Starting phenix.real_space_refine on Sat Jan 20 08:05:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b54_12018/01_2024/7b54_12018.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b54_12018/01_2024/7b54_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b54_12018/01_2024/7b54_12018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b54_12018/01_2024/7b54_12018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b54_12018/01_2024/7b54_12018.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b54_12018/01_2024/7b54_12018.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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 Residue "X TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 21": "OD1" <-> "OD2" Residue "X GLU 26": "OE1" <-> "OE2" Residue "X GLU 34": "OE1" <-> "OE2" Residue "X GLU 36": "OE1" <-> "OE2" Residue "X TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 45": "OD1" <-> "OD2" Residue "X TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 76": "OD1" <-> "OD2" Residue "X ASP 88": "OD1" <-> "OD2" Residue "X TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 192": "OE1" <-> "OE2" Residue "X ASP 194": "OD1" <-> "OD2" Residue "X GLU 224": "OE1" <-> "OE2" Residue "X PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 265": "OE1" <-> "OE2" Residue "X ASP 271": "OD1" <-> "OD2" Residue "X GLU 290": "OE1" <-> "OE2" Residue "X GLU 304": "OE1" <-> "OE2" Residue "X GLU 308": "OE1" <-> "OE2" Residue "X TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 324": "OD1" <-> "OD2" Residue "X TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 331": "OE1" <-> "OE2" Residue "X GLU 341": "OE1" <-> "OE2" Residue "X ASP 349": "OD1" <-> "OD2" Residue "X GLU 352": "OE1" <-> "OE2" Residue "X GLU 375": "OE1" <-> "OE2" Residue "X GLU 378": "OE1" <-> "OE2" Residue "X GLU 396": "OE1" <-> "OE2" Residue "X ASP 409": "OD1" <-> "OD2" Residue "X GLU 504": "OE1" <-> "OE2" Residue "X ASP 508": "OD1" <-> "OD2" Residue "X ASP 517": "OD1" <-> "OD2" Residue "X GLU 572": "OE1" <-> "OE2" Residue "X GLU 573": "OE1" <-> "OE2" Residue "X TYR 574": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 601": "OD1" <-> "OD2" Residue "X ASP 608": "OD1" <-> "OD2" Residue "X GLU 611": "OE1" <-> "OE2" Residue "X ASP 657": "OD1" <-> "OD2" Residue "X ASP 666": "OD1" <-> "OD2" Residue "X GLU 668": "OE1" <-> "OE2" Residue "X GLU 798": "OE1" <-> "OE2" Residue "X GLU 815": "OE1" <-> "OE2" Residue "X TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 883": "OD1" <-> "OD2" Residue "X ASP 907": "OD1" <-> "OD2" Residue "X ASP 913": "OD1" <-> "OD2" Residue "X TYR 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 976": "OD1" <-> "OD2" Residue "X GLU 1003": "OE1" <-> "OE2" Residue "X ASP 1011": "OD1" <-> "OD2" Residue "X ASP 1025": "OD1" <-> "OD2" Residue "X ASP 1028": "OD1" <-> "OD2" Residue "X GLU 1041": "OE1" <-> "OE2" Residue "X TYR 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 1047": "OE1" <-> "OE2" Residue "X GLU 1095": "OE1" <-> "OE2" Residue "X GLU 1105": "OE1" <-> "OE2" Residue "X TYR 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 1144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 1157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 1158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 1161": "OD1" <-> "OD2" Residue "X ASP 1171": "OD1" <-> "OD2" Residue "X GLU 1174": "OE1" <-> "OE2" Residue "X GLU 1189": "OE1" <-> "OE2" Residue "X PHE 1191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 1199": "OE1" <-> "OE2" Residue "X ASP 1220": "OD1" <-> "OD2" Residue "X PHE 1240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 1253": "OD1" <-> "OD2" Residue "X ASP 1259": "OD1" <-> "OD2" Residue "X TYR 1282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 1294": "OE1" <-> "OE2" Residue "X GLU 1313": "OE1" <-> "OE2" Residue "X ASP 1353": "OD1" <-> "OD2" Residue "X ASP 1435": "OD1" <-> "OD2" Residue "X GLU 1436": "OE1" <-> "OE2" Residue "X ASP 1446": "OD1" <-> "OD2" Residue "X GLU 1464": "OE1" <-> "OE2" Residue "X GLU 1474": "OE1" <-> "OE2" Residue "X ASP 1495": "OD1" <-> "OD2" Residue "X GLU 