Starting phenix.real_space_refine on Thu Sep 26 16:22:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/09_2024/7jgj_22328.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/09_2024/7jgj_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_22328/09_2024/7jgj_22328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/09_2024/7jgj_22328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/09_2024/7jgj_22328.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgj_22328/09_2024/7jgj_22328.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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. Time to flip 34 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.38, per 1000 atoms: 0.55 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 - 3.00 Amino acid : True - 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: 3.18 Conformation dependent library (CDL) restraints added in 1.6 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: 1.61 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: 5.21 Time building geometry restraints manager: 3.71 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: 0.00 - 13.42: 18392 13.42 - 26.84: 11 26.84 - 40.26: 1 40.26 - 53.68: 0 53.68 - 67.10: 1 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 3.120 nonbonded pdb=" O GLU H 12 " pdb=" N SER H 118 " model vdw 2.430 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 9.530 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.040 Process input model: 31.250 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.680 ------------------------------------------------------------------------------- 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 % Allowed : 16.33 % Favored : 70.99 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP H 194 HIS 0.012 0.002 HIS A1487 PHE 0.028 0.003 PHE L 138 TYR 0.053 0.004 TYR L 35 ARG 0.010 0.002 ARG A 699 *********************** 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 : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 727 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.8723 (m-80) REVERT: A 733 ILE cc_start: 0.8162 (pt) cc_final: 0.7905 (mm) REVERT: A 768 TYR cc_start: 0.9460 (OUTLIER) cc_final: 0.9204 (m-10) REVERT: A 783 PHE cc_start: 0.9236 (t80) cc_final: 0.8953 (t80) REVERT: A 835 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8165 (p0) REVERT: A 870 ILE cc_start: 0.9378 (mm) cc_final: 0.9063 (mm) REVERT: A 915 PHE cc_start: 0.9031 (t80) cc_final: 0.8278 (t80) REVERT: A 930 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7787 (p0) REVERT: A 972 VAL cc_start: 0.9641 (OUTLIER) cc_final: 0.9365 (t) REVERT: A 980 ASN cc_start: 0.9769 (OUTLIER) cc_final: 0.9339 (t0) REVERT: A 1003 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9118 (tp) REVERT: A 1048 SER cc_start: 0.8045 (OUTLIER) cc_final: 0.7711 (p) REVERT: A 1133 TYR cc_start: 0.9334 (m-80) cc_final: 0.8812 (m-80) REVERT: A 1204 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8887 (pp) REVERT: A 1206 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: A 1207 TYR cc_start: 0.9798 (m-10) cc_final: 0.9515 (m-80) REVERT: A 1209 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9283 (mt) REVERT: A 1221 PHE cc_start: 0.9221 (m-80) cc_final: 0.9019 (t80) REVERT: A 1263 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9076 (mm) REVERT: A 1308 GLU cc_start: 0.9462 (OUTLIER) cc_final: 0.9128 (pm20) REVERT: A 1316 TYR cc_start: 0.9740 (t80) cc_final: 0.9484 (t80) REVERT: A 1352 LEU cc_start: 0.9460 (tt) cc_final: 0.9160 (tt) REVERT: A 1390 GLU cc_start: 0.9778 (mm-30) cc_final: 0.9293 (mm-30) REVERT: A 1397 LEU cc_start: 0.9114 (mp) cc_final: 0.8858 (mp) REVERT: A 1405 TRP cc_start: 0.9186 (t60) cc_final: 0.8701 (t60) REVERT: A 1406 PHE cc_start: 0.9643 (t80) cc_final: 0.9289 (t80) REVERT: A 1466 PHE cc_start: 0.8466 (p90) cc_final: 0.7658 (p90) REVERT: A 1480 ASP cc_start: 0.9712 (m-30) cc_final: 0.9498 (m-30) REVERT: A 1510 ASP cc_start: 0.9649 (m-30) cc_final: 0.9174 (p0) REVERT: A 1511 HIS cc_start: 0.9749 (t70) cc_final: 0.9434 (t-90) REVERT: A 1532 LEU cc_start: 0.9429 (pp) cc_final: 0.8908 (pp) REVERT: A 1535 ASP cc_start: 0.4338 (OUTLIER) cc_final: 0.3863 (m-30) REVERT: A 1561 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8651 (ppp) REVERT: A 1593 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8391 (ptt) REVERT: A 1605 GLU cc_start: 0.8976 (mp0) cc_final: 0.8628 (mt-10) REVERT: A 1610 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8465 (p) REVERT: A 1616 LEU cc_start: 0.9171 (mt) cc_final: 0.8808 (mp) REVERT: A 1625 LEU cc_start: 0.8498 (mt) cc_final: 0.8170 (mt) REVERT: A 1643 ASP cc_start: 0.9541 (m-30) cc_final: 0.8943 (p0) REVERT: A 1688 PHE cc_start: 0.9656 (m-80) cc_final: 0.9236 (m-80) REVERT: A 1692 TYR cc_start: 0.9189 (m-10) cc_final: 0.8829 (m-80) REVERT: A 1694 MET cc_start: 0.9762 (ppp) cc_final: 0.9297 (ppp) REVERT: A 1741 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6375 (pp) REVERT: A 1760 ILE cc_start: 0.9454 (pt) cc_final: 0.9224 (pt) REVERT: A 1789 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7227 (tt) REVERT: A 1798 ASP cc_start: 0.8976 (OUTLIER) cc_final: 0.8706 (p0) REVERT: A 1808 LEU cc_start: 0.9632 (tp) cc_final: 0.9412 (tp) REVERT: A 