Starting phenix.real_space_refine on Thu Mar 5 02:55:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z12_14438/03_2026/7z12_14438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z12_14438/03_2026/7z12_14438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z12_14438/03_2026/7z12_14438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z12_14438/03_2026/7z12_14438.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z12_14438/03_2026/7z12_14438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z12_14438/03_2026/7z12_14438.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= -0.000 sd= 0.043 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 110 5.16 5 C 11465 2.51 5 N 3159 2.21 5 O 3618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18352 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1650 Classifications: {'peptide': 221} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 209} Chain: "C" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "A" Number of atoms: 15071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1853, 15071 Classifications: {'peptide': 1853} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 20, 'PCIS': 2, 'PTRANS': 48, 'TRANS': 1782} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 3.60, per 1000 atoms: 0.20 Number of scatterers: 18352 At special positions: 0 Unit cell: (111.488, 156.416, 159.744, 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 110 16.00 O 3618 8.00 N 3159 7.00 C 11465 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 169 " - pdb=" SG CYS B 225 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 107 " distance=2.02 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 213 " distance=2.04 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: 1.34 Conformation dependent library (CDL) restraints added in 748.2 milliseconds 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4292 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 16 sheets defined 39.9% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'B' and resid 216 through 218 No H-bonds generated for 'chain 'B' and resid 216 through 218' Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.932A pdb=" N VAL C 102 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 147 Processing helix chain 'C' and resid 201 through 207 Processing helix chain 'A' and resid 11 through 16 Processing helix chain 'A' and resid 24 through 29 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 51 through 54 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.543A pdb=" N GLU A 103 " --> pdb=" O PRO A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 4.246A pdb=" N LEU A 113 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 142 removed outlier: 4.401A pdb=" N ALA A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 206 through 218 removed outlier: 4.063A pdb=" N ALA A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.995A pdb=" N VAL A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.918A pdb=" N LEU A 235 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 284 through 295 Processing helix chain 'A' and resid 319 through 328 removed outlier: 3.820A pdb=" N LYS A 323 " --> pdb=" O CYS A 319 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP A 324 " --> pdb=" O SER A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 366 through 378 removed outlier: 3.795A pdb=" N VAL A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N PHE A 373 " --> pdb=" O TYR A 369 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 588 through 592 Processing helix chain 'A' and resid 609 through 632 Processing helix chain 'A' and resid 641 through 661 Processing helix chain 'A' and resid 672 through 687 removed outlier: 4.762A pdb=" N PHE A 685 " --> pdb=" O PHE A 681 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS A 687 " --> pdb=" O LYS A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 714 Processing helix chain 'A' and resid 715 through 728 removed outlier: 3.511A pdb=" N ILE A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 751 through 756 removed outlier: 4.250A pdb=" N ASP A 754 " --> pdb=" O PRO A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 786 removed outlier: 4.127A pdb=" N ASP A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 781 " --> pdb=" O LYS A 777 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A 786 " --> pdb=" O ILE A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 816 removed outlier: 3.825A pdb=" N GLU A 806 " --> pdb=" O LYS A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 851 removed outlier: 3.534A pdb=" N LYS A 850 " --> pdb=" O ILE A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 890 Processing helix chain 'A' and resid 896 through 905 Processing helix chain 'A' and resid 971 through 973 No H-bonds generated for 'chain 'A' and resid 971 through 973' Processing helix chain 'A' and resid 974 through 979 Processing helix chain 'A' and resid 1025 through 1049 removed outlier: 4.149A pdb=" N THR A1030 " --> pdb=" O GLY A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1103 through 1125 removed outlier: 3.717A pdb=" N ASP A1109 " --> pdb=" O GLU A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1128 through 1133 Processing helix chain 'A' and resid 1140 through 1157 removed outlier: 3.930A pdb=" N LYS A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1166 removed outlier: 3.845A pdb=" N ILE A1165 " --> pdb=" O TRP A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1181 Processing helix chain 'A' and resid 1188 through 1197 removed outlier: 4.243A pdb=" N LYS A1194 " --> pdb=" O ILE A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1258 Processing helix chain 'A' and resid 1266 through 1271 Processing helix chain 'A' and resid 1294 through 1302 Processing helix chain 'A' and resid 1308 through 1313 Processing helix chain 'A' and resid 1313 through 1318 Processing helix chain 'A' and resid 1343 through 1348 Processing helix chain 'A' and resid 1349 through 1360 Processing helix chain 'A' and resid 1368 through 1380 removed outlier: 3.938A pdb=" N LEU A1372 " --> pdb=" O HIS A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1426 Processing helix chain 'A' and resid 1448 through 1477 removed outlier: 4.131A pdb=" N PHE A1454 " --> pdb=" O SER A1450 " (cutoff:3.500A) Processing helix chain 'A' and resid 1501 through 1530 removed outlier: 4.573A pdb=" N LYS A1507 " --> pdb=" O ARG A1503 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TYR A1508 " --> pdb=" O LYS A1504 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS A1521 " --> pdb=" O GLN A1517 