Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 20:21:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/04_2023/7jgj_22328.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/04_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_22328/04_2023/7jgj_22328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/04_2023/7jgj_22328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/04_2023/7jgj_22328.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/04_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 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. 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 6.92, per 1000 atoms: 0.52 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: 5.40 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: 0.96 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: 5.74 Time building geometry restraints manager: 5.82 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 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: 2.290 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: 7.930 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 37.540 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 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 : 1.742 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 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: 0.2529 time to fit residues: 159.9892 Evaluate side-chains 236 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 199 time to evaluate : 1.633 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 0.2144 time to fit residues: 14.3248 ------------------------------------------------------------------------------- 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 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 959 ASN ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7300 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 13593 Z= 0.256 Angle : 0.777 9.364 18405 Z= 0.420 Chirality : 0.057 1.089 2033 Planarity : 0.005 0.072 2378 Dihedral : 6.043 57.740 1852 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.59 % Favored : 94.23 % 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: -2.08 (0.19), residues: 1699 helix: -0.21 (0.24), residues: 430 sheet: -1.59 (0.25), residues: 385 loop : -1.88 (0.19), residues: 884 *********************** 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 265 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 259 time to evaluate : 1.750 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: 6 outliers final: 3 residues processed: 263 average time/residue: 0.2378 time to fit residues: 94.4480 Evaluate side-chains 180 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 177 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1251 time to fit residues: 2.7860 ------------------------------------------------------------------------------- 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: 6.9990 chunk 47 optimal weight: 7.9990 chunk 127 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 166 optimal weight: 9.9990 chunk 136 optimal weight: 0.5980 chunk 152 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 ASN ** A1508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1511 HIS ** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1759 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 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 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 13593 Z= 0.324 Angle : 0.752 8.908 18405 Z= 0.407 Chirality : 0.047 0.423 2033 Planarity : 0.005 0.053 2378 Dihedral : 6.031 48.859 1852 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 29.15 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.42 % Favored : 93.47 % 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: -2.08 (0.19), residues: 1699 helix: -0.34 (0.23), residues: 416 sheet: -1.66 (0.26), residues: 381 loop : -1.74 (0.19), residues: 902 *********************** 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 215 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 212 time to evaluate : 1.674 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 outliers start: 3 outliers final: 2 residues processed: 215 average time/residue: 0.2348 time to fit residues: 76.6961 Evaluate side-chains 145 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.621 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1504 time to fit residues: 2.8778 ------------------------------------------------------------------------------- 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: 9.9990 chunk 115 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 73 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** 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** ** 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** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN ** L 136 ASN ** 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: 0.7601 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.049 13593 Z= 0.389 Angle : 0.814 11.050 18405 Z= 0.445 Chirality : 0.047 0.292 2033 Planarity : 0.006 0.056 2378 Dihedral : 6.487 44.171 1852 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 41.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.83 % Favored : 92.05 % Rotamer Outliers : 0.14 % 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: -2.41 (0.19), residues: 1699 helix: -1.10 (0.22), residues: 415 sheet: -1.61 (0.26), residues: 369 loop : -1.81 (0.19), residues: 915 *********************** 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 190 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 188 time to evaluate : 1.615 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: 2 outliers final: 0 residues processed: 190 average time/residue: 0.2287 time to fit residues: 67.3986 Evaluate side-chains 132 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 1.605 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1510 ------------------------------------------------------------------------------- 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: 0.4980 chunk 92 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 112 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 146 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- 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 879 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN A1220 GLN ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1508 GLN ** A1522 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 136 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 13593 Z= 0.335 Angle : 0.751 9.042 18405 Z= 0.409 Chirality : 0.046 0.283 2033 Planarity : 0.005 0.057 2378 Dihedral : 6.455 41.293 1852 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 38.