/7jgj_22328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/02_2023/7jgj_22328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/02_2023/7jgj_22328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/02_2023/7jgj_22328.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/02_2023/7jgj_22328.pdb" } resolution = 4.8 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= 0.021 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 Process input model Symmetric amino acids flipped Residue "A GLU 681": "OE1" <-> "OE2" Residue "A GLU 735": "OE1" <-> "OE2" Residue "A GLU 810": "OE1" <-> "OE2" Residue "A ARG 816": "NH1" <-> "NH2" Residue "A ARG 826": "NH1" <-> "NH2" Residue "A ARG 896": "NH1" <-> "NH2" Residue "A TYR 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1010": "OE1" <-> "OE2" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1070": "OE1" <-> "OE2" Residue "A GLU 1235": "OE1" <-> "OE2" Residue "A ASP 1240": "OD1" <-> "OD2" Residue "A ARG 1247": "NH1" <-> "NH2" Residue "A GLU 1255": "OE1" <-> "OE2" Residue "A ARG 1296": "NH1" <-> "NH2" Residue "A ARG 1442": "NH1" <-> "NH2" Residue "A ARG 1524": "NH1" <-> "NH2" Residue "A ARG 1621": "NH1" <-> "NH2" Residue "A ARG 1622": "NH1" <-> "NH2" Residue "A GLU 1698": "OE1" <-> "OE2" Residue "A ARG 1716": "NH1" <-> "NH2" Residue "A ARG 1773": "NH1" <-> "NH2" Residue "A GLU 1850": "OE1" <-> "OE2" Residue "A ARG 1875": "NH1" <-> "NH2" Residue "A ARG 1955": "NH1" <-> "NH2" Residue "L GLU 2": "OE1" <-> "OE2" Residue "L PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 104": "OE1" <-> "OE2" Residue "L GLU 153": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H ASP 52": "OD1" <-> "OD2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 13324 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 10070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1277, 10070 Classifications: {'peptide': 1277} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 33, 'TRANS': 1243} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1626 Classifications: {'peptide': 212} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 201} Chain: "H" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1628 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 202} Time building chain proxies: 7.87, per 1000 atoms: 0.59 Number of scatterers: 13324 At special positions: 0 Unit cell: (82.368, 136.448, 143.936, 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 36 16.00 O 2656 8.00 N 2239 7.00 C 8393 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.05 Simple disulfide: pdb=" SG CYS L 133 " - pdb=" SG CYS L 193 " distance=2.05 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 201 " distance=2.02 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: 5.10 Conformation dependent library (CDL) restraints added in 1.9 seconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB GLN A 979 " pdb=" CB TYR A1141 " pdb=" CB VAL A1465 " pdb=" CB ALA A1478 " pdb=" CB GLN A1612 " pdb=" CB ARG A1622 " pdb=" CB VAL A1905 " pdb=" CB SER L 115 " pdb=" CB PRO L 118 " pdb=" CB ASN L 136 " pdb=" CB SER L 173 " pdb=" CB PRO H 132 " Number of C-beta restraints generated: 3154 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 28 sheets defined 27.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 782 through 793 Processing helix chain 'A' and resid 807 through 809 No H-bonds generated for 'chain 'A' and resid 807 through 809' Processing helix chain 'A' and resid 1075 through 1082 removed outlier: 3.506A pdb=" N VAL A1082 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1130 removed outlier: 3.653A pdb=" N LEU A1129 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1144 removed outlier: 3.629A pdb=" N LEU A1144 " --> pdb=" O LYS A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1174 Processing helix chain 'A' and resid 1224 through 1238 removed outlier: 4.348A pdb=" N ILE A1228 " --> pdb=" O ASP A1224 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A1231 " --> pdb=" O SER A1227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A1233 " --> pdb=" O VAL A1229 " (cutoff:3.500A) Proline residue: A1234 - end of helix Processing helix chain 'A' and resid 1243 through 1250 Processing helix chain 'A' and resid 1257 through 1262 removed outlier: 4.440A pdb=" N GLU A1260 " --> pdb=" O LYS A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1273 Processing helix chain 'A' and resid 1273 through 1283 Processing helix chain 'A' and resid 1292 through 1306 removed outlier: 4.095A pdb=" N ARG A1296 " --> pdb=" O ASN A1292 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR A1298 " --> pdb=" O VAL A1294 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A1299 " --> pdb=" O THR A1295 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A1305 " --> pdb=" O ASP A1301 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN A1306 " --> pdb=" O LYS A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1321 Processing helix chain 'A' and resid 1330 through 1336 Processing helix chain 'A' and resid 1337 through 