Starting phenix.real_space_refine on Tue Aug 4 18:20:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rao_19021/08_2026/8rao_19021.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rao_19021/08_2026/8rao_19021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rao_19021/08_2026/8rao_19021.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rao_19021/08_2026/8rao_19021.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rao_19021/08_2026/8rao_19021.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rao_19021/08_2026/8rao_19021.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 8 Type Number sf(0) Gaussians P 11 5.49 5 Mg 1 5.21 5 S 31 5.16 5 Be 1 3.05 5 C 3604 2.51 5 N 1010 2.21 5 O 1120 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5781 Number of models: 1 Model: "" Number of chains: 3 Chain: "O" Number of atoms: 5557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 694, 5557 Classifications: {'peptide': 694} Link IDs: {'PTRANS': 28, 'TRANS': 665} Chain breaks: 2 Chain: "P" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 192 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 3} Link IDs: {'rna2p': 4, 'rna3p': 4} Chain: "O" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.18, per 1000 atoms: 0.20 Number of scatterers: 5781 At special positions: 0 Unit cell: (77.7, 102.9, 96.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 31 16.00 P 11 15.00 Mg 1 11.99 F 3 9.00 O 1120 8.00 N 1010 7.00 C 3604 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.46 Conformation dependent library (CDL) restraints added in 248.0 milliseconds 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1312 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 4 sheets defined 52.9% alpha, 15.6% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'O' and resid 1095 through 1110 Processing helix chain 'O' and resid 1113 through 1121 Processing helix chain 'O' and resid 1136 through 1140 Processing helix chain 'O' and resid 1149 through 1175 Proline residue: O1159 - end of helix Processing helix chain 'O' and resid 1203 through 1210 Processing helix chain 'O' and resid 1232 through 1239 removed outlier: 3.629A pdb=" N PHE O1236 " --> pdb=" O SER O1232 " (cutoff:3.500A) Processing helix chain 'O' and resid 1268 through 1274 Processing helix chain 'O' and resid 1288 through 1301 Processing helix chain 'O' and resid 1302 through 1305 removed outlier: 6.161A pdb=" N ASP O1305 " --> pdb=" O GLU O1302 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1302 through 1305' Processing helix chain 'O' and resid 1306 through 1313 Processing helix chain 'O' and resid 1322 through 1334 removed outlier: 3.616A pdb=" N ILE O1326 " --> pdb=" O ASP O1322 " (cutoff:3.500A) Processing helix chain 'O' and resid 1336 through 1349 Processing helix chain 'O' and resid 1362 through 1377 Processing helix chain 'O' and resid 1412 through 1425 removed outlier: 3.617A pdb=" N SER O1425 " --> pdb=" O LEU O1421 " (cutoff:3.500A) Processing helix chain 'O' and resid 1452 through 1455 Processing helix chain 'O' and resid 1456 through 1465 Processing helix chain 'O' and resid 1531 through 1562 Processing helix chain 'O' and resid 1570 through 1573 removed outlier: 3.702A pdb=" N ALA O1573 " --> pdb=" O SER O1570 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1570 through 1573' Processing helix chain 'O' and resid 1574 through 1581 Processing helix chain 'O' and resid 1592 through 1595 removed outlier: 3.589A pdb=" N CYS O1595 " --> pdb=" O ALA O1592 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1592 through 1595' Processing helix chain 'O' and resid 1596 through 1602 Processing helix chain 'O' and resid 1603 through 1606 removed outlier: 3.819A pdb=" N TYR O1606 " --> pdb=" O PRO O1603 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1603 through 1606' Processing helix chain 'O' and resid 1626 through 1632 Processing helix chain 'O' and resid 1637 through 1646 Processing helix chain 'O' and resid 1658 through 1669 removed outlier: 4.550A pdb=" N PHE O1664 " --> pdb=" O SER O1660 " (cutoff:3.500A) Proline residue: O1665 - end of helix Processing helix chain 'O' and resid 1679 through 1684 Processing helix chain 'O' and resid 1686 through 1691 removed outlier: 4.041A pdb=" N GLN O1690 " --> pdb=" O ARG O1686 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU O1691 " --> pdb=" O PRO O1687 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 1686 through 1691' Processing helix chain 'O' and resid 1718 through 1737 removed outlier: 3.955A pdb=" N ILE O1722 " --> pdb=" O ASN O1718 " (cutoff:3.500A) Processing helix chain 'O' and resid 1752 through 1767 Processing helix chain 'O' and resid 1769 through 1774 removed outlier: 3.996A pdb=" N LYS O1773 " --> pdb=" O GLY O1769 " (cutoff:3.500A) Processing helix chain 'O' and resid 1805 through 1809 removed