Starting phenix.real_space_refine on Wed Mar 4 14:50:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7b54_12018/03_2026/7b54_12018.cif Found real_map, /net/cci-nas-00/data/ceres_data/7b54_12018/03_2026/7b54_12018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7b54_12018/03_2026/7b54_12018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7b54_12018/03_2026/7b54_12018.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7b54_12018/03_2026/7b54_12018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7b54_12018/03_2026/7b54_12018.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 95 5.16 5 C 8850 2.51 5 N 2424 2.21 5 O 2779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14148 Number of models: 1 Model: "" Number of chains: 1 Chain: "X" Number of atoms: 14148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1732, 14148 Classifications: {'peptide': 1732} Modifications used: {'COO': 1} Link IDs: {'CIS': 5, 'PCIS': 1, 'PTRANS': 46, 'TRANS': 1679} Chain breaks: 10 Time building chain proxies: 2.92, per 1000 atoms: 0.21 Number of scatterers: 14148 At special positions: 0 Unit cell: (104.58, 135.29, 141.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 95 16.00 O 2779 8.00 N 2424 7.00 C 8850 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS X 52 " - pdb=" SG CYS X 228 " distance=2.02 Simple disulfide: pdb=" SG CYS X 67 " - pdb=" SG CYS X 106 " distance=2.03 Simple disulfide: pdb=" SG CYS X 305 " - pdb=" SG CYS X 322 " distance=2.03 Simple disulfide: pdb=" SG CYS X 645 " - pdb=" SG CYS X 747 " distance=2.03 Simple disulfide: pdb=" SG CYS X 771 " - pdb=" SG CYS X 910 " distance=2.03 Simple disulfide: pdb=" SG CYS X 785 " - pdb=" SG CYS X 803 " distance=2.03 Simple disulfide: pdb=" SG CYS X 799 " - pdb=" SG CYS X 966 " distance=2.03 Simple disulfide: pdb=" SG CYS X 807 " - pdb=" SG CYS X 964 " distance=2.03 Simple disulfide: pdb=" SG CYS X 975 " - pdb=" SG CYS X1099 " distance=2.03 Simple disulfide: pdb=" SG CYS X 987 " - pdb=" SG CYS X1005 " distance=2.03 Simple disulfide: pdb=" SG CYS X1149 " - pdb=" SG CYS X1180 " distance=2.03 Simple disulfide: pdb=" SG CYS X1219 " - pdb=" SG CYS X1418 " distance=2.03 Simple disulfide: pdb=" SG CYS X1230 " - pdb=" SG CYS X1273 " distance=2.03 Simple disulfide: pdb=" SG CYS X1251 " - pdb=" SG CYS X1264 " distance=2.03 Simple disulfide: pdb=" SG CYS X1344 " - pdb=" SG CYS X1437 " distance=2.03 Simple disulfide: pdb=" SG CYS X1462 " - pdb=" SG CYS X1546 " distance=2.03 Simple disulfide: pdb=" SG CYS X1476 " - pdb=" SG CYS X1501 " distance=2.03 Simple disulfide: pdb=" SG CYS X1486 " - pdb=" SG CYS X1576 " distance=2.03 Simple disulfide: pdb=" SG CYS X1505 " - pdb=" SG CYS X1574 " distance=2.02 Simple disulfide: pdb=" SG CYS X1596 " - pdb=" SG CYS X1632 " distance=2.02 Simple disulfide: pdb=" SG CYS X1688 " - pdb=" SG CYS X1782 " distance=2.02 Simple disulfide: pdb=" SG CYS X1689 " - pdb=" SG CYS X1906 " distance=2.03 Simple disulfide: pdb=" SG CYS X1807 " - pdb=" SG CYS X1909 " distance=2.03 Simple disulfide: pdb=" SG CYS X1821 " - pdb=" SG CYS X1838 " distance=2.04 Simple disulfide: pdb=" SG CYS X1842 " - pdb=" SG CYS X1961 " distance=2.03 Simple disulfide: pdb=" SG CYS X1896 " - pdb=" SG CYS X1907 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 564.8 milliseconds 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3270 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 2 sheets defined 53.6% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'X' and resid 10 through 16 Processing helix chain 'X' and resid 22 through 29 Processing helix chain 'X' and resid 36 through 40 removed outlier: 3.727A pdb=" N SER X 40 " --> pdb=" O TYR X 37 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 54 removed outlier: 3.732A pdb=" N LYS X 53 " --> pdb=" O ASN X 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 99 through 105 Processing helix chain 'X' and resid 107 through 112 removed outlier: 3.790A pdb=" N GLU X 111 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing helix chain 'X' and resid 120 through 142 removed outlier: 3.892A pdb=" N PHE X 124 " --> pdb=" O ASP X 120 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 168 removed outlier: 3.616A pdb=" N ALA X 160 " --> pdb=" O GLU X 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 176 through 194 Processing helix chain 'X' and resid 208 through 218 Processing helix chain 'X' and resid 218 through 228 removed outlier: 4.066A pdb=" N VAL X 222 " --> pdb=" O ASN X 218 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N CYS X 228 " --> pdb=" O GLU X 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 274 through 300 removed outlier: 3.949A pdb=" N GLN X 292 " --> pdb=" O TYR X 288 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET X 298 " --> pdb=" O LEU X 294 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU X 299 " --> pdb=" O ILE X 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 316 through 349 removed outlier: 3.642A pdb=" N SER X 320 " --> pdb=" O THR X 316 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS X 327 " --> pdb=" O LYS X 323 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS X 334 " --> pdb=" O CYS X 330 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP X 349 " --> pdb=" O ASN X 345 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 377 removed outlier: 3.748A pdb=" N ASP X 372 " --> pdb=" O ASP X 368 " (cutoff:3.500A) Processing helix chain 'X' and resid 572 through 575 removed outlier: 3.529A pdb=" N ALA X 575 " --> pdb=" O GLU X 572 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 572 through 575' Processing helix chain 'X' and