Starting phenix.real_space_refine on Sat Sep 28 22:33:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgd_22323/09_2024/7jgd_22323.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgd_22323/09_2024/7jgd_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgd_22323/09_2024/7jgd_22323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgd_22323/09_2024/7jgd_22323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgd_22323/09_2024/7jgd_22323.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgd_22323/09_2024/7jgd_22323.cif" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: 9.60, per 1000 atoms: 0.47 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: 5.53 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.33 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: 7.00 Time building geometry restraints manager: 6.63 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: 2.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.380 Extract box with map and model: 0.830 Check model and map are aligned: 0.150 Set scattering table: 0.180 Process input model: 42.660 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.460 ------------------------------------------------------------------------------- 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 12020 Z= 0.111 Angle : 0.430 9.951 16142 Z= 0.256 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 : 11.45 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (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 TRP 0.009 0.001 TRP A1670 HIS 0.004 0.001 HIS A1897 PHE 0.006 0.001 PHE A 652 TYR 0.009 0.001 TYR A1867 ARG 0.004 0.000 ARG A1692 *********************** 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 fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.4519 time to fit residues: 67.6564 Evaluate side-chains 90 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 0.0030 chunk 68 optimal weight: 0.5980 chunk 83 optimal weight: 0.0050 chunk 129 optimal weight: 0.6980 overall best weight: 0.3804 ------------------------------------------------------------------------------- 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 643 ASN ** A 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1542 ASN A1850 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.0709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12020 Z= 0.138 Angle : 0.417 10.455 16142 Z= 0.225 Chirality : 0.054 1.707 1662 Planarity : 0.003 0.045 2065 Dihedral : 2.773 14.158 1543 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.31 % Allowed : 3.46 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.24), residues: 1379 helix: 2.79 (0.19), residues: 806 sheet: 0.56 (2.00), residues: 10 loop : -2.74 (0.22), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 560 HIS 0.004 0.001 HIS A1186 PHE 0.009 0.001 PHE A 652 TYR 0.013 0.001 TYR A1530 ARG 0.005 0.000 ARG A 302 *********************** 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 98 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1250 ILE cc_start: 0.7733 (OUTLIER) cc_final: 0.7060 (pt) outliers start: 4 outliers final: 2 residues processed: 95 average time/residue: 0.4777 time to fit residues: 66.4667 Evaluate side-chains 93 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1542 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 129 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1305 HIS A1674 ASN ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1901 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12020 Z= 0.221 Angle : 0.476 10.559 16142 Z= 0.262 Chirality : 0.055 1.713 1662 Planarity : 0.003 0.044 2065 Dihedral : 3.278 17.086 1543 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.85 % Allowed : 4.69 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.24), residues: 1379 helix: 2.57 (0.19), residues: 802 sheet: 0.48 (1.86), residues: 10 loop : -2.83 (0.22), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 985 HIS 0.003 0.001 HIS A 261 PHE 0.016 0.001 PHE A 652 TYR 0.018 0.001 TYR A 923 ARG 0.007 0.001 ARG A 231 *********************** 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 116 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLU cc_start: 0.5676 (tm-30) cc_final: 0.5263 (tm-30) REVERT: A 143 HIS cc_start: 0.6552 (m-70) cc_final: 0.6290 (m170) REVERT: A 594 LYS cc_start: 0.6110 (OUTLIER) cc_final: 0.5298 (tmmt) REVERT: A 775 GLN cc_start: 0.7551 (tm-30) cc_final: 0.7225 (tt0) REVERT: A 1146 PHE cc_start: 0.7466 (t80) cc_final: 0.7144 (t80) REVERT: A 1250 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7299 (pt) outliers start: 11 outliers final: 6 residues processed: 110 average time/residue: 0.4569 time to fit residues: 73.3475 Evaluate side-chains 104 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LYS Chi-restraints