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR A1524 " --> pdb=" O ASP A1520 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A1525 " --> pdb=" O LYS A1521 " (cutoff:3.500A) Processing helix chain 'A' and resid 1534 through 1541 removed outlier: 4.396A pdb=" N GLU A1541 " --> pdb=" O ASP A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1543 through 1547 removed outlier: 3.715A pdb=" N ILE A1547 " --> pdb=" O PRO A1544 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1555 Processing helix chain 'A' and resid 1558 through 1565 Processing helix chain 'A' and resid 1567 through 1574 removed outlier: 4.529A pdb=" N SER A1572 " --> pdb=" O ASP A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1630 Processing helix chain 'A' and resid 1635 through 1643 removed outlier: 3.877A pdb=" N ILE A1639 " --> pdb=" O GLU A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1674 removed outlier: 3.559A pdb=" N GLU A1656 " --> pdb=" O GLU A1652 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1703 Processing helix chain 'A' and resid 1712 through 1725 Processing helix chain 'A' and resid 1730 through 1743 Processing helix chain 'A' and resid 1755 through 1776 Processing helix chain 'A' and resid 1793 through 1821 Processing helix chain 'A' and resid 1827 through 1831 Processing helix chain 'A' and resid 1837 through 1867 Proline residue: A1851 - end of helix removed outlier: 3.788A pdb=" N ILE A1854 " --> pdb=" O ASN A1850 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A1865 " --> pdb=" O ASN A1861 " (cutoff:3.500A) Processing helix chain 'A' and resid 1887 through 1896 Processing helix chain 'A' and resid 1923 through 1927 removed outlier: 4.054A pdb=" N LEU A1926 " --> pdb=" O ASN A1923 " (cutoff:3.500A) Processing helix chain 'A' and resid 1941 through 1948 removed outlier: 3.661A pdb=" N GLU A1945 " --> pdb=" O ASP A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1956 Processing helix chain 'A' and resid 1957 through 1985 removed outlier: 3.912A pdb=" N ASN A1978 " --> pdb=" O ASN A1974 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A1981 " --> pdb=" O ASP A1977 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'B' and resid 77 through 79 removed outlier: 5.222A pdb=" N TRP B 66 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ARG B 57 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASN B 131 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79 removed outlier: 5.222A pdb=" N TRP B 66 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ARG B 57 " --> pdb=" O TRP B 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 149 through 153 removed outlier: 3.866A pdb=" N GLY B 168 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 169 " --> pdb=" O SER B 209 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 210 " --> pdb=" O HIS B 193 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 153 removed outlier: 3.866A pdb=" N GLY B 168 " --> pdb=" O LEU B 153 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS B 169 " --> pdb=" O SER B 209 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 180 through 183 removed outlier: 3.612A pdb=" N THR B 180 " --> pdb=" O ASN B 228 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR B 223 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 23 through 26 removed outlier: 4.407A pdb=" N PHE C 90 " --> pdb=" O CYS C 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 31 through 32 Processing sheet with id=AA9, first strand: chain 'C' and resid 72 through 73 removed outlier: 6.497A pdb=" N TRP C 54 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR C 68 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU C 52 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 72 through 73 removed outlier: 6.497A pdb=" N TRP C 54 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N TYR C 68 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU C 52 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 151 through 158 removed outlier: 4.673A pdb=" N TYR C 192 " --> pdb=" O ASN C 157 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 163 through 169 Processing sheet with id=AB4, first strand: chain 'A' and resid 500 through 501 Processing sheet with id=AB5, first strand: chain 'A' and resid 569 through 570 Processing sheet with id=AB6, first strand: chain 'A' and resid 854 through 856 removed outlier: 7.711A pdb=" N ALA A 855 " --> pdb=" O SER A 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 923 through 925 708 hydrogen bonds defined for protein. 1980 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: 3.32 Time building geometry restraints manager: 1.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3688 1.33 - 1.45: 4515 1.45 - 1.57: 10385 1.57 - 1.69: 1 1.69 - 1.81: 134 Bond restraints: 18723 Sorted by residual: bond pdb=" CA SER A 564 " pdb=" CB SER A 564 " ideal model delta sigma weight residual 1.530 1.456 0.074 1.69e-02 3.50e+03 1.91e+01 bond pdb=" C TYR A 632 " pdb=" N PRO A 633 " ideal model delta sigma weight residual 1.335 1.368 -0.033 8.70e-03 1.32e+04 1.42e+01 bond pdb=" CA LYS A1203 " pdb=" C LYS A1203 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.34e-02 5.57e+03 1.40e+01 bond pdb=" CA SER A 700 " pdb=" CB SER A 700 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.55e-02 4.16e+03 1.21e+01 bond pdb=" CA SER A 703 " pdb=" CB SER A 703 " ideal model delta sigma weight residual 1.531 1.477 0.055 1.58e-02 4.01e+03 1.19e+01 ... (remaining 18718 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 24810 3.36 - 6.72: 381 6.72 - 10.07: 31 10.07 - 13.43: 4 13.43 - 16.79: 2 Bond angle restraints: 25228 Sorted by residual: angle pdb=" N LYS A1203 " pdb=" CA LYS A1203 " pdb=" C LYS A1203 " ideal model delta sigma weight residual 110.80 127.59 -16.79 2.13e+00 2.20e-01 6.21e+01 angle pdb=" C LYS A 562 " pdb=" CA LYS A 562 " pdb=" CB LYS A 562 " ideal model delta sigma weight residual 110.42 95.99 14.43 1.99e+00 2.53e-01 5.26e+01 angle pdb=" C THR A 694 " pdb=" CA THR A 694 " pdb=" CB THR A 694 " ideal model delta sigma weight residual 115.89 106.54 9.35 1.32e+00 5.74e-01 5.01e+01 angle pdb=" N ILE A 7 " pdb=" CA ILE A 7 " pdb=" C ILE A 7 " ideal model delta sigma weight residual 113.20 106.56 6.64 9.60e-01 1.09e+00 4.78e+01 angle pdb=" C TYR A 701 " pdb=" CA TYR A 701 " pdb=" CB TYR A 701 " ideal model delta sigma weight residual 109.84 119.97 -10.13 1.50e+00 4.44e-01 4.56e+01 ... (remaining 25223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.57: 10771 25.57 - 51.13: 553 51.13 - 76.70: 61 76.70 - 102.26: 18 102.26 - 127.83: 1 Dihedral angle restraints: 11404 sinusoidal: 4716 harmonic: 6688 Sorted