resid 582 through 586 Processing helix chain 'X' and resid 609 through 632 Processing helix chain 'X' and resid 641 through 661 Processing helix chain 'X' and resid 671 through 684 removed outlier: 3.528A pdb=" N LEU X 684 " --> pdb=" O ASN X 680 " (cutoff:3.500A) Processing helix chain 'X' and resid 703 through 727 removed outlier: 5.651A pdb=" N LYS X 717 " --> pdb=" O ASN X 713 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYR X 718 " --> pdb=" O THR X 714 " (cutoff:3.500A) Processing helix chain 'X' and resid 757 through 778 removed outlier: 4.448A pdb=" N TRP X 766 " --> pdb=" O PHE X 762 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ASN X 769 " --> pdb=" O GLU X 765 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN X 773 " --> pdb=" O ASN X 769 " (cutoff:3.500A) Processing helix chain 'X' and resid 779 through 784 Processing helix chain 'X' and resid 803 through 816 Processing helix chain 'X' and resid 830 through 852 Processing helix chain 'X' and resid 881 through 893 Processing helix chain 'X' and resid 896 through 905 Processing helix chain 'X' and resid 906 through 911 removed outlier: 3.967A pdb=" N CYS X 910 " --> pdb=" O ASP X 907 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY X 911 " --> pdb=" O ASN X 908 " (cutoff:3.500A) Processing helix chain 'X' and resid 941 through 945 Processing helix chain 'X' and resid 970 through 977 Processing helix chain 'X' and resid 1025 through 1053 Processing helix chain 'X' and resid 1094 through 1130 removed outlier: 4.288A pdb=" N TYR X1127 " --> pdb=" O SER X1123 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP X1128 " --> pdb=" O LYS X1124 " (cutoff:3.500A) Processing helix chain 'X' and resid 1141 through 1158 removed outlier: 3.921A pdb=" N TYR X1153 " --> pdb=" O CYS X1149 " (cutoff:3.500A) Processing helix chain 'X' and resid 1169 through 1181 Processing helix chain 'X' and resid 1188 through 1201 Processing helix chain 'X' and resid 1266 through 1271 Processing helix chain 'X' and resid 1274 through 1278 Processing helix chain 'X' and resid 1292 through 1318 Processing helix chain 'X' and resid 1342 through 1360 Processing helix chain 'X' and resid 1368 through 1378 Processing helix chain 'X' and resid 1398 through 1427 removed outlier: 3.504A pdb=" N ASN X1402 " --> pdb=" O THR X1398 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TRP X1404 " --> pdb=" O ASN X1400 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ARG X1410 " --> pdb=" O LYS X1406 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLU X1411 " --> pdb=" O GLY X1407 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS X1425 " --> pdb=" O THR X1421 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS X1426 " --> pdb=" O LYS X1422 " (cutoff:3.500A) Processing helix chain 'X' and resid 1443 through 1447 removed outlier: 3.837A pdb=" N ASP X1446 " --> pdb=" O THR X1443 " (cutoff:3.500A) Processing helix chain 'X' and resid 1448 through 1477 Processing helix chain 'X' and resid 1499 through 1530 removed outlier: 4.530A pdb=" N GLN X1517 " --> pdb=" O SER X1513 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU X1518 " --> pdb=" O GLU X1514 " (cutoff:3.500A) Processing helix chain 'X' and resid 1534 through 1543 Processing helix chain 'X' and resid 1550 through 1555 Processing helix chain 'X' and resid 1558 through 1565 Processing helix chain 'X' and resid 1567 through 1569 No H-bonds generated for 'chain 'X' and resid 1567 through 1569' Processing helix chain 'X' and resid 1570 through 1575 Processing helix chain 'X' and resid 1635 through 1643 removed outlier: 4.100A pdb=" N ILE X1639 " --> pdb=" O GLU X1635 " (cutoff:3.500A) Processing helix chain 'X' and resid 1650 through 1674 removed outlier: 3.539A pdb=" N TYR X1673 " --> pdb=" O LEU X1669 " (cutoff:3.500A) Processing helix chain 'X' and resid 1679 through 1703 Processing helix chain 'X' and resid 1712 through 1725 Processing helix chain 'X' and resid 1730 through 1744 Processing helix chain 'X' and resid 1755 through 1776 Processing helix chain 'X' and resid 1793 through 1822 Processing helix chain 'X' and resid 1827 through 1832 Processing helix chain 'X' and resid 1837 through 1867 removed outlier: 3.775A pdb=" N ALA X1841 " --> pdb=" O GLU X1837 " (cutoff:3.500A) Proline residue: X1851 - end of helix removed outlier: 3.784A pdb=" N ILE X1854 " --> pdb=" O ASN X1850 " (cutoff:3.500A) Processing helix chain 'X' and resid 1887 through 1894 removed outlier: 3.618A pdb=" N LYS X1894 " --> pdb=" O ASP X1890 " (cutoff:3.500A) Processing helix chain 'X' and resid 1942 through 1948 removed outlier: 3.526A pdb=" N ASN X1948 " --> pdb=" O ASN X1944 " (cutoff:3.500A) Processing helix chain 'X' and resid 1951 through 1984 removed outlier: 4.069A pdb=" N ALA X1956 " --> pdb=" O LYS X1952 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N HIS X1957 " --> pdb=" O LYS X1953 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N MET X1959 " --> pdb=" O SER X1955 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LYS X1960 " --> pdb=" O ALA X1956 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN X1974 " --> pdb=" O GLU X1970 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU X1975 " --> pdb=" O GLU X1971 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 569 through 570 Processing sheet with id=AA2, first strand: chain 'X' and resid 923 through 925 652 hydrogen bonds defined for protein. 