Starting phenix.real_space_refine on Mon Jun 16 11:39:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z12_14438/06_2025/7z12_14438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z12_14438/06_2025/7z12_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7z12_14438/06_2025/7z12_14438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z12_14438/06_2025/7z12_14438.map" model { file = "/net/cci-nas-00/data/ceres_data/7z12_14438/06_2025/7z12_14438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z12_14438/06_2025/7z12_14438.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.38, per 1000 atoms: 0.67 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: 4.77 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.08 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: 7.45 Time building geometry restraints manager: 5.65 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: 5.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 45.610 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.820 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.050 0.002 TRP A 223 HIS 0.010 0.002 HIS A 888 PHE 0.039 0.003 PHE B 46 TYR 0.045 0.002 TYR A 701 ARG 0.012 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.15078 ( 679) hydrogen bonds : angle 7.87736 ( 1980) SS BOND : bond 0.00547 ( 4) SS BOND : angle 1.01449 ( 8) covalent geometry : bond 0.00676 (18723) covalent geometry : angle 1.03342 (25228) *********************** 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 : 1.993 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: 0.8037 (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: 0.6667 (pm20) REVERT: A 1634 TYR cc_start: 0.8705 (m-80) cc_final: 0.8122 (m-80) outliers start: 28 outliers final: 7 residues processed: 183 average time/residue: 1.3797 time to fit residues: 284.9304 Evaluate side-chains 127 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 118 time to evaluate : 1.941 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 0.5980 chunk 172 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 chunk 92 optimal weight: 0.2980 chunk 178 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 133 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.131820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.088712 restraints weight = 50361.200| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 3.95 r_work: 0.3159 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18727 Z= 0.183 Angle : 0.853 10.539 25236 Z= 0.461 Chirality : 0.049 0.358 2644 Planarity : 0.006 0.106 3273 Dihedral : 9.227 93.861 2504 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.40 % Allowed : 13.73 % Favored : 85.87 % Rotamer: Outliers : 1.47 % Allowed : 9.12 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 1.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.17), residues: 2272 helix: -0.53 (0.18), residues: 813 sheet: -0.25 (0.36), residues: 212 loop : -3.14 (0.16), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 223 HIS 0.008 0.001 HIS A 888 PHE 0.021 0.002 PHE A1031 TYR 0.032 0.002 TYR A1314 ARG 0.006 0.001 ARG A1417 Details of bonding type rmsd hydrogen bonds : bond 0.05438 ( 679) hydrogen bonds : angle 7.10975 ( 1980) SS BOND : bond 0.00510 ( 4) SS BOND : angle 0.65168 ( 8) covalent geometry : bond 0.00384 (18723) covalent geometry : angle 0.85341 (25228) *********************** 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 169 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 139 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 ASP cc_start: 0.7960 (t0) cc_final: 0.7604 (t0) REVERT: B 92 ASP cc_start: 0.8448 (t0) cc_final: 0.7905 (t0) REVERT: B 108 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8824 (tm-30) REVERT: B 151 PHE cc_start: 0.7688 (m-10) cc_final: 0.7382 (m-80) REVERT: C 