1514": "OE1" <-> "OE2" Residue "X GLU 1518": "OE1" <-> "OE2" Residue "X GLU 1545": "OE1" <-> "OE2" Residue "X TYR 1565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 1598": "OE1" <-> "OE2" Residue "X ASP 1600": "OD1" <-> "OD2" Residue "X GLU 1645": "OE1" <-> "OE2" Residue "X GLU 1656": "OE1" <-> "OE2" Residue "X GLU 1722": "OE1" <-> "OE2" Residue "X ASP 1731": "OD1" <-> "OD2" Residue "X ASP 1752": "OD1" <-> "OD2" Residue "X ASP 1762": "OD1" <-> "OD2" Residue "X GLU 1774": "OE1" <-> "OE2" Residue "X GLU 1777": "OE1" <-> "OE2" Residue "X GLU 1800": "OE1" <-> "OE2" Residue "X GLU 1801": "OE1" <-> "OE2" Residue "X GLU 1805": "OE1" <-> "OE2" Residue "X GLU 1808": "OE1" <-> "OE2" Residue "X GLU 1815": "OE1" <-> "OE2" Residue "X ASP 1828": "OD1" <-> "OD2" Residue "X ASP 1832": "OD1" <-> "OD2" Residue "X GLU 1945": "OE1" <-> "OE2" Residue "X ASP 1951": "OD1" <-> "OD2" Residue "X TYR 1954": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/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: 7.21, per 1000 atoms: 0.51 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 - 3.50 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: 5.37 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.31 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: 4.01 Time building geometry restraints manager: 5.83 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: 98.17 - 105.35: 173 105.35 - 112.53: 7171 112.53 - 119.71: 5060 119.71 - 126.89: 6821 126.89 - 134.08: 188 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 2.440 nonbonded pdb=" OG SER X1726 " pdb=" OD1 ASN X1728 " model vdw 2.159 2.440 nonbonded pdb=" OE2 GLU X 624 " pdb=" OG SER X 651 " model vdw 2.177 2.440 nonbonded pdb=" NH1 ARG X 157 " pdb=" OE2 GLU X 282 " model vdw 2.194 2.520 nonbonded pdb=" OH TYR X1118 " pdb=" O VAL X1139 " model vdw 2.208 2.440 ... (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: 4.060 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: 17.670 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.580 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.830 ------------------------------------------------------------------------------- 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 14435 Z= 0.289 Angle : 0.773 8.954 19413 Z= 0.449 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 (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: -1.25 (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 TRP 0.055 0.002 TRP X 558 HIS 0.009 0.001 HIS X 845 PHE 0.020 0.002 PHE X1121 TYR 0.042 0.002 TYR X 655 ARG 0.009 0.001 ARG X 157 *********************** 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 fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 1.601 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: 0.3431 time to fit residues: 38.2692 Evaluate side-chains 59 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 146 optimal weight: 0.6980 chunk 131 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** ** X1903 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.0699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14435 Z= 0.200 Angle : 0.655 8.964 19413 Z= 0.356 Chirality : 0.042 0.208 1989 Planarity : 0.005 0.089 2520 Dihedral : 6.621 50.999 1881 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.11 % Favored : 87.49 % 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 (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: -0.97 (0.21), residues: 1710 helix: 1.39 (0.18), residues: 871 sheet: -5.38 (0.71), residues: 10 loop : -3.05 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP X 214 HIS 0.008 0.001 HIS X 845 PHE 0.017 0.002 PHE X1121 TYR 0.024 0.001 TYR X 655 ARG 0.007 0.000 ARG X 157 *********************** 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 76 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 1.