Starting phenix.real_space_refine on Thu Mar 5 08:07:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jgd_22323/03_2026/7jgd_22323.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jgd_22323/03_2026/7jgd_22323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jgd_22323/03_2026/7jgd_22323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jgd_22323/03_2026/7jgd_22323.map" model { file = "/net/cci-nas-00/data/ceres_data/7jgd_22323/03_2026/7jgd_22323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jgd_22323/03_2026/7jgd_22323.cif" } resolution = 3.38 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= 1.000 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: 5 Type Number sf(0) Gaussians S 86 5.16 5 C 7421 2.51 5 N 2009 2.21 5 O 2271 1.98 5 H 8505 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 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: 20292 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 20292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1435, 20292 Classifications: {'peptide': 1435} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 39, 'TRANS': 1395} Chain breaks: 27 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 3} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 3.45, per 1000 atoms: 0.17 Number of scatterers: 20292 At special positions: 0 Unit cell: (106, 109.18, 145.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 O 2271 8.00 N 2009 7.00 C 7421 6.00 H 8505 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 228 " distance=2.03 Simple disulfide: pdb=" SG CYS A 67 " - pdb=" SG CYS A 106 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS A 645 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A 771 " - pdb=" SG CYS A 910 " distance=2.03 Simple disulfide: pdb=" SG CYS A 785 " - pdb=" SG CYS A 803 " distance=2.03 Simple disulfide: pdb=" SG CYS A 799 " - pdb=" SG CYS A 966 " distance=2.03 Simple disulfide: pdb=" SG CYS A 807 " - pdb=" SG CYS A 964 " distance=2.03 Simple disulfide: pdb=" SG CYS A 817 " - pdb=" SG CYS A 929 " distance=2.03 Simple disulfide: pdb=" SG CYS A 975 " - pdb=" SG CYS A1099 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS A1005 " distance=2.03 Simple disulfide: pdb=" SG CYS A1097 " - pdb=" SG CYS A1202 " distance=2.03 Simple disulfide: pdb=" SG CYS A1149 " - pdb=" SG CYS A1180 " distance=2.04 Simple disulfide: pdb=" SG CYS A1219 " - pdb=" SG CYS A1418 " distance=2.03 Simple disulfide: pdb=" SG CYS A1230 " - pdb=" SG CYS A1273 " distance=2.03 Simple disulfide: pdb=" SG CYS A1251 " - pdb=" SG CYS A1264 " distance=2.03 Simple disulfide: pdb=" SG CYS A1344 " - pdb=" SG CYS A1437 " distance=2.03 Simple disulfide: pdb=" SG CYS A1462 " - pdb=" SG CYS A1546 " distance=2.03 Simple disulfide: pdb=" SG CYS A1476 " - pdb=" SG CYS A1501 " distance=2.03 Simple disulfide: pdb=" SG CYS A1505 " - pdb=" SG CYS A1574 " distance=2.03 Simple disulfide: pdb=" SG CYS A1596 " - pdb=" SG CYS A1632 " distance=2.03 Simple disulfide: pdb=" SG CYS A1688 " - pdb=" SG CYS A1782 " distance=2.03 Simple disulfide: pdb=" SG CYS A1689 " - pdb=" SG CYS A1906 " distance=2.03 Simple disulfide: pdb=" SG CYS A1807 " - pdb=" SG CYS A1909 " distance=2.03 Simple disulfide: pdb=" SG CYS A1821 " - pdb=" SG CYS A1838 " distance=2.03 Simple disulfide: pdb=" SG CYS A1842 " - pdb=" SG CYS A1933 " distance=2.03 Simple disulfide: pdb=" SG CYS A1896 " - pdb=" SG CYS A1907 " distance=2.03 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: 1.76 Conformation dependent library (CDL) restraints added in 601.4 milliseconds 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 1 sheets defined 58.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 99 through 105 removed outlier: 4.136A pdb=" N ARG A 102 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU A 105 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 143 removed outlier: 3.944A pdb=" N PHE A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 165 Processing helix chain 'A' and resid 176 through 191 removed outlier: 3.540A pdb=" N GLU A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 223 removed outlier: 4.039A pdb=" N TRP A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 removed outlier: 5.347A pdb=" N THR A 227 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY A 229 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 306 removed outlier: 3.521A pdb=" N ASN A 293 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR A 306 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 355 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.699A pdb=" N GLN A 585 " --> pdb=" O PRO A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 636 Proline residue: A 