1917 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: 2.57 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4404 1.33 - 1.46: 2382 1.46 - 1.58: 7533 1.58 - 1.70: 1 1.70 - 1.82: 115 Bond restraints: 14435 Sorted by residual: bond pdb=" CA ASN X 597 " pdb=" CB ASN X 597 " ideal model delta sigma weight residual 1.526 1.585 -0.059 1.76e-02 3.23e+03 1.12e+01 bond pdb=" C SER X 951 " pdb=" N PRO X 952 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.42e+00 bond pdb=" C TYR X1565 " pdb=" N PRO X1566 " ideal model delta sigma weight residual 1.337 1.322 0.015 9.80e-03 1.04e+04 2.32e+00 bond pdb=" CB CYS X1961 " pdb=" SG CYS X1961 " ideal model delta sigma weight residual 1.808 1.761 0.047 3.30e-02 9.18e+02 2.02e+00 bond pdb=" CG LEU X1947 " pdb=" CD1 LEU X1947 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.95e+00 ... (remaining 14430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 18710 1.79 - 3.58: 548 3.58 - 5.37: 120 5.37 - 7.16: 24 7.16 - 8.95: 11 Bond angle restraints: 19413 Sorted by residual: angle pdb=" N TYR X 366 " pdb=" CA TYR X 366 " pdb=" CB TYR X 366 " ideal model delta sigma weight residual 114.17 107.78 6.39 1.14e+00 7.69e-01 3.14e+01 angle pdb=" N LYS X1894 " pdb=" CA LYS X1894 " pdb=" C LYS X1894 " ideal model delta sigma weight residual 112.59 106.56 6.03 1.22e+00 6.72e-01 2.44e+01 angle pdb=" C CYS X 256 " pdb=" N ARG X 257 " pdb=" CA ARG X 257 " ideal model delta sigma weight residual 121.70 130.26 -8.56 1.80e+00 3.09e-01 2.26e+01 angle pdb=" C GLU X1648 " pdb=" N LYS X1649 " pdb=" CA LYS X1649 " ideal model delta sigma weight residual 121.54 130.49 -8.95 1.91e+00 2.74e-01 2.20e+01 angle pdb=" C GLN X 524 " pdb=" N ASP X 525 " pdb=" CA ASP X 525 " ideal model delta sigma weight residual 121.54 129.67 -8.13 1.91e+00 2.74e-01 1.81e+01 ... (remaining 19408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 7974 17.87 - 35.74: 700 35.74 - 53.61: 112 53.61 - 71.48: 53 71.48 - 89.35: 23 Dihedral angle restraints: 8862 sinusoidal: 3775 harmonic: 5087 Sorted by residual: dihedral pdb=" CA TYR X 701 " pdb=" C TYR X 701 " pdb=" N SER X 702 " pdb=" CA SER X 702 " ideal model delta harmonic sigma weight residual -180.00 -128.60 -51.40 0 5.00e+00 4.00e-02 1.06e+02 dihedral pdb=" CA SER X 951 " pdb=" C SER X 951 " pdb=" N PRO X 952 " pdb=" CA PRO X 952 " ideal model delta harmonic sigma weight residual 180.00 130.74 49.26 0 5.00e+00 4.00e-02 9.71e+01 dihedral pdb=" CB CYS X1821 " pdb=" SG CYS X1821 " pdb=" SG CYS X1838 " pdb=" CB CYS X1838 " ideal model delta sinusoidal sigma weight residual 93.00 6.31 86.69 1 1.00e+01 1.00e-02 9.05e+01 ... (remaining 8859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1567 0.052 - 0.105: 376 0.105 - 0.157: 40 0.157 - 0.210: 4 0.210 - 0.262: 2 Chirality restraints: 1989 Sorted by residual: chirality pdb=" CB ILE X 753 " pdb=" CA ILE X 753 " pdb=" CG1 ILE X 753 " pdb=" CG2 ILE X 753 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CB ILE X1905 " pdb=" CA ILE X1905 " pdb=" CG1 ILE X1905 " pdb=" CG2 ILE X1905 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB ILE X 689 " pdb=" CA ILE X 689 " pdb=" CG1 ILE X 689 " pdb=" CG2 ILE X 689 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.31e-01 ... (remaining 1986 not shown) Planarity restraints: 2520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP X 766 " 0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C TRP X 766 " -0.069 2.00e-02 2.50e+03 pdb=" O TRP X 766 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL X 767 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS X 671 " 0.019 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C LYS X 671 " -0.068 2.00e-02 2.50e+03 pdb=" O LYS X 671 " 0.025 2.00e-02 2.50e+03 pdb=" N ASP X 672 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER X 951 " -0.060 5.00e-02 4.00e+02 9.19e-02 1.35e+01 pdb=" N PRO X 952 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO X 952 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO X 952 " -0.050 5.00e-02 4.00e+02 ... (remaining 2517 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 251 2.64 - 3.21: 14651 3.21 - 3.77: 23441 3.77 - 4.34: 31474 4.34 - 4.90: 49810 Nonbonded interactions: 119627 Sorted by model distance: nonbonded pdb=" OH TYR X1100 " pdb=" O ALA X1198 " model vdw 2.081 3.040 nonbonded pdb=" OG SER X1726 " pdb=" OD1 ASN X1728 " model vdw 2.159 3.040 nonbonded pdb=" OE2 GLU X 624 " pdb=" OG SER X 651 " model vdw 2.177 3.040 nonbonded pdb=" NH1 ARG X 157 " pdb=" OE2 GLU X 282 " model vdw 2.194 3.120 nonbonded pdb=" OH TYR X1118 " pdb=" O VAL X1139 " model vdw 2.208 3.040 ... (remaining 119622 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: 8.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.670 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.005 0.059 14461 Z= 0.215 Angle : 0.777 9.176 19465 Z= 0.450 Chirality : 0.045 0.262 1989 Planarity : 0.005 0.092 2520 Dihedral : 14.530 89.355 5514 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.46 % Favored : 87.13 % Rotamer: Outliers : 0.19 % Allowed : 0.64 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.21), residues: 1710 helix: 1.14 (0.18), residues: 873 sheet: -5.33 (0.83), residues: 12 loop : -3.16 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 157 TYR 0.042 0.002 TYR X 655 PHE 0.020 0.002 PHE X1121 TRP 0.055 0.002 TRP X 558 HIS 0.009 0.001 HIS X 845 Details of bonding type rmsd covalent geometry : bond 0.00461 (14435) covalent geometry : angle 0.77332 (19413) SS BOND : bond 0.00445 ( 26) SS BOND : angle 1.65772 ( 52) hydrogen bonds : bond 0.09904 ( 652) hydrogen bonds : angle 5.05558 ( 1917) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.570 Fit side-chains revert: symmetry clash REVERT: X 854 LYS cc_start: 0.9062 (mppt) cc_final: 0.8842 (mppt) REVERT: X 1412 MET cc_start: 0.9322 (mmp) cc_final: 0.8813 (mmm) REVERT: X 1432 PHE cc_start: 0.7343 (m-80) cc_final: 0.6869 (m-80) REVERT: X 1647 MET cc_start: 0.7376 (mpp) cc_final: 0.7071 (mpp) outliers start: 3 outliers final: 1 residues processed: 78 average time/residue: 0.1475 time to fit residues: 16.5412 Evaluate side-chains 59 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 1900 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1356 ASN X1449 GLN ** X1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.107914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.072704 restraints weight = 43631.102| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 4.27 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.0765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14461 Z= 0.198 Angle : 0.694 8.967 19465 Z= 0.379 Chirality : 0.044 0.224 1989 Planarity : 0.005 0.089 2520 Dihedral : 6.736 50.732 1881 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.35 % Allowed : 12.22 % Favored : 87.43 % Rotamer: Outliers : 0.45 % Allowed : 5.74 % Favored : 93.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.21), residues: 1710 helix: 1.34 (0.18), residues: 862 sheet: -5.30 (0.70), residues: 10 loop : -3.07 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 157 TYR 0.027 0.002 TYR X 655 PHE 0.019 0.002 PHE X1121 TRP 0.022 0.002 TRP X 214 HIS 0.007 0.001 HIS X 845 Details of bonding type rmsd covalent geometry : bond 0.00439 (14435) covalent geometry : angle 0.69258 (19413) SS BOND : bond 0.00432 ( 26) SS BOND : angle 1.09473 ( 52) hydrogen bonds : bond 0.04516 ( 652) hydrogen bonds : angle 4.75403 ( 1917) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 133 ARG cc_start: 0.8106 (tpt170) cc_final: 0.7894 (tpm170) REVERT: X 298 MET cc_start: 0.7432 (ppp) cc_final: 0.6886 (mmt) REVERT: X 573 GLU cc_start: 0.8455 (tp30) cc_final: 0.8245 (tp30) REVERT: X 624 GLU cc_start: 0.8461 (tp30) cc_final: 0.8213 (tp30) REVERT: X 854 LYS cc_start: 0.8976 (mppt) cc_final: 0.8703 (mppt) REVERT: X 1412 MET cc_start: 0.9408 (mmp) cc_final: 0.8856 (mmm) REVERT: X 1442 PRO cc_start: 0.8455 (Cg_endo) cc_final: 0.8227 (Cg_exo) REVERT: X 1647 MET cc_start: 0.7418 (mpp) cc_final: 0.6979 (mpp) REVERT: X 1943 MET cc_start: 0.8204 (tmm) cc_final: 0.7873 (tmm) outliers start: 7 outliers final: 1 residues processed: 67 average time/residue: 0.1429 time to fit residues: 13.7090 Evaluate side-chains 60 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 207 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 44 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 4 optimal weight: 8.9990 chunk 165 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.109388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.074591 restraints weight = 44203.209| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 4.30 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14461 Z= 0.130 Angle : 0.634 8.959 19465 Z= 0.344 Chirality : 0.041 0.174 1989 Planarity : 0.005 0.088 2520 Dihedral : 6.430 52.986 1879 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.17 % Favored : 88.48 % Rotamer: Outliers : 0.96 % Allowed : 7.59 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.21), residues: 1710 helix: 1.45 (0.18), residues: 870 sheet: -5.28 (0.68), residues: 10 loop : -3.05 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 853 TYR 0.017 0.001 TYR X 655 PHE 0.017 0.002 PHE X 159 TRP 0.016 0.001 TRP X 560 HIS 0.005 0.001 HIS X1787 Details of bonding type rmsd covalent geometry : bond 0.00276 (14435) covalent geometry : angle 0.63325 (19413) SS BOND : bond 0.00317 ( 26) SS BOND : angle 0.90946 ( 52) hydrogen bonds : bond 0.04061 ( 652) hydrogen bonds : angle 4.55522 ( 1917) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 134 ASN cc_start: 0.7892 (m-40) cc_final: 0.7504 (m110) REVERT: X 298 MET cc_start: 0.7467 (ppp) cc_final: 0.6881 (mmt) REVERT: X 573 GLU cc_start: 0.8329 (tp30) cc_final: 0.8021 (tp30) REVERT: X 624 GLU cc_start: 0.8322 (tp30) cc_final: 0.8106 (tp30) REVERT: X 706 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7902 (tm-30) REVERT: X 1044 TYR cc_start: 0.8881 (t80) cc_final: 0.8617 (t80) REVERT: X 1047 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8633 (mm-30) REVERT: X 1307 GLU cc_start: 0.9327 (pp20) cc_final: 0.8927 (pp20) REVERT: X 1412 MET cc_start: 0.9378 (mmp) cc_final: 0.8832 (mmm) REVERT: X 1442 PRO cc_start: 0.8280 (Cg_endo) cc_final: 0.8063 (Cg_exo) REVERT: X 1647 MET cc_start: 0.7493 (mpp) cc_final: 0.7074 (mpp) REVERT: X 1866 ILE cc_start: 0.8927 (tp) cc_final: 0.8632 (tp) REVERT: X 1943 MET cc_start: 0.8260 (tmm) cc_final: 0.7779 (tmm) outliers start: 15 outliers final: 8 residues processed: 94 average time/residue: 0.1321 time to fit residues: 18.0192 Evaluate side-chains 74 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 137 GLU Chi-restraints excluded: chain X residue 207 TYR Chi-restraints excluded: chain X residue 306 THR Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 949 VAL Chi-restraints excluded: chain X residue 1186 HIS Chi-restraints excluded: chain X residue 1190 ILE Chi-restraints excluded: chain X residue 1961 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 2 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 676 ASN ** X1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1948 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 = 0.4037 r_free = 0.4037 target = 0.108262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.073001 restraints weight = 44197.982| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 4.45 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14461 Z= 