by residual: dihedral pdb=" CA CYS A1202 " pdb=" C CYS A1202 " pdb=" N LYS A1203 " pdb=" CA LYS A1203 " ideal model delta harmonic sigma weight residual 180.00 52.17 127.83 0 5.00e+00 4.00e-02 6.54e+02 dihedral pdb=" CA ASP A 698 " pdb=" C ASP A 698 " pdb=" N THR A 699 " pdb=" CA THR A 699 " ideal model delta harmonic sigma weight residual 180.00 93.79 86.21 0 5.00e+00 4.00e-02 2.97e+02 dihedral pdb=" CA LEU A 236 " pdb=" C LEU A 236 " pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta harmonic sigma weight residual 180.00 -120.77 -59.23 0 5.00e+00 4.00e-02 1.40e+02 ... (remaining 11401 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2236 0.074 - 0.148: 356 0.148 - 0.221: 43 0.221 - 0.295: 4 0.295 - 0.369: 5 Chirality restraints: 2644 Sorted by residual: chirality pdb=" CB ILE A 118 " pdb=" CA ILE A 118 " pdb=" CG1 ILE A 118 " pdb=" CG2 ILE A 118 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.40e+00 chirality pdb=" CA LYS A1203 " pdb=" N LYS A1203 " pdb=" C LYS A1203 " pdb=" CB LYS A1203 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB VAL A 945 " pdb=" CA VAL A 945 " pdb=" CG1 VAL A 945 " pdb=" CG2 VAL A 945 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 2641 not shown) Planarity restraints: 3273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 632 " 0.099 5.00e-02 4.00e+02 1.51e-01 3.63e+01 pdb=" N PRO A 633 " -0.261 5.00e-02 4.00e+02 pdb=" CA PRO A 633 " 0.083 5.00e-02 4.00e+02 pdb=" CD PRO A 633 " 0.079 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 951 " 0.076 5.00e-02 4.00e+02 1.15e-01 2.13e+01 pdb=" N PRO A 952 " -0.199 5.00e-02 4.00e+02 pdb=" CA PRO A 952 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 952 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A1822 " -0.064 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A1823 " 0.166 5.00e-02 4.00e+02 pdb=" CA PRO A1823 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A1823 " -0.052 5.00e-02 4.00e+02 ... (remaining 3270 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.67: 3 1.67 - 2.48: 215 2.48 - 3.29: 23048 3.29 - 4.09: 48917 4.09 - 4.90: 86547 Warning: very small nonbonded interaction distances. Nonbonded interactions: 158730 Sorted by model distance: nonbonded pdb=" NZ LYS A 690 " pdb=" CE LYS A 691 " model vdw 0.865 3.520 nonbonded pdb=" NZ LYS A 690 " pdb=" CD LYS A 691 " model vdw 1.321 3.520 nonbonded pdb=" CE LYS A 690 " pdb=" CE LYS A 691 " model vdw 1.539 3.840 nonbonded pdb=" NZ LYS A 690 " pdb=" NZ LYS A 691 " model vdw 1.982 3.200 nonbonded pdb=" OG1 THR A 872 " pdb=" O GLU A 874 " model vdw 2.019 3.040 ... (remaining 158725 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 individual isotropic 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: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 16.180 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.007 0.079 18727 Z= 0.332 Angle : 1.033 16.790 25236 Z= 0.609 Chirality : 0.056 0.369 2644 Planarity : 0.006 0.151 3273 Dihedral : 15.278 127.830 7100 Min Nonbonded Distance : 0.865 Molprobity Statistics. All-atom Clashscore : 31.24 Ramachandran Plot: Outliers : 1.14 % Allowed : 14.96 % Favored : 83.89 % Rotamer: Outliers : 1.37 % Allowed : 1.08 % Favored : 97.55 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 2.78 % Twisted General : 1.36 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.16), residues: 2272 helix: -0.96 (0.17), residues: 835 sheet: -0.49 (0.37), residues: 208 loop : -3.22 (0.16), residues: 1229 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 43 TYR 0.045 0.002 TYR A 701 PHE 0.039 0.003 PHE B 46 TRP 0.050 0.002 TRP A 223 HIS 0.010 0.002 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00676 (18723) covalent geometry : angle 1.03342 (25228) SS BOND : bond 0.00547 ( 4) SS BOND : angle 1.01449 ( 8) hydrogen bonds : bond 0.15078 ( 679) hydrogen bonds : angle 7.87736 ( 1980) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8457 (t0) cc_final: 0.8171 (t0) REVERT: B 118 ASP cc_start: 0.7893 (m-30) cc_final: 0.7664 (m-30) REVERT: C 36 ASP cc_start: 0.8666 (m-30) cc_final: 0.8036 (m-30) REVERT: C 186 ASP cc_start: 0.8673 (t70) cc_final: 0.8334 (t0) REVERT: A 7 ILE cc_start: 0.3728 (OUTLIER) cc_final: 0.3288 (pp) REVERT: A 198 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: A 1634 TYR cc_start: 0.8705 (m-80) cc_final: 0.8122 (m-80) REVERT: A 1980 ILE cc_start: 0.8044 (OUTLIER) cc_final: 0.7801 (tp) outliers start: 28 outliers final: 7 residues processed: 183 average time/residue: 0.6046 time to fit residues: 123.8904 Evaluate side-chains 128 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 556 LYS Chi-restraints excluded: chain A residue 683 LYS Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain A residue 691 LYS Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 699 THR Chi-restraints excluded: chain A residue 700 SER Chi-restraints excluded: chain A residue 1980 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.0980 chunk 227 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0970 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.5980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 GLN C 46 GLN C 156 ASN C 157 ASN A 233 ASN ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 524 GLN A 528 GLN A 867 ASN A1008 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1125 GLN ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1373 GLN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1522 GLN A1659 GLN ** A1861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.132618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.089666 restraints weight = 50599.348| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 3.94 r_work: 0.3178 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18727 Z= 0.176 Angle : 0.857 10.776 25236 Z= 0.462 Chirality : 0.049 0.374 2644 Planarity : 0.006 0.105 3273 Dihedral : 9.214 96.825 2506 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.56 % Favored : 86.05 % Rotamer: Outliers : 1.67 % Allowed : 8.73 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 1.22 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.17), residues: 2272 helix: -0.49 (0.18), residues: 810 sheet: -0.24 (0.36), residues: 222 loop : -3.15 (0.16), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1417 TYR 0.032 0.002 TYR A1314 PHE 0.022 0.002 PHE A 276 TRP 0.019 0.002 TRP A 223 HIS 0.008 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00368 (18723) covalent geometry : angle 0.85744 (25228) SS BOND : bond 0.00485 ( 4) SS BOND : angle 0.64034 ( 8) hydrogen bonds : bond 0.05377 ( 679) hydrogen bonds : angle 7.07790 ( 