633 - end of helix Processing helix chain 'A' and resid 642 through 661 removed outlier: 4.140A pdb=" N LYS A 646 " --> pdb=" O GLU A 642 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 686 removed outlier: 3.716A pdb=" N LEU A 675 " --> pdb=" O LYS A 671 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 723 removed outlier: 3.885A pdb=" N LEU A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LYS A 717 " --> pdb=" O ASN A 713 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N TYR A 718 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 785 removed outlier: 3.574A pdb=" N GLN A 773 " --> pdb=" O ASN A 769 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 815 Processing helix chain 'A' and resid 830 through 852 removed outlier: 3.519A pdb=" N ARG A 834 " --> pdb=" O PRO A 830 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN A 852 " --> pdb=" O ASP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 893 Processing helix chain 'A' and resid 896 through 905 Processing helix chain 'A' and resid 970 through 978 Processing helix chain 'A' and resid 1028 through 1052 removed outlier: 3.737A pdb=" N LYS A1040 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A1043 " --> pdb=" O ASN A1039 " (cutoff:3.500A) Processing helix chain 'A' and resid 1093 through 1128 removed outlier: 3.767A pdb=" N ASP A1128 " --> pdb=" O LYS A1124 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1158 removed outlier: 3.717A pdb=" N LYS A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A1157 " --> pdb=" O TYR A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1180 removed outlier: 4.215A pdb=" N GLU A1174 " --> pdb=" O SER A1170 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N PHE A1175 " --> pdb=" O ASP A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1186 through 1206 removed outlier: 3.812A pdb=" N CYS A1202 " --> pdb=" O ALA A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1271 removed outlier: 3.598A pdb=" N GLN A1270 " --> pdb=" O PRO A1266 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN A1271 " --> pdb=" O PRO A1267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1266 through 1271' Processing helix chain 'A' and resid 1296 through 1318 Processing helix chain 'A' and resid 1342 through 1360 Processing helix chain 'A' and resid 1366 through 1380 Processing helix chain 'A' and resid 1403 through 1428 Processing helix chain 'A' and resid 1449 through 1476 Processing helix chain 'A' and resid 1500 through 1530 Processing helix chain 'A' and resid 1534 through 1542 removed outlier: 3.855A pdb=" N LEU A1538 " --> pdb=" O SER A1534 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN A1542 " --> pdb=" O LEU A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1555 Processing helix chain 'A' and resid 1570 through 1575 Processing helix chain 'A' and resid 1627 through 1631 removed outlier: 3.686A pdb=" N LEU A1631 " --> pdb=" O ARG A1628 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1643 removed outlier: 4.257A pdb=" N ILE A1639 " --> pdb=" O GLU A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1646 through 1674 removed outlier: 4.620A pdb=" N GLU A1652 " --> pdb=" O GLU A1648 " (cutoff:3.500A) Processing helix chain 'A' and resid 1675 through 1678 Processing helix chain 'A' and resid 1680 through 1704 removed outlier: 3.832A pdb=" N ASN A1684 " --> pdb=" O ILE A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1710 through 1724 removed outlier: 4.069A pdb=" N TYR A1715 " --> pdb=" O GLU A1711 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1744 Processing helix chain 'A' and resid 1755 through 1774 removed outlier: 3.632A pdb=" N GLU A1774 " --> pdb=" O TYR A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1793 through 1821 Processing helix chain 'A' and resid 1837 through 1866 Proline residue: A1851 - end of helix removed outlier: 4.297A pdb=" N ILE A1854 " --> pdb=" O ASN A1850 " (cutoff:3.500A) Processing helix chain 'A' and resid 1887 through 1892 Processing helix chain 'A' and resid 1915 through 1920 Processing helix chain 'A' and resid 1930 through 1949 Proline residue: A1939 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 920 through 923 609 hydrogen bonds defined for protein. 