1342 removed outlier: 3.713A pdb=" N PHE A1341 " --> pdb=" O PRO A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1358 removed outlier: 3.662A pdb=" N LEU A1352 " --> pdb=" O PRO A1348 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A1353 " --> pdb=" O LEU A1349 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1364 Processing helix chain 'A' and resid 1367 through 1375 Processing helix chain 'A' and resid 1384 through 1395 removed outlier: 3.690A pdb=" N LYS A1394 " --> pdb=" O GLU A1390 " (cutoff:3.500A) Processing helix chain 'A' and resid 1401 through 1410 Processing helix chain 'A' and resid 1421 through 1430 Processing helix chain 'A' and resid 1438 through 1445 Processing helix chain 'A' and resid 1448 through 1452 removed outlier: 4.506A pdb=" N ASN A1452 " --> pdb=" O LYS A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1453 through 1459 Processing helix chain 'A' and resid 1480 through 1483 Processing helix chain 'A' and resid 1491 through 1519 Processing helix chain 'A' and resid 1522 through 1527 removed outlier: 3.516A pdb=" N GLU A1525 " --> pdb=" O GLN A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1558 through 1564 Processing helix chain 'A' and resid 1597 through 1610 removed outlier: 3.773A pdb=" N THR A1601 " --> pdb=" O ASP A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1662 Processing helix chain 'A' and resid 1676 through 1705 removed outlier: 3.635A pdb=" N TYR A1696 " --> pdb=" O TYR A1692 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A1701 " --> pdb=" O LEU A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1707 through 1714 Processing helix chain 'A' and resid 1742 through 1749 removed outlier: 3.800A pdb=" N LEU A1749 " --> pdb=" O GLU A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1751 through 1759 Processing helix chain 'A' and resid 1798 through 1810 Processing helix chain 'A' and resid 1817 through 1823 Processing helix chain 'A' and resid 1826 through 1834 Processing helix chain 'A' and resid 1848 through 1857 Processing helix chain 'A' and resid 1863 through 1882 removed outlier: 3.940A pdb=" N LEU A1882 " --> pdb=" O GLN A1878 " (cutoff:3.500A) Processing helix chain 'A' and resid 1904 through 1921 removed outlier: 3.522A pdb=" N GLN A1914 " --> pdb=" O ALA A1910 " (cutoff:3.500A) Processing helix chain 'A' and resid 1934 through 1951 Processing helix chain 'L' and resid 120 through 127 removed outlier: 3.634A pdb=" N SER L 126 " --> pdb=" O GLU L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 188 Processing helix chain 'H' and resid 135 through 139 Processing sheet with id=AA1, first strand: chain 'A' and resid 699 through 700 removed outlier: 5.894A pdb=" N TYR A 714 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 732 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 736 through 737 removed outlier: 3.550A pdb=" N GLU A 736 " --> pdb=" O VAL A 743 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER A 732 " --> pdb=" O THR A 747 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AA4, first strand: chain 'A' and resid 797 through 799 removed outlier: 6.397A pdb=" N TYR A 798 " --> pdb=" O GLY A 829 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 828 " --> pdb=" O THR A 853 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 855 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS A 884 " --> pdb=" O VAL A 854 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 804 through 805 removed outlier: 7.046A pdb=" N LEU A 804 " --> pdb=" O TYR A 839 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER A 858 " --> pdb=" O TYR A 836 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 864 removed outlier: 5.095A pdb=" N VAL A 862 " --> pdb=" O VAL A 891 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE A 915 " --> pdb=" O THR A 951 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N THR A 953 " --> pdb=" O PHE A 915 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLY A 917 " --> pdb=" O THR A 953 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N SER A 955 " --> pdb=" O GLY A 917 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP A 986 " --> pdb=" O ALA A 950 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N VAL A 952 " --> pdb=" O ASP A 986 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ASN A 988 " --> pdb=" O VAL A 952 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE A 954 " --> pdb=" O ASN A 988 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 869 through 871 Processing sheet with id=AA8, first strand: chain 'A' and resid 904 through 905 Processing sheet with id=AA9, first strand: chain 'A' and resid 944 through 946 Processing sheet with id=AB1, first strand: chain 'A' and resid 964 through 965 Processing sheet with id=AB2, first strand: chain 'A' and resid 1054 through 1055 Processing sheet with id=AB3, first strand: chain 'A' and resid 1159 through 1161 removed outlier: 3.621A pdb=" N MET A1161 " --> pdb=" O LYS A1180 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS A1180 " --> pdb=" O MET A1161 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1207 through 1209 removed outlier: 4.014A pdb=" N LEU A1214 " --> pdb=" O LEU A1209 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1324 through 1325 Processing sheet with id=AB6, first strand: chain 'A' and resid 1465 through 1467 removed outlier: 3.533A pdb=" N PHE A1476 " --> pdb=" O LEU A1533 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N LEU A1532 " --> pdb=" O VAL A1586 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1736 through 1739 Processing sheet with id=AB8, first strand: chain 'A' and resid 1836 through 1839 Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.728A pdb=" N MET L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AC3, first strand: chain 'L' and resid 128 through 134 Processing sheet with id=AC4, first strand: chain 'L' and resid 152 through 154 removed outlier: 3.614A pdb=" N THR L 192 " --> pdb=" O LYS L 148 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR L 191 " --> pdb=" O PHE L 208 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE L 208 " --> pdb=" O TYR L 191 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.602A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 16 through 23 removed outlier: 5.240A pdb=" N ALA H 16 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 129 through 130 Processing sheet with id=AC8, first strand: chain 'H' and resid 141 through 143 Processing sheet with id=AC9, first strand: chain 'H' and resid 171 through 177 removed outlier: 4.434A pdb=" N SER H 184 " --> pdb=" O PRO H 173 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 203 through 205 removed outlier: 3.905A pdb=" N VAL H 203 " --> pdb=" O VAL H 212 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL H 212 " --> pdb=" O VAL H 203 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1110 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: 5.11 Time building geometry restraints manager: 5.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2274 1.30 - 1.45: 3670 1.45 - 1.59: 7585 1.59 - 1.74: 0 1.74 - 1.88: 64 Bond restraints: 13593 Sorted by residual: bond pdb=" CA CYS L 23 " pdb=" C CYS L 23 " ideal model delta sigma weight residual 1.522 1.406 0.116 1.20e-02 6.94e+03 9.38e+01 bond pdb=" C CYS L 23 " pdb=" O CYS L 23 " ideal model delta sigma weight residual 1.236 1.346 -0.110 1.21e-02 6.83e+03 8.26e+01 bond pdb=" CA CYS L 23 " pdb=" CB CYS L 23 " ideal model delta sigma weight residual 1.531 1.403 0.127 1.52e-02 4.33e+03 7.02e+01 bond pdb=" C TYR A1440 " pdb=" O TYR A1440 " ideal model delta sigma weight residual 1.236 1.160 0.076 1.15e-02 7.56e+03 4.41e+01 bond pdb=" C LEU A1209 " pdb=" O LEU A1209 " ideal model delta sigma weight residual 1.232 1.159 0.073 1.35e-02 5.49e+03 2.92e+01 ... (remaining 13588 not shown) Histogram of bond angle deviations from ideal: 53.45 - 70.90: 1 70.90 - 88.36: 1 88.36 - 105.82: 351 105.82 - 123.27: 15659 123.27 - 140.73: 2393 Bond angle restraints: 18405 Sorted by residual: angle pdb=" CA TYR A1392 " pdb=" C TYR A1392 " pdb=" O TYR A1392 " ideal model delta sigma weight residual 120.55 53.45 67.10 1.06e+00 8.90e-01 4.01e+03 angle pdb=" O TYR A1392 " pdb=" C TYR A1392 " pdb=" N ARG A1393 " ideal model delta sigma weight residual 122.12 87.43 34.69 1.06e+00 8.90e-01 1.07e+03 angle pdb=" CA TYR A1392 " pdb=" C TYR A1392 " pdb=" N ARG A1393 " ideal model delta sigma weight residual 117.30 140.73 -23.43 1.16e+00 7.43e-01 4.08e+02 angle pdb=" C PRO L 118 " pdb=" CA PRO L 118 " pdb=" CB PRO L 118 " ideal model delta sigma weight residual 110.92 132.43 -21.51 1.22e+00 6.72e-01 3.11e+02 angle pdb=" C GLY A1801 " pdb=" N ARG A1802 " pdb=" CA ARG A1802 " ideal model delta sigma weight residual 120.44 139.14 -18.70 1.36e+00 5.41e-01 1.89e+02 ... (remaining 18400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.52: 7467 25.52 - 51.05: 568 51.05 - 76.57: 90 76.57 - 102.09: 11 102.09 - 127.61: 2 Dihedral angle restraints: 8138 sinusoidal: 3183 harmonic: 4955 Sorted by residual: dihedral pdb=" CA ALA H 105 " pdb=" C ALA H 105 " pdb=" N MET H 106 " pdb=" CA MET H 106 " ideal model delta harmonic sigma weight residual -180.00 -52.39 -127.61 0 5.00e+00 4.00e-02 6.51e+02 dihedral pdb=" CA GLU H 154 " pdb=" C GLU H 154 " pdb=" N PRO H 155 " pdb=" CA PRO H 155 " ideal model delta harmonic sigma weight residual 180.00 71.88 108.12 0 5.00e+00 4.00e-02 4.68e+02 dihedral pdb=" CA PHE H 152 " pdb=" C PHE H 152 " pdb=" N PRO H 153 " pdb=" CA PRO H 153 " ideal model delta harmonic sigma weight residual 0.00 -44.96 44.96 0 5.00e+00 4.00e-02 8.08e+01 ... (remaining 8135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.995: 2020 0.995 - 1.989: 0 1.989 - 2.983: 1 2.983 - 3.978: 11 3.978 - 4.972: 1 Chirality restraints: 2033 Sorted by residual: chirality pdb=" CB THR A1018 " pdb=" CA THR A1018 " pdb=" OG1 THR A1018 " pdb=" CG2 THR A1018 " both_signs ideal model delta sigma weight residual False 2.55 -2.42 4.97 2.00e-01 2.50e+01 6.18e+02 chirality pdb=" CA SER L 173 " pdb=" N