1980) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 ASP cc_start: 0.7951 (t0) cc_final: 0.7588 (t0) REVERT: B 92 ASP cc_start: 0.8432 (t0) cc_final: 0.7884 (t0) REVERT: B 108 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8840 (tm-30) REVERT: B 151 PHE cc_start: 0.7698 (m-10) cc_final: 0.7409 (m-80) REVERT: C 36 ASP cc_start: 0.8745 (m-30) cc_final: 0.8176 (m-30) REVERT: C 157 ASN cc_start: 0.9024 (m-40) cc_final: 0.8768 (m110) REVERT: C 161 ARG cc_start: 0.9230 (tmt90) cc_final: 0.9012 (tpt-90) REVERT: C 186 ASP cc_start: 0.8599 (t70) cc_final: 0.8088 (t0) REVERT: A 1 MET cc_start: 0.4889 (OUTLIER) cc_final: 0.4647 (ppp) REVERT: A 7 ILE cc_start: 0.3815 (OUTLIER) cc_final: 0.3324 (pp) REVERT: A 141 GLN cc_start: 0.8907 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 198 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7340 (pm20) REVERT: A 567 GLU cc_start: 0.8273 (pm20) cc_final: 0.7914 (mp0) REVERT: A 984 GLN cc_start: 0.6770 (mp10) cc_final: 0.6421 (mp10) REVERT: A 1590 LYS cc_start: 0.5141 (tmtt) cc_final: 0.4508 (tptt) REVERT: A 1597 TYR cc_start: 0.8688 (m-10) cc_final: 0.8426 (m-80) REVERT: A 1764 MET cc_start: 0.9464 (mmt) cc_final: 0.9053 (mtt) REVERT: A 1866 ILE cc_start: 0.8982 (tp) cc_final: 0.8745 (tp) REVERT: A 1897 HIS cc_start: 0.8205 (t70) cc_final: 0.7961 (t70) REVERT: A 1943 MET cc_start: 0.9014 (mmm) cc_final: 0.8811 (mmm) outliers start: 34 outliers final: 9 residues processed: 170 average time/residue: 0.6319 time to fit residues: 121.1655 Evaluate side-chains 126 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 867 ASN Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 1097 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 157 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 219 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 202 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 184 ASN B 200 GLN C 229 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 345 ASN A 353 GLN ** A 867 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1356 ASN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1749 ASN A1765 GLN ** A1861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1972 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.130578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.086896 restraints weight = 51069.144| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.99 r_work: 0.3116 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18727 Z= 0.214 Angle : 0.810 9.899 25236 Z= 0.437 Chirality : 0.048 0.292 2644 Planarity : 0.005 0.096 3273 Dihedral : 8.511 91.074 2486 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.34 % Favored : 86.27 % Rotamer: Outliers : 1.57 % Allowed : 12.65 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 1.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.17), residues: 2272 helix: -0.31 (0.18), residues: 822 sheet: -0.18 (0.36), residues: 214 loop : -3.08 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 43 TYR 0.027 0.002 TYR A1314 PHE 0.022 0.002 PHE A1121 TRP 0.018 0.001 TRP A 283 HIS 0.010 0.002 HIS A1957 Details of bonding type rmsd covalent geometry : bond 0.00467 (18723) covalent geometry : angle 0.80956 (25228) SS BOND : bond 0.00529 ( 4) SS BOND : angle 0.68655 ( 8) hydrogen bonds : bond 0.05083 ( 679) hydrogen bonds : angle 6.79868 ( 1980) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8409 (t0) cc_final: 0.7822 (t0) REVERT: B 108 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8813 (tm-30) REVERT: B 151 PHE cc_start: 0.7924 (m-10) cc_final: 0.7656 (m-80) REVERT: C 36 ASP cc_start: 0.8738 (m-30) cc_final: 0.8255 (m-30) REVERT: C 157 ASN cc_start: 0.9099 (m-40) cc_final: 0.8835 (m110) REVERT: C 186 ASP cc_start: 0.8596 (t70) cc_final: 0.8102 (t70) REVERT: A 7 ILE cc_start: 0.4037 (OUTLIER) cc_final: 0.3548 (pp) REVERT: A 141 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8679 (tm-30) REVERT: A 198 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.7334 (pm20) REVERT: A 567 GLU cc_start: 0.8404 (pm20) cc_final: 0.8010 (mp0) REVERT: A 850 LYS cc_start: 0.8281 (ptpp) cc_final: 0.8041 (pttt) REVERT: A 890 ILE cc_start: 0.8470 (tt) cc_final: 0.8144 (tt) REVERT: A 1119 ASN cc_start: 0.8760 (m-40) cc_final: 0.8507 (p0) REVERT: A 1298 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.8632 (pp20) REVERT: A 1527 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8434 (mp0) REVERT: A 1597 TYR cc_start: 0.8812 (m-10) cc_final: 0.8541 (m-80) REVERT: A 1711 GLU cc_start: 0.8542 (tt0) cc_final: 0.8262 (tp30) REVERT: A 1764 MET cc_start: 0.9447 (OUTLIER) cc_final: 0.9123 (mtt) REVERT: A 1866 ILE cc_start: 0.8976 (tp) cc_final: 0.8679 (tp) outliers start: 32 outliers final: 12 residues processed: 154 average time/residue: 0.5813 time to fit residues: 102.3980 Evaluate side-chains 130 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1764 MET Chi-restraints excluded: chain A residue 1905 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 132 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 65 optimal weight: 0.0770 chunk 72 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 88 optimal weight: 4.9990 chunk 218 optimal weight: 0.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN A1092 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** 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 = 0.4243 r_free = 0.4243 target = 0.131638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.088039 restraints weight = 50780.125| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.95 r_work: 0.3192 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18727 Z= 0.178 Angle : 0.774 10.919 25236 Z= 0.415 Chirality : 0.047 0.281 2644 Planarity : 0.005 0.096 3273 Dihedral : 8.187 84.117 2486 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.20 % Favored : 86.40 % Rotamer: Outliers : 2.55 % Allowed : 14.12 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.95 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.17), residues: 2272 helix: -0.23 (0.18), residues: 833 sheet: -0.08 (0.36), residues: 222 loop : -3.00 (0.16), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 161 TYR 0.025 0.002 TYR A1314 PHE 0.021 0.002 PHE B 195 TRP 0.017 0.001 TRP A 223 HIS 0.007 0.002 HIS A1345 Details of bonding type rmsd covalent geometry : bond 0.00382 (18723) covalent geometry : angle 0.77401 (25228) SS BOND : bond 0.00413 ( 4) SS BOND : angle 0.69007 ( 8) hydrogen bonds : bond 0.04653 ( 679) hydrogen bonds : angle 6.48856 ( 1980) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8557 (t0) cc_final: 0.7996 (t0) REVERT: B 108 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8870 (tm-30) REVERT: B 151 PHE cc_start: 0.8077 (m-10) cc_final: 0.7819 (m-80) REVERT: C 36 ASP cc_start: 0.8806 (m-30) cc_final: 0.8328 (m-30) REVERT: C 142 GLU cc_start: 0.8504 (pp20) cc_final: 0.8287 (pp20) REVERT: C 144 LEU cc_start: 0.9358 (pp) cc_final: 0.9149 (mm) REVERT: C 157 ASN cc_start: 0.9144 (m-40) cc_final: 0.8775 (m-40) REVERT: C 186 ASP cc_start: 0.8614 (t70) cc_final: 0.8130 (t70) REVERT: A 7 ILE cc_start: 0.4161 (OUTLIER) cc_final: 0.3673 (pp) REVERT: A 141 GLN cc_start: 0.8847 (tm-30) cc_final: 0.8574 (tm-30) REVERT: A 198 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.6882 (pm20) REVERT: A 233 ASN cc_start: 0.7457 (t0) cc_final: 0.7216 (t0) REVERT: A 577 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8963 (m) REVERT: A 1109 ASP cc_start: 0.8890 (OUTLIER) cc_final: 0.8589 (p0) REVERT: A 1119 ASN cc_start: 0.8777 (m-40) cc_final: 0.8441 (p0) REVERT: A 1252 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.5967 (tptp) REVERT: A 1298 GLU cc_start: 0.9403 (OUTLIER) cc_final: 0.8739 (pp20) REVERT: A 1357 MET cc_start: 0.9243 (tmm) cc_final: 0.8813 (ppp) REVERT: A 1527 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8453 (mp0) REVERT: A 1711 GLU cc_start: 0.8526 (tt0) cc_final: 0.8239 (tp30) REVERT: A 1764 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.9144 (mtt) REVERT: A 1822 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.6114 (m-30) REVERT: A 1866 ILE cc_start: 0.8929 (tp) cc_final: 0.8566 (tp) REVERT: A 1945 GLU cc_start: 0.8874 (mp0) cc_final: 0.8663 (mp0) outliers start: 52 outliers final: 15 residues processed: 176 average time/residue: 0.5603 time to fit residues: 112.2510 Evaluate side-chains 138 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 509 ASN Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 867 ASN Chi-restraints excluded: chain A residue 877 CYS Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1252 LYS Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1731 ASP Chi-restraints excluded: chain A residue 1764 MET Chi-restraints excluded: chain A residue 1822 ASP Chi-restraints excluded: chain A residue 1905 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 21 optimal weight: 1.9990 chunk 197 optimal weight: 1.9990 chunk 214 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 151 optimal weight: 0.0370 chunk 167 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 150 optimal weight: 0.0770 chunk 158 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 ASN C 229 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 HIS A 867 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.132693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089222 restraints weight = 50347.803| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.98 r_work: 0.3175 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 18727 Z= 0.153 Angle : 0.765 10.706 25236 Z= 0.409 Chirality : 0.046 0.285 2644 Planarity : 0.005 0.086 3273 Dihedral : 7.962 81.711 2486 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.34 % Favored : 86.40 % Rotamer: Outliers : 2.40 % Allowed : 15.84 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.82 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.17), residues: 2272 helix: -0.12 (0.18), residues: 835 sheet: 0.03 (0.37), residues: 212 loop : -2.89 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 43 TYR 0.023 0.002 TYR A1314 PHE 0.023 0.002 PHE A1121 TRP 0.021 0.001 TRP A 223 HIS 0.007 0.001 HIS A 845 Details of bonding type rmsd covalent geometry : bond 0.00326 (18723) covalent geometry : angle 0.76469 (25228) SS BOND : bond 0.00368 ( 4) SS BOND : angle 0.54116 ( 8) hydrogen bonds : bond 0.04420 ( 679) hydrogen bonds : angle 6.29561 ( 1980) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8496 (t0) cc_final: 0.7931 (t0) REVERT: B 108 GLU cc_start: 0.9239 (tm-30) cc_final: 0.8911 (tm-30) REVERT: C 36 ASP cc_start: 0.8783 (m-30) cc_final: 0.8317 (m-30) REVERT: C 144 LEU cc_start: 0.9384 (pp) cc_final: 0.9169 (mp) REVERT: C 157 ASN cc_start: 0.9117 (m-40) cc_final: 0.8788 (m-40) REVERT: C 186 ASP cc_start: 0.8591 (t70) cc_final: 0.8078 (t70) REVERT: A 7 ILE cc_start: 0.4042 (OUTLIER) cc_final: 0.3571 (pp) REVERT: A 141 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8697 (tm-30) REVERT: A 198 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.6867 (pm20) REVERT: A 577 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8845 (m) REVERT: A 1109 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8553 (p0) REVERT: A 1119 ASN cc_start: 0.8746 (m-40) cc_final: 0.8398 (p0) REVERT: A 1298 GLU cc_start: 0.9422 (OUTLIER) cc_final: 0.8807 (pp20) REVERT: A 1343 PHE cc_start: 0.9314 (m-80) cc_final: 0.8923 (m-80) REVERT: A 1357 MET cc_start: 0.9269 (tmm) cc_final: 0.8889 (ppp) REVERT: A 1527 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8422 (mp0) REVERT: A 1681 ASP cc_start: 0.8880 (m-30) cc_final: 0.8660 (t70) REVERT: A 1711 GLU cc_start: 0.8533 (tt0) cc_final: 0.8242 (tp30) REVERT: A 1764 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.9147 (mtt) REVERT: A 1866 ILE cc_start: 0.8884 (tp) cc_final: 0.8509 (tp) outliers start: 49 outliers final: 16 residues processed: 172 average time/residue: 0.5902 time to fit residues: 115.9915 Evaluate side-chains 141 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 867 ASN Chi-restraints excluded: chain A residue 877 CYS Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1384 THR Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1764 MET Chi-restraints excluded: chain A residue 1905 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 0 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 173 optimal weight: 0.7980 chunk 184 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN A 867 ASN ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1400 ASN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** 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 = 0.4244 r_free = 0.4244 target = 0.132199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.088664 restraints weight = 50081.288| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.94 r_work: 0.3166 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18727 Z= 0.168 Angle : 0.761 9.839 25236 Z= 0.406 Chirality : 0.047 0.289 2644 Planarity : 0.005 0.086 3273 Dihedral : 7.793 80.262 2486 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.42 % Favored : 86.31 % Rotamer: Outliers : 2.40 % Allowed : 16.72 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.82 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.17), residues: 2272 helix: -0.05 (0.18), residues: 