outlier: 3.873A pdb=" N LEU O1808 " --> pdb=" O VAL O1805 " (cutoff:3.500A) Processing helix chain 'O' and resid 1810 through 1819 removed outlier: 3.606A pdb=" N MET O1814 " --> pdb=" O ASP O1810 " (cutoff:3.500A) Processing helix chain 'O' and resid 1830 through 1836 removed outlier: 3.871A pdb=" N LYS O1836 " --> pdb=" O ARG O1832 " (cutoff:3.500A) Processing helix chain 'O' and resid 1837 through 1850 Processing helix chain 'O' and resid 1865 through 1876 removed outlier: 3.783A pdb=" N GLN O1869 " --> pdb=" O ASN O1865 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 1188 through 1191 removed outlier: 3.655A pdb=" N ASN O1257 " --> pdb=" O THR O1253 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR O1249 " --> pdb=" O THR O1261 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG O1263 " --> pdb=" O VAL O1247 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL O1247 " --> pdb=" O ARG O1263 " (cutoff:3.500A) removed outlier: 8.635A pdb=" N HIS O1265 " --> pdb=" O ALA O1245 " (cutoff:3.500A) removed outlier: 8.886A pdb=" N ALA O1245 " --> pdb=" O HIS O1265 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASP O1215 " --> pdb=" O VAL O1247 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU O1216 " --> pdb=" O VAL O1285 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N SER O1182 " --> pdb=" O ALA O1202 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA O1202 " --> pdb=" O SER O1182 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE O1184 " --> pdb=" O SER O1200 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER O1200 " --> pdb=" O ILE O1184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'O' and resid 1439 through 1441 removed outlier: 6.606A pdb=" N ILE O1406 " --> pdb=" O ILE O1565 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N SER O1567 " --> pdb=" O ILE O1406 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ILE O1408 " --> pdb=" O SER O1567 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL O1587 " --> pdb=" O ILE O1612 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N VAL O1614 " --> pdb=" O VAL O1587 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE O1589 " --> pdb=" O VAL O1614 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLY O1351 " --> pdb=" O CYS O1611 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET O1613 " --> pdb=" O GLY O1351 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER O1353 " --> pdb=" O MET O1613 " (cutoff:3.500A) removed outlier: 8.791A pdb=" N TYR O1649 " --> pdb=" O PHE O1352 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU O1354 " --> pdb=" O TYR O1649 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 1427 through 1428 Processing sheet with id=AA4, first strand: chain 'O' and resid 1775 through 1778 removed outlier: 6.779A pdb=" N ILE O1746 " --> pdb=" O ASP O1776 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ASN O1778 " --> pdb=" O ILE O1746 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ILE O1748 " --> pdb=" O ASN O1778 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY O1747 " --> pdb=" O LEU O1792 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N SER O1794 " --> pdb=" O GLY O1747 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE O1749 " --> pdb=" O SER O1794 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N GLU O1789 " --> pdb=" O SER O1824 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N TRP O1826 " --> pdb=" O GLU O1789 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE O1791 " --> pdb=" O TRP O1826 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU O1828 " --> pdb=" O ILE O1791 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE O1793 " --> pdb=" O LEU O1828 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N ALA O1854 " --> pdb=" O TYR O1697 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N PHE O1699 " --> pdb=" O ALA O1854 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA O1856 " --> pdb=" O PHE O1699 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N ASP O1701 " --> pdb=" O ALA O1856 " (cutoff:3.500A) 256 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1854 1.34 - 1.45: 742 1.45 - 1.57: 3239 1.57 - 1.69: 20 1.69 - 1.81: 49 Bond restraints: 5904 Sorted by residual: bond pdb=" F2 BEF O3003 " pdb="BE BEF O3003 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" F3 BEF O3003 " pdb="BE BEF O3003 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" F1 BEF O3003 " pdb="BE BEF O3003 " ideal model delta sigma weight residual 1.476 1.534 -0.058 2.00e-02 2.50e+03 8.42e+00 bond pdb=" N1 C P 4 " pdb=" C2 C P 4 " ideal model delta sigma weight residual 1.397 1.410 -0.013 1.00e-02 1.00e+04 1.58e+00 bond pdb=" C4 ADP O3001 " pdb=" C5 ADP O3001 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.02e+00 ... (remaining 5899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 