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 134 ASN cc_start: 0.7835 (m-40) cc_final: 0.7571 (m110) REVERT: X 298 MET cc_start: 0.7317 (ppp) cc_final: 0.6825 (mmt) REVERT: X 624 GLU cc_start: 0.8202 (tp30) cc_final: 0.7917 (tp30) REVERT: X 1412 MET cc_start: 0.9323 (mmp) cc_final: 0.8807 (mmm) REVERT: X 1442 PRO cc_start: 0.8237 (Cg_endo) cc_final: 0.8012 (Cg_exo) REVERT: X 1647 MET cc_start: 0.7445 (mpp) cc_final: 0.7041 (mpp) REVERT: X 1866 ILE cc_start: 0.9000 (tp) cc_final: 0.8745 (tp) REVERT: X 1943 MET cc_start: 0.8104 (tmm) cc_final: 0.7759 (tmm) outliers start: 7 outliers final: 2 residues processed: 72 average time/residue: 0.3410 time to fit residues: 35.6797 Evaluate side-chains 63 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 61 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 150 ASN 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 87 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 157 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 140 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 126 optimal weight: 0.0370 overall best weight: 0.7458 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1833 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1903 ASN ** X1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14435 Z= 0.181 Angle : 0.617 8.979 19413 Z= 0.333 Chirality : 0.041 0.162 1989 Planarity : 0.004 0.087 2520 Dihedral : 6.308 53.349 1879 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.75 % Favored : 87.84 % Rotamer: Outliers : 1.02 % Allowed : 7.84 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.60 % 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: -0.80 (0.21), residues: 1710 helix: 1.58 (0.18), residues: 870 sheet: -5.56 (0.73), residues: 10 loop : -3.02 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 560 HIS 0.006 0.001 HIS X 845 PHE 0.018 0.002 PHE X 159 TYR 0.019 0.001 TYR X 655 ARG 0.006 0.000 ARG X 157 *********************** 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 91 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 134 ASN cc_start: 0.7781 (m-40) cc_final: 0.7468 (m110) REVERT: X 187 PHE cc_start: 0.8484 (t80) cc_final: 0.8233 (t80) REVERT: X 191 ARG cc_start: 0.8091 (mtm-85) cc_final: 0.7873 (ptp-170) REVERT: X 298 MET cc_start: 0.7394 (ppp) cc_final: 0.6850 (mmt) REVERT: X 624 GLU cc_start: 0.8168 (tp30) cc_final: 0.7967 (tp30) REVERT: X 1307 GLU cc_start: 0.9260 (pp20) cc_final: 0.8872 (pp20) REVERT: X 1412 MET cc_start: 0.9292 (mmp) cc_final: 0.8782 (mmm) REVERT: X 1647 MET cc_start: 0.7603 (mpp) cc_final: 0.7118 (mpp) REVERT: X 1866 ILE cc_start: 0.8981 (tp) cc_final: 0.8694 (tp) REVERT: X 1943 MET cc_start: 0.8312 (tmm) cc_final: 0.7834 (tmm) outliers start: 16 outliers final: 8 residues processed: 89 average time/residue: 0.3132 time to fit residues: 41.1742 Evaluate side-chains 73 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 137 GLU Chi-restraints excluded: chain X residue 150 ASN Chi-restraints excluded: chain X residue 207 TYR Chi-restraints excluded: chain X residue 306 THR 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 1961 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 155 optimal weight: 3.9990 chunk 118 optimal weight: 8.9990 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 157 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 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 676 ASN X1143 ASN X1225 ASN ** X1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14435 Z= 0.176 Angle : 0.610 8.986 19413 Z= 0.327 Chirality : 0.040 0.163 1989 Planarity : 0.004 0.083 2520 Dihedral : 6.190 55.423 1879 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.58 % Favored : 88.07 % Rotamer: Outliers : 1.15 % Allowed : 9.25 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.60 % 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: -0.75 (0.21), residues: 1710 helix: 1.66 (0.18), residues: 868 sheet: -5.42 (0.75), residues: 10 loop : -3.02 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP X 214 HIS 0.005 0.001 HIS X 845 PHE 0.016 0.001 PHE X1121 TYR 0.015 0.001 TYR X1127 ARG 0.006 0.000 ARG X 853 *********************** 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 91 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 134 ASN cc_start: 0.7753 (m-40) cc_final: 0.7414 (m110) REVERT: X 298 MET cc_start: 0.7430 (ppp) cc_final: 0.6931 (mmt) REVERT: X 560 TRP cc_start: 0.8986 (OUTLIER) cc_final: 0.8773 (m-10) REVERT: X 1044 TYR cc_start: 0.8679 (t80) cc_final: 0.8437 (t80) REVERT: X 1307 GLU cc_start: 0.9271 (pp20) cc_final: 0.8886 (pp20) REVERT: X 1412 MET cc_start: 0.9281 (mmp) cc_final: 0.8774 (mmm) REVERT: X 1647 MET cc_start: 0.7643 (mpp) cc_final: 0.7165 (mpp) REVERT: X 1866 ILE cc_start: 0.8987 (tp) cc_final: 0.8685 (tp) REVERT: X 1943 MET cc_start: 0.8396 (tmm) cc_final: 0.7877 (tmm) outliers start: 18 outliers final: 12 residues processed: 89 average time/residue: 0.3055 time to fit residues: 39.9958 Evaluate side-chains 75 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 62 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 137 GLU Chi-restraints excluded: chain X residue 150 ASN 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 560 TRP Chi-restraints excluded: chain X residue 801 THR Chi-restraints excluded: chain X residue 1141 LEU Chi-restraints excluded: chain X residue 1190 ILE Chi-restraints excluded: chain X residue 1559 ILE 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 139 optimal weight: 0.0010 chunk 94 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 85 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 42 optimal weight: 0.0570 overall best weight: 0.7906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 585 GLN X 678 GLN X1143 ASN X1225 ASN ** X1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14435 Z= 0.182 Angle : 0.605 8.968 19413 Z= 0.325 Chirality : 0.040 0.159 1989 Planarity : 0.004 0.080 2520 Dihedral : 6.105 56.449 1879 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.87 % Favored : 87.72 % Rotamer: Outliers : 1.47 % Allowed : 9.82 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.60 % 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: -0.68 (0.21), residues: 1710 helix: 1.73 (0.18), residues: 869 sheet: -5.36 (0.80), residues: 10 loop : -3.01 (0.20), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 223 HIS 0.004 0.001 HIS X 845 PHE 0.017 0.001 PHE X 159 TYR 0.015 0.001 TYR X1127 ARG 0.006 0.000 ARG X 853 *********************** 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 91 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 68 time to evaluate : 1.692 Fit side-chains revert: symmetry clash REVERT: X 133 ARG cc_start: 0.7641 (tpm170) cc_final: 0.6793 (tpt170) REVERT: X 134 ASN cc_start: 0.7715 (m-40) cc_final: 0.6978 (m110) REVERT: X 152 CYS cc_start: 0.7241 (t) cc_final: 0.6924 (t) REVERT: X 191 ARG cc_start: 0.8022 (mtm-85) cc_final: 0.7777 (ptp-170) REVERT: X 257 ARG cc_start: 0.6454 (mmt180) cc_final: 0.6163 (mmt180) REVERT: X 298 MET cc_start: 0.7449 (ppp) cc_final: 0.6972 (mmt) REVERT: X 1166 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8989 (pttm) REVERT: X 1307 GLU cc_start: 0.9268 (pp20) cc_final: 0.8866 (pp20) REVERT: X 1412 MET cc_start: 0.9276 (mmp) cc_final: 0.8790 (mmm) REVERT: X 1647 MET cc_start: 0.7675 (mpp) cc_final: 0.7165 (mpp) REVERT: X 1866 ILE cc_start: 0.8994 (tp) cc_final: 0.8691 (tp) REVERT: X 1943 MET cc_start: 0.8507 (tmm) cc_final: 0.7988 (tmm) outliers start: 23 outliers final: 15 residues processed: 88 average time/residue: 0.3250 time to fit residues: 41.5106 Evaluate side-chains 75 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 59 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 150 ASN 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 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 1961 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 56 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 167 optimal weight: 0.6980 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X1143 ASN X1225 ASN ** X1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 0.040 14435 Z= 0.198 Angle : 0.612 10.111 19413 Z= 0.328 Chirality : 0.040 0.158 1989 Planarity : 0.004 0.079 2520 Dihedral : 6.073 56.862 1879 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.40 % Favored : 88.19 % Rotamer: Outliers : 1.34 % Allowed : 10.91 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.21), residues: 1710 helix: 1.78 (0.18), residues: 