836 sheet: 0.06 (0.36), residues: 221 loop : -2.78 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 43 TYR 0.024 0.002 TYR A1044 PHE 0.027 0.002 PHE A1121 TRP 0.022 0.001 TRP A 223 HIS 0.006 0.001 HIS A 888 Details of bonding type rmsd covalent geometry : bond 0.00363 (18723) covalent geometry : angle 0.76090 (25228) SS BOND : bond 0.00336 ( 4) SS BOND : angle 0.67178 ( 8) hydrogen bonds : bond 0.04385 ( 679) hydrogen bonds : angle 6.14997 ( 1980) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 130 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8428 (t0) cc_final: 0.7865 (t0) REVERT: B 108 GLU cc_start: 0.9289 (tm-30) cc_final: 0.8940 (tm-30) REVERT: B 151 PHE cc_start: 0.7660 (m-80) cc_final: 0.7283 (m-80) REVERT: C 36 ASP cc_start: 0.8724 (m-30) cc_final: 0.8255 (m-30) REVERT: C 142 GLU cc_start: 0.8335 (pp20) cc_final: 0.8097 (pp20) REVERT: C 157 ASN cc_start: 0.9138 (m-40) cc_final: 0.8800 (m-40) REVERT: C 186 ASP cc_start: 0.8590 (t70) cc_final: 0.8077 (t70) REVERT: A 7 ILE cc_start: 0.4107 (OUTLIER) cc_final: 0.3605 (pp) REVERT: A 141 GLN cc_start: 0.8881 (tm-30) cc_final: 0.8641 (tm-30) REVERT: A 198 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8187 (pp30) REVERT: A 233 ASN cc_start: 0.7265 (t0) cc_final: 0.6961 (t0) REVERT: A 577 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8832 (m) REVERT: A 1048 GLN cc_start: 0.8789 (tp40) cc_final: 0.8342 (mp10) REVERT: A 1109 ASP cc_start: 0.8955 (OUTLIER) cc_final: 0.8578 (p0) REVERT: A 1119 ASN cc_start: 0.8745 (m-40) cc_final: 0.8369 (p0) REVERT: A 1298 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.9160 (mp0) REVERT: A 1343 PHE cc_start: 0.9409 (m-80) cc_final: 0.9089 (m-80) REVERT: A 1527 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8484 (mp0) REVERT: A 1681 ASP cc_start: 0.8914 (m-30) cc_final: 0.8688 (t70) REVERT: A 1711 GLU cc_start: 0.8568 (tt0) cc_final: 0.8193 (tp30) REVERT: A 1764 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.9124 (mtt) REVERT: A 1866 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8476 (tp) REVERT: A 1985 LEU cc_start: 0.7181 (OUTLIER) cc_final: 0.6882 (pp) outliers start: 49 outliers final: 20 residues processed: 172 average time/residue: 0.5892 time to fit residues: 115.7598 Evaluate side-chains 146 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 696 GLU Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 877 CYS Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 942 ASP Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1384 THR Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1764 MET Chi-restraints excluded: chain A residue 1866 ILE Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1985 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.8980 chunk 108 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 191 optimal weight: 1.9990 chunk 186 optimal weight: 0.9990 chunk 227 optimal weight: 1.9990 chunk 67 optimal weight: 0.0670 chunk 30 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 867 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** 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 = 0.4261 r_free = 0.4261 target = 0.133257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.089834 restraints weight = 50383.052| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.98 r_work: 0.3187 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18727 Z= 0.149 Angle : 0.764 9.612 25236 Z= 0.406 Chirality : 0.047 0.320 2644 Planarity : 0.005 0.082 3273 Dihedral : 7.608 78.114 2486 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.90 % Favored : 86.84 % Rotamer: Outliers : 2.35 % Allowed : 17.61 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.63 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.17), residues: 2272 helix: 0.05 (0.19), residues: 832 sheet: 0.18 (0.37), residues: 215 loop : -2.73 (0.16), residues: 1225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 102 TYR 0.023 0.001 TYR B 79 PHE 0.025 0.002 PHE A1121 TRP 0.030 0.001 TRP A 223 HIS 0.006 0.001 HIS A 725 Details of bonding type rmsd covalent geometry : bond 0.00318 (18723) covalent geometry : angle 0.76399 (25228) SS BOND : bond 0.00496 ( 4) SS BOND : angle 0.74713 ( 8) hydrogen bonds : bond 0.04210 ( 679) hydrogen bonds : angle 5.96892 ( 1980) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 138 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8387 (t0) cc_final: 0.7817 (t0) REVERT: B 108 GLU cc_start: 0.9287 (tm-30) cc_final: 0.8925 (tm-30) REVERT: B 151 PHE cc_start: 0.7543 (m-80) cc_final: 0.7208 (m-80) REVERT: C 36 ASP cc_start: 0.8750 (m-30) cc_final: 0.8276 (m-30) REVERT: C 153 CYS cc_start: 0.7948 (t) cc_final: 0.7651 (t) REVERT: C 157 ASN cc_start: 0.9107 (m-40) cc_final: 0.8757 (m-40) REVERT: C 186 ASP cc_start: 0.8597 (t70) cc_final: 0.8084 (t70) REVERT: A 7 ILE cc_start: 0.4039 (OUTLIER) cc_final: 0.3563 (pp) REVERT: A 198 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8237 (pp30) REVERT: A 234 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7035 (m-30) REVERT: A 504 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8372 (mm-30) REVERT: A 509 ASN cc_start: 0.7632 (p0) cc_final: 0.7360 (p0) REVERT: A 577 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8789 (m) REVERT: A 1048 GLN cc_start: 0.8837 (tp40) cc_final: 0.8441 (mp10) REVERT: A 1109 ASP cc_start: 0.8941 (OUTLIER) cc_final: 0.8583 (p0) REVERT: A 1119 ASN cc_start: 0.8703 (m-40) cc_final: 0.8292 (p0) REVERT: A 1298 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.9136 (mp0) REVERT: A 1357 MET cc_start: 0.9221 (tmm) cc_final: 0.8974 (ppp) REVERT: A 1412 MET cc_start: 0.9007 (tpt) cc_final: 0.8641 (mpp) REVERT: A 1527 GLU cc_start: 0.8849 (mm-30) cc_final: 0.8561 (mp0) REVERT: A 1681 ASP cc_start: 0.8886 (m-30) cc_final: 0.8666 (t70) REVERT: A 1711 GLU cc_start: 0.8533 (tt0) cc_final: 0.8142 (tp30) REVERT: A 1764 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.9136 (mtt) REVERT: A 1866 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8452 (tp) REVERT: A 1973 LEU cc_start: 0.9184 (tp) cc_final: 0.8970 (tm) REVERT: A 1985 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6975 (pp) outliers start: 48 outliers final: 18 residues processed: 180 average time/residue: 0.5936 time to fit residues: 121.9806 Evaluate side-chains 146 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 279 TRP Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 867 ASN Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1384 THR Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1764 MET Chi-restraints excluded: chain A residue 1866 