1809 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: 4.29 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 8492 1.04 - 1.23: 282 1.23 - 1.43: 4859 1.43 - 1.63: 6789 1.63 - 1.82: 103 Bond restraints: 20525 Sorted by residual: bond pdb=" N PRO A1266 " pdb=" CA PRO A1266 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.31e-02 5.83e+03 1.05e+00 bond pdb=" CG LEU A 294 " pdb=" CD1 LEU A 294 " ideal model delta sigma weight residual 1.521 1.549 -0.028 3.30e-02 9.18e+02 7.36e-01 bond pdb=" CG LEU A 294 " pdb=" CD2 LEU A 294 " ideal model delta sigma weight residual 1.521 1.549 -0.028 3.30e-02 9.18e+02 7.32e-01 bond pdb=" N ASN A1001 " pdb=" CA ASN A1001 " ideal model delta sigma weight residual 1.468 1.459 0.009 1.24e-02 6.50e+03 5.39e-01 bond pdb=" CA PRO A1266 " pdb=" C PRO A1266 " ideal model delta sigma weight residual 1.514 1.518 -0.004 5.50e-03 3.31e+04 4.96e-01 ... (remaining 20520 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.13: 35612 7.13 - 14.25: 2 14.25 - 21.38: 0 21.38 - 28.51: 5 28.51 - 35.63: 7 Bond angle restraints: 35626 Sorted by residual: angle pdb=" CB SER A 832 " pdb=" CA SER A 832 " pdb=" HA SER A 832 " ideal model delta sigma weight residual 109.00 73.37 35.63 3.00e+00 1.11e-01 1.41e+02 angle pdb=" N SER A 832 " pdb=" CA SER A 832 " pdb=" HA SER A 832 " ideal model delta sigma weight residual 110.00 75.86 34.14 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C SER A 832 " pdb=" CA SER A 832 " pdb=" HA SER A 832 " ideal model delta sigma weight residual 109.00 75.11 33.89 3.00e+00 1.11e-01 1.28e+02 angle pdb=" SD MET A 186 " pdb=" CE MET A 186 " pdb=" HE2 MET A 186 " ideal model delta sigma weight residual 109.00 79.23 29.77 3.00e+00 1.11e-01 9.85e+01 angle pdb=" SD MET A 186 " pdb=" CE MET A 186 " pdb=" HE3 MET A 186 " ideal model delta sigma weight residual 109.00 79.23 29.77 3.00e+00 1.11e-01 9.84e+01 ... (remaining 35621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 9282 17.70 - 35.39: 630 35.39 - 53.09: 152 53.09 - 70.78: 35 70.78 - 88.48: 12 Dihedral angle restraints: 10111 sinusoidal: 5282 harmonic: 4829 Sorted by residual: dihedral pdb=" CB CYS A 152 " pdb=" SG CYS A 152 " pdb=" SG CYS A 259 " pdb=" CB CYS A 259 " ideal model delta sinusoidal sigma weight residual -86.00 -21.36 -64.64 1 1.00e+01 1.00e-02 5.49e+01 dihedral pdb=" CB CYS A1596 " pdb=" SG CYS A1596 " pdb=" SG CYS A1632 " pdb=" CB CYS A1632 " ideal model delta sinusoidal sigma weight residual 93.00 149.13 -56.13 1 1.00e+01 1.00e-02 4.25e+01 dihedral pdb=" CB CYS A 807 " pdb=" SG CYS A 807 " pdb=" SG CYS A 964 " pdb=" CB CYS A 964 " ideal model delta sinusoidal sigma weight residual 93.00 136.25 -43.25 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 10108 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.339: 1660 0.339 - 0.678: 1 0.678 - 1.018: 0 1.018 - 1.357: 0 1.357 - 1.696: 1 Chirality restraints: 1662 Sorted by residual: chirality pdb=" CG LEU A 294 " pdb=" CB LEU A 294 " pdb=" CD1 LEU A 294 " pdb=" CD2 LEU A 294 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.19e+01 chirality pdb=" CA SER A 832 " pdb=" N SER A 832 " pdb=" C SER A 832 " pdb=" CB SER A 832 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ILE A1265 " pdb=" N ILE A1265 " pdb=" C ILE A1265 " pdb=" CB ILE A1265 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1659 not shown) Planarity restraints: 3145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 951 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO A 952 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 952 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 952 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 72 " -0.026 5.00e-02 4.00e+02 3.96e-02 2.51e+00 pdb=" N PRO A 73 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A1001 " -0.006 2.00e-02 2.50e+03 1.12e-02 1.25e+00 pdb=" C ASN A1001 " 0.019 2.00e-02 2.50e+03 pdb=" O ASN A1001 " -0.007 2.00e-02 2.50e+03 pdb=" N TYR A1002 " -0.007 2.00e-02 2.50e+03 ... (remaining 3142 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 601 2.18 - 2.79: 34923 2.79 - 3.39: 49464 3.39 - 4.00: 59959 4.00 - 4.60: 96821 Nonbonded interactions: 241768 Sorted by model distance: nonbonded pdb=" HZ1 LYS A 291 " pdb=" OE1 GLN A 292 " model vdw 1.579 2.450 nonbonded pdb=" OD1 ASP A 749 " pdb=" H ILE A 750 " model vdw 1.629 2.450 nonbonded pdb=" OE1 GLU A1447 " pdb=" H GLU A1447 " model vdw 1.635 2.450 nonbonded pdb=" OD2 ASP A1700 " pdb="HH22 ARG A1797 " model vdw 1.637 2.450 nonbonded pdb=" OD1 ASN A1586 " pdb=" H ALA A1587 " model vdw 1.658 2.450 ... (remaining 241763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.390 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: 0.120 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.570 Find NCS groups from input model: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 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 : 0.002 0.028 12047 Z= 0.092 Angle : 0.434 9.951 16196 Z= 0.258 Chirality : 0.053 1.696 1662 Planarity : 0.002 0.051 2065 Dihedral : 12.943 88.476 4562 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.18 (0.24), residues: 