1818 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8704 (mtm) REVERT: A 1889 ASP cc_start: 0.8645 (OUTLIER) cc_final: 0.7979 (p0) REVERT: A 1912 MET cc_start: 0.9779 (tpp) cc_final: 0.9234 (ttp) REVERT: A 1940 LYS cc_start: 0.9530 (mttm) cc_final: 0.9294 (mtmm) REVERT: A 1945 LYS cc_start: 0.9620 (pttm) cc_final: 0.9372 (tptp) REVERT: A 1947 TYR cc_start: 0.9416 (t80) cc_final: 0.8920 (t80) REVERT: L 32 ILE cc_start: 0.9779 (OUTLIER) cc_final: 0.9563 (tp) REVERT: L 88 PHE cc_start: 0.9584 (t80) cc_final: 0.8644 (t80) REVERT: L 95 PHE cc_start: 0.9213 (m-10) cc_final: 0.8893 (m-10) REVERT: L 190 SER cc_start: 0.0372 (OUTLIER) cc_final: -0.0052 (p) REVERT: L 191 TYR cc_start: 0.8143 (m-80) cc_final: 0.7753 (m-10) REVERT: L 208 PHE cc_start: 0.4221 (OUTLIER) cc_final: 0.3438 (m-80) REVERT: H 44 SER cc_start: 0.9045 (OUTLIER) cc_final: 0.8845 (t) REVERT: H 64 PHE cc_start: 0.9175 (m-80) cc_final: 0.8921 (m-80) REVERT: H 126 SER cc_start: 0.8548 (OUTLIER) cc_final: 0.8341 (p) REVERT: H 184 SER cc_start: 0.9727 (OUTLIER) cc_final: 0.9517 (p) outliers start: 184 outliers final: 37 residues processed: 437 average time/residue: 0.2543 time to fit residues: 162.1668 Evaluate side-chains 283 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 218 time to evaluate : 1.527 ------------------------------------------------------------------------------- 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: 0.5980 chunk 128 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 875 ASN ** 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 A1044 ASN A1166 GLN A1203 ASN ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1508 GLN ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1623 ASN ** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1950 GLN ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13593 Z= 0.298 Angle : 0.796 9.418 18405 Z= 0.436 Chirality : 0.059 1.096 2033 Planarity : 0.006 0.070 2378 Dihedral : 6.221 57.959 1852 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.71 % Favored : 94.11 % Rotamer: Outliers : 0.28 % Allowed : 4.89 % Favored : 94.83 % Cbeta Deviations : 0.19 % 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: -2.16 (0.19), residues: 1699 helix: -0.41 (0.23), residues: 436 sheet: -1.67 (0.25), residues: 376 loop : -1.84 (0.19), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1894 HIS 0.010 0.002 HIS A 977 PHE 0.023 0.003 PHE A 993 TYR 0.048 0.003 TYR A1861 ARG 0.007 0.001 ARG A1592 *********************** 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 263 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 259 time to evaluate : 1.544 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: A 783 PHE cc_start: 0.9406 (t80) cc_final: 0.9030 (t80) REVERT: A 857 LEU cc_start: 0.9694 (tt) cc_final: 0.9422 (mp) REVERT: A 870 ILE cc_start: 0.9459 (mm) cc_final: 0.9195 (pt) REVERT: A 878 THR cc_start: 0.9099 (p) cc_final: 0.8761 (p) REVERT: A 934 LEU cc_start: 0.9247 (mm) cc_final: 0.8800 (tp) REVERT: A 972 VAL cc_start: 0.9670 (t) cc_final: 0.9451 (t) REVERT: A 1003 LEU cc_start: 0.9593 (mm) cc_final: 0.9038 (tp) REVERT: A 1133 TYR cc_start: 0.9192 (m-80) cc_final: 0.8938 (m-80) REVERT: A 1162 MET cc_start: 0.9424 (tpt) cc_final: 0.9197 (tpt) REVERT: A 1207 TYR cc_start: 0.9734 (m-10) cc_final: 0.9292 (m-80) REVERT: A 1266 GLN cc_start: 0.9549 (mp10) cc_final: 0.9269 (mp10) REVERT: A 1316 TYR cc_start: 0.9786 (t80) cc_final: 0.9425 (t80) REVERT: A 1332 ASP cc_start: 0.9071 (m-30) cc_final: 0.8819 (m-30) REVERT: A 1352 LEU cc_start: 0.9397 (tt) cc_final: 0.8968 (tt) REVERT: A 1370 ASP cc_start: 0.9388 (t0) cc_final: 0.9008 (p0) REVERT: A 1371 THR cc_start: 0.9651 (m) cc_final: 0.9057 (m) REVERT: A 1406 PHE cc_start: 0.9835 (t80) cc_final: 0.9563 (t80) REVERT: A 1443 ILE cc_start: 0.9165 (tt) cc_final: 0.8732 (tt) REVERT: A 1480 ASP cc_start: 0.9674 (m-30) cc_final: 0.9448 (p0) REVERT: A 1532 LEU cc_start: 0.9095 (pp) cc_final: 0.6674 (pp) REVERT: A 1534 TYR cc_start: 0.8949 (m-10) cc_final: 0.8593 (m-10) REVERT: A 1561 MET cc_start: 0.9100 (ppp) cc_final: 0.8720 (ppp) REVERT: A 1630 PHE cc_start: 0.9550 (m-10) cc_final: 0.9288 (m-10) REVERT: A 1693 MET cc_start: 0.9729 (tmm) cc_final: 0.9337 (ptp) REVERT: A 1694 MET cc_start: 0.9704 (ppp) cc_final: 0.9326 (ppp) REVERT: A 1799 LEU cc_start: 0.9470 (pp) cc_final: 0.9264 (mm) REVERT: A 1800 MET cc_start: 0.9518 (mmm) cc_final: 0.8706 (mmt) REVERT: A 1804 ILE cc_start: 0.9801 (tt) cc_final: 0.9560 (mt) REVERT: A 1806 TYR cc_start: 0.8173 (m-10) cc_final: 0.7665 (m-80) REVERT: A 1818 MET cc_start: 0.9244 (mtp) cc_final: 0.8826 (mtm) REVERT: A 1911 LEU cc_start: 0.9503 (mm) cc_final: 0.9296 (pp) REVERT: A 1912 MET cc_start: 0.9733 (tpp) cc_final: 0.9479 (mtp) REVERT: A 1940 LYS cc_start: 0.9619 (mttm) cc_final: 0.9405 (mtpp) REVERT: A 1947 TYR cc_start: 0.9580 (t80) cc_final: 0.9344 (t80) REVERT: A 1954 PHE cc_start: 0.8988 (m-80) cc_final: 0.8743 (m-80) REVERT: L 21 MET cc_start: 0.8421 (pmm) cc_final: 0.8062 (pmm) REVERT: L 34 TRP cc_start: 0.8730 (m100) cc_final: 0.7007 (m100) REVERT: L 87 CYS cc_start: 0.8960 (p) cc_final: 0.8330 (p) REVERT: L 191 TYR cc_start: 0.7522 (m-80) cc_final: 0.7287 (m-10) REVERT: H 10 GLU cc_start: 0.6134 (mp0) cc_final: 