867 sheet: -5.29 (0.84), residues: 10 loop : -3.03 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP X 223 HIS 0.010 0.001 HIS X1787 PHE 0.015 0.001 PHE X1121 TYR 0.016 0.001 TYR X1127 ARG 0.006 0.000 ARG X 157 *********************** 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 81 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 1.763 Fit side-chains REVERT: X 187 PHE cc_start: 0.8304 (t80) cc_final: 0.8080 (t80) REVERT: X 298 MET cc_start: 0.7458 (ppp) cc_final: 0.7001 (mmt) REVERT: X 1166 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8996 (pttm) REVERT: X 1307 GLU cc_start: 0.9277 (pp20) cc_final: 0.8874 (pp20) REVERT: X 1412 MET cc_start: 0.9264 (mmp) cc_final: 0.8789 (mmm) REVERT: X 1647 MET cc_start: 0.7680 (mpp) cc_final: 0.7167 (mpp) REVERT: X 1866 ILE cc_start: 0.9021 (tp) cc_final: 0.8718 (tp) REVERT: X 1943 MET cc_start: 0.8540 (tmm) cc_final: 0.8009 (tmm) outliers start: 21 outliers final: 15 residues processed: 77 average time/residue: 0.3275 time to fit residues: 37.1876 Evaluate side-chains 70 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 54 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 150 ASN 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 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 1746 THR Chi-restraints excluded: chain X residue 1838 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 161 optimal weight: 0.4980 chunk 18 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 104 optimal weight: 0.0970 chunk 101 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X1143 ASN X1225 ASN ** X1356 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14435 Z= 0.173 Angle : 0.604 10.632 19413 Z= 0.323 Chirality : 0.040 0.158 1989 Planarity : 0.004 0.078 2520 Dihedral : 6.022 57.810 1879 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.40 % Favored : 88.25 % Rotamer: Outliers : 1.34 % Allowed : 11.10 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.42 % 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: -0.63 (0.21), residues: 1710 helix: 1.81 (0.18), residues: 867 sheet: -5.15 (0.87), residues: 10 loop : -3.04 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP X 223 HIS 0.011 0.001 HIS X1787 PHE 0.018 0.001 PHE X 159 TYR 0.016 0.001 TYR X1127 ARG 0.010 0.000 ARG X 853 *********************** 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 82 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 1.635 Fit side-chains revert: symmetry clash REVERT: X 134 ASN cc_start: 0.7393 (m-40) cc_final: 0.7085 (m110) REVERT: X 298 MET cc_start: 0.7469 (ppp) cc_final: 0.7052 (mmt) REVERT: X 1166 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9004 (pttm) REVERT: X 1307 GLU cc_start: 0.9281 (pp20) cc_final: 0.8882 (pp20) REVERT: X 1412 MET cc_start: 0.9258 (mmp) cc_final: 0.8799 (mmm) REVERT: X 1647 MET cc_start: 0.7712 (mpp) cc_final: 0.7186 (mpp) REVERT: X 1866 ILE cc_start: 0.8990 (tp) cc_final: 0.8686 (tp) REVERT: X 1943 MET cc_start: 0.8499 (tmm) cc_final: 0.8255 (tmm) outliers start: 21 outliers final: 15 residues processed: 79 average time/residue: 0.3114 time to fit residues: 36.9203 Evaluate side-chains 72 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 56 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 150 ASN 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 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 1746 THR Chi-restraints excluded: chain X residue 1838 CYS Chi-restraints excluded: chain X residue 1961 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 103 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 131 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X1225 ASN X1356 ASN ** X1674 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X1833 ASN ** X1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14435 Z= 0.245 Angle : 0.635 18.534 19413 Z= 0.337 Chirality : 0.041 0.159 1989 Planarity : 0.005 0.091 2520 Dihedral : 6.047 56.963 1879 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.81 % Favored : 87.84 % Rotamer: Outliers : 1.53 % Allowed : 11.48 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.48 % 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: -0.65 (0.21), residues: 1710 helix: 1.80 (0.18), residues: 867 sheet: -5.32 (0.82), residues: 10 loop : -3.05 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP X 223 HIS 0.010 0.001 HIS X1787 PHE 0.017 0.001 PHE X1031 TYR 0.016 0.001 TYR X1127 ARG 0.005 0.000 ARG X 133 *********************** 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 82 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 58 time to evaluate : 1.744 Fit side-chains revert: symmetry clash REVERT: X 134 ASN cc_start: 0.7452 (m-40) cc_final: 0.7125 (m110) REVERT: X 185 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8939 (pm20) REVERT: X 298 MET cc_start: 0.7473 (ppp) cc_final: 0.7068 (mmt) REVERT: X 1166 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.9011 (pttm) REVERT: X 1307 GLU cc_start: 0.9301 (pp20) cc_final: 0.8895 (pp20) REVERT: X 1412 MET cc_start: 0.9272 (mmp) cc_final: 0.8792 (mmm) REVERT: X 1647 MET cc_start: 0.7757 (mpp) cc_final: 0.7230 (mpp) REVERT: X 1866 ILE cc_start: 0.9037 (tp) cc_final: 0.8736 (tp) REVERT: X 1943 MET cc_start: 0.8569 (tmm) cc_final: 0.8315 (tmm) outliers start: 24 outliers final: 15 residues processed: 80 average time/residue: 0.2947 time to fit residues: 35.2273 Evaluate side-chains 73 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 56 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 150 ASN 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 673 LEU Chi-restraints excluded: chain X residue 797 THR Chi-restraints excluded: chain X residue 801 THR 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 1672 GLN Chi-restraints excluded: chain X residue 1746 THR Chi-restraints excluded: chain X residue 1838 CYS Chi-restraints excluded: chain X residue 1905 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 159 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 154 optimal weight: 0.6980 chunk 102 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X1143 ASN X1225 ASN ** X1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14435 Z= 0.169 Angle : 0.614 18.499 19413 Z= 0.324 Chirality : 0.040 0.159 1989 Planarity : 0.004 0.082 2520 Dihedral : 6.010 57.740 1879 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.64 % Favored : 87.95 % Rotamer: Outliers : 1.47 % Allowed : 11.80 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.42 % 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: -0.59 (0.21), residues: 1710 helix: 1.88 (0.18), residues: 861 sheet: -4.97 (0.95), residues: 10 loop : -3.03 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP X 223 HIS 0.010 0.001 HIS X1787 PHE 0.020 0.001 PHE X 159 TYR 0.016 0.001 TYR X1127 ARG 0.012 0.000 ARG X 853 *********************** 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 83 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 60 time to evaluate : 1.623 Fit side-chains REVERT: X 134 ASN cc_start: 0.7428 (m-40) cc_final: 0.7092 (m110) REVERT: X 185 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8987 (pm20) REVERT: X 298 MET cc_start: 0.7473 (ppp) cc_final: 0.7077 (mmt) REVERT: X 1166 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.9061 (pttm) REVERT: X 1307 GLU cc_start: 0.9285 (pp20) cc_final: 0.8883 (pp20) REVERT: X 1412 MET cc_start: 0.9236 (mmp) cc_final: 0.8802 (mmm) REVERT: X 1647 MET cc_start: 0.7704 (mpp) cc_final: 0.7190 (mpp) REVERT: X 1866 ILE cc_start: 0.8993 (tp) cc_final: 0.8691 (tp) REVERT: X 1943 MET cc_start: 0.8478 (tmm) cc_final: 0.8228 (tmm) outliers start: 23 outliers final: 18 residues processed: 81 average time/residue: 0.3049 time to fit residues: 37.0115 Evaluate side-chains 77 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 57 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 150 ASN 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 673 LEU Chi-restraints excluded: chain X residue 780 ASP Chi-restraints excluded: chain X residue 797 THR Chi-restraints excluded: chain X residue 801 THR Chi-restraints excluded: chain X residue 910 CYS 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 1672 