SER L 173 " pdb=" C SER L 173 " pdb=" CB SER L 173 " both_signs ideal model delta sigma weight residual False 2.51 -1.37 3.88 2.00e-01 2.50e+01 3.76e+02 chirality pdb=" CA TYR A1141 " pdb=" N TYR A1141 " pdb=" C TYR A1141 " pdb=" CB TYR A1141 " both_signs ideal model delta sigma weight residual False 2.51 -1.20 3.71 2.00e-01 2.50e+01 3.45e+02 ... (remaining 2030 not shown) Planarity restraints: 2378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A1627 " -0.043 2.00e-02 2.50e+03 8.59e-02 7.38e+01 pdb=" C PRO A1627 " 0.149 2.00e-02 2.50e+03 pdb=" O PRO A1627 " -0.057 2.00e-02 2.50e+03 pdb=" N GLU A1628 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 940 " 0.036 2.00e-02 2.50e+03 7.21e-02 5.20e+01 pdb=" C GLY A 940 " -0.125 2.00e-02 2.50e+03 pdb=" O GLY A 940 " 0.048 2.00e-02 2.50e+03 pdb=" N LYS A 941 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1358 " 0.029 2.00e-02 2.50e+03 5.97e-02 3.57e+01 pdb=" C SER A1358 " -0.103 2.00e-02 2.50e+03 pdb=" O SER A1358 " 0.038 2.00e-02 2.50e+03 pdb=" N GLY A1359 " 0.036 2.00e-02 2.50e+03 ... (remaining 2375 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.30: 2 2.30 - 2.95: 6468 2.95 - 3.60: 21866 3.60 - 4.25: 34373 4.25 - 4.90: 54023 Nonbonded interactions: 116732 Sorted by model distance: nonbonded pdb=" N TYR A1392 " pdb=" O TYR A1392 " model vdw 1.656 2.496 nonbonded pdb=" O TYR A1392 " pdb=" CB TYR A1392 " model vdw 2.131 2.752 nonbonded pdb=" N TYR H 94 " pdb=" O TYR H 94 " model vdw 2.382 2.496 nonbonded pdb=" OD1 ASN A1402 " pdb=" N ASN A1403 " model vdw 2.395 2.520 nonbonded pdb=" O GLU H 12 " pdb=" N SER H 118 " model vdw 2.430 2.520 ... (remaining 116727 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 8393 2.51 5 N 2239 2.21 5 O 2656 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 8.130 Check model and map are aligned: 0.150 Process input model: 36.550 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.120 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 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 : 0.013 0.127 13593 Z= 0.843 Angle : 2.215 67.103 18405 Z= 1.662 Chirality : 0.307 4.972 2033 Planarity : 0.009 0.086 2378 Dihedral : 17.489 127.612 4972 Min Nonbonded Distance : 1.656 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 1.24 % Allowed : 7.18 % Favored : 91.58 % Rotamer Outliers : 12.68 % Cbeta Deviations : 1.07 % Peptide Plane: Cis-proline : 7.02 % Cis-general : 0.06 % Twisted Proline : 3.51 % Twisted General : 0.06 % 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: -2.09 (0.18), residues: 1699 helix: -0.08 (0.24), residues: 416 sheet: -1.92 (0.27), residues: 298 loop : -1.83 (0.17), residues: 985 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 301 time to evaluate : 1.653 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 outliers start: 184 outliers final: 37 residues processed: 437 average time/residue: 0.2505 time to fit residues: 158.7480 Evaluate side-chains 236 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 199 time to evaluate : 1.580 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 0.2260 time to fit residues: 14.5921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 153 optimal weight: 0.0020 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN ** A1166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1508 GLN ** A1511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1558 ASN A1570 ASN A1623 ASN ** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN H 139 ASN ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 13593 Z= 0.268 Angle : 0.792 9.451 18405 Z= 0.428 Chirality : 0.059 1.149 2033 Planarity : 0.006 0.070 2378 Dihedral : 6.063 59.234 1852 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.77 % Favored : 94.06 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.06 % Twisted Proline : 1.75 % Twisted General : 0.06 % 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 (0.19), residues: 1699 helix: -0.25 (0.24), residues: 431 sheet: -1.62 (0.25), residues: 382 loop : -1.86 (0.19), residues: 886 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 258 time to evaluate : 1.503 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 outliers start: 6 outliers final: 4 residues processed: 262 average time/residue: 0.2336 time to fit residues: 91.7728 Evaluate side-chains 177 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 173 time to evaluate : 1.646 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1408 time to fit residues: 3.2796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 104 optimal weight: 0.0570 chunk 42 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 ASN A1508 GLN ** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 13593 Z= 0.248 Angle : 0.708 8.184 18405 Z= 0.380 Chirality : 0.047 0.452 2033 Planarity : 0.005 0.058 2378 Dihedral : 5.819 50.588 1852 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.12 % Favored : 93.76 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.06 % Twisted Proline : 1.75 % Twisted General : 0.06 % 