1379 helix: 3.08 (0.19), residues: 773 sheet: 0.27 (2.05), residues: 10 loop : -2.60 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1692 TYR 0.009 0.001 TYR A1867 PHE 0.006 0.001 PHE A 652 TRP 0.009 0.001 TRP A1670 HIS 0.004 0.001 HIS A1897 Details of bonding type rmsd covalent geometry : bond 0.00178 (12020) covalent geometry : angle 0.42998 (16142) SS BOND : bond 0.00173 ( 27) SS BOND : angle 1.15294 ( 54) hydrogen bonds : bond 0.11533 ( 609) hydrogen bonds : angle 3.75949 ( 1809) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2039 time to fit residues: 30.6996 Evaluate side-chains 90 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 ASN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 ASN ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1674 ASN A1850 ASN ** A1871 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 = 0.4618 r_free = 0.4618 target = 0.235128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.185028 restraints weight = 33546.812| |-----------------------------------------------------------------------------| r_work (start): 0.4179 rms_B_bonded: 3.19 r_work: 0.3980 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12047 Z= 0.158 Angle : 0.489 10.644 16196 Z= 0.268 Chirality : 0.056 1.710 1662 Planarity : 0.004 0.048 2065 Dihedral : 3.170 16.551 1543 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.54 % Allowed : 4.00 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.75 (0.24), residues: 1379 helix: 2.55 (0.19), residues: 806 sheet: 0.51 (1.92), residues: 10 loop : -2.85 (0.22), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 302 TYR 0.022 0.001 TYR A 923 PHE 0.015 0.001 PHE A 652 TRP 0.008 0.001 TRP A 560 HIS 0.005 0.001 HIS A1186 Details of bonding type rmsd covalent geometry : bond 0.00357 (12020) covalent geometry : angle 0.48510 (16142) SS BOND : bond 0.00476 ( 27) SS BOND : angle 1.14581 ( 54) hydrogen bonds : bond 0.03852 ( 609) hydrogen bonds : angle 3.45650 ( 1809) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 594 LYS cc_start: 0.6246 (OUTLIER) cc_final: 0.5692 (tmmt) REVERT: A 775 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7385 (tt0) REVERT: A 1250 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.6922 (pt) outliers start: 7 outliers final: 3 residues processed: 105 average time/residue: 0.2074 time to fit residues: 31.5557 Evaluate side-chains 99 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1536 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 116 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 ASN A 888 HIS A 903 ASN A 983 ASN A1522 GLN ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1901 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.227775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.177501 restraints weight = 33648.719| |-----------------------------------------------------------------------------| r_work (start): 0.4077 rms_B_bonded: 3.09 r_work: 0.3886 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12047 Z= 0.180 Angle : 0.533 10.674 16196 Z= 0.295 Chirality : 0.056 1.712 1662 Planarity : 0.004 0.061 2065 Dihedral : 3.815 21.177 1543 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.69 % Allowed : 6.99 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.35 (0.23), residues: 1379 helix: 2.14 (0.19), residues: 812 sheet: 0.80 (1.97), residues: 10 loop : -2.94 (0.22), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 231 TYR 0.027 0.002 TYR A 923 PHE 0.016 0.002 PHE A1121 TRP 0.010 0.001 TRP A1111 HIS 0.005 0.001 HIS A1186 Details of bonding type rmsd covalent geometry : bond 0.00410 (12020) covalent geometry : angle 0.52948 (16142) SS BOND : bond 0.00394 ( 27) SS BOND : angle 1.19848 ( 54) hydrogen bonds : bond 0.04788 ( 609) hydrogen bonds : angle 3.65477 ( 1809) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.6982 (m-70) cc_final: 0.6661 (m170) REVERT: A 594 LYS cc_start: 0.6507 (OUTLIER) cc_final: 0.5220 (ttmt) REVERT: A 723 MET cc_start: 0.7766 (mtm) cc_final: 0.7523 (mtm) REVERT: A 775 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7434 (tt0) REVERT: A 845 HIS cc_start: 0.9010 (OUTLIER) cc_final: 0.8804 (m-70) REVERT: A 1147 PHE cc_start: 0.8728 (t80) cc_final: 0.8515 (t80) REVERT: A 1250 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7283 (pt) REVERT: A 1537 ASP cc_start: 0.6441 (m-30) cc_final: 0.5908 (p0) outliers start: 9 outliers final: 4 residues processed: 106 average time/residue: 0.2105 time to fit residues: 32.2025 Evaluate side-chains 101 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1546 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 116 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN A1033 ASN A1192 ASN A1305 HIS A1550 ASN A1643 ASN ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.226051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.174914 restraints weight = 33575.958| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.99 r_work: 0.3876 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12047 Z= 0.182 Angle : 0.522 10.019 16196 Z= 0.287 Chirality : 0.056 1.703 1662 Planarity : 0.004 0.046 2065 Dihedral : 3.968 26.117 1543 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.92 % Allowed : 8.53 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.23 (0.23), residues: 1379 helix: 2.04 (0.19), residues: 811 sheet: 0.28 (1.94), residues: 10 loop : -2.96 (0.22), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 851 TYR 0.015 0.002 TYR A 923 PHE 0.016 0.001 PHE A1147 TRP 0.010 0.001 TRP A 214 HIS 0.003 0.001 HIS A1186 Details of bonding type rmsd covalent geometry : bond 0.00416 (12020) covalent geometry : angle 0.51811 (16142) SS BOND : bond 0.00410 ( 27) SS BOND : angle 1.20365 ( 54) hydrogen bonds : bond 0.04517 ( 609) hydrogen bonds : angle 3.59147 ( 1809) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 LEU cc_start: 0.5527 (mp) cc_final: 0.5307 (tp) REVERT: A 263 GLU cc_start: 0.4755 (OUTLIER) cc_final: 0.4152 (mp0) REVERT: A 594 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.5490 (ttmt) REVERT: A 775 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7389 (tt0) REVERT: A 854 LYS cc_start: 0.7005 (mptt) cc_final: 0.6550 (mmtt) REVERT: A 1250 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7503 (pt) REVERT: A 1537 ASP cc_start: 0.6579 (m-30) cc_final: 0.6167 (p0) REVERT: A 1924 LYS cc_start: 0.5490 (tptt) cc_final: 0.5273 (tptp) outliers start: 12 outliers final: 8 residues processed: 108 average time/residue: 0.2004 time to fit residues: 31.6321 Evaluate side-chains 103 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1536 SER Chi-restraints excluded: chain A residue 1674 ASN Chi-restraints excluded: chain A residue 1781 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 117 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 chunk 53 optimal weight: 0.0870 chunk 132 optimal weight: 0.5980 chunk 82 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 96 optimal weight: 0.0170 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1033 ASN A1192 ASN ** A1871 ASN ** 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 = 0.4587 r_free = 0.4587 target = 0.229919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.177513 restraints weight = 33886.228| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 3.56 r_work: 0.3905 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12047 Z= 0.113 Angle : 0.454 10.018 16196 Z= 0.246 Chirality : 0.054 1.701 1662 Planarity : 0.003 0.039 2065 Dihedral : 3.668 22.190 1543 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.77 % Allowed : 9.38 % Favored : 89.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.49 (0.23), residues: 1379 helix: 2.30 (0.19), residues: 806 sheet: 0.34 (1.98), residues: 10 loop : -2.89 (0.22), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 851 TYR 0.012 0.001 TYR A 923 PHE 0.011 0.001 PHE A 652 TRP 0.010 0.001 TRP A 214 HIS 0.003 0.001 HIS A1897 Details of bonding type rmsd covalent geometry : bond 0.00256 (12020) covalent geometry : angle 0.45100 (16142) SS BOND : bond 0.00287 ( 27) SS BOND : angle 1.01720 ( 54) hydrogen bonds : bond 0.04001 ( 609) hydrogen bonds : angle 3.37330 ( 1809) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 594 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.5436 (ttmt) REVERT: A 775 GLN cc_start: 0.7916 (tm-30) cc_final: 0.7369 (tt0) REVERT: A 854 LYS cc_start: 0.7101 (mptt) cc_final: 0.6620 (mmtt) REVERT: A 1173 PHE cc_start: 0.8051 (OUTLIER) cc_final: 0.7598 (t80) REVERT: A 1249 TRP cc_start: 0.7220 (m100) cc_final: 0.6647 (m100) REVERT: A 1250 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7539 (pt) REVERT: A 1537 ASP cc_start: 0.6671 (m-30) cc_final: 0.6302 (p0) outliers start: 10 outliers final: 6 residues processed: 99 average time/residue: 0.2049 time to fit residues: 29.2740 Evaluate side-chains 101 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1173 PHE Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1546 CYS Chi-restraints excluded: chain A residue 1781 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 39 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 29 optimal weight: 0.0010 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 ASN A1192 ASN A1305 HIS ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1923 