0.187 Angle : 0.650 8.905 19465 Z= 0.352 Chirality : 0.042 0.164 1989 Planarity : 0.005 0.098 2520 Dihedral : 6.362 52.962 1879 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.46 % Favored : 88.19 % Rotamer: Outliers : 1.34 % Allowed : 8.67 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.21), residues: 1710 helix: 1.49 (0.18), residues: 867 sheet: -5.38 (0.67), residues: 10 loop : -3.06 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 853 TYR 0.016 0.001 TYR X1314 PHE 0.018 0.002 PHE X1121 TRP 0.022 0.001 TRP X 214 HIS 0.005 0.001 HIS X1787 Details of bonding type rmsd covalent geometry : bond 0.00416 (14435) covalent geometry : angle 0.64883 (19413) SS BOND : bond 0.00404 ( 26) SS BOND : angle 0.98840 ( 52) hydrogen bonds : bond 0.04156 ( 652) hydrogen bonds : angle 4.58203 ( 1917) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 0.391 Fit side-chains revert: symmetry clash REVERT: X 134 ASN cc_start: 0.7816 (m-40) cc_final: 0.7520 (m110) REVERT: X 152 CYS cc_start: 0.7185 (t) cc_final: 0.6933 (t) REVERT: X 298 MET cc_start: 0.7592 (ppp) cc_final: 0.7034 (mmt) REVERT: X 573 GLU cc_start: 0.8472 (tp30) cc_final: 0.8145 (tp30) REVERT: X 624 GLU cc_start: 0.8416 (tp30) cc_final: 0.8197 (tp30) REVERT: X 1166 LYS cc_start: 0.9432 (OUTLIER) cc_final: 0.9149 (pttm) REVERT: X 1307 GLU cc_start: 0.9356 (pp20) cc_final: 0.8963 (pp20) REVERT: X 1412 MET cc_start: 0.9389 (mmp) cc_final: 0.8831 (mmm) REVERT: X 1647 MET cc_start: 0.7595 (mpp) cc_final: 0.7138 (mpp) REVERT: X 1866 ILE cc_start: 0.9011 (tp) cc_final: 0.8691 (tp) REVERT: X 1943 MET cc_start: 0.8450 (tmm) cc_final: 0.7929 (tmm) outliers start: 21 outliers final: 13 residues processed: 87 average time/residue: 0.1182 time to fit residues: 15.0059 Evaluate side-chains 75 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 207 TYR Chi-restraints excluded: chain X residue 306 THR Chi-restraints excluded: chain X residue 559 ILE Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 801 THR Chi-restraints excluded: chain X residue 949 VAL Chi-restraints excluded: chain X residue 1141 LEU Chi-restraints excluded: chain X residue 1166 LYS Chi-restraints excluded: chain X residue 1186 HIS Chi-restraints excluded: chain X residue 1190 ILE Chi-restraints excluded: chain X residue 1559 ILE Chi-restraints excluded: chain X residue 1672 GLN Chi-restraints excluded: chain X residue 1838 CYS Chi-restraints excluded: chain X residue 1961 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 4 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 97 optimal weight: 0.2980 chunk 170 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 585 GLN X1765 GLN ** X1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.109289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.074090 restraints weight = 43817.311| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 4.29 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14461 Z= 0.133 Angle : 0.621 8.964 19465 Z= 0.335 Chirality : 0.041 0.162 1989 Planarity : 0.005 0.087 2520 Dihedral : 6.236 54.508 1879 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.35 % Favored : 88.30 % Rotamer: Outliers : 1.02 % Allowed : 10.08 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.21), residues: 1710 helix: 1.58 (0.18), residues: 866 sheet: -5.08 (0.72), residues: 10 loop : -3.05 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 853 TYR 0.019 0.001 TYR X1044 PHE 0.017 0.002 PHE X 159 TRP 0.018 0.001 TRP X 223 HIS 0.006 0.001 HIS X1787 Details of bonding type rmsd covalent geometry : bond 0.00286 (14435) covalent geometry : angle 0.62027 (19413) SS BOND : bond 0.00321 ( 26) SS BOND : angle 0.92157 ( 52) hydrogen bonds : bond 0.03936 ( 652) hydrogen bonds : angle 4.49706 ( 1917) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 0.532 Fit side-chains REVERT: X 134 ASN cc_start: 0.7951 (m-40) cc_final: 0.7558 (m110) REVERT: X 185 GLN cc_start: 0.9013 (OUTLIER) cc_final: 0.8765 (pm20) REVERT: X 298 MET cc_start: 0.7536 (ppp) cc_final: 0.7071 (mmt) REVERT: X 573 GLU cc_start: 0.8432 (tp30) cc_final: 0.8082 (tp30) REVERT: X 624 GLU cc_start: 0.8401 (tp30) cc_final: 0.8160 (tp30) REVERT: X 706 GLU cc_start: 0.8524 (tm-30) cc_final: 0.7925 (tm-30) REVERT: X 1166 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9176 (pttm) REVERT: X 1307 GLU cc_start: 0.9361 (pp20) cc_final: 0.8958 (pp20) REVERT: X 1412 MET cc_start: 0.9373 (mmp) cc_final: 0.8841 (mmm) REVERT: X 1647 MET cc_start: 0.7602 (mpp) cc_final: 0.7136 (mpp) REVERT: X 1866 ILE cc_start: 0.8973 (tp) cc_final: 0.8662 (tp) REVERT: X 1943 MET cc_start: 0.8445 (tmm) cc_final: 0.7936 (tmm) outliers start: 16 outliers final: 13 residues processed: 83 average time/residue: 0.1277 time to fit residues: 15.6043 Evaluate side-chains 75 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 185 GLN Chi-restraints excluded: chain X residue 207 TYR Chi-restraints excluded: chain X residue 306 THR Chi-restraints excluded: chain X residue 558 TRP Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 801 THR Chi-restraints excluded: chain X residue 949 VAL Chi-restraints excluded: chain X residue 1141 LEU Chi-restraints excluded: chain X residue 1166 LYS Chi-restraints excluded: chain X residue 1186 HIS Chi-restraints excluded: chain X residue 1190 ILE Chi-restraints excluded: chain X residue 1622 VAL Chi-restraints excluded: chain X residue 1838 CYS Chi-restraints excluded: chain X residue 1961 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 57 optimal weight: 4.9990 chunk 38 optimal weight: 20.0000 chunk 153 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 164 