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: -2.07 (0.19), residues: 1699 helix: -0.31 (0.23), residues: 425 sheet: -1.64 (0.26), residues: 376 loop : -1.77 (0.19), residues: 898 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 227 time to evaluate : 1.747 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 outliers start: 3 outliers final: 1 residues processed: 229 average time/residue: 0.2350 time to fit residues: 83.1850 Evaluate side-chains 160 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 159 time to evaluate : 1.502 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1584 time to fit residues: 2.3868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 17 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 154 optimal weight: 6.9990 chunk 163 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1759 ASN ** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 36 GLN L 68 ASN L 136 ASN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 211 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 13593 Z= 0.389 Angle : 0.821 11.620 18405 Z= 0.445 Chirality : 0.048 0.292 2033 Planarity : 0.006 0.054 2378 Dihedral : 6.382 46.143 1852 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 39.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.36 % Favored : 92.53 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.06 % Twisted Proline : 1.75 % 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: -2.33 (0.19), residues: 1699 helix: -0.92 (0.22), residues: 414 sheet: -1.58 (0.26), residues: 367 loop : -1.81 (0.19), residues: 918 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 1.636 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: 3 outliers final: 1 residues processed: 197 average time/residue: 0.2402 time to fit residues: 72.2654 Evaluate side-chains 139 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 138 time to evaluate : 1.677 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1632 time to fit residues: 2.5268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1950 GLN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 211 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 13593 Z= 0.271 Angle : 0.699 7.890 18405 Z= 0.379 Chirality : 0.044 0.224 2033 Planarity : 0.005 0.066 2378 Dihedral : 6.141 42.536 1852 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 33.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.53 % Favored : 92.35 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.06 % Twisted Proline : 1.75 % 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: -2.20 (0.19), residues: 1699 helix: -0.66 (0.23), residues: 412 sheet: -1.64 (0.27), residues: 360 loop : -1.74 (0.19), residues: 927 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 1.488 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: 1 outliers final: 0 residues processed: 196 average time/residue: 0.2531 time to fit residues: 76.0265 Evaluate side-chains 129 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.651 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 13 optimal weight: 0.0370 chunk 85 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 overall best weight: 4.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.5424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 13593 Z= 0.289 Angle : 0.702 10.111 18405 Z= 0.382 Chirality : 0.044 0.243 2033 Planarity : 0.006 0.113 2378 Dihedral : 6.169 39.853 1852 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 35.88 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.36 % Favored : 91.52 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.06 % Twisted Proline : 1.75 % 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 (0.19), residues: 1699 helix: -0.77 (0.23), residues: 418 sheet: -1.59 (0.27), residues: 361 loop : -1.79 (0.20), residues: 920 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 1.580 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: 0 residues processed: 189 average time/residue: 0.2384 time to fit residues: 69.1877 Evaluate side-chains 131 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 1.596 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 137 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 162 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 GLN ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1522 GLN A1720 ASN ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 13593 Z= 0.211 Angle : 0.645 7.006 18405 Z= 0.349 Chirality : 0.043 0.220 2033 Planarity : 0.005 0.073 2378 Dihedral : 5.891 38.458 1852 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 29.