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.227222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.174510 restraints weight = 33745.711| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 3.63 r_work: 0.3873 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12047 Z= 0.156 Angle : 0.492 10.025 16196 Z= 0.269 Chirality : 0.055 1.702 1662 Planarity : 0.003 0.041 2065 Dihedral : 3.849 22.575 1543 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 1.23 % Allowed : 9.68 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.30 (0.23), residues: 1379 helix: 2.12 (0.19), residues: 814 sheet: 0.21 (2.02), residues: 10 loop : -3.00 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 851 TYR 0.015 0.001 TYR A 923 PHE 0.014 0.001 PHE A 652 TRP 0.009 0.001 TRP A 665 HIS 0.003 0.001 HIS A 845 Details of bonding type rmsd covalent geometry : bond 0.00355 (12020) covalent geometry : angle 0.48885 (16142) SS BOND : bond 0.00369 ( 27) SS BOND : angle 1.10431 ( 54) hydrogen bonds : bond 0.04347 ( 609) hydrogen bonds : angle 3.50195 ( 1809) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 111 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 LYS cc_start: 0.6592 (OUTLIER) cc_final: 0.5596 (ttmt) REVERT: A 775 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7375 (tt0) REVERT: A 854 LYS cc_start: 0.7125 (mptt) cc_final: 0.6653 (mmtt) REVERT: A 1173 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7595 (t80) REVERT: A 1249 TRP cc_start: 0.7255 (m100) cc_final: 0.7025 (m100) REVERT: A 1250 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7533 (pt) REVERT: A 1537 ASP cc_start: 0.6761 (m-30) cc_final: 0.6332 (p0) outliers start: 16 outliers final: 11 residues processed: 107 average time/residue: 0.1925 time to fit residues: 29.9087 Evaluate side-chains 107 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1173 PHE Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1536 SER Chi-restraints excluded: chain A residue 1546 CYS Chi-restraints excluded: chain A residue 1674 ASN Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1821 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 30.0000 chunk 122 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 86 optimal weight: 9.9990 chunk 46 optimal weight: 0.4980 chunk 95 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 ASN A1192 ASN ** A1871 ASN ** 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 = 0.4564 r_free = 0.4564 target = 0.227225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.174618 restraints weight = 33725.575| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.41 r_work: 0.3878 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12047 Z= 0.146 Angle : 0.486 10.006 16196 Z= 0.265 Chirality : 0.055 1.700 1662 Planarity : 0.003 0.040 2065 Dihedral : 3.849 26.910 1543 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.38 % Allowed : 10.15 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.30 (0.23), residues: 1379 helix: 2.12 (0.19), residues: 814 sheet: 0.08 (2.01), residues: 10 loop : -2.98 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 851 TYR 0.014 0.001 TYR A 923 PHE 0.013 0.001 PHE A 652 TRP 0.008 0.001 TRP A 214 HIS 0.005 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00335 (12020) covalent geometry : angle 0.48289 (16142) SS BOND : bond 0.00350 ( 27) SS BOND : angle 1.06177 ( 54) hydrogen bonds : bond 0.04285 ( 609) hydrogen bonds : angle 3.47505 ( 1809) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.7000 (m-70) cc_final: 0.6692 (m170) REVERT: A 594 LYS cc_start: 0.6653 (OUTLIER) cc_final: 0.5612 (ttmt) REVERT: A 775 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7347 (tt0) REVERT: A 854 LYS cc_start: 0.7143 (mptt) cc_final: 0.6663 (mmtt) REVERT: A 978 ARG cc_start: 0.7634 (tpp80) cc_final: 0.6969 (tpp80) REVERT: A 1173 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7620 (t80) REVERT: A 1249 TRP cc_start: 0.7261 (m100) cc_final: 0.7055 (m100) REVERT: A 1250 ILE cc_start: 0.7957 (OUTLIER) cc_final: 0.7547 (pt) REVERT: A 1839 LYS cc_start: 0.5684 (pttt) cc_final: 0.5148 (mtpp) REVERT: A 1924 LYS cc_start: 0.5388 (tptt) cc_final: 0.5079 (tptp) outliers start: 18 outliers final: 13 residues processed: 112 average time/residue: 0.2040 time to fit residues: 32.6657 Evaluate side-chains 111 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 910 CYS Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1173 PHE Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1536 SER Chi-restraints excluded: chain A residue 1546 CYS Chi-restraints excluded: chain A residue 1674 ASN Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1821 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 49 optimal weight: 0.6980 chunk 