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1833 ASN X1897 HIS ** X1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.106656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.071022 restraints weight = 44273.978| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 4.27 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 14461 Z= 0.298 Angle : 0.705 9.151 19465 Z= 0.384 Chirality : 0.045 0.165 1989 Planarity : 0.005 0.089 2520 Dihedral : 6.410 56.404 1879 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.40 % Favored : 87.19 % Rotamer: Outliers : 1.66 % Allowed : 10.46 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.54 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.21), residues: 1710 helix: 1.46 (0.18), residues: 863 sheet: -5.75 (0.55), residues: 10 loop : -3.07 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 257 TYR 0.019 0.002 TYR X1314 PHE 0.021 0.002 PHE X1121 TRP 0.031 0.002 TRP X 214 HIS 0.007 0.001 HIS X1709 Details of bonding type rmsd covalent geometry : bond 0.00668 (14435) covalent geometry : angle 0.70385 (19413) SS BOND : bond 0.00540 ( 26) SS BOND : angle 1.15997 ( 52) hydrogen bonds : bond 0.04435 ( 652) hydrogen bonds : angle 4.67289 ( 1917) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.509 Fit side-chains REVERT: X 134 ASN cc_start: 0.8147 (m-40) cc_final: 0.7758 (m110) REVERT: X 185 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8818 (pm20) REVERT: X 298 MET cc_start: 0.7554 (ppp) cc_final: 0.7077 (mmt) REVERT: X 573 GLU cc_start: 0.8508 (tp30) cc_final: 0.8185 (tp30) REVERT: X 1166 LYS cc_start: 0.9428 (OUTLIER) cc_final: 0.9135 (pttm) REVERT: X 1412 MET cc_start: 0.9392 (mmp) cc_final: 0.8850 (mmm) REVERT: X 1432 PHE cc_start: 0.7470 (m-80) cc_final: 0.6828 (m-80) REVERT: X 1647 MET cc_start: 0.7786 (mpp) cc_final: 0.7240 (mpp) REVERT: X 1943 MET cc_start: 0.8627 (tmm) cc_final: 0.8211 (tmm) outliers start: 26 outliers final: 15 residues processed: 82 average time/residue: 0.1346 time to fit residues: 16.0604 Evaluate side-chains 73 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 185 GLN Chi-restraints excluded: chain X residue 207 TYR Chi-restraints excluded: chain X residue 306 THR Chi-restraints excluded: chain X residue 559 ILE Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 801 THR Chi-restraints excluded: chain X residue 949 VAL Chi-restraints excluded: chain X residue 1141 LEU Chi-restraints excluded: chain X residue 1166 LYS Chi-restraints excluded: chain X residue 1186 HIS Chi-restraints excluded: chain X residue 1190 ILE Chi-restraints excluded: chain X residue 1559 ILE Chi-restraints excluded: chain X residue 1622 VAL Chi-restraints excluded: chain X residue 1672 GLN Chi-restraints excluded: chain X residue 1838 CYS Chi-restraints excluded: chain X residue 1905 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 165 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.109036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.074263 restraints weight = 44122.730| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.21 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14461 Z= 0.137 Angle : 0.638 10.296 19465 Z= 0.344 Chirality : 0.041 0.164 1989 Planarity : 0.005 0.082 2520 Dihedral : 6.295 57.482 1879 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.35 % Favored : 88.30 % Rotamer: Outliers : 1.15 % Allowed : 11.48 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.60 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.21), residues: 1710 helix: 1.54 (0.18), residues: 869 sheet: -5.30 (0.63), residues: 10 loop : -3.04 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG X 133 TYR 0.015 0.001 TYR X1127 PHE 0.016 0.001 PHE X1121 TRP 0.025 0.001 TRP X 223 HIS 0.006 0.001 HIS X1787 Details of bonding type rmsd covalent geometry : bond 0.00296 (14435) covalent geometry : angle 0.63688 (19413) SS BOND : bond 0.00293 ( 26) SS BOND : angle 0.94047 ( 52) hydrogen bonds : bond 0.04016 ( 652) hydrogen bonds : angle 4.52274 ( 1917) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 63 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: X 134 ASN cc_start: 0.7948 (m-40) cc_final: 0.7562 (m110) REVERT: X 257 ARG cc_start: 0.6601 (mpt180) cc_final: 0.6003 (mmt180) REVERT: X 573 GLU cc_start: 0.8392 (tp30) cc_final: 0.8050 (tp30) REVERT: X 624 GLU cc_start: 0.8310 (tp30) cc_final: 0.8042 (tp30) REVERT: X 1166 LYS cc_start: 0.9400 (OUTLIER) cc_final: 0.9127 (pttm) REVERT: X 1412 MET cc_start: 0.9353 (mmp) cc_final: 0.8803 (mmm) REVERT: X 1432 PHE cc_start: 0.7319 (m-80) cc_final: 0.6749 (m-80) REVERT: X 1442 PRO cc_start: 0.8566 (Cg_endo) cc_final: 0.8357 (Cg_exo) REVERT: X 1647 MET cc_start: 0.7648 (mpp) cc_final: 0.7142 (mpp) REVERT: X 1866 ILE cc_start: 0.9016 (tp) cc_final: 0.8700 (tp) REVERT: X 1943 MET cc_start: 0.8471 (tmm) cc_final: 0.8074 (tmm) outliers start: 18 outliers final: 14 residues processed: 79 average time/residue: 0.1452 time to fit residues: 16.4874 Evaluate side-chains 70 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 207 TYR Chi-restraints excluded: chain X residue 306 THR Chi-restraints excluded: chain X residue 558 TRP Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 797 THR Chi-restraints excluded: chain X residue 801 THR Chi-restraints excluded: chain X residue 949 VAL Chi-restraints excluded: chain X residue 1141 LEU Chi-restraints excluded: chain X residue 1166 LYS Chi-restraints excluded: chain X residue 1186 HIS Chi-restraints excluded: chain X residue 1190 ILE Chi-restraints excluded: chain X residue 1559 ILE Chi-restraints excluded: chain X residue 1622 VAL