0.5932 (mp0) REVERT: H 59 ASN cc_start: 0.8347 (m-40) cc_final: 0.7254 (m-40) REVERT: H 61 ASN cc_start: 0.9469 (t0) cc_final: 0.9090 (t0) REVERT: H 64 PHE cc_start: 0.9419 (m-80) cc_final: 0.9030 (m-80) REVERT: H 83 LEU cc_start: 0.9882 (mp) cc_final: 0.9670 (mm) REVERT: H 183 LEU cc_start: 0.9691 (tt) cc_final: 0.9387 (pp) outliers start: 4 outliers final: 2 residues processed: 261 average time/residue: 0.2373 time to fit residues: 92.7624 Evaluate side-chains 191 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 189 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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: 5.9990 chunk 47 optimal weight: 0.9980 chunk 127 optimal weight: 0.0970 chunk 104 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 153 optimal weight: 8.9990 chunk 166 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 GLN ** 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 977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 979 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1345 ASN A1362 ASN ** A1508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1686 ASN ** A1833 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 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13593 Z= 0.215 Angle : 0.692 7.648 18405 Z= 0.372 Chirality : 0.048 0.462 2033 Planarity : 0.005 0.053 2378 Dihedral : 5.851 49.897 1852 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 0.21 % Allowed : 4.27 % Favored : 95.52 % 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: -2.06 (0.19), residues: 1699 helix: -0.21 (0.23), residues: 425 sheet: -1.71 (0.25), residues: 378 loop : -1.77 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1864 HIS 0.012 0.002 HIS A1511 PHE 0.047 0.003 PHE L 117 TYR 0.044 0.002 TYR A1392 ARG 0.009 0.001 ARG A 960 *********************** 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 242 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 239 time to evaluate : 1.739 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: A 680 LEU cc_start: 0.9727 (mm) cc_final: 0.9395 (mm) REVERT: A 783 PHE cc_start: 0.9384 (t80) cc_final: 0.9008 (t80) REVERT: A 846 PHE cc_start: 0.9224 (m-80) cc_final: 0.8899 (m-80) REVERT: A 870 ILE cc_start: 0.9466 (mm) cc_final: 0.9246 (pt) REVERT: A 898 VAL cc_start: 0.9257 (t) cc_final: 0.8759 (t) REVERT: A 1003 LEU cc_start: 0.9557 (mm) cc_final: 0.9072 (tp) REVERT: A 1133 TYR cc_start: 0.9455 (m-80) cc_final: 0.8952 (m-80) REVERT: A 1162 MET cc_start: 0.9570 (tpt) cc_final: 0.9368 (tpt) REVERT: A 1207 TYR cc_start: 0.9693 (m-10) cc_final: 0.9275 (m-80) REVERT: A 1266 GLN cc_start: 0.9574 (mp10) cc_final: 0.9297 (mp10) REVERT: A 1316 TYR cc_start: 0.9672 (t80) cc_final: 0.9264 (t80) REVERT: A 1332 ASP cc_start: 0.9282 (m-30) cc_final: 0.8849 (m-30) REVERT: A 1392 TYR cc_start: 0.9638 (m-80) cc_final: 0.9401 (m-80) REVERT: A 1406 PHE cc_start: 0.9788 (t80) cc_final: 0.9514 (t80) REVERT: A 1443 ILE cc_start: 0.9244 (tt) cc_final: 0.8817 (tt) REVERT: A 1466 PHE cc_start: 0.9125 (p90) cc_final: 0.8367 (p90) REVERT: A 1507 ARG cc_start: 0.9215 (mtm-85) cc_final: 0.9014 (mmm-85) REVERT: A 1532 LEU cc_start: 0.9102 (pp) cc_final: 0.6824 (pp) REVERT: A 1534 TYR cc_start: 0.9028 (m-10) cc_final: 0.8550 (m-10) REVERT: A 1561 MET cc_start: 0.9049 (ppp) cc_final: 0.8675 (ppp) REVERT: A 1630 PHE cc_start: 0.9575 (m-10) cc_final: 0.9307 (m-10) REVERT: A 1688 PHE cc_start: 0.9416 (m-80) cc_final: 0.8982 (m-80) REVERT: A 1694 MET cc_start: 0.9719 (ppp) cc_final: 0.9448 (ppp) REVERT: A 1799 LEU cc_start: 0.9437 (pp) cc_final: 0.9214 (mt) REVERT: A 1800 MET cc_start: 0.9573 (mmm) cc_final: 0.8301 (mmm) REVERT: A 1806 TYR cc_start: 0.7997 (m-10) cc_final: 0.7585 (m-80) REVERT: A 1808 LEU cc_start: 0.9685 (tp) cc_final: 0.9130 (tp) REVERT: A 1818 MET cc_start: 0.9282 (mtp) cc_final: 0.8602 (mmm) REVERT: A 1872 TYR cc_start: 0.9498 (m-10) cc_final: 0.9141 (m-80) REVERT: A 1912 MET cc_start: 0.9737 (tpp) cc_final: 0.9499 (mtp) REVERT: A 1925 TRP cc_start: 0.8315 (t-100) cc_final: 0.8011 (t-100) REVERT: A 1940 LYS cc_start: 0.9595 (mttm) cc_final: 0.9354 (mtpp) REVERT: A 1947 TYR cc_start: 0.9574 (t80) cc_final: 0.9353 (t80) REVERT: A 1954 PHE cc_start: 0.8990 (m-80) cc_final: 0.8748 (m-80) REVERT: L 21 MET cc_start: 0.8342 (pmm) cc_final: 0.7920 (pmm) REVERT: L 34 TRP cc_start: 0.8470 (m100) cc_final: 0.6565 (m100) REVERT: L 74 ILE cc_start: 0.9336 (mp) cc_final: 0.9061 (mp) REVERT: L 87 CYS cc_start: 0.8860 (p) cc_final: 0.8273 (p) REVERT: L 103 LEU cc_start: 0.9576 (tp) cc_final: 0.9370 (tp) REVERT: L 117 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6604 (m-10) REVERT: L 191 TYR cc_start: 0.7514 (m-80) cc_final: 0.7288 (m-10) REVERT: H 34 MET cc_start: 0.8567 (mmp) cc_final: 0.8145 (mmm) REVERT: H 64 PHE cc_start: 0.9396 (m-80) cc_final: 0.9076 (m-10) REVERT: H 81 MET cc_start: 0.9501 (tpt) cc_final: 0.9184 (tpt) REVERT: H 183 LEU cc_start: 0.9688 (tt) cc_final: 0.9396 (pp) outliers start: 3 outliers final: 1 residues processed: 241 average time/residue: 0.2476 time to fit residues: 89.3899 Evaluate side-chains 187 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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: 10.0000 chunk 115 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 17 optimal weight: 0.4980 chunk 73 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 154 optimal weight: 0.4980 chunk 163 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 overall best weight: 5.