120 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 ASN A1427 ASN ** A1871 ASN ** 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 = 0.4560 r_free = 0.4560 target = 0.226828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.174219 restraints weight = 33712.186| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 3.38 r_work: 0.3869 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12047 Z= 0.146 Angle : 0.486 10.001 16196 Z= 0.265 Chirality : 0.055 1.700 1662 Planarity : 0.003 0.039 2065 Dihedral : 3.843 25.030 1543 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.31 % Allowed : 10.45 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.31 (0.23), residues: 1379 helix: 2.12 (0.19), residues: 814 sheet: 0.06 (2.01), residues: 10 loop : -2.98 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 851 TYR 0.014 0.001 TYR A 923 PHE 0.013 0.001 PHE A 652 TRP 0.009 0.001 TRP A 665 HIS 0.007 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00334 (12020) covalent geometry : angle 0.48285 (16142) SS BOND : bond 0.00342 ( 27) SS BOND : angle 1.05607 ( 54) hydrogen bonds : bond 0.04300 ( 609) hydrogen bonds : angle 3.46844 ( 1809) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.7036 (m-70) cc_final: 0.6741 (m170) REVERT: A 182 ASN cc_start: 0.7420 (t0) cc_final: 0.7106 (m110) REVERT: A 594 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.5620 (ttmt) REVERT: A 775 GLN cc_start: 0.7970 (tm-30) cc_final: 0.7385 (tt0) REVERT: A 854 LYS cc_start: 0.7161 (mptt) cc_final: 0.6674 (mmtt) REVERT: A 1173 PHE cc_start: 0.8054 (OUTLIER) cc_final: 0.7682 (t80) REVERT: A 1250 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7567 (pt) REVERT: A 1753 ARG cc_start: 0.6312 (ttm170) cc_final: 0.6066 (ttm-80) REVERT: A 1839 LYS cc_start: 0.5736 (pttt) cc_final: 0.5196 (mtpp) REVERT: A 1924 LYS cc_start: 0.5455 (tptt) cc_final: 0.5117 (tptp) outliers start: 17 outliers final: 13 residues processed: 109 average time/residue: 0.2056 time to fit residues: 32.5865 Evaluate side-chains 113 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 910 CYS Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1015 THR Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1173 PHE Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1536 SER Chi-restraints excluded: chain A residue 1546 CYS Chi-restraints excluded: chain A residue 1674 ASN Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1821 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 99 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 113 optimal weight: 0.1980 chunk 26 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 83 optimal weight: 0.4980 chunk 47 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 ASN A1048 GLN ** A1871 ASN ** 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 = 0.4548 r_free = 0.4548 target = 0.225874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.174876 restraints weight = 32746.007| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 3.27 r_work: 0.3868 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12047 Z= 0.119 Angle : 0.465 10.010 16196 Z= 0.251 Chirality : 0.055 1.701 1662 Planarity : 0.003 0.037 2065 Dihedral : 3.741 25.537 1543 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.08 % Allowed : 11.15 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.43 (0.23), residues: 1379 helix: 2.21 (0.19), residues: 814 sheet: 0.18 (2.01), residues: 10 loop : -2.92 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 851 TYR 0.012 0.001 TYR A 923 PHE 0.012 0.001 PHE A1031 TRP 0.015 0.001 TRP A1249 HIS 0.005 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00271 (12020) covalent geometry : angle 0.46221 (16142) SS BOND : bond 0.00303 ( 27) SS BOND : angle 1.00448 ( 54) hydrogen bonds : bond 0.04048 ( 609) hydrogen bonds : angle 3.37493 ( 1809) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 108 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.7042 (m-70) cc_final: 0.6740 (m170) REVERT: A 231 ARG cc_start: 0.6488 (ttp80) cc_final: 0.6135 (tpt90) REVERT: A 594 LYS cc_start: 0.6609 (OUTLIER) cc_final: 0.5536 (ttmt) REVERT: A 775 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7324 (tt0) REVERT: A 854 LYS cc_start: 0.7127 (mptt) cc_final: 0.6622 (mmtt) REVERT: A 978 ARG cc_start: 0.7632 (tpp80) cc_final: 0.6974 (tpp80) REVERT: A 1173 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7597 (t80) REVERT: A 1250 ILE cc_start: 0.7961 (OUTLIER) cc_final: 0.7552 (pt) REVERT: A 1753 ARG cc_start: 0.6273 (ttm170) cc_final: 0.6027 (ttm-80) REVERT: A 1924 LYS cc_start: 0.5288 (tptt) cc_final: 0.4964 (tptp) outliers start: 14 outliers final: 10 residues processed: 105 