excluded: chain A residue 923 TYR Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1172 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 888 HIS ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN A1192 ASN ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1522 GLN ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12020 Z= 0.278 Angle : 0.530 10.219 16142 Z= 0.296 Chirality : 0.056 1.702 1662 Planarity : 0.004 0.046 2065 Dihedral : 3.874 23.119 1543 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.61 % Allowed : 6.99 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1379 helix: 2.14 (0.19), residues: 810 sheet: 0.03 (1.84), residues: 10 loop : -2.89 (0.22), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1249 HIS 0.003 0.001 HIS A 888 PHE 0.016 0.002 PHE A 652 TYR 0.018 0.002 TYR A 923 ARG 0.006 0.001 ARG A 231 *********************** 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 109 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.6527 (m-70) cc_final: 0.6280 (m170) REVERT: A 594 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.5262 (ttmt) REVERT: A 775 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7327 (tt0) REVERT: A 1250 ILE cc_start: 0.7885 (OUTLIER) cc_final: 0.7516 (pt) outliers start: 8 outliers final: 5 residues processed: 103 average time/residue: 0.4952 time to fit residues: 75.5905 Evaluate side-chains 101 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LYS 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 1537 ASP Chi-restraints excluded: chain A residue 1546 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 275 GLN ** A 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1033 ASN ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 ASN ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12020 Z= 0.293 Angle : 0.539 9.995 16142 Z= 0.299 Chirality : 0.056 1.700 1662 Planarity : 0.004 0.045 2065 Dihedral : 4.041 24.545 1543 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.15 % Allowed : 7.76 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.23), residues: 1379 helix: 2.00 (0.19), residues: 809 sheet: -0.21 (1.82), residues: 10 loop : -2.94 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1249 HIS 0.002 0.001 HIS A1305 PHE 0.015 0.002 PHE A 652 TYR 0.017 0.002 TYR A 923 ARG 0.006 0.001 ARG A 851 *********************** 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 114 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 263 GLU cc_start: 0.4650 (OUTLIER) cc_final: 0.4246 (mp0) REVERT: A 594 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.5387 (ttmt) REVERT: A 775 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7259 (tt0) REVERT: A 854 LYS cc_start: 0.7255 (mptt) cc_final: 0.6929 (mmtt) REVERT: A 1172 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8016 (t) REVERT: A 1250 ILE cc_start: 0.7981 (OUTLIER) cc_final: 0.7648 (pt) REVERT: A 1924 LYS cc_start: 0.5076 (tptp) cc_final: 0.4866 (tptt) outliers start: 15 outliers final: 11 residues processed: 110 average time/residue: 0.4540 time to fit residues: 73.8495 Evaluate side-chains 110 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.732 ------------------------------------------------------------------------------- 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 923 TYR 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 1172 THR 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 1537 ASP Chi-restraints excluded: chain A residue 1546 CYS Chi-restraints excluded: chain A residue 1674 ASN 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 46 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 45 optimal weight: 0.3980 chunk 72 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 A1550 ASN ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12020 Z= 0.203 Angle : 0.478 10.014 16142 Z= 0.262 Chirality : 0.055 1.701 1662 Planarity : 0.003 0.041 2065 Dihedral : 3.867 23.512 1543 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.92 % Allowed : 8.99 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1379 helix: 2.12 (0.19), residues: 807 sheet: -0.16 (1.90), residues: 10 loop : -2.90 (0.22), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A1249 HIS 0.003 0.001 HIS A1897 PHE 0.012 0.001 PHE A 652 TYR 0.013 0.001 TYR A 923 ARG 0.007 0.000 ARG A 851 *********************** 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 105 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 594 LYS cc_start: 0.6376 (OUTLIER) cc_final: 0.5400 (ttmt) REVERT: A 775 GLN cc_start: 0.7675 (tm-30) cc_final: 0.7192 (tt0) REVERT: A 854 LYS cc_start: 0.7261 (mptt) cc_final: 0.6937 (mmtt) REVERT: A 1172 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.7978 (t) REVERT: A 1250 ILE cc_start: 0.7943 (OUTLIER) cc_final: 0.7625 (pt) outliers start: 12 outliers final: 8 residues processed: 102 average time/residue: 0.4894 time to fit residues: 72.4168 Evaluate side-chains 103 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.612 ------------------------------------------------------------------------------- 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 1097 CYS Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1536 SER Chi-restraints excluded: chain A residue 1537 ASP Chi-restraints excluded: chain A residue 1546 CYS Chi-restraints excluded: chain A residue 1781 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 A1305 HIS ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1923 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12020 Z= 0.229 Angle : 0.498 9.991 16142 Z= 0.274 Chirality : 0.055 1.701 1662 Planarity : 0.004 0.041 2065 Dihedral : 3.927 27.494 1543 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 1.15 % Allowed : 9.61 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.23), residues: 1379 helix: 2.10 (0.18), residues: 809 sheet: -0.33 (1.87), residues: 10 loop : -2.91 (0.22), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1249 HIS 0.006 0.001 HIS A 261 PHE 0.014 0.001 PHE A 652 TYR 0.015 0.001 TYR A 923 ARG 0.008 0.000 ARG A 851 *********************** 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 109 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.6629 (m-70) cc_final: 0.6393 (m170) REVERT: A 573 GLU cc_start: 0.6798 (tt0) cc_final: 0.6452 (tt0) REVERT: A 594 LYS cc_start: 0.6478 (OUTLIER) cc_final: 0.5464 (ttmt) REVERT: A 775 GLN cc_start: 0.7692 (tm-30) cc_final: 0.7217 (tt0) REVERT: A 854 LYS cc_start: 0.7262 (mptt) cc_final: 0.6949 (mmtt) REVERT: A 1172 THR cc_start: 0.8291 (OUTLIER) cc_final: 0.7956 (t) REVERT: A 1177 ILE cc_start: 0.7863 (pt) cc_final: 0.7661 (mt) REVERT: A 1250 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7679 (pt) outliers start: 15 outliers final: 10 residues processed: 106 average time/residue: 0.4682 time to fit residues: 72.5221 Evaluate side-chains 104 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 1097 CYS Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1172 THR 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 1537 ASP Chi-restraints excluded: chain A residue 1546 CYS Chi-restraints excluded: chain A residue 1674 ASN Chi-restraints excluded: chain A residue 1781 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 0.0470 chunk 93 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 108 optimal weight: 0.0470 chunk 125 optimal weight: 0.8980 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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 A1427 ASN ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12020 Z= 0.161 Angle : 0.457 10.009 16142 Z= 0.247 Chirality : 0.054 1.700 1662 Planarity : 0.003 0.039 2065 Dihedral : 3.730 24.992 1543 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.08 % Allowed : 9.76 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1379 helix: 2.24 (0.18), residues: 812 sheet: -0.06 (1.96), residues: 10 loop : -2.89 (0.22), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1249 HIS 0.005 0.001 HIS A 261 PHE 0.012 0.001 PHE A1031 TYR 0.011 0.001 TYR A 923 ARG 0.008 0.000 ARG A 851 *********************** 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 104 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.6611 (m-70) cc_final: 0.6373 (m170) REVERT: A 573 GLU cc_start: 0.6749 (tt0) cc_final: 0.6423 (tt0) REVERT: A 594 LYS cc_start: 0.6342 (OUTLIER) cc_final: 0.5322 (ttmt) REVERT: A 775 GLN cc_start: 0.7670 (tm-30) cc_final: 0.7187 (tt0) REVERT: A 854 LYS cc_start: 0.7271 (mptt) cc_final: 0.6947 (mmtt) REVERT: A 1172 THR cc_start: 0.8210 (OUTLIER) cc_final: 0.7890 (t) REVERT: A 1250 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7598 (pt) outliers start: 14 outliers final: 10 residues processed: 102 average time/residue: 0.4771 time to fit residues: 71.0999 Evaluate side-chains 102 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 89 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 1097 CYS Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1172 THR Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1536 SER Chi-restraints excluded: chain A residue 1537 ASP 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 132 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 0.4980 chunk 77 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** ** A 908 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12020 Z= 0.204 Angle : 0.481 10.013 16142 Z= 0.262 Chirality : 0.055 1.700 1662 Planarity : 0.003 0.039 2065 Dihedral : 3.797 25.631 1543 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.08 % Allowed : 10.07 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.23), residues: 