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1379 GLN ** A1508 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** ** A1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 ASN L 211 ASN ** H 5 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: 0.7555 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13593 Z= 0.351 Angle : 0.751 11.048 18405 Z= 0.410 Chirality : 0.047 0.332 2033 Planarity : 0.005 0.053 2378 Dihedral : 6.112 44.988 1852 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 29.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 0.21 % Allowed : 4.27 % Favored : 95.52 % 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: -2.15 (0.19), residues: 1699 helix: -0.50 (0.23), residues: 420 sheet: -1.61 (0.26), residues: 364 loop : -1.79 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A1448 HIS 0.008 0.002 HIS A1608 PHE 0.035 0.003 PHE L 117 TYR 0.032 0.003 TYR A1861 ARG 0.005 0.001 ARG A1802 *********************** 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 210 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 207 time to evaluate : 1.434 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: A 680 LEU cc_start: 0.9688 (mm) cc_final: 0.9436 (mt) REVERT: A 783 PHE cc_start: 0.9459 (t80) cc_final: 0.9087 (t80) REVERT: A 846 PHE cc_start: 0.9289 (m-80) cc_final: 0.9031 (m-80) REVERT: A 929 TYR cc_start: 0.4786 (p90) cc_final: 0.4538 (p90) REVERT: A 987 ILE cc_start: 0.9259 (mt) cc_final: 0.8750 (mt) REVERT: A 1003 LEU cc_start: 0.9572 (mm) cc_final: 0.8916 (tp) REVERT: A 1161 MET cc_start: 0.8683 (pmm) cc_final: 0.8454 (pmm) REVERT: A 1207 TYR cc_start: 0.9726 (m-10) cc_final: 0.9267 (m-80) REVERT: A 1266 GLN cc_start: 0.9591 (mp10) cc_final: 0.9359 (mp10) REVERT: A 1332 ASP cc_start: 0.9345 (m-30) cc_final: 0.9095 (m-30) REVERT: A 1370 ASP cc_start: 0.9622 (m-30) cc_final: 0.9109 (p0) REVERT: A 1392 TYR cc_start: 0.9675 (m-80) cc_final: 0.9329 (m-80) REVERT: A 1406 PHE cc_start: 0.9788 (t80) cc_final: 0.9536 (t80) REVERT: A 1440 TYR cc_start: 0.9823 (t80) cc_final: 0.9566 (t80) REVERT: A 1532 LEU cc_start: 0.9212 (pp) cc_final: 0.7760 (pp) REVERT: A 1534 TYR cc_start: 0.9228 (m-10) cc_final: 0.8865 (m-10) REVERT: A 1561 MET cc_start: 0.9081 (ppp) cc_final: 0.8812 (ppp) REVERT: A 1594 LEU cc_start: 0.9357 (tp) cc_final: 0.9136 (tp) REVERT: A 1694 MET cc_start: 0.9755 (ppp) cc_final: 0.9487 (ppp) REVERT: A 1799 LEU cc_start: 0.9377 (pp) cc_final: 0.9093 (mp) REVERT: A 1800 MET cc_start: 0.9609 (mmm) cc_final: 0.8804 (tpp) REVERT: A 1806 TYR cc_start: 0.8253 (m-10) cc_final: 0.7915 (m-80) REVERT: A 1808 LEU cc_start: 0.9606 (tp) cc_final: 0.9012 (tp) REVERT: A 1818 MET cc_start: 0.9134 (mtp) cc_final: 0.8476 (mmm) REVERT: A 1911 LEU cc_start: 0.9553 (mm) cc_final: 0.9341 (pp) REVERT: A 1912 MET cc_start: 0.9744 (tpp) cc_final: 0.9500 (mtp) REVERT: A 1925 TRP cc_start: 0.8356 (t-100) cc_final: 0.8041 (t-100) REVERT: A 1940 LYS cc_start: 0.9621 (mttm) cc_final: 0.9373 (mtpp) REVERT: A 1944 PHE cc_start: 0.9903 (t80) cc_final: 0.9679 (t80) REVERT: L 21 MET cc_start: 0.8611 (pmm) cc_final: 0.8133 (pmm) REVERT: L 34 TRP cc_start: 0.8852 (m100) cc_final: 0.7069 (m100) REVERT: L 74 ILE cc_start: 0.9401 (mp) cc_final: 0.9176 (mp) REVERT: L 87 CYS cc_start: 0.8725 (p) cc_final: 0.8103 (p) REVERT: L 117 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.6877 (m-80) REVERT: H 18 MET cc_start: 0.7894 (tmm) cc_final: 0.7600 (tmm) REVERT: H 64 PHE cc_start: 0.9341 (m-80) cc_final: 0.9010 (m-10) outliers start: 3 outliers final: 1 residues processed: 210 average time/residue: 0.2345 time to fit residues: 75.3326 Evaluate side-chains 165 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 1.544 ------------------------------------------------------------------------------- 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: 9.9990 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 121 optimal weight: 0.0970 chunk 67 optimal weight: 2.9990 chunk 139 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 83 optimal weight: 5.9990 chunk 146 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1508 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** ** A1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 211 ASN ** H 5 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 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13593 Z= 0.237 Angle : 0.677 8.779 18405 Z= 0.367 Chirality : 0.045 0.317 2033 Planarity : 0.005 0.047 2378 Dihedral : 5.893 41.571 1852 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 23.