average time/residue: 0.2073 time to fit residues: 31.6142 Evaluate side-chains 107 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 910 CYS Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1173 PHE Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1536 SER Chi-restraints excluded: chain A residue 1546 CYS Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1821 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 109 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 132 optimal weight: 0.2980 chunk 123 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 ASN ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.226113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.173322 restraints weight = 33701.056| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 3.57 r_work: 0.3859 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12047 Z= 0.152 Angle : 0.494 10.018 16196 Z= 0.269 Chirality : 0.055 1.702 1662 Planarity : 0.003 0.039 2065 Dihedral : 3.864 25.425 1543 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 1.00 % Allowed : 11.07 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.34 (0.23), residues: 1379 helix: 2.13 (0.19), residues: 814 sheet: -0.03 (2.01), residues: 10 loop : -2.94 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 851 TYR 0.015 0.001 TYR A 923 PHE 0.013 0.001 PHE A 652 TRP 0.021 0.001 TRP A1249 HIS 0.005 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00347 (12020) covalent geometry : angle 0.49047 (16142) SS BOND : bond 0.00358 ( 27) SS BOND : angle 1.07442 ( 54) hydrogen bonds : bond 0.04317 ( 609) hydrogen bonds : angle 3.47979 ( 1809) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 117 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.7047 (m-70) cc_final: 0.6754 (m170) REVERT: A 594 LYS cc_start: 0.6738 (OUTLIER) cc_final: 0.5667 (ttmt) REVERT: A 775 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7371 (tt0) REVERT: A 854 LYS cc_start: 0.7167 (mptt) cc_final: 0.6703 (mmtt) REVERT: A 978 ARG cc_start: 0.7741 (tpp80) cc_final: 0.7090 (tpp80) REVERT: A 1173 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.7787 (t80) REVERT: A 1199 GLU cc_start: 0.7506 (tt0) cc_final: 0.7090 (tp30) REVERT: A 1250 ILE cc_start: 0.8015 (OUTLIER) cc_final: 0.7633 (pt) REVERT: A 1753 ARG cc_start: 0.6303 (ttm170) cc_final: 0.6058 (ttm-80) REVERT: A 1839 LYS cc_start: 0.5675 (pttt) cc_final: 0.5177 (mtpp) REVERT: A 1924 LYS cc_start: 0.5590 (tptt) cc_final: 0.5304 (tptp) outliers start: 13 outliers final: 10 residues processed: 114 average time/residue: 0.2242 time to fit residues: 36.8836 Evaluate side-chains 113 residues out of total 1304 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 CYS Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 845 HIS Chi-restraints excluded: chain A residue 910 CYS Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1097 CYS Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1173 PHE Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1536 SER Chi-restraints excluded: chain A residue 1546 CYS Chi-restraints excluded: chain A residue 1781 LEU Chi-restraints excluded: chain A residue 1821 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 5 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 91 optimal weight: 0.2980 chunk 13 optimal weight: 0.0370 chunk 77 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 56 optimal weight: 0.0770 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 ASN ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4580 r_free = 0.4580 target = 0.228961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.176527 restraints weight = 33807.454| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 3.59 r_work: 0.3896 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12047 Z= 0.101 Angle : 0.451 10.016 16196 Z= 0.242 Chirality : 0.054 1.699 1662 Planarity : 0.003 0.036 2065 Dihedral : 3.658 25.467 1543 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.85 % Allowed : 11.38 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.54 (0.23), residues: 1379 helix: 2.33 (0.18), residues: 812 sheet: 0.23 (2.02), residues: 10 loop : -2.90 (0.22), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 631 TYR 0.010 0.001 TYR A 923 PHE 0.013 0.001 PHE A1031 TRP 0.022 0.001 TRP A1249 HIS 0.003 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00228 (12020) covalent geometry : angle 0.44865 (16142) SS BOND : bond 0.00270 ( 27) SS BOND : angle 0.95659 ( 54) hydrogen bonds : bond 0.03833 ( 609) hydrogen bonds : angle 3.29542 ( 1809) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4168.85 seconds wall clock time: 71 minutes 46.83 seconds (4306.83 seconds total)