36 ASP cc_start: 0.8749 (m-30) cc_final: 0.8162 (m-30) REVERT: C 157 ASN cc_start: 0.9030 (m-40) cc_final: 0.8769 (m110) REVERT: C 186 ASP cc_start: 0.8628 (t70) cc_final: 0.8132 (t0) REVERT: A 1 MET cc_start: 0.4884 (OUTLIER) cc_final: 0.4638 (ppp) REVERT: A 7 ILE cc_start: 0.3893 (OUTLIER) cc_final: 0.3381 (pp) REVERT: A 141 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8685 (tm-30) REVERT: A 198 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7247 (pm20) REVERT: A 567 GLU cc_start: 0.8278 (pm20) cc_final: 0.7933 (mp0) REVERT: A 984 GLN cc_start: 0.6770 (mp10) cc_final: 0.6412 (mp10) REVERT: A 1590 LYS cc_start: 0.5031 (tmtt) cc_final: 0.4377 (tptt) REVERT: A 1597 TYR cc_start: 0.8708 (m-10) cc_final: 0.8446 (m-80) REVERT: A 1764 MET cc_start: 0.9476 (mmt) cc_final: 0.9075 (mtt) REVERT: A 1897 HIS cc_start: 0.8244 (t70) cc_final: 0.8023 (t70) REVERT: A 1943 MET cc_start: 0.9038 (mmm) cc_final: 0.8816 (mmm) outliers start: 30 outliers final: 7 residues processed: 160 average time/residue: 1.3793 time to fit residues: 249.7789 Evaluate side-chains 122 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 226 ASN 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 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 194 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 223 optimal weight: 1.9990 chunk 145 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 218 optimal weight: 0.9990 chunk 119 optimal weight: 0.1980 chunk 188 optimal weight: 0.8980 chunk 132 optimal weight: 0.0870 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** 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** ** A1315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1356 ASN ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1522 GLN A1749 ASN ** A1861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.132397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.089159 restraints weight = 49979.709| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.94 r_work: 0.3163 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18727 Z= 0.162 Angle : 0.792 10.180 25236 Z= 0.428 Chirality : 0.047 0.313 2644 Planarity : 0.005 0.091 3273 Dihedral : 8.498 89.274 2486 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.40 % Allowed : 12.85 % Favored : 86.75 % Rotamer: Outliers : 1.57 % Allowed : 12.46 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 1.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.17), residues: 2272 helix: -0.28 (0.18), residues: 822 sheet: -0.15 (0.36), residues: 224 loop : -3.08 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 223 HIS 0.008 0.001 HIS A1957 PHE 0.026 0.002 PHE A1121 TYR 0.027 0.002 TYR A1314 ARG 0.007 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04912 ( 679) hydrogen bonds : angle 6.78518 ( 1980) SS BOND : bond 0.00471 ( 4) SS BOND : angle 0.56604 ( 8) covalent geometry : bond 0.00342 (18723) covalent geometry : angle 0.79217 (25228) *********************** 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 164 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8435 (t0) cc_final: 0.7849 (t0) REVERT: B 108 GLU cc_start: 0.9113 (tm-30) cc_final: 0.8811 (tm-30) REVERT: B 151 PHE cc_start: 0.7812 (m-10) cc_final: 0.7538 (m-80) REVERT: C 36 ASP cc_start: 0.8742 (m-30) cc_final: 0.8256 (m-30) REVERT: C 157 ASN cc_start: 0.9073 (m-40) cc_final: 0.8826 (m110) REVERT: C 186 ASP cc_start: 0.8612 (t70) cc_final: 0.8127 (t70) REVERT: A 7 ILE cc_start: 0.3972 (OUTLIER) cc_final: 0.3510 (pp) REVERT: A 141 GLN cc_start: 0.8886 (tm-30) cc_final: 0.8667 (tm-30) REVERT: A 198 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: A 567 GLU cc_start: 0.8304 (pm20) cc_final: 0.7912 (mp0) REVERT: A 890 ILE cc_start: 0.8323 (tt) cc_final: 0.8024 (tt) REVERT: A 1119 ASN cc_start: 0.8719 (m-40) cc_final: 0.8492 (p0) REVERT: A 1298 GLU cc_start: 0.9352 (OUTLIER) cc_final: 0.8618 (pp20) REVERT: A 1357 MET cc_start: 0.9296 (tmm) cc_final: 0.8776 (ppp) REVERT: A 1527 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8400 (mp0) REVERT: A 1597 TYR cc_start: 0.8766 (m-10) cc_final: 0.8513 (m-80) REVERT: A 1711 GLU cc_start: 0.8478 (tt0) cc_final: 0.8223 (tp30) REVERT: A 1764 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.9121 (mtt) REVERT: A 1866 ILE cc_start: 0.8902 (tp) cc_final: 0.8560 (tp) REVERT: A 1897 HIS cc_start: 0.8130 (t70) cc_final: 0.7929 (t70) REVERT: A 1943 MET cc_start: 0.9005 (mmm) cc_final: 0.8797 (mmm) outliers start: 32 outliers final: 11 residues processed: 156 average time/residue: 1.2322 time to fit residues: 221.3408 Evaluate side-chains 127 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain C residue 144 LEU 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 273 VAL Chi-restraints excluded: chain A residue 509 ASN 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 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 187 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 149 optimal weight: 0.1980 chunk 138 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 226 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 19 optimal weight: 0.0470 overall best weight: 0.5480 ------------------------------------------------------------------------------- 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 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** 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** A1972 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.133183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089548 restraints weight = 50268.700| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 3.97 r_work: 0.3184 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18727 Z= 0.155 Angle : 0.768 10.167 25236 Z= 0.412 Chirality : 0.046 0.290 2644 Planarity : 0.005 0.089 3273 Dihedral : 8.184 86.943 2486 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.16 % Favored : 86.53 % Rotamer: Outliers : 2.11 % Allowed : 14.12 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.91 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.17), residues: 2272 helix: -0.17 (0.18), residues: 831 sheet: -0.02 (0.37), residues: 214 loop : -2.93 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 283 HIS 0.008 0.001 HIS A1345 PHE 0.023 0.002 PHE A1121 TYR 0.025 0.001 TYR A1314 ARG 0.004 0.001 ARG C 161 Details of bonding type rmsd hydrogen bonds : bond 0.04574 ( 679) hydrogen bonds : angle 6.51390 ( 1980) SS BOND : bond 0.00331 ( 4) SS BOND : angle 0.63552 ( 8) covalent geometry : bond 0.00327 (18723) covalent geometry : angle 0.76796 (25228) *********************** 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 181 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 138 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8479 (t0) cc_final: 0.7933 (t0) REVERT: B 108 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8874 (tm-30) REVERT: B 151 PHE cc_start: 0.7848 (m-10) cc_final: 0.7589 (m-80) REVERT: C 36 ASP cc_start: 0.8766 (m-30) cc_final: 0.8271 (m-30) REVERT: C 157 ASN cc_start: 0.9102 (m-40) cc_final: 0.8784 (m-40) REVERT: C 161 ARG cc_start: 0.9051 (tpt90) cc_final: 0.8850 (tpt-90) REVERT: C 186 ASP cc_start: 0.8592 (t70) cc_final: 0.8085 (t70) REVERT: A 7 ILE cc_start: 0.4035 (OUTLIER) cc_final: 0.3583 (pp) REVERT: A 141 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8662 (tm-30) REVERT: A 198 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7051 (pm20) REVERT: A 577 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8815 (m) REVERT: A 1119 ASN cc_start: 0.8700 (m-40) cc_final: 0.8437 (p0) REVERT: A 1298 GLU cc_start: 0.9397 (OUTLIER) cc_final: 