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 0.14 % Allowed : 2.41 % Favored : 97.45 % 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: -2.11 (0.19), residues: 1699 helix: -0.37 (0.23), residues: 428 sheet: -1.79 (0.27), residues: 350 loop : -1.74 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 36 HIS 0.007 0.002 HIS A1608 PHE 0.044 0.002 PHE L 117 TYR 0.033 0.002 TYR L 191 ARG 0.005 0.001 ARG A1052 *********************** 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 214 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 212 time to evaluate : 1.682 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: A 680 LEU cc_start: 0.9681 (mm) cc_final: 0.9394 (mt) REVERT: A 783 PHE cc_start: 0.9438 (t80) cc_final: 0.9079 (t80) REVERT: A 846 PHE cc_start: 0.9297 (m-80) cc_final: 0.9043 (m-80) REVERT: A 926 THR cc_start: 0.8566 (p) cc_final: 0.8282 (p) REVERT: A 929 TYR cc_start: 0.4571 (p90) cc_final: 0.4285 (p90) REVERT: A 1003 LEU cc_start: 0.9579 (mm) cc_final: 0.8961 (tp) REVERT: A 1161 MET cc_start: 0.8842 (pmm) cc_final: 0.8628 (pmm) REVERT: A 1207 TYR cc_start: 0.9660 (m-10) cc_final: 0.9156 (m-80) REVERT: A 1266 GLN cc_start: 0.9590 (mp10) cc_final: 0.9355 (mp10) REVERT: A 1370 ASP cc_start: 0.9611 (m-30) cc_final: 0.9090 (p0) REVERT: A 1392 TYR cc_start: 0.9678 (m-80) cc_final: 0.9368 (m-80) REVERT: A 1406 PHE cc_start: 0.9741 (t80) cc_final: 0.9498 (t80) REVERT: A 1532 LEU cc_start: 0.9306 (pp) cc_final: 0.7904 (pp) REVERT: A 1534 TYR cc_start: 0.9230 (m-10) cc_final: 0.8884 (m-10) REVERT: A 1561 MET cc_start: 0.9122 (ppp) cc_final: 0.8849 (ppp) REVERT: A 1568 VAL cc_start: 0.9681 (p) cc_final: 0.9388 (m) REVERT: A 1588 TYR cc_start: 0.9193 (m-80) cc_final: 0.8746 (m-80) REVERT: A 1692 TYR cc_start: 0.9495 (m-10) cc_final: 0.9285 (m-10) REVERT: A 1694 MET cc_start: 0.9777 (ppp) cc_final: 0.9477 (ppp) REVERT: A 1799 LEU cc_start: 0.9426 (pp) cc_final: 0.9156 (mp) REVERT: A 1800 MET cc_start: 0.9603 (mmm) cc_final: 0.8690 (tpp) REVERT: A 1806 TYR cc_start: 0.8105 (m-10) cc_final: 0.7582 (m-80) REVERT: A 1814 PHE cc_start: 0.9598 (p90) cc_final: 0.9309 (p90) REVERT: A 1872 TYR cc_start: 0.9539 (m-10) cc_final: 0.9136 (m-80) REVERT: A 1911 LEU cc_start: 0.9534 (mm) cc_final: 0.9308 (pp) REVERT: A 1912 MET cc_start: 0.9740 (tpp) cc_final: 0.9538 (mtp) REVERT: A 1925 TRP cc_start: 0.8327 (t-100) cc_final: 0.8024 (t-100) REVERT: A 1940 LYS cc_start: 0.9597 (mttm) cc_final: 0.9362 (mtpp) REVERT: A 1944 PHE cc_start: 0.9868 (t80) cc_final: 0.9626 (t80) REVERT: L 21 MET cc_start: 0.8678 (pmm) cc_final: 0.8257 (pmm) REVERT: L 34 TRP cc_start: 0.8723 (m100) cc_final: 0.6811 (m100) REVERT: L 74 ILE cc_start: 0.9382 (mp) cc_final: 0.9165 (mp) REVERT: L 87 CYS cc_start: 0.8692 (p) cc_final: 0.8130 (p) REVERT: L 117 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6687 (m-10) REVERT: H 18 MET cc_start: 0.7940 (tmm) cc_final: 0.7703 (tmm) REVERT: H 64 PHE cc_start: 0.9296 (m-80) cc_final: 0.9078 (m-80) REVERT: H 104 TYR cc_start: 0.9047 (p90) cc_final: 0.8292 (m-80) REVERT: H 106 MET cc_start: 0.8340 (ppp) cc_final: 0.7945 (ppp) REVERT: H 183 LEU cc_start: 0.9640 (tt) cc_final: 0.9306 (pp) outliers start: 2 outliers final: 0 residues processed: 213 average time/residue: 0.2275 time to fit residues: 74.5615 Evaluate side-chains 165 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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: 10.0000 chunk 95 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 13 optimal weight: 0.0040 chunk 85 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A 885 GLN ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1824 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 ASN ** 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: 0.7625 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13593 Z= 0.320 Angle : 0.731 10.265 18405 Z= 0.398 Chirality : 0.046 0.317 2033 Planarity : 0.005 0.051 2378 Dihedral : 6.134 32.687 1852 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 31.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.53 % Favored : 92.41 % Rotamer: Outliers : 0.07 % Allowed : 4.14 % Favored : 95.80 % 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: -2.38 (0.19), residues: 1699 helix: -0.75 (0.23), residues: 433 sheet: -1.75 (0.27), residues: 339 loop : -1.92 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1448 HIS 0.007 0.002 HIS A1937 PHE 0.034 0.003 PHE L 117 TYR 0.029 0.002 TYR A1861 ARG 0.005 0.001 ARG A1052 *********************** 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 197 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 1.563 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: A 680 LEU cc_start: 0.9695 (mm) cc_final: 0.9441 (mt) REVERT: A 783 PHE cc_start: 0.9469 (t80) cc_final: 0.9125 (t80) REVERT: A 929 TYR cc_start: 0.5184 (p90) cc_final: 0.4870 (p90) REVERT: A 1003 LEU cc_start: 0.9560 (mm) cc_final: 0.8948 (tp) REVERT: A 1207 TYR cc_start: 0.9648 (m-10) cc_final: 0.9111 (m-80) REVERT: A 1332 ASP cc_start: 0.9334 (m-30) cc_final: 0.9072 (m-30) REVERT: A 1370 ASP cc_start: 0.9635 (m-30) cc_final: 0.9126 (p0) REVERT: A 1392 TYR cc_start: 0.9652 (m-80) cc_final: 0.9367 (m-80) REVERT: A 1406 PHE cc_start: 0.9724 (t80) cc_final: 0.9508 (t80) REVERT: A 1532 LEU cc_start: 0.9378 (pp) cc_final: 0.8006 (pp) REVERT: A 1534 TYR cc_start: 0.9302 (m-10) cc_final: 0.8888 (m-10) REVERT: A 1561 MET cc_start: 0.9146 (ppp) cc_final: 0.8884 (ppp) REVERT: A 1588 TYR cc_start: 0.9246 (m-80) cc_final: 0.8827 (m-80) REVERT: A 1694 MET cc_start: 0.9782 (ppp) cc_final: 0.9556 (ppp) REVERT: A 1800 MET cc_start: 0.9626 (mmm) cc_final: 0.9213 (tpp) REVERT: A 1814 PHE cc_start: 0.9443 (p90) cc_final: 