Starting phenix.real_space_refine (version: dev) on Sat May 14 16:48:09 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgd_22323/05_2022/7jgd_22323.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgd_22323/05_2022/7jgd_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_22323/05_2022/7jgd_22323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgd_22323/05_2022/7jgd_22323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgd_22323/05_2022/7jgd_22323.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jgd_22323/05_2022/7jgd_22323.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: 10.24, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 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: 15.37 Conformation dependent library (CDL) restraints added in 1.7 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: 0.48 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: 6.47 Time building geometry restraints manager: 16.09 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: 73.37 - 85.49: 10 85.49 - 97.61: 0 97.61 - 109.74: 12967 109.74 - 121.86: 18935 121.86 - 133.99: 3714 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: 8218 17.70 - 35.39: 590 35.39 - 53.09: 99 53.09 - 70.78: 16 70.78 - 88.48: 12 Dihedral angle restraints: 8935 sinusoidal: 4106 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 8932 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 1.850 nonbonded pdb=" OD1 ASP A 749 " pdb=" H ILE A 750 " model vdw 1.629 1.850 nonbonded pdb=" OE1 GLU A1447 " pdb=" H GLU A1447 " model vdw 1.635 1.850 nonbonded pdb=" OD2 ASP A1700 " pdb="HH22 ARG A1797 " model vdw 1.637 1.850 nonbonded pdb=" OD1 ASN A1586 " pdb=" H ALA A1587 " model vdw 1.658 1.850 ... (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 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. 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.850 Extract box with map and model: 6.960 Check model and map are aligned: 0.300 Convert atoms to be neutral: 0.170 Process input model: 59.560 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 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 : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.4788 time to fit residues: 72.7489 Evaluate side-chains 90 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.673 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3916 ------------------------------------------------------------------------------- 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: 0.9990 chunk 60 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 68 optimal weight: 0.6980 chunk 83 optimal weight: 0.0870 chunk 129 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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** A1542 ASN A1674 ASN ** A1684 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1850 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: 0.6798 moved from start: 0.1072 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= 0.202 Angle : 0.471 10.718 16142 Z= 0.257 Chirality : 0.055 1.708 1662 Planarity : 0.003 0.045 2065 Dihedral : 3.136 16.568 1543 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer Outliers : 0.46 % 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: 0.84 (0.24), residues: 1379 helix: 2.63 (0.19), residues: 804 sheet: 0.70 (1.90), residues: 10 loop : -2.82 (0.22), residues: 565 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2758 Ramachandran restraints generated. 1379 Oldfield, 0 Emsley, 1379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 37 is missing expected H atoms. Skipping. Residue TYR 46 is missing expected H atoms. Skipping. Residue LYS 69 is missing expected H atoms. Skipping. Residue LYS 70 is missing expected H atoms. Skipping. Residue LEU 71 is missing expected H atoms. Skipping. Residue ALA 163 is missing expected H atoms. Skipping. Residue ALA 230 is missing expected H atoms. Skipping. Residue SER 232 is missing expected H atoms. Skipping. Residue LEU 618 is missing expected H atoms. Skipping. Residue ILE 619 is missing expected H atoms. Skipping. Residue VAL 620 is missing expected H atoms. Skipping. Residue SER 621 is missing expected H atoms. Skipping. Residue LYS 626 is missing expected H atoms. Skipping. Residue LEU 628 is missing expected H atoms. Skipping. Residue LYS 629 is missing expected H atoms. Skipping. Residue LYS 630 is missing expected H atoms. Skipping. Residue TYR 632 is missing expected H atoms. Skipping. Residue ALA 816 is missing expected H atoms. Skipping. Residue SER 829 is missing expected H atoms. Skipping. Residue SER 832 is missing expected H atoms. Skipping. Residue LYS 833 is missing expected H atoms. Skipping. Residue ILE 838 is missing expected H atoms. Skipping. Residue TYR 839 is missing expected H atoms. Skipping. Residue TYR 842 is missing expected H atoms. Skipping. Residue SER 843 is missing expected H atoms. Skipping. Residue LYS 844 is missing expected H atoms. Skipping. Residue ILE 846 is missing expected H atoms. Skipping. Residue ALA 849 is missing expected H atoms. Skipping. Residue LYS 854 is missing expected H atoms. Skipping. Residue ALA 855 is missing expected H atoms. Skipping. Residue THR 857 is missing expected H atoms. Skipping. Residue THR 896 is missing expected H atoms. Skipping. Residue SER 898 is missing expected H atoms. Skipping. Residue SER 899 is missing expected H atoms. Skipping. Residue TYR 900 is missing expected H atoms. Skipping. Residue LEU 901 is missing expected H atoms. Skipping. Residue