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.77 % Favored : 91.11 % Rotamer Outliers : 0.14 % 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: -2.45 (0.19), residues: 1699 helix: -1.06 (0.22), residues: 414 sheet: -1.71 (0.27), residues: 357 loop : -1.85 (0.19), residues: 928 *********************** 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 183 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 181 time to evaluate : 1.536 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: 2 outliers final: 0 residues processed: 183 average time/residue: 0.2193 time to fit residues: 62.7031 Evaluate side-chains 126 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.470 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0137 ------------------------------------------------------------------------------- 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: 10.0000 chunk 147 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 163 optimal weight: 7.9990 chunk 135 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1511 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 GLN ** 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** ** A1950 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 136 ASN ** L 155 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: 0.7628 moved from start: 0.5526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 13593 Z= 0.309 Angle : 0.733 7.572 18405 Z= 0.400 Chirality : 0.045 0.287 2033 Planarity : 0.005 0.054 2378 Dihedral : 6.397 40.075 1852 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 38.59 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.71 % Favored : 91.17 % 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: -2.50 (0.19), residues: 1699 helix: -1.04 (0.22), residues: 410 sheet: -1.82 (0.26), residues: 365 loop : -1.87 (0.19), residues: 924 *********************** 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 183 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 1.680 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: 183 average time/residue: 0.2333 time to fit residues: 66.4246 Evaluate side-chains 124 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.613 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1766 ------------------------------------------------------------------------------- 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: 1.9990 chunk 93 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 162 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 ASN ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1522 GLN ** 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** A1950 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.5632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 13593 Z= 0.202 Angle : 0.664 9.018 18405 Z= 0.357 Chirality : 0.043 0.222 2033 Planarity : 0.004 0.050 2378 Dihedral : 5.898 38.342 1852 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 28.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.47 % Favored : 92.41 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.77 % Cis-general : 0.06 % Twisted Proline : 1.75 % Twisted General : 0.00 % 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: -2.13 (0.19), residues: 1699 helix: -0.50 (0.24), residues: 409 sheet: -1.58 (0.27), residues: 348 loop : -1.77 (0.20), residues: 942 *********************** 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 199 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 199 average time/residue: 0.2504 time to fit residues: 78.4338 Evaluate side-chains 130 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1434 ------------------------------------------------------------------------------- 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: 9.9990 chunk 97 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 764 ASN ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5893 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= 0.283 Angle : 0.711 11.599 18405 Z= 0.383 Chirality : 0.044 0.240 2033 Planarity : 0.005 0.048 2378 Dihedral : 6.080 37.714 1852 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 36.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.71 % Favored : 91.17 % 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: -2.34 (0.19), residues: 1699 helix: -0.84 (0.23), residues: 422 sheet: -1.63 (0.27), residues: 351 loop : -1.86 (0.20), residues: 926 *********************** 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 186 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2196 time to fit residues: 63.9936 Evaluate side-chains 127 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.599 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1609 ------------------------------------------------------------------------------- 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: 3.9990 chunk 142 optimal weight: 9.9990 chunk 151 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 13593 Z= 0.249 Angle : 0.680 7.883 18405 Z= 0.369 Chirality : 0.044 0.209 2033 Planarity : 0.005 0.049 2378 Dihedral : 6.008 36.851 1852 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 33.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.95 % Favored : 91.94 % 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: -2.25 (0.19), residues: 1699 helix: -0.72 (0.23), residues: 422 sheet: -1.54 (0.27), residues: 345 loop : -1.85 (0.20), residues: 932 *********************** 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 185 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 1.703 Fit side-chains 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: 185 average time/residue: 0.2218 time to fit residues: 64.7311 Evaluate side-chains 133 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.466 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0672 ------------------------------------------------------------------------------- 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: 0.2980 chunk 76 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 168 optimal weight: 0.5980 chunk 154 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 GLN ** 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** ** H 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.6206 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= 0.260 Angle : 0.693 11.859 18405 Z= 0.374 Chirality : 0.043 0.228 2033 Planarity : 0.005 0.047 2378 Dihedral : 6.037 36.308 1852 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 34.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.30 % Favored : 91.58 % 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: -2.24 (0.19), residues: 1699 helix: -0.73 (0.23), residues: 423 sheet: -1.55 (0.27), residues: 354 loop : -1.82 (0.20), residues: 922 ********************** 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 190 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.692 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: 190 average time/residue: 0.2348 time to fit residues: 68.6424 Evaluate side-chains 133 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1133 ------------------------------------------------------------------------------- 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: 8.9990 chunk 123 optimal weight: 3.9990 chunk 19 optimal weight: 0.0970 chunk 37 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 56 optimal weight: 0.4980 chunk 137 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 ASN ** A1166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1345 ASN ** 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 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.039254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.026682 restraints weight = 103498.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.028316 restraints weight = 60960.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.029598 restraints weight = 41384.139| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5199 moved from start: 0.6278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13593 Z= 0.184 Angle : 0.656 7.998 18405 Z= 0.350 Chirality : 0.043 0.189 2033 Planarity : 0.004 0.049 2378 Dihedral : 5.631 35.811 1852 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 26.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.12 % Favored : 92.76 % 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: -2.02 (0.20), residues: 1699 helix: -0.32 (0.24), residues: 421 sheet: -1.43 (0.27), residues: 341 loop : -1.80 (0.20), residues: 937 =============================================================================== Job complete usr+sys time: 2643.64 seconds wall clock time: 50 minutes 17.79 seconds (3017.79 seconds total)