0.9221 (p90) REVERT: A 1911 LEU cc_start: 0.9542 (mm) cc_final: 0.9315 (pp) REVERT: A 1925 TRP cc_start: 0.8401 (t-100) cc_final: 0.8086 (t-100) REVERT: A 1944 PHE cc_start: 0.9847 (t80) cc_final: 0.9605 (t80) REVERT: L 34 TRP cc_start: 0.8916 (m100) cc_final: 0.7521 (m100) REVERT: L 87 CYS cc_start: 0.8665 (p) cc_final: 0.8186 (p) REVERT: L 178 LEU cc_start: 0.8902 (tp) cc_final: 0.8687 (tp) REVERT: H 18 MET cc_start: 0.8076 (tmm) cc_final: 0.7804 (tmm) REVERT: H 106 MET cc_start: 0.8486 (ppp) cc_final: 0.8162 (ppp) REVERT: H 141 MET cc_start: 0.8105 (tpp) cc_final: 0.7847 (tpp) outliers start: 1 outliers final: 1 residues processed: 197 average time/residue: 0.2330 time to fit residues: 69.9268 Evaluate side-chains 149 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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: 2.9990 chunk 93 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 162 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN ** 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** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1494 ASN A1508 GLN A1575 ASN ** A1608 HIS ** 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** ** A1937 HIS ** 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 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13593 Z= 0.207 Angle : 0.663 9.979 18405 Z= 0.356 Chirality : 0.044 0.277 2033 Planarity : 0.005 0.052 2378 Dihedral : 5.773 35.142 1852 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.53 % Favored : 93.41 % Rotamer: Outliers : 0.07 % Allowed : 2.55 % Favored : 97.38 % 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: -2.16 (0.20), residues: 1699 helix: -0.37 (0.24), residues: 431 sheet: -1.54 (0.28), residues: 326 loop : -1.93 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP H 109 HIS 0.008 0.001 HIS A1608 PHE 0.043 0.002 PHE L 117 TYR 0.034 0.002 TYR A1806 ARG 0.007 0.001 ARG A1621 *********************** 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 212 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 680 LEU cc_start: 0.9702 (mm) cc_final: 0.9428 (mt) REVERT: A 783 PHE cc_start: 0.9419 (t80) cc_final: 0.9065 (t80) REVERT: A 1003 LEU cc_start: 0.9516 (mm) cc_final: 0.8923 (tp) REVERT: A 1127 GLU cc_start: 0.9721 (pp20) cc_final: 0.9455 (pp20) REVERT: A 1207 TYR cc_start: 0.9689 (m-10) cc_final: 0.9138 (m-80) REVERT: A 1266 GLN cc_start: 0.9587 (mp10) cc_final: 0.9331 (mp10) REVERT: A 1332 ASP cc_start: 0.9288 (m-30) cc_final: 0.9019 (m-30) REVERT: A 1370 ASP cc_start: 0.9599 (m-30) cc_final: 0.9073 (p0) REVERT: A 1392 TYR cc_start: 0.9635 (m-80) cc_final: 0.9359 (m-80) REVERT: A 1406 PHE cc_start: 0.9823 (t80) cc_final: 0.9534 (t80) REVERT: A 1532 LEU cc_start: 0.9404 (pp) cc_final: 0.8027 (pp) REVERT: A 1534 TYR cc_start: 0.9307 (m-10) cc_final: 0.8914 (m-10) REVERT: A 1561 MET cc_start: 0.9115 (ppp) cc_final: 0.8835 (ppp) REVERT: A 1568 VAL cc_start: 0.9769 (p) cc_final: 0.9410 (m) REVERT: A 1588 TYR cc_start: 0.9150 (m-80) cc_final: 0.8683 (m-80) REVERT: A 1593 MET cc_start: 0.9348 (ppp) cc_final: 0.8780 (ppp) REVERT: A 1692 TYR cc_start: 0.9519 (m-10) cc_final: 0.9287 (m-10) REVERT: A 1694 MET cc_start: 0.9761 (ppp) cc_final: 0.9480 (ppp) REVERT: A 1799 LEU cc_start: 0.9460 (pp) cc_final: 0.9138 (mp) REVERT: A 1800 MET cc_start: 0.9562 (mmm) cc_final: 0.8599 (tpp) REVERT: A 1814 PHE cc_start: 0.9252 (p90) cc_final: 0.9004 (p90) REVERT: A 1872 TYR cc_start: 0.9596 (m-10) cc_final: 0.9177 (m-80) REVERT: A 1912 MET cc_start: 0.9657 (mtm) cc_final: 0.9248 (ptm) REVERT: A 1925 TRP cc_start: 0.8321 (t-100) cc_final: 0.8008 (t-100) REVERT: A 1940 LYS cc_start: 0.9566 (mttm) cc_final: 0.9359 (mtpp) REVERT: A 1944 PHE cc_start: 0.9830 (t80) cc_final: 0.9574 (t80) REVERT: L 21 MET cc_start: 0.8810 (pmm) cc_final: 0.8389 (pmm) REVERT: L 34 TRP cc_start: 0.8485 (m100) cc_final: 0.7185 (m100) REVERT: L 45 LEU cc_start: 0.9673 (tp) cc_final: 0.9467 (tp) REVERT: L 74 ILE cc_start: 0.9393 (mp) cc_final: 0.9192 (mp) REVERT: L 87 CYS cc_start: 0.8590 (p) cc_final: 0.8204 (p) REVERT: L 178 LEU cc_start: 0.8975 (tp) cc_final: 0.8768 (tp) REVERT: H 64 PHE cc_start: 0.9608 (m-80) cc_final: 0.9314 (m-80) REVERT: H 106 MET cc_start: 0.8404 (ppp) cc_final: 0.7919 (ppp) REVERT: H 141 MET cc_start: 0.8161 (tpp) cc_final: 0.7883 (tpp) outliers start: 1 outliers final: 0 residues processed: 212 average time/residue: 0.2261 time to fit residues: 73.2130 Evaluate side-chains 158 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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: 7.9990 chunk 97 optimal weight: 9.9990 chunk 49 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 148 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN ** 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** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1025 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1220 GLN ** A1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** 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** ** A1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.5936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 13593 Z= 0.505 Angle : 0.924 11.626 18405 Z= 0.502 Chirality : 0.051 0.303 2033 Planarity : 0.007 0.078 2378 Dihedral : 6.845 35.928 1852 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 43.