0.8700 (pp20) REVERT: A 1527 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8428 (mp0) REVERT: A 1597 TYR cc_start: 0.8813 (m-10) cc_final: 0.8611 (m-80) REVERT: A 1711 GLU cc_start: 0.8527 (tt0) cc_final: 0.8255 (tp30) REVERT: A 1764 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.9145 (mtt) REVERT: A 1866 ILE cc_start: 0.8905 (tp) cc_final: 0.8550 (tp) REVERT: A 1976 ILE cc_start: 0.8203 (mt) cc_final: 0.8000 (mt) outliers start: 43 outliers final: 14 residues processed: 172 average time/residue: 1.1544 time to fit residues: 230.3122 Evaluate side-chains 137 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 144 LEU 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 1298 GLU Chi-restraints excluded: chain A residue 1633 LEU Chi-restraints excluded: chain A residue 1731 ASP Chi-restraints excluded: chain A residue 1764 MET 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 193 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 184 optimal weight: 0.5980 chunk 65 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 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 = 0.4231 r_free = 0.4231 target = 0.131686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.087348 restraints weight = 51340.989| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 4.03 r_work: 0.3194 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18727 Z= 0.186 Angle : 0.772 9.566 25236 Z= 0.414 Chirality : 0.047 0.270 2644 Planarity : 0.005 0.085 3273 Dihedral : 7.973 81.903 2486 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.29 % Favored : 86.40 % Rotamer: Outliers : 2.21 % Allowed : 15.89 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.86 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.17), residues: 2272 helix: -0.12 (0.18), residues: 834 sheet: -0.01 (0.36), residues: 225 loop : -2.92 (0.16), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 223 HIS 0.008 0.001 HIS A1957 PHE 0.029 0.002 PHE A1343 TYR 0.023 0.002 TYR A1314 ARG 0.008 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 679) hydrogen bonds : angle 6.35946 ( 1980) SS BOND : bond 0.00397 ( 4) SS BOND : angle 0.69209 ( 8) covalent geometry : bond 0.00407 (18723) covalent geometry : angle 0.77155 (25228) *********************** 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 171 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 126 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8522 (t0) cc_final: 0.7944 (t0) REVERT: B 108 GLU cc_start: 0.9259 (tm-30) cc_final: 0.8931 (tm-30) REVERT: C 36 ASP cc_start: 0.8772 (m-30) cc_final: 0.8291 (m-30) REVERT: C 157 ASN cc_start: 0.9149 (m-40) cc_final: 0.8782 (m-40) REVERT: C 186 ASP cc_start: 0.8629 (t70) cc_final: 0.8130 (t70) REVERT: A 7 ILE cc_start: 0.4214 (OUTLIER) cc_final: 0.3709 (pp) REVERT: A 198 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8066 (pp30) REVERT: A 233 ASN cc_start: 0.7435 (t0) cc_final: 0.7047 (t0) REVERT: A 577 THR cc_start: 0.9200 (OUTLIER) cc_final: 0.8885 (m) REVERT: A 1119 ASN cc_start: 0.8735 (m-40) cc_final: 0.8415 (p0) REVERT: A 1252 LYS cc_start: 0.7299 (mmtt) cc_final: 0.5702 (tptt) REVERT: A 1298 GLU cc_start: 0.9419 (OUTLIER) cc_final: 0.9202 (pm20) REVERT: A 1357 MET cc_start: 0.9329 (tmm) cc_final: 0.8868 (ppp) REVERT: A 1527 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8505 (mp0) REVERT: A 1597 TYR cc_start: 0.8763 (m-80) cc_final: 0.8558 (m-80) REVERT: A 1711 GLU cc_start: 0.8558 (tt0) cc_final: 0.8292 (tp30) REVERT: A 1764 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.9125 (mtt) REVERT: A 1866 ILE cc_start: 0.8928 (tp) cc_final: 0.8562 (tp) outliers start: 45 outliers final: 18 residues processed: 166 average time/residue: 1.2467 time to fit residues: 238.8786 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 : 1.