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.18 % Favored : 92.70 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.06 % Twisted Proline : 1.75 % 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: -2.10 (0.19), residues: 1699 helix: -0.38 (0.24), residues: 417 sheet: -1.36 (0.28), residues: 342 loop : -1.90 (0.19), residues: 940 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 1.742 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: 1 outliers final: 0 residues processed: 204 average time/residue: 0.2267 time to fit residues: 71.8025 Evaluate side-chains 134 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.532 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 0.0030 chunk 97 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN A1305 ASN ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1720 ASN ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.5908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 13593 Z= 0.333 Angle : 0.764 11.845 18405 Z= 0.410 Chirality : 0.046 0.250 2033 Planarity : 0.005 0.067 2378 Dihedral : 6.250 37.775 1852 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 41.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.48 % Favored : 91.41 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.06 % Twisted Proline : 1.75 % Twisted General : 0.06 % 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: -2.40 (0.19), residues: 1699 helix: -0.87 (0.23), residues: 423 sheet: -1.61 (0.26), residues: 369 loop : -1.93 (0.20), residues: 907 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 184 average time/residue: 0.2327 time to fit residues: 66.5796 Evaluate side-chains 129 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 91 optimal weight: 0.0970 chunk 66 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 160 optimal weight: 30.0000 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1179 ASN A1203 ASN A1305 ASN ** A1511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.6105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 13593 Z= 0.296 Angle : 0.717 8.862 18405 Z= 0.389 Chirality : 0.045 0.228 2033 Planarity : 0.005 0.054 2378 Dihedral : 6.202 38.092 1852 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 38.21 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.59 % Favored : 91.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.06 % Twisted Proline : 1.75 % Twisted General : 0.06 % 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: -2.44 (0.19), residues: 1699 helix: -0.86 (0.22), residues: 428 sheet: -1.74 (0.26), residues: 362 loop : -1.94 (0.20), residues: 909 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.462 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: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2299 time to fit residues: 65.4269 Evaluate side-chains 129 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 134 optimal weight: 9.9990 chunk 13 optimal weight: 0.0980 chunk 103 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS ** A1166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 13593 Z= 0.249 Angle : 0.677 8.780 18405 Z= 0.367 Chirality : 0.043 0.229 2033 Planarity : 0.005 0.054 2378 Dihedral : 6.014 36.991 1852 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 35.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.06 % Favored : 91.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.06 % Twisted Proline : 1.75 % 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: -2.28 (0.19), residues: 1699 helix: -0.63 (0.23), residues: 424 sheet: -1.63 (0.27), residues: 364 loop : -1.89 (0.20), residues: 911 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.688 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: 0 outliers final: 0 residues processed: 187 average time/residue: 0.2367 time to fit residues: 68.4447 Evaluate side-chains 130 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.578 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 137 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 7 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN ** A1511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1686 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 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 = 0.2878 r_free = 0.2878 target = 0.037567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.025738 restraints weight = 110674.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2538 r_free = 0.2538 target = 0.027309 restraints weight = 64656.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.028505 restraints weight = 43820.648| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4988 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 : 0.004 0.035 13593 Z= 0.258 Angle : 0.693 12.229 18405 Z= 0.376 Chirality : 0.044 0.222 2033 Planarity : 0.005 0.053 2378 Dihedral : 6.064 37.016 1852 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 35.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.77 % Favored : 91.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.06 % Twisted Proline : 1.75 % 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: -2.32 (0.19), residues: 1699 helix: -0.63 (0.23), residues: 423 sheet: -1.63 (0.27), residues: 364 loop : -1.95 (0.20), residues: 912 =============================================================================== Job complete usr+sys time: 2676.93 seconds wall clock time: 50 minutes 24.19 seconds (3024.19 seconds total)