GLN Chi-restraints excluded: chain X residue 1746 THR Chi-restraints excluded: chain X residue 1838 CYS Chi-restraints excluded: chain X residue 1905 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 164 optimal weight: 0.0770 chunk 100 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 172 optimal weight: 0.0020 chunk 158 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 106 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.7148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X1143 ASN X1225 ASN ** X1948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14435 Z= 0.174 Angle : 0.610 18.019 19413 Z= 0.322 Chirality : 0.040 0.157 1989 Planarity : 0.004 0.077 2520 Dihedral : 5.936 58.377 1879 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.41 % Allowed : 11.46 % Favored : 88.13 % Rotamer: Outliers : 1.28 % Allowed : 12.18 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.21), residues: 1710 helix: 1.92 (0.18), residues: 861 sheet: -4.81 (1.08), residues: 10 loop : -3.02 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP X 223 HIS 0.009 0.001 HIS X1787 PHE 0.015 0.001 PHE X1031 TYR 0.017 0.001 TYR X1127 ARG 0.005 0.000 ARG X 157 ********************** 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 79 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 59 time to evaluate : 1.848 Fit side-chains REVERT: X 134 ASN cc_start: 0.7412 (m-40) cc_final: 0.7070 (m110) REVERT: X 298 MET cc_start: 0.7478 (ppp) cc_final: 0.7090 (mmt) REVERT: X 1166 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.9090 (pttm) REVERT: X 1307 GLU cc_start: 0.9285 (pp20) cc_final: 0.8888 (pp20) REVERT: X 1412 MET cc_start: 0.9216 (mmp) cc_final: 0.8812 (mmm) REVERT: X 1647 MET cc_start: 0.7685 (mpp) cc_final: 0.7209 (mpp) REVERT: X 1866 ILE cc_start: 0.8966 (tp) cc_final: 0.8653 (tp) REVERT: X 1943 MET cc_start: 0.8500 (tmm) cc_final: 0.8255 (tmm) outliers start: 20 outliers final: 16 residues processed: 78 average time/residue: 0.3228 time to fit residues: 37.6541 Evaluate side-chains 74 residues out of total 1568 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 57 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 150 ASN 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 673 LEU Chi-restraints excluded: chain X residue 780 ASP Chi-restraints excluded: chain X residue 797 THR Chi-restraints excluded: chain X residue 801 THR Chi-restraints excluded: chain X residue 910 CYS 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 1672 GLN Chi-restraints excluded: chain X residue 1746 THR Chi-restraints excluded: chain X residue 1838 CYS Chi-restraints excluded: chain X residue 1905 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 173 random chunks: chunk 146 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 57 optimal weight: 0.0870 chunk 141 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 chunk 120 optimal weight: 0.0870 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X1225 ASN ** 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 = 0.4056 r_free = 0.4056 target = 0.110446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.074641 restraints weight = 43550.778| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 4.40 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14435 Z= 0.167 Angle : 0.618 17.553 19413 Z= 0.327 Chirality : 0.040 0.157 1989 Planarity : 0.004 0.077 2520 Dihedral : 5.902 58.625 1879 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.40 % Favored : 88.25 % Rotamer: Outliers : 1.02 % Allowed : 12.56 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.30 % Twisted Proline : 2.17 % Twisted General : 0.42 % 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: -0.55 (0.21), residues: 1710 helix: 1.89 (0.18), residues: 867 sheet: -4.77 (1.07), residues: 10 loop : -3.02 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP X 223 HIS 0.012 0.001 HIS X1787 PHE 0.019 0.001 PHE X 159 TYR 0.017 0.001 TYR X1127 ARG 0.011 0.000 ARG X 853 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2850.48 seconds wall clock time: 53 minutes 42.12 seconds (3222.12 seconds total)