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.24 % Favored : 90.64 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % 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: -2.83 (0.19), residues: 1699 helix: -1.39 (0.21), residues: 433 sheet: -1.91 (0.28), residues: 323 loop : -2.13 (0.19), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A1448 HIS 0.012 0.003 HIS A1654 PHE 0.036 0.004 PHE L 117 TYR 0.038 0.003 TYR A1207 ARG 0.010 0.001 ARG A1621 *********************** 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 172 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 1.551 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: A 680 LEU cc_start: 0.9658 (mm) cc_final: 0.9356 (mt) REVERT: A 783 PHE cc_start: 0.9417 (t80) cc_final: 0.9150 (t80) REVERT: A 1003 LEU cc_start: 0.9517 (mm) cc_final: 0.8897 (tp) REVERT: A 1332 ASP cc_start: 0.9400 (m-30) cc_final: 0.9179 (m-30) REVERT: A 1370 ASP cc_start: 0.9661 (m-30) cc_final: 0.9185 (p0) REVERT: A 1513 ASP cc_start: 0.9434 (t0) cc_final: 0.8898 (m-30) REVERT: A 1674 PHE cc_start: 0.9861 (m-80) cc_final: 0.9651 (m-80) REVERT: A 1694 MET cc_start: 0.9756 (ppp) cc_final: 0.9513 (ppp) REVERT: A 1925 TRP cc_start: 0.8470 (t-100) cc_final: 0.8133 (t-100) REVERT: A 1944 PHE cc_start: 0.9770 (t80) cc_final: 0.9449 (t80) REVERT: L 21 MET cc_start: 0.8951 (pmm) cc_final: 0.8607 (pmm) REVERT: L 34 TRP cc_start: 0.8664 (m100) cc_final: 0.7276 (m100) REVERT: L 87 CYS cc_start: 0.8467 (p) cc_final: 0.8213 (p) REVERT: L 178 LEU cc_start: 0.8831 (tp) cc_final: 0.8617 (tp) REVERT: H 34 MET cc_start: 0.9143 (mmp) cc_final: 0.8917 (mmm) REVERT: H 64 PHE cc_start: 0.9512 (m-80) cc_final: 0.9252 (m-10) REVERT: H 106 MET cc_start: 0.8559 (ppp) cc_final: 0.8326 (ppp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.2311 time to fit residues: 60.3935 Evaluate side-chains 129 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 1.570 ------------------------------------------------------------------------------- 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: 5.9990 chunk 142 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN ** 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** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 HIS ** A1166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1508 GLN ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1636 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** A1927 ASN ** A1937 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.5921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13593 Z= 0.228 Angle : 0.706 12.727 18405 Z= 0.379 Chirality : 0.046 0.274 2033 Planarity : 0.005 0.077 2378 Dihedral : 6.095 35.390 1852 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 26.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.42 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % 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: -2.47 (0.19), residues: 1699 helix: -0.78 (0.22), residues: 438 sheet: -1.68 (0.27), residues: 332 loop : -2.08 (0.19), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 36 HIS 0.010 0.002 HIS A 977 PHE 0.042 0.002 PHE L 117 TYR 0.046 0.002 TYR A1692 ARG 0.006 0.001 ARG A1621 *********************** 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 192 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 680 LEU cc_start: 0.9668 (mm) cc_final: 0.9387 (mt) REVERT: A 783 PHE cc_start: 0.9373 (t80) cc_final: 0.9072 (t80) REVERT: A 1003 LEU cc_start: 0.9472 (mm) cc_final: 0.8879 (tp) REVERT: A 1127 GLU cc_start: 0.9735 (pp20) cc_final: 0.9434 (pp20) REVERT: A 1207 TYR cc_start: 0.9524 (m-10) cc_final: 0.8792 (m-10) REVERT: A 1260 GLU cc_start: 0.9428 (mp0) cc_final: 0.9205 (mp0) REVERT: A 1266 GLN cc_start: 0.9596 (mp10) cc_final: 0.9317 (mp10) REVERT: A 1332 ASP cc_start: 0.9312 (m-30) cc_final: 0.9028 (m-30) REVERT: A 1370 ASP cc_start: 0.9616 (m-30) cc_final: 0.9104 (p0) REVERT: A 1392 TYR cc_start: 0.9667 (m-80) cc_final: 0.9453 (m-80) REVERT: A 1406 PHE cc_start: 0.9903 (t80) cc_final: 0.9548 (t80) REVERT: A 1513 ASP cc_start: 0.9315 (t0) cc_final: 0.8791 (m-30) REVERT: A 1532 LEU cc_start: 0.9230 (pp) cc_final: 0.7977 (pp) REVERT: A 1534 TYR cc_start: 0.9041 (m-10) cc_final: 0.8562 (m-10) REVERT: A 1561 MET cc_start: 0.9217 (ppp) cc_final: 0.8950 (ppp) REVERT: A 1692 TYR cc_start: 0.9537 (m-80) cc_final: 0.9331 (m-80) REVERT: A 1694 MET cc_start: 0.9757 (ppp) cc_final: 0.9514 (ppp) REVERT: A 1695 GLU cc_start: 0.9559 (pt0) cc_final: 0.9214 (pt0) REVERT: A 1818 MET cc_start: 0.9369 (tmm) cc_final: 0.9128 (tmm) REVERT: A 1912 MET cc_start: 0.9697 (mtm) cc_final: 0.9214 (ptm) REVERT: A 1925 TRP cc_start: 0.8329 (t-100) cc_final: 0.7995 (t-100) REVERT: A 1944 PHE cc_start: 0.9721 (t80) cc_final: 0.9371 (t80) REVERT: L 21 MET cc_start: 0.8856 (pmm) cc_final: 0.8437 (pmm) REVERT: L 34 TRP cc_start: 0.8427 (m100) cc_final: 0.6910 (m100) REVERT: L 87 CYS cc_start: 0.8389 (p) cc_final: 0.8067 (p) REVERT: L 88 PHE cc_start: 0.9463 (t80) cc_final: 0.9244 (t80) REVERT: H 34 MET cc_start: 0.8873 (mmp) cc_final: 0.8668 (mmm) REVERT: H 64 PHE cc_start: 0.9491 (m-80) cc_final: 0.9207 (m-10) REVERT: H 