ILE Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1985 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 182 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 192 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 142 optimal weight: 0.4980 chunk 216 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN A 523 ASN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** 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 = 0.4238 r_free = 0.4238 target = 0.131720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.087905 restraints weight = 50090.814| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 3.99 r_work: 0.3148 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18727 Z= 0.199 Angle : 0.795 12.741 25236 Z= 0.419 Chirality : 0.048 0.370 2644 Planarity : 0.005 0.083 3273 Dihedral : 7.340 54.038 2483 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.76 % Favored : 86.97 % Rotamer: Outliers : 1.86 % Allowed : 18.93 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.63 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.17), residues: 2272 helix: 0.05 (0.19), residues: 832 sheet: 0.16 (0.36), residues: 224 loop : -2.73 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 43 TYR 0.025 0.002 TYR A1044 PHE 0.026 0.002 PHE A1121 TRP 0.038 0.001 TRP A 223 HIS 0.006 0.001 HIS A1957 Details of bonding type rmsd covalent geometry : bond 0.00441 (18723) covalent geometry : angle 0.79459 (25228) SS BOND : bond 0.00385 ( 4) SS BOND : angle 0.91817 ( 8) hydrogen bonds : bond 0.04357 ( 679) hydrogen bonds : angle 5.93419 ( 1980) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8406 (t0) cc_final: 0.7823 (t0) REVERT: B 108 GLU cc_start: 0.9300 (tm-30) cc_final: 0.8934 (tm-30) REVERT: C 36 ASP cc_start: 0.8746 (m-30) cc_final: 0.8269 (m-30) REVERT: C 142 GLU cc_start: 0.8661 (pp20) cc_final: 0.8448 (pp20) REVERT: C 144 LEU cc_start: 0.9366 (pp) cc_final: 0.9164 (mm) REVERT: C 153 CYS cc_start: 0.7869 (t) cc_final: 0.7541 (t) REVERT: C 157 ASN cc_start: 0.9124 (m-40) cc_final: 0.8755 (m-40) REVERT: C 186 ASP cc_start: 0.8594 (t70) cc_final: 0.8068 (t70) REVERT: A 7 ILE cc_start: 0.4097 (OUTLIER) cc_final: 0.3568 (pp) REVERT: A 141 GLN cc_start: 0.8748 (tm-30) cc_final: 0.8522 (tm-30) REVERT: A 198 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8282 (pp30) REVERT: A 233 ASN cc_start: 0.7247 (t0) cc_final: 0.6865 (t0) REVERT: A 234 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7004 (m-30) REVERT: A 504 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8362 (mm-30) REVERT: A 577 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8922 (m) REVERT: A 697 GLN cc_start: 0.8720 (mm-40) cc_final: 0.8330 (mm-40) REVERT: A 1044 TYR cc_start: 0.8823 (t80) cc_final: 0.8541 (t80) REVERT: A 1048 GLN cc_start: 0.8847 (tp40) cc_final: 0.8302 (mp10) REVERT: A 1109 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8611 (p0) REVERT: A 1298 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.9171 (mp0) REVERT: A 1357 MET cc_start: 0.9229 (tmm) cc_final: 0.8994 (ppp) REVERT: A 1527 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8569 (mp0) REVERT: A 1681 ASP cc_start: 0.8910 (m-30) cc_final: 0.8694 (t70) REVERT: A 1711 GLU cc_start: 0.8560 (tt0) cc_final: 0.8228 (tp30) REVERT: A 1764 MET cc_start: 0.9410 (OUTLIER) cc_final: 0.9115 (mtt) REVERT: A 1866 ILE cc_start: 0.8917 (OUTLIER) cc_final: 0.8562 (tp) REVERT: A 1985 LEU cc_start: 0.7183 (OUTLIER) cc_final: 0.6869 (pp) outliers start: 38 outliers final: 18 residues processed: 155 average time/residue: 0.5876 time to fit residues: 103.6626 Evaluate side-chains 143 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 867 ASN Chi-restraints excluded: chain A residue 877 CYS Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1384 THR Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1764 MET Chi-restraints excluded: chain A residue 1866 ILE Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1985 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 134 optimal weight: 1.9990 chunk 127 optimal weight: 0.5980 chunk 213 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 59 optimal weight: 0.0570 chunk 83 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 ASN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** 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 = 0.4265 r_free = 0.4265 target = 0.133499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.090109 restraints weight = 50274.285| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 4.01 r_work: 0.3194 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18727 Z= 0.151 Angle : 0.778 12.408 25236 Z= 0.409 Chirality : 0.047 0.376 2644 Planarity : 0.005 0.099 3273 Dihedral : 7.245 51.930 2483 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.54 % Favored : 87.24 % Rotamer: Outliers : 1.72 % Allowed : 18.93 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.91 (0.17), residues: 2272 helix: 0.11 (0.18), residues: 841 sheet: 0.19 (0.37), residues: 212 loop : -2.69 (0.16), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 43 TYR 0.023 0.001 TYR A1044 PHE 0.024 0.002 PHE A1121 TRP 0.047 0.001 TRP A 223 HIS 0.017 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00324 (18723) covalent geometry : angle 0.77847 (25228) SS BOND : bond 0.00353 ( 4) SS BOND : angle 0.60169 ( 8) hydrogen bonds : bond 0.04109 ( 679) hydrogen bonds : angle 5.81773 ( 1980) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8415 (t0) cc_final: 0.7823 (t0) REVERT: B 108 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8945 (tm-30) REVERT: C 36 ASP cc_start: 0.8808 (m-30) cc_final: 0.8345 (m-30) REVERT: C 142 GLU cc_start: 0.8607 (pp20) cc_final: 0.8384 (pp20) REVERT: C 153 CYS cc_start: 0.7960 (t) cc_final: 0.7665 (t) REVERT: C 157 ASN cc_start: 0.9087 (m-40) cc_final: 0.8720 (m-40) REVERT: C 186 ASP cc_start: 0.8577 (t70) cc_final: 0.8074 (t70) REVERT: A 7 ILE cc_start: 0.4004 (OUTLIER) cc_final: 0.3502 (pp) REVERT: A 137 GLU cc_start: 0.9099 (tp30) cc_final: 0.8576 (pt0) REVERT: A 142 ASN cc_start: 0.9379 (OUTLIER) cc_final: 0.8747 (p0) REVERT: A 198 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8186 (pp30) REVERT: A 234 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7142 (m-30) REVERT: A 504 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8363 (mm-30) REVERT: A 577 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8810 (m) REVERT: A 690 LYS cc_start: 0.7855 (tptp) cc_final: 0.7524 (ttpp) REVERT: A 1298 GLU cc_start: 0.9443 (OUTLIER) cc_final: 0.9188 (mp0) REVERT: A 1343 PHE cc_start: 0.9308 (m-10) cc_final: 0.8916 (m-80) REVERT: A 1357 MET cc_start: 0.9243 (tmm) cc_final: 0.9019 (ppp) REVERT: A 1527 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8604 (mp0) REVERT: A 1620 GLU cc_start: 0.9100 (tp30) cc_final: 0.8636 (tp30) REVERT: A 1681 ASP cc_start: 0.8886 (m-30) cc_final: 0.8658 (t70) REVERT: A 1711 GLU cc_start: 0.8508 (tt0) cc_final: 0.8126 (tp30) REVERT: A 1764 MET cc_start: 0.9379 (mmt) cc_final: 0.9132 (mtt) REVERT: A 1866 ILE cc_start: 0.8847 (tp) cc_final: 0.8461 (tp) REVERT: A 1985 LEU cc_start: 0.7223 (OUTLIER) cc_final: 0.6913 (pp) outliers start: 35 outliers final: 19 residues processed: 157 average time/residue: 0.6054 time to fit residues: 108.6596 Evaluate side-chains 143 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 877 CYS Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1042 ILE Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1384 THR Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1985 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 220 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 chunk 46 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 233 ASN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1586 ASN ** A1957 HIS ** 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 = 0.4213 r_free = 0.4213 target = 0.130243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.086407 restraints weight = 50287.777| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 3.94 r_work: 0.3100 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 18727 Z= 0.264 Angle : 0.834 12.726 25236 Z= 0.439 Chirality : 0.049 0.389 2644 Planarity : 0.005 0.093 3273 Dihedral : 7.320 54.134 2483 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.34 % Favored : 86.44 % Rotamer: Outliers : 1.52 % Allowed : 19.42 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.63 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.17), residues: 2272 helix: 0.10 (0.19), residues: 831 sheet: 0.06 (0.37), residues: 221 loop : -2.77 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 161 TYR 0.022 0.002 TYR B 79 PHE 0.028 0.002 PHE A1121 TRP 0.056 0.002 TRP A 223 HIS 0.010 0.002 HIS A1957 Details of bonding type rmsd covalent geometry : bond 0.00591 (18723) covalent geometry : angle 0.83403 (25228) SS BOND : bond 0.00536 ( 4) SS BOND : angle 0.85142 ( 8) hydrogen bonds : bond 0.04607 ( 679) hydrogen bonds : angle 5.92632 ( 1980) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4544 Ramachandran restraints generated. 2272 Oldfield, 0 Emsley, 2272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 121 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8393 (t0) cc_final: 0.7825 (t0) REVERT: B 108 GLU cc_start: 0.9288 (tm-30) cc_final: 0.8870 (tm-30) REVERT: C 36 ASP cc_start: 0.8721 (m-30) cc_final: 0.8258 (m-30) REVERT: C 153 CYS cc_start: 0.8050 (t) cc_final: 0.7704 (t) REVERT: C 157 ASN cc_start: 0.9083 (m-40) cc_final: 0.8744 (m-40) REVERT: C 186 ASP cc_start: 0.8483 (t70) cc_final: 0.7959 (t70) REVERT: A 7 ILE cc_start: 0.3984 (OUTLIER) cc_final: 0.3486 (pp) REVERT: A 198 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8221 (pp30) REVERT: A 234 ASP cc_start: 0.7612 (OUTLIER) cc_final: 0.7038 (m-30) REVERT: A 236 LEU cc_start: 0.0469 (OUTLIER) cc_final: 0.0104 (mt) REVERT: A 504 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8368 (mm-30) REVERT: A 577 THR cc_start: 0.9300 (OUTLIER) cc_final: 0.8966 (m) REVERT: A 697 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8519 (mm-40) REVERT: A 1048 GLN cc_start: 0.8974 (tt0) cc_final: 0.8484 (tm-30) REVERT: A 1298 GLU cc_start: 0.9437 (OUTLIER) cc_final: 0.9177 (mp0) REVERT: A 1357 MET cc_start: 0.9270 (tmm) cc_final: 0.9054 (ppp) REVERT: A 1527 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8600 (mp0) REVERT: A 1711 GLU cc_start: 0.8559 (tt0) cc_final: 0.8352 (tt0) REVERT: A 1764 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.9098 (mtt) REVERT: A 1866 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8616 (tp) REVERT: A 1985 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6984 (pp) outliers start: 31 outliers final: 17 residues processed: 149 average time/residue: 0.5949 time to fit residues: 101.2281 Evaluate side-chains 138 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 112 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 272 TYR Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 877 CYS Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 949 VAL Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1203 LYS Chi-restraints excluded: chain A residue 1298 GLU Chi-restraints excluded: chain A residue 1363 VAL Chi-restraints excluded: chain A residue 1384 THR Chi-restraints excluded: chain A residue 1597 TYR Chi-restraints excluded: chain A residue 1764 MET Chi-restraints excluded: chain A residue 1866 ILE Chi-restraints excluded: chain A residue 1905 ILE Chi-restraints excluded: chain A residue 1985 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 217 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 97 optimal weight: 0.0170 chunk 100 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 110 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 229 ASN ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 ASN ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 867 ASN A1008 ASN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1957 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.132967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.089537 restraints weight = 50423.859| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 4.09 r_work: 0.3169 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18727 Z= 0.151 Angle : 0.790 13.362 25236 Z= 0.414 Chirality : 0.047 0.425 2644 Planarity : 0.005 0.092 3273 Dihedral : 7.202 52.477 2483 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.18 % Allowed : 12.37 % Favored : 87.46 % Rotamer: Outliers : 1.47 % Allowed : 19.86 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.63 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.17), residues: 2272 helix: 0.12 (0.19), residues: 838 sheet: 0.26 (0.39), residues: 202 loop : -2.71 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 161 TYR 0.024 0.001 TYR A1044 PHE 0.024 0.002 PHE A1121 TRP 0.060 0.001 TRP A 223 HIS 0.006 0.001 HIS A 845 Details of bonding type rmsd covalent geometry : bond 0.00330 (18723) covalent geometry : angle 0.78956 (25228) SS BOND : bond 0.00367 ( 4) SS BOND : angle 0.60952 ( 8) hydrogen bonds : bond 0.04171 ( 679) hydrogen bonds : angle 5.74741 ( 1980) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8010.22 seconds wall clock time: 137 minutes 49.49 seconds (8269.49 seconds total)