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 144 LEU 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 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 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 1731 ASP 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 151 optimal weight: 20.0000 chunk 89 optimal weight: 0.0570 chunk 124 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 131 optimal weight: 0.6980 chunk 74 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 194 optimal weight: 0.0570 overall best weight: 0.4616 ------------------------------------------------------------------------------- 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 345 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 GLN ** A1110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.133595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090293 restraints weight = 50696.624| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 4.04 r_work: 0.3197 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18727 Z= 0.145 Angle : 0.750 9.731 25236 Z= 0.402 Chirality : 0.046 0.272 2644 Planarity : 0.005 0.083 3273 Dihedral : 7.751 79.566 2486 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 12.98 % Favored : 86.75 % Rotamer: Outliers : 2.11 % Allowed : 17.12 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.17), residues: 2272 helix: -0.00 (0.19), residues: 831 sheet: 0.11 (0.37), residues: 210 loop : -2.72 (0.16), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 223 HIS 0.007 0.001 HIS A 845 PHE 0.020 0.002 PHE A1121 TYR 0.023 0.001 TYR A1044 ARG 0.012 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 679) hydrogen bonds : angle 6.13223 ( 1980) SS BOND : bond 0.00248 ( 4) SS BOND : angle 0.52614 ( 8) covalent geometry : bond 0.00304 (18723) covalent geometry : angle 0.75024 (25228) *********************** 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 186 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8486 (t0) cc_final: 0.7911 (t0) REVERT: B 108 GLU cc_start: 0.9291 (tm-30) cc_final: 0.8942 (tm-30) REVERT: B 151 PHE cc_start: 0.7579 (m-80) cc_final: 0.7357 (m-80) REVERT: C 36 ASP cc_start: 0.8815 (m-30) cc_final: 0.8341 (m-30) REVERT: C 142 GLU cc_start: 0.8515 (pp20) cc_final: 0.8245 (pp20) REVERT: C 157 ASN cc_start: 0.9132 (m-40) cc_final: 0.8785 (m-40) REVERT: C 186 ASP cc_start: 0.8609 (t70) cc_final: 0.8088 (t70) REVERT: A 7 ILE cc_start: 0.4045 (OUTLIER) cc_final: 0.3567 (pp) REVERT: A 141 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8574 (tm-30) REVERT: A 198 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8141 (pp30) REVERT: A 233 ASN cc_start: 0.7303 (t0) cc_final: 0.6915 (t0) REVERT: A 504 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8393 (mm-30) REVERT: A 567 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8325 (mp0) REVERT: A 577 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8780 (m) REVERT: A 690 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7550 (tptp) REVERT: A 867 ASN cc_start: 0.6068 (OUTLIER) cc_final: 0.4121 (m110) REVERT: A 1048 GLN cc_start: 0.8829 (tp40) cc_final: 0.8435 (mp10) REVERT: A 1119 ASN cc_start: 0.8694 (m-40) cc_final: 0.8305 (p0) REVERT: A 1298 GLU cc_start: 0.9389 (OUTLIER) cc_final: 0.9138 (mp0) REVERT: A 1343 PHE cc_start: 0.9336 (m-10) cc_final: 0.8972 (m-80) REVERT: A 1357 MET cc_start: 0.9309 (tmm) cc_final: 0.8918 (ppp) REVERT: A 1527 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8495 (mp0) REVERT: A 1681 ASP cc_start: 0.8851 (m-30) cc_final: 0.8636 (t70) REVERT: A 1711 GLU cc_start: 0.8514 (tt0) cc_final: 0.8159 (tp30) REVERT: A 1731 ASP cc_start: 0.9286 (OUTLIER) cc_final: 0.9083 (p0) REVERT: A 1764 MET cc_start: 0.9400 (mmt) cc_final: 0.9116 (mtt) REVERT: A 1866 ILE cc_start: 0.8837 (tp) cc_final: 0.8397 (tp) REVERT: A 1945 GLU cc_start: 0.8788 (mp0) cc_final: 0.8570 (mp0) REVERT: A 1976 ILE cc_start: 0.8289 (mt) cc_final: 0.7929 (mt) REVERT: A 1985 LEU cc_start: 0.7154 (OUTLIER) cc_final: 0.6888 (pp) outliers start: 43 outliers final: 13 residues processed: 178 average time/residue: 1.2805 time to fit residues: 260.1880 Evaluate side-chains 143 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 200 GLN 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 690 LYS 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 922 THR Chi-restraints excluded: chain A residue 949 VAL 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 1633 LEU Chi-restraints excluded: chain A residue 1731 ASP 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 38 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 176 optimal weight: 7.9990 chunk 69 optimal weight: 0.3980 chunk 101 optimal weight: 0.2980 chunk 4 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 GLN ** A1110 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 = 0.4237 r_free = 0.4237 target = 0.131712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.087979 restraints weight = 50294.403| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.98 r_work: 0.3147 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18727 Z= 0.199 Angle : 0.780 9.372 25236 Z= 0.416 Chirality : 0.047 0.330 2644 Planarity : 0.005 0.081 3273 Dihedral : 7.428 50.393 2483 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 13.12 % Favored : 86.62 % Rotamer: Outliers : 2.40 % Allowed : 17.56 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.17), residues: 2272 helix: -0.03 (0.18), residues: 842 sheet: 0.15 (0.36), residues: 225 loop : -2.76 (0.16), residues: 1205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 223 HIS 0.006 0.001 HIS A 725 PHE 0.023 0.002 PHE A1121 TYR 0.021 0.002 TYR B 79 ARG 0.009 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 679) hydrogen bonds : angle 6.05969 ( 1980) SS BOND : bond 0.00722 ( 4) SS BOND : angle 1.27164 ( 8) covalent geometry : bond 0.00442 (18723) covalent geometry : angle 0.77993 (25228) *********************** 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 175 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 126 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8417 (t0) cc_final: 0.7843 (t0) REVERT: B 108 GLU cc_start: 0.9297 (tm-30) cc_final: 0.8930 (tm-30) REVERT: B 151 PHE cc_start: 0.7688 (m-80) cc_final: 0.7390 (m-80) REVERT: C 36 ASP cc_start: 0.8709 (m-30) cc_final: 0.8222 (m-30) REVERT: C 142 GLU cc_start: 0.8475 (pp20) cc_final: 0.8261 (pp20) REVERT: C 153 CYS cc_start: 0.7766 (t) cc_final: 0.7447 (t) REVERT: C 157 ASN cc_start: 0.9139 (m-40) cc_final: 0.8795 (m-40) REVERT: C 161 ARG cc_start: 0.9203 (mmm-85) cc_final: 0.8991 (mmm-85) REVERT: C 186 ASP cc_start: 0.8602 (t70) cc_final: 0.8057 (t70) REVERT: A 7 ILE cc_start: 0.4141 (OUTLIER) cc_final: 0.3608 (pp) REVERT: A 142 ASN cc_start: 0.9466 (m-40) cc_final: 0.9247 (m110) REVERT: A 198 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8219 (pp30) REVERT: A 233 ASN cc_start: 0.7256 (t0) cc_final: 0.6852 (t0) REVERT: A 298 MET cc_start: 0.7038 (ppp) cc_final: 0.6082 (pmm) REVERT: A 504 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8328 (mm-30) REVERT: A 509 ASN cc_start: 0.7661 (p0) cc_final: 0.7422 (p0) REVERT: A 577 THR cc_start: 0.9213 (OUTLIER) cc_final: 0.8876 (m) REVERT: A 697 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8527 (mm-40) REVERT: A 867 ASN cc_start: 0.6641 (OUTLIER) cc_final: 0.4517 (m110) REVERT: A 1048 GLN cc_start: 0.8858 (tp40) cc_final: 0.8467 (mp10) REVERT: A 1119 ASN cc_start: 0.8759 (m-40) cc_final: 0.8407 (p0) REVERT: A 1298 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.9173 (mp0) REVERT: A 1357 MET cc_start: 0.9252 (tmm) cc_final: 0.8957 (ppp) REVERT: A 1412 MET cc_start: 0.9053 (tpt) cc_final: 0.8672 (mpp) REVERT: A 1527 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8542 (mp0) REVERT: A 1681 ASP cc_start: 0.8913 (m-30) cc_final: 0.8695 (t70) REVERT: A 1711 GLU cc_start: 0.8541 (tt0) cc_final: 0.8228 (tp30) REVERT: A 1731 ASP cc_start: 0.9364 (OUTLIER) cc_final: 0.9154 (p0) REVERT: A 1764 MET cc_start: 0.9414 (OUTLIER) cc_final: 0.9120 (mtt) REVERT: A 1866 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8543 (tp) REVERT: A 1943 MET cc_start: 0.8955 (mmm) cc_final: 0.8755 (mmm) REVERT: A 1985 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6988 (pp) outliers start: 49 outliers final: 19 residues processed: 169 average time/residue: 1.1522 time to fit residues: 225.1560 Evaluate side-chains 145 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain C residue 143 GLN 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 534 VAL Chi-restraints excluded: chain A residue 555 LYS Chi-restraints excluded: chain A residue 577 THR 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 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 1633 LEU Chi-restraints excluded: chain A residue 1731 ASP 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 130 optimal weight: 0.0870 chunk 192 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 186 optimal weight: 0.7980 chunk 179 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.132988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089384 restraints weight = 50151.047| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 4.02 r_work: 0.3178 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18727 Z= 0.155 Angle : 0.777 13.579 25236 Z= 0.410 Chirality : 0.047 0.358 2644 Planarity : 0.005 0.082 3273 Dihedral : 7.306 52.267 2483 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.59 % Favored : 87.19 % Rotamer: Outliers : 2.21 % Allowed : 18.24 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.91 % Twisted Proline : 1.39 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.17), residues: 2272 helix: 0.05 (0.18), residues: 839 sheet: 0.24 (0.37), residues: 215 loop : -2.69 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 223 HIS 0.006 0.001 HIS A 725 PHE 0.021 0.002 PHE A1121 TYR 0.029 0.001 TYR A1314 ARG 0.012 0.001 ARG C 43 Details of bonding type rmsd hydrogen bonds : bond 0.04228 ( 679) hydrogen bonds : angle 5.96317 ( 1980) SS BOND : bond 0.00335 ( 4) SS BOND : angle 0.79242 ( 8) covalent geometry : bond 0.00336 (18723) covalent geometry : angle 0.77667 (25228) *********************** 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 174 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 129 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 92 ASP cc_start: 0.8377 (t0) cc_final: 0.7804 (t0) REVERT: B 108 GLU cc_start: 0.9287 (tm-30) cc_final: 0.8955 (tm-30) REVERT: B 151 PHE cc_start: 0.7617 (m-80) cc_final: 0.7350 (m-80) REVERT: C 36 ASP cc_start: 0.8766 (m-30) cc_final: 0.8293 (m-30) REVERT: C 142 GLU cc_start: 0.8446 (pp20) cc_final: 0.8231 (pp20) REVERT: C 153 CYS cc_start: 0.7886 (t) cc_final: 0.7609 (t) REVERT: C 157 ASN cc_start: 0.9117 (m-40) cc_final: 0.8762 (m-40) REVERT: C 161 ARG cc_start: 0.9237 (mmm-85) cc_final: 0.8873 (mmm-85) REVERT: C 186 ASP cc_start: 0.8603 (t70) cc_final: 0.8074 (t70) REVERT: A 7 ILE cc_start: 0.4008 (OUTLIER) cc_final: 0.3504 (pp) REVERT: A 198 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8187 (pp30) REVERT: A 298 MET cc_start: 0.7040 (ppp) cc_final: 0.6187 (pmm) REVERT: A 504 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8363 (mm-30) REVERT: A 509 ASN cc_start: 0.7714 (p0) cc_final: 0.7487 (p0) REVERT: A 577 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8783 (m) REVERT: A 690 