SER 902 is missing expected H atoms. Skipping. Residue VAL 904 is missing expected H atoms. Skipping. Residue LEU 905 is missing expected H atoms. Skipping. Residue TYR 981 is missing expected H atoms. Skipping. Residue SER 986 is missing expected H atoms. Skipping. Residue ALA 1185 is missing expected H atoms. Skipping. Residue LYS 1194 is missing expected H atoms. Skipping. Residue LEU 1195 is missing expected H atoms. Skipping. Residue LYS 1196 is missing expected H atoms. Skipping. Residue ALA 1198 is missing expected H atoms. Skipping. Residue LYS 1200 is missing expected H atoms. Skipping. Residue SER 1207 is missing expected H atoms. Skipping. Residue THR 1208 is missing expected H atoms. Skipping. Residue SER 1430 is missing expected H atoms. Skipping. Residue THR 1846 is missing expected H atoms. Skipping. Residue TYR 1867 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 1.736 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 107 average time/residue: 0.4484 time to fit residues: 70.1027 Evaluate side-chains 97 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1973 time to fit residues: 3.4596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 88 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 129 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 643 ASN A 903 ASN A1305 HIS ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1901 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.1560 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= 0.202 Angle : 0.462 10.226 16142 Z= 0.251 Chirality : 0.055 1.705 1662 Planarity : 0.003 0.042 2065 Dihedral : 3.335 18.593 1543 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.46 % 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: 0.73 (0.24), residues: 1379 helix: 2.52 (0.19), residues: 807 sheet: 1.06 (2.00), residues: 10 loop : -2.85 (0.22), residues: 562 *********************** 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 107 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 101 time to evaluate : 1.776 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 104 average time/residue: 0.4655 time to fit residues: 70.6136 Evaluate side-chains 90 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 1.698 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2223 time to fit residues: 3.6043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 67 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 275 GLN ** A 983 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 ASN ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1542 ASN ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1901 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 12020 Z= 0.314 Angle : 0.552 10.012 16142 Z= 0.306 Chirality : 0.057 1.703 1662 Planarity : 0.004 0.046 2065 Dihedral : 3.977 24.138 1543 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer Outliers : 0.61 % 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: 0.26 (0.23), residues: 1379 helix: 2.07 (0.19), residues: 810 sheet: 0.24 (1.83), residues: 10 loop : -2.95 (0.22), residues: 559 *********************** 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 107 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 105 average time/residue: 0.4328 time to fit residues: 67.5518 Evaluate side-chains 99 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 2.140 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2128 time to fit residues: 4.6793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 57 optimal weight: 0.0870 chunk 117 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 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: 0.7762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1192 ASN ** A1305 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 ASN ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1897 HIS A1901 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 1.164 12020 Z= 1.193 Angle : 0.938 96.224 16142 Z= 0.394 Chirality : 0.055 1.698 1662 Planarity : 0.004 0.066 2065 Dihedral : 3.846 24.238 1543 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.07 % 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: 0.34 (0.23), residues: 1379 helix: 2.15 (0.19), residues: 809 sheet: 0.20 (1.87), residues: 10 loop : -2.94 (0.21), residues: 560 *********************** 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 101 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.694 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 98 average time/residue: 0.4720 time to fit residues: 68.4925 Evaluate side-chains 96 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 92 time to evaluate : 1.821 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2354 time to fit residues: 4.1438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 138 optimal weight: 0.0270 chunk 114 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 888 HIS A1542 ASN A1550 ASN ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1897 HIS A1901 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 1.166 12020 Z= 1.193 Angle : 0.948 99.871 16142 Z= 0.386 Chirality : 0.055 1.698 1662 Planarity : 0.003 0.052 2065 Dihedral : 3.718 23.696 1543 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.07 % 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: 2.28 (0.19), residues: 807 sheet: 0.33 (1.94), residues: 10 loop : -2.92 (0.22), residues: 562 *********************** 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 100 