106 MET cc_start: 0.8409 (ppp) cc_final: 0.8121 (ppp) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.2252 time to fit residues: 66.6756 Evaluate side-chains 140 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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: 0.9980 chunk 76 optimal weight: 0.2980 chunk 111 optimal weight: 8.9990 chunk 168 optimal weight: 0.9980 chunk 154 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 chunk 13 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 GLN ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1237 GLN A1508 GLN ** A1604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1636 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** ** 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: 0.7634 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13593 Z= 0.200 Angle : 0.694 9.132 18405 Z= 0.370 Chirality : 0.045 0.227 2033 Planarity : 0.005 0.074 2378 Dihedral : 5.786 33.548 1852 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.59 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -2.27 (0.19), residues: 1699 helix: -0.49 (0.23), residues: 435 sheet: -1.48 (0.27), residues: 343 loop : -2.06 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 109 HIS 0.009 0.001 HIS A 977 PHE 0.037 0.002 PHE L 117 TYR 0.043 0.002 TYR A1692 ARG 0.006 0.001 ARG A1621 ********************** 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 194 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 680 LEU cc_start: 0.9650 (mm) cc_final: 0.9384 (mt) REVERT: A 783 PHE cc_start: 0.9365 (t80) cc_final: 0.9092 (t80) REVERT: A 980 ASN cc_start: 0.9673 (m-40) cc_final: 0.8835 (t0) REVERT: A 1127 GLU cc_start: 0.9721 (pp20) cc_final: 0.9431 (pp20) REVERT: A 1207 TYR cc_start: 0.9524 (m-10) cc_final: 0.8836 (m-10) REVERT: A 1266 GLN cc_start: 0.9637 (mp10) cc_final: 0.9388 (mp10) REVERT: A 1332 ASP cc_start: 0.9269 (m-30) cc_final: 0.8992 (m-30) REVERT: A 1370 ASP cc_start: 0.9553 (m-30) cc_final: 0.9007 (p0) REVERT: A 1406 PHE cc_start: 0.9815 (t80) cc_final: 0.9601 (t80) REVERT: A 1513 ASP cc_start: 0.9310 (t0) cc_final: 0.8819 (m-30) REVERT: A 1532 LEU cc_start: 0.9329 (pp) cc_final: 0.8093 (pp) REVERT: A 1534 TYR cc_start: 0.9111 (m-10) cc_final: 0.8684 (m-10) REVERT: A 1561 MET cc_start: 0.9213 (ppp) cc_final: 0.8854 (ppp) REVERT: A 1692 TYR cc_start: 0.9534 (m-80) cc_final: 0.9298 (m-80) REVERT: A 1694 MET cc_start: 0.9733 (ppp) cc_final: 0.9418 (ppp) REVERT: A 1695 GLU cc_start: 0.9538 (pt0) cc_final: 0.9123 (pt0) REVERT: A 1800 MET cc_start: 0.9620 (tpp) cc_final: 0.8979 (tpp) REVERT: A 1818 MET cc_start: 0.9382 (tmm) cc_final: 0.9147 (tmm) REVERT: A 1912 MET cc_start: 0.9723 (mtm) cc_final: 0.9265 (ptm) REVERT: A 1925 TRP cc_start: 0.8378 (t-100) cc_final: 0.8049 (t-100) REVERT: A 1940 LYS cc_start: 0.9557 (mttm) cc_final: 0.9345 (mtpp) REVERT: A 1944 PHE cc_start: 0.9706 (t80) cc_final: 0.9452 (t80) REVERT: L 21 MET cc_start: 0.8877 (pmm) cc_final: 0.8555 (pmm) REVERT: L 34 TRP cc_start: 0.8239 (m100) cc_final: 0.6759 (m100) REVERT: L 88 PHE cc_start: 0.9538 (t80) cc_final: 0.9296 (t80) REVERT: H 64 PHE cc_start: 0.9515 (m-80) cc_final: 0.9233 (m-10) REVERT: H 81 MET cc_start: 0.8198 (mmp) cc_final: 0.7962 (mmm) REVERT: H 106 MET cc_start: 0.8323 (ppp) cc_final: 0.7995 (ppp) REVERT: H 141 MET cc_start: 0.8197 (tpp) cc_final: 0.7990 (tpp) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2380 time to fit residues: 70.5488 Evaluate side-chains 142 residues out of total 1473 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.591 ------------------------------------------------------------------------------- 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: 0.9990 chunk 19 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 137 optimal weight: 6.9990 chunk 17 optimal weight: 0.0050 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 885 GLN ** A 907 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1013 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1345 ASN A1508 GLN ** A1608 HIS ** 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** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.038774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.026233 restraints weight = 101224.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2553 r_free = 0.2553 target = 0.027885 restraints weight = 58194.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2599 r_free = 0.2599 target = 0.029172 restraints weight = 39193.344| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5280 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 0.047 13593 Z= 0.200 Angle : 0.686 14.612 18405 Z= 0.363 Chirality : 0.044 0.231 2033 Planarity : 0.005 0.068 2378 Dihedral : 5.629 32.459 1852 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.30 % Favored : 92.58 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -0.37 (0.23), residues: 425 sheet: -1.39 (0.27), residues: 347 loop : -2.05 (0.19), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 109 HIS 0.009 0.001 HIS A 977 PHE 0.031 0.002 PHE L 117 TYR 0.039 0.002 TYR A1692 ARG 0.006 0.001 ARG A1621 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2864.59 seconds wall clock time: 52 minutes 48.13 seconds (3168.13 seconds total)