Chi-restraints excluded: chain X residue 1672 GLN Chi-restraints excluded: chain X residue 1838 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 153 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 110 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 678 GLN ** X1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1948 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 = 0.4042 r_free = 0.4042 target = 0.109057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.073443 restraints weight = 43833.556| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.36 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14461 Z= 0.142 Angle : 0.658 20.971 19465 Z= 0.349 Chirality : 0.041 0.160 1989 Planarity : 0.005 0.081 2520 Dihedral : 6.203 57.009 1879 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.58 % Favored : 88.07 % Rotamer: Outliers : 1.21 % Allowed : 11.93 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.21), residues: 1710 helix: 1.56 (0.18), residues: 868 sheet: -5.15 (0.64), residues: 10 loop : -3.07 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG X 133 TYR 0.016 0.001 TYR X1127 PHE 0.017 0.001 PHE X 187 TRP 0.031 0.001 TRP X 223 HIS 0.006 0.001 HIS X1787 Details of bonding type rmsd covalent geometry : bond 0.00312 (14435) covalent geometry : angle 0.65652 (19413) SS BOND : bond 0.00308 ( 26) SS BOND : angle 0.96903 ( 52) hydrogen bonds : bond 0.03976 ( 652) hydrogen bonds : angle 4.50494 ( 1917) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.521 Fit side-chains REVERT: X 134 ASN cc_start: 0.7960 (m-40) cc_final: 0.7543 (m110) REVERT: X 257 ARG cc_start: 0.6682 (mpt180) cc_final: 0.6221 (mmt180) REVERT: X 298 MET cc_start: 0.7024 (tpt) cc_final: 0.6749 (ppp) REVERT: X 573 GLU cc_start: 0.8421 (tp30) cc_final: 0.8069 (tp30) REVERT: X 624 GLU cc_start: 0.8305 (tp30) cc_final: 0.8037 (tp30) REVERT: X 1166 LYS cc_start: 0.9409 (OUTLIER) cc_final: 0.9164 (pttm) REVERT: X 1412 MET cc_start: 0.9362 (mmp) cc_final: 0.8837 (mmm) REVERT: X 1442 PRO cc_start: 0.8455 (Cg_endo) cc_final: 0.8224 (Cg_exo) REVERT: X 1647 MET cc_start: 0.7626 (mpp) cc_final: 0.7130 (mpp) REVERT: X 1866 ILE cc_start: 0.8999 (tp) cc_final: 0.8679 (tp) REVERT: X 1943 MET cc_start: 0.8481 (tmm) cc_final: 0.8085 (tmm) outliers start: 19 outliers final: 16 residues processed: 75 average time/residue: 0.1411 time to fit residues: 15.1496 Evaluate side-chains 75 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 207 TYR Chi-restraints excluded: chain X residue 306 THR Chi-restraints excluded: chain X residue 558 TRP Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 797 THR Chi-restraints excluded: chain X residue 801 THR Chi-restraints excluded: chain X residue 949 VAL Chi-restraints excluded: chain X residue 1141 LEU Chi-restraints excluded: chain X residue 1166 LYS Chi-restraints excluded: chain X residue 1190 ILE Chi-restraints excluded: chain X residue 1559 ILE Chi-restraints excluded: chain X residue 1622 VAL Chi-restraints excluded: chain X residue 1672 GLN Chi-restraints excluded: chain X residue 1838 CYS Chi-restraints excluded: chain X residue 1961 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 148 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 chunk 129 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 172 optimal weight: 0.7980 chunk 33 optimal weight: 0.3980 chunk 64 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.108527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.073035 restraints weight = 43566.329| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 4.30 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14461 Z= 0.173 Angle : 0.655 18.811 19465 Z= 0.350 Chirality : 0.042 0.161 1989 Planarity : 0.005 0.082 2520 Dihedral : 6.198 56.932 1879 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.64 % Favored : 88.01 % Rotamer: Outliers : 1.34 % Allowed : 12.18 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.21), residues: 1710 helix: 1.59 (0.18), residues: 862 sheet: -5.21 (0.64), residues: 10 loop : -3.04 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG X 133 TYR 0.016 0.001 TYR X1127 PHE 0.017 0.001 PHE X1121 TRP 0.037 0.001 TRP X 223 HIS 0.005 0.001 HIS X1787 Details of bonding type rmsd covalent geometry : bond 0.00384 (14435) covalent geometry : angle 0.65432 (19413) SS BOND : bond 0.00346 ( 26) SS BOND : angle 0.98583 ( 52) hydrogen bonds : bond 0.04032 ( 652) hydrogen bonds : angle 4.51150 ( 1917) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.502 Fit side-chains REVERT: X 134 ASN cc_start: 0.8018 (m-40) cc_final: 0.7639 (m110) REVERT: X 257 ARG cc_start: 0.6596 (mpt180) cc_final: 0.6182 (mmt180) REVERT: X 298 MET cc_start: 0.7142 (tpt) cc_final: 0.6787 (ppp) REVERT: X 573 GLU cc_start: 0.8470 (tp30) cc_final: 0.8120 (tp30) REVERT: X 624 GLU cc_start: 0.8360 (tp30) cc_final: 0.8062 (tp30) REVERT: X 1166 LYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9176 (pttm) REVERT: X 1412 MET cc_start: 0.9358 (mmp) cc_final: 0.8843 (mmm) REVERT: X 1432 PHE cc_start: 0.7358 (m-80) cc_final: 0.6767 (m-80) REVERT: X 1442 PRO cc_start: 0.8501 (Cg_endo) cc_final: 0.8283 (Cg_exo) REVERT: X 1647 MET cc_start: 0.7690 (mpp) cc_final: 0.7177 (mpp) REVERT: X 1866 ILE cc_start: 0.9025 (tp) cc_final: 0.8684 (tp) REVERT: X 1943 MET cc_start: 0.8535 (tmm) cc_final: 0.8130 (tmm) outliers start: 21 outliers final: 16 residues processed: 74 average time/residue: 0.1384 time to fit residues: 14.8999 Evaluate side-chains 74 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 207 TYR Chi-restraints excluded: chain X residue 306 THR Chi-restraints excluded: chain X residue 558 TRP Chi-restraints excluded: chain X residue 559 ILE Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 797 THR Chi-restraints excluded: chain X residue 801 THR Chi-restraints excluded: chain X residue 949 VAL Chi-restraints excluded: chain X residue 1141 LEU Chi-restraints excluded: chain X residue 1166 LYS Chi-restraints excluded: chain X residue 1186 HIS Chi-restraints excluded: chain X residue 1190 ILE Chi-restraints excluded: chain X residue 1559 ILE Chi-restraints excluded: chain X residue 1622 VAL Chi-restraints excluded: chain X residue 1672 GLN Chi-restraints excluded: chain X residue 1838 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 38 optimal weight: 20.0000 chunk 40 optimal weight: 40.0000 chunk 16 optimal weight: 10.0000 chunk 120 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.0980 chunk 1 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 138 optimal weight: 0.0170 chunk 125 optimal weight: 10.0000 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.109059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.073878 restraints weight = 43960.814| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 4.25 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14461 Z= 0.147 Angle : 0.649 18.715 19465 Z= 0.345 Chirality : 0.041 0.160 1989 Planarity : 0.005 0.081 2520 Dihedral : 6.152 57.381 1879 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.11 % Favored : 88.54 % Rotamer: Outliers : 1.21 % Allowed : 12.44 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.21), residues: 1710 helix: 1.60 (0.18), residues: 868 sheet: -5.08 (0.67), residues: 10 loop : -3.03 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG X 853 TYR 0.017 0.001 TYR X1127 PHE 0.016 0.001 PHE X1121 TRP 0.047 0.001 TRP X 223 HIS 0.006 0.001 HIS X1787 Details of bonding type rmsd covalent geometry : bond 0.00324 (14435) covalent geometry : angle 0.64841 (19413) SS BOND : bond 0.00314 ( 26) SS BOND : angle 0.94745 ( 52) hydrogen bonds : bond 0.03924 ( 652) hydrogen bonds : angle 4.47946 ( 1917) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3420 Ramachandran restraints generated. 1710 Oldfield, 0 Emsley, 1710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 63 time to evaluate : 0.512 Fit side-chains REVERT: X 133 ARG cc_start: 0.8086 (tpt90) cc_final: 0.7863 (tpm170) REVERT: X 134 ASN cc_start: 0.8062 (m-40) cc_final: 0.7755 (m110) REVERT: X 257 ARG cc_start: 0.6626 (mpt180) cc_final: 0.6221 (mmt180) REVERT: X 298 MET cc_start: 0.7039 (tpt) cc_final: 0.6732 (ppp) REVERT: X 573 GLU cc_start: 0.8431 (tp30) cc_final: 0.8083 (tp30) REVERT: X 624 GLU cc_start: 0.8291 (tp30) cc_final: 0.8045 (tp30) REVERT: X 1166 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9156 (pttm) REVERT: X 1412 MET cc_start: 0.9343 (mmp) cc_final: 0.8866 (mmm) REVERT: X 1432 PHE cc_start: 0.7341 (m-80) cc_final: 0.6734 (m-80) REVERT: X 1442 PRO cc_start: 0.8482 (Cg_endo) cc_final: 0.8261 (Cg_exo) REVERT: X 1647 MET cc_start: 0.7635 (mpp) cc_final: 0.7166 (mpp) REVERT: X 1866 ILE cc_start: 0.9017 (tp) cc_final: 0.8695 (tp) REVERT: X 1903 ASN cc_start: 0.8165 (m-40) cc_final: 0.7630 (p0) REVERT: X 1943 MET cc_start: 0.8524 (tmm) cc_final: 0.8149 (tmm) outliers start: 19 outliers final: 17 residues processed: 78 average time/residue: 0.1242 time to fit residues: 14.2405 Evaluate side-chains 78 residues out of total 1568 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 207 TYR Chi-restraints excluded: chain X residue 306 THR Chi-restraints excluded: chain X residue 558 TRP Chi-restraints excluded: chain X residue 559 ILE Chi-restraints excluded: chain X residue 595 LEU Chi-restraints excluded: chain X residue 797 THR Chi-restraints excluded: chain X residue 801 THR Chi-restraints excluded: chain X residue 949 VAL Chi-restraints excluded: chain X residue 1141 LEU Chi-restraints excluded: chain X residue 1166 LYS Chi-restraints excluded: chain X residue 1186 HIS Chi-restraints excluded: chain X residue 1190 ILE Chi-restraints excluded: chain X residue 1559 ILE Chi-restraints excluded: chain X residue 1622 VAL Chi-restraints excluded: chain X residue 1672 GLN Chi-restraints excluded: chain X residue 1838 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 52 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 143 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 14 optimal weight: 0.0040 chunk 109 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.108570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.073037 restraints weight = 43625.538| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 4.36 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14461 Z= 0.170 Angle : 0.651 18.157 19465 Z= 0.348 Chirality : 0.042 0.163 1989 Planarity : 0.005 0.081 2520 Dihedral : 6.161 57.031 1879 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.52 % Favored : 88.13 % Rotamer: Outliers : 1.21 % Allowed : 12.56 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.21), residues: 1710 helix: 1.63 (0.18), residues: 862 sheet: -5.12 (0.68), residues: 10 loop : -3.01 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG X 133 TYR 0.017 0.001 TYR X1127 PHE 0.016 0.001 PHE X1121 TRP 0.053 0.002 TRP X 223 HIS 0.006 0.001 HIS X1787 Details of bonding type rmsd covalent geometry : bond 0.00378 (14435) covalent geometry : angle 0.64990 (19413) SS BOND : bond 0.00342 ( 26) SS BOND : angle 1.00130 ( 52) hydrogen bonds : bond 0.03990 ( 652) hydrogen bonds : angle 4.48476 ( 1917) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3258.26 seconds wall clock time: 56 minutes 54.51 seconds (3414.51 seconds total)