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.735 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 98 average time/residue: 0.4558 time to fit residues: 65.9795 Evaluate side-chains 93 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 1.884 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2105 time to fit residues: 4.3610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 84 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1923 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 1.165 12020 Z= 1.195 Angle : 0.959 100.487 16142 Z= 0.392 Chirality : 0.055 1.699 1662 Planarity : 0.003 0.045 2065 Dihedral : 3.818 25.428 1543 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.07 % 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: 0.41 (0.23), residues: 1379 helix: 2.21 (0.19), residues: 811 sheet: 0.03 (1.90), residues: 10 loop : -2.93 (0.22), residues: 558 *********************** 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 98 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 95 average time/residue: 0.5280 time to fit residues: 75.2407 Evaluate side-chains 92 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 1.828 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2050 time to fit residues: 3.5558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0770 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 12 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1542 ASN ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.191 12020 Z= 0.279 Angle : 0.492 13.867 16142 Z= 0.272 Chirality : 0.055 1.699 1662 Planarity : 0.004 0.081 2065 Dihedral : 3.846 29.652 1543 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer Outliers : 0.23 % 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: 0.44 (0.23), residues: 1379 helix: 2.26 (0.19), residues: 809 sheet: 0.17 (1.94), residues: 10 loop : -2.92 (0.22), residues: 560 *********************** 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 96 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 95 average time/residue: 0.4811 time to fit residues: 67.8904 Evaluate side-chains 96 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 1.848 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2242 time to fit residues: 3.8546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 77 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** ** A 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1305 HIS ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 12020 Z= 0.245 Angle : 0.502 10.005 16142 Z= 0.275 Chirality : 0.055 1.701 1662 Planarity : 0.004 0.080 2065 Dihedral : 3.888 30.682 1543 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.38 (0.23), residues: 1379 helix: 2.18 (0.19), residues: 811 sheet: -0.05 (1.92), residues: 10 loop : -2.93 (0.22), residues: 558 *********************** 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 93 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 1.816 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.4627 time to fit residues: 62.9998 Evaluate side-chains 91 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 1.642 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 94 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 113 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1871 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 1.199 12020 Z= 1.209 Angle : 1.011 104.095 16142 Z= 0.429 Chirality : 0.056 1.700 1662 Planarity : 0.005 0.130 2065 Dihedral : 3.892 30.221 1543 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.19), residues: 811 sheet: -0.06 (1.92), residues: 10 loop : -2.92 (0.22), residues: 558 ********************** 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 93 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 1.973 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 93 average time/residue: 0.4920 time to fit residues: 67.0132 Evaluate side-chains 92 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 1.730 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2271 time to fit residues: 3.3012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 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: 4.9990 chunk 20 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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 852 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1427 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 = 0.4537 r_free = 0.4537 target = 0.225583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.171740 restraints weight = 33699.442| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 3.44 r_work: 0.3988 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3964 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work: 0.3937 rms_B_bonded: 3.31 restraints_weight: 0.1250 r_work: 0.3902 rms_B_bonded: 3.65 restraints_weight: 0.0625 r_work: 0.3856 rms_B_bonded: 4.23 restraints_weight: 0.0312 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 1.173 12020 Z= 1.202 Angle : 0.951 96.491 16142 Z= 0.405 Chirality : 0.055 1.699 1662 Planarity : 0.004 0.100 2065 Dihedral : 3.878 29.453 1543 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.07 % 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 (0.19), residues: 811 sheet: -0.06 (1.93), residues: 10 loop : -2.93 (0.22), residues: 558 =============================================================================== Job complete usr+sys time: 3426.66 seconds wall clock time: 62 minutes 20.31 seconds (3740.31 seconds total)