7951 2.52 - 5.04: 43 5.04 - 7.55: 6 7.55 - 10.07: 0 10.07 - 12.59: 2 Bond angle restraints: 8002 Sorted by residual: angle pdb=" C1' C P 4 " pdb=" N1 C P 4 " pdb=" C2 C P 4 " ideal model delta sigma weight residual 118.80 125.43 -6.63 1.10e+00 8.26e-01 3.63e+01 angle pdb=" N1 C P 4 " pdb=" C2 C P 4 " pdb=" O2 C P 4 " ideal model delta sigma weight residual 118.90 121.89 -2.99 6.00e-01 2.78e+00 2.48e+01 angle pdb=" C1' C P 4 " pdb=" N1 C P 4 " pdb=" C6 C P 4 " ideal model delta sigma weight residual 120.80 115.60 5.20 1.20e+00 6.94e-01 1.88e+01 angle pdb=" F2 BEF O3003 " pdb="BE BEF O3003 " pdb=" F3 BEF O3003 " ideal model delta sigma weight residual 119.96 107.37 12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" O2 C P 4 " pdb=" C2 C P 4 " pdb=" N3 C P 4 " ideal model delta sigma weight residual 121.90 118.98 2.92 7.00e-01 2.04e+00 1.74e+01 ... (remaining 7997 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.90: 3556 23.90 - 47.80: 57 47.80 - 71.70: 26 71.70 - 95.60: 4 95.60 - 119.51: 2 Dihedral angle restraints: 3645 sinusoidal: 1614 harmonic: 2031 Sorted by residual: dihedral pdb=" O4' C P 4 " pdb=" C1' C P 4 " pdb=" N1 C P 4 " pdb=" C2 C P 4 " ideal model delta sinusoidal sigma weight residual 200.00 102.01 97.99 1 1.50e+01 4.44e-03 4.86e+01 dihedral pdb=" O1B ADP O3001 " pdb=" O3A ADP O3001 " pdb=" PB ADP O3001 " pdb=" PA ADP O3001 " ideal model delta sinusoidal sigma weight residual -60.00 -179.51 119.51 1 2.00e+01 2.50e-03 3.58e+01 dihedral pdb=" O5' C P 8 " pdb=" C5' C P 8 " pdb=" C4' C P 8 " pdb=" C3' C P 8 " ideal model delta sinusoidal sigma weight residual 55.00 114.85 -59.85 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 3642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 580 0.025 - 0.051: 178 0.051 - 0.076: 45 0.076 - 0.101: 46 0.101 - 0.126: 38 Chirality restraints: 887 Sorted by residual: chirality pdb=" CA ILE O1280 " pdb=" N ILE O1280 " pdb=" C ILE O1280 " pdb=" CB ILE O1280 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" C2' C P 4 " pdb=" C3' C P 4 " pdb=" O2' C P 4 " pdb=" C1' C P 4 " both_signs ideal model delta sigma weight residual False -2.62 -2.74 0.13 2.00e-01 2.50e+01 3.92e-01 chirality pdb=" CA ILE O1825 " pdb=" N ILE O1825 " pdb=" C ILE O1825 " pdb=" CB ILE O1825 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 884 not shown) Planarity restraints: 997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER O1647 " 0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO O1648 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO O1648 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO O1648 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU O1222 " -0.014 5.00e-02 4.00e+02 2.19e-02 7.70e-01 pdb=" N PRO O1223 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO O1223 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO O1223 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY O1357 " 0.013 5.00e-02 4.00e+02 1.97e-02 6.21e-01 pdb=" N PRO O1358 " -0.034 5.00e-02 4.00e+02 pdb=" CA PRO O1358 " 0.010 5.00e-02 4.00e+02 pdb=" CD PRO O1358 " 0.011 5.00e-02 4.00e+02 ... (remaining 994 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 59 2.59 - 3.17: 5264 3.17 - 3.75: 9127 3.75 - 4.32: 13028 4.32 - 4.90: 21362 Nonbonded interactions: 48840 Sorted by model distance: nonbonded pdb=" OG1 THR O1364 " pdb="MG MG O3002 " model vdw 2.016 2.170 nonbonded pdb=" O2B ADP O3001 " pdb="MG MG O3002 " model vdw 2.016 2.170 nonbonded pdb=" OE2 GLU O1591 " pdb=" F1 BEF O3003 " model vdw 2.166 2.990 nonbonded pdb=" O TYR O1125 " pdb=" NH1 ARG O1173 " model vdw 2.167 3.120 nonbonded pdb=" OG SER O1332 " pdb=" O LYS O1430 " model vdw 2.174 3.040 ... (remaining 48835 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.160 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 5904 Z= 0.119 Angle : 0.475 12.589 8002 Z= 0.272 Chirality : 0.039 0.126 887 Planarity : 0.002 0.027 997 Dihedral : 10.681 119.506 2333 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.69 (0.34), residues: 688 helix: 3.31 (0.31), residues: 333 sheet: 0.87 (0.44), residues: 129 loop : -0.05 (0.42), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O1820 TYR 0.004 0.000 TYR O1195 PHE 0.006 0.001 PHE O1860 TRP 0.003 0.000 TRP O1688 HIS 0.002 0.000 HIS O1574 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.12 ( 5904) covalent geometry : angle 0.47504 / 0.27 ( 8002) hydrogen bonds : bond 0.13236 / 9.36 ( 256) hydrogen bonds : angle 4.24797 / 3.21 ( 735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1105 MET cc_start: 0.9440 (tpt) cc_final: 0.9046 (tpt) REVERT: O 1157 MET cc_start: 0.9183 (mmm) cc_final: 0.8705 (mmm) REVERT: O 1162 LEU cc_start: 0.9747 (mt) cc_final: 0.9500 (pp) REVERT: O 1294 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9174 (mt-10) REVERT: O 1439 LEU cc_start: 0.6606 