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7474 (tptp) REVERT: A 850 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7753 (pttt) REVERT: A 867 ASN cc_start: 0.6516 (OUTLIER) cc_final: 0.4343 (m110) REVERT: A 1044 TYR cc_start: 0.8841 (t80) cc_final: 0.8366 (t80) REVERT: A 1048 GLN cc_start: 0.8811 (tp40) cc_final: 0.8123 (mp10) REVERT: A 1298 GLU cc_start: 0.9433 (OUTLIER) cc_final: 0.9180 (mp0) REVERT: A 1357 MET cc_start: 0.9235 (tmm) cc_final: 0.8932 (ppp) REVERT: A 1527 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8540 (mp0) REVERT: A 1681 ASP cc_start: 0.8903 (m-30) cc_final: 0.8684 (t70) REVERT: A 1711 GLU cc_start: 0.8507 (tt0) cc_final: 0.8181 (tp30) REVERT: A 1764 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.9126 (mtt) REVERT: A 1866 ILE cc_start: 0.8848 (tp) cc_final: 0.8448 (tp) REVERT: A 1985 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6893 (pp) outliers start: 45 outliers final: 18 residues processed: 166 average time/residue: 1.2309 time to fit residues: 233.8415 Evaluate side-chains 144 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 2.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 PHE Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain C residue 143 GLN 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 534 VAL Chi-restraints excluded: chain A residue 577 THR Chi-restraints excluded: chain A residue 690 LYS Chi-restraints excluded: chain A residue 778 VAL Chi-restraints excluded: chain A residue 850 LYS 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 1042 ILE 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 1905 ILE Chi-restraints excluded: chain A residue 1985 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.8664 > 50: distance: 34 - 57: 3.873 distance: 41 - 62: 17.135 distance: 45 - 70: 24.402 distance: 48 - 57: 3.163 distance: 49 - 78: 21.874 distance: 57 - 58: 8.512 distance: 58 - 59: 15.563 distance: 58 - 61: 15.700 distance: 59 - 60: 11.686 distance: 59 - 62: 12.589 distance: 60 - 83: 17.303 distance: 62 - 63: 9.973 distance: 63 - 64: 10.656 distance: 63 - 66: 6.713 distance: 64 - 65: 9.219 distance: 64 - 70: 14.946 distance: 65 - 91: 14.945 distance: 66 - 67: 19.933 distance: 67 - 68: 12.224 distance: 67 - 69: 11.915 distance: 70 - 71: 7.560 distance: 71 - 72: 6.561 distance: 71 - 74: 12.180 distance: 72 - 73: 4.397 distance: 72 - 78: 3.020 distance: 73 - 99: 26.519 distance: 74 - 75: 11.989 distance: 75 - 76: 24.185 distance: 75 - 77: 8.565 distance: 78 - 79: 18.149 distance: 79 - 80: 15.986 distance: 79 - 82: 18.479 distance: 80 - 81: 10.140 distance: 80 - 83: 7.724 distance: 81 - 107: 12.835 distance: 83 - 84: 4.537 distance: 84 - 85: 8.704 distance: 84 - 87: 15.389 distance: 85 - 86: 13.239 distance: 85 - 91: 10.475 distance: 87 - 88: 8.010 distance: 88 - 89: 14.146 distance: 88 - 90: 16.391 distance: 91 - 92: 5.670 distance: 92 - 93: 18.633 distance: 92 - 95: 4.473 distance: 93 - 94: 10.272 distance: 93 - 99: 27.334 distance: 95 - 96: 14.890 distance: 95 - 97: 7.615 distance: 96 - 98: 4.126 distance: 99 - 100: 22.184 distance: 100 - 101: 24.830 distance: 100 - 103: 21.286 distance: 101 - 102: 21.977 distance: 101 - 107: 15.681 distance: 103 - 104: 33.068 distance: 103 - 105: 11.497 distance: 104 - 106: 14.992 distance: 107 - 108: 33.606 distance: 108 - 109: 29.540 distance: 108 - 111: 12.964 distance: 109 - 110: 10.996 distance: 111 - 112: 22.944 distance: 112 - 113: 9.892 distance: 113 - 114: 22.835 distance: 114 - 115: 23.382 distance: 115 - 116: 29.184 distance: 115 - 117: 20.474 distance: 118 - 119: 13.545 distance: 119 - 120: 8.299 distance: 120 - 121: 24.514 distance: 120 - 122: 43.998 distance: 122 - 123: 19.225 distance: 123 - 124: 16.613 distance: 123 - 126: 10.368 distance: 124 - 125: 19.914 distance: 124 - 129: 22.495 distance: 126 - 128: 8.965