1379 helix: 2.19 (0.18), residues: 814 sheet: -0.24 (1.98), residues: 10 loop : -2.95 (0.22), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1249 HIS 0.006 0.001 HIS A 261 PHE 0.012 0.001 PHE A 652 TYR 0.014 0.001 TYR A 923 ARG 0.007 0.000 ARG A 851 *********************** 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 fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.6651 (m-70) cc_final: 0.6413 (m170) REVERT: A 594 LYS cc_start: 0.6440 (OUTLIER) cc_final: 0.5357 (ttmt) REVERT: A 775 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7223 (tt0) REVERT: A 854 LYS cc_start: 0.7240 (mptt) cc_final: 0.6927 (mmtt) REVERT: A 1172 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7895 (t) REVERT: A 1177 ILE cc_start: 0.7902 (pt) cc_final: 0.7679 (mt) REVERT: A 1250 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7676 (pt) REVERT: A 1934 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7437 (mp0) outliers start: 14 outliers final: 11 residues processed: 106 average time/residue: 0.4634 time to fit residues: 71.9548 Evaluate side-chains 104 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 90 time to evaluate : 1.617 ------------------------------------------------------------------------------- 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 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 1172 THR Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1536 SER Chi-restraints excluded: chain A residue 1537 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.0970 chunk 82 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 142 optimal weight: 0.4980 chunk 131 optimal weight: 0.9980 chunk 113 optimal weight: 0.0770 chunk 11 optimal weight: 10.0000 chunk 87 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 182 ASN ** A 218 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12020 Z= 0.151 Angle : 0.450 10.017 16142 Z= 0.242 Chirality : 0.054 1.699 1662 Planarity : 0.003 0.036 2065 Dihedral : 3.653 24.905 1543 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.92 % Allowed : 10.45 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1379 helix: 2.33 (0.18), residues: 814 sheet: -0.01 (1.97), residues: 10 loop : -2.88 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1249 HIS 0.005 0.001 HIS A 261 PHE 0.011 0.001 PHE A1147 TYR 0.015 0.001 TYR A1567 ARG 0.007 0.000 ARG A 851 ********************** 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 106 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 HIS cc_start: 0.6624 (m-70) cc_final: 0.6387 (m170) REVERT: A 594 LYS cc_start: 0.6327 (OUTLIER) cc_final: 0.5294 (ttmt) REVERT: A 775 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7155 (tt0) REVERT: A 854 LYS cc_start: 0.7203 (mptt) cc_final: 0.6932 (mmtt) REVERT: A 978 ARG cc_start: 0.7506 (tpp80) cc_final: 0.6803 (tpp80) REVERT: A 1172 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7801 (t) REVERT: A 1177 ILE cc_start: 0.7763 (pt) cc_final: 0.7534 (mt) REVERT: A 1250 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7624 (pt) outliers start: 12 outliers final: 9 residues processed: 105 average time/residue: 0.4633 time to fit residues: 71.4265 Evaluate side-chains 103 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 91 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 LYS 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 1172 THR Chi-restraints excluded: chain A residue 1250 ILE Chi-restraints excluded: chain A residue 1536 SER Chi-restraints excluded: chain A residue 1537 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 113 optimal weight: 0.0870 chunk 47 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 99 optimal weight: 0.0060 overall best weight: 0.6176 ------------------------------------------------------------------------------- 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 = 0.4570 r_free = 0.4570 target = 0.228073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.176085 restraints weight = 33799.714| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 3.85 r_work: 0.3860 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12020 Z= 0.176 Angle : 0.462 10.008 16142 Z= 0.250 Chirality : 0.054 1.699 1662 Planarity : 0.003 0.037 2065 Dihedral : 3.671 25.147 1543 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 0.92 % Allowed : 10.45 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1379 helix: 2.31 (0.18), residues: 814 sheet: -0.21 (1.96), residues: 10 loop : -2.90 (0.23), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1249 HIS 0.005 0.001 HIS A 261 PHE 0.012 0.001 PHE A1031 TYR 0.012 0.001 TYR A 923 ARG 0.006 0.000 ARG A 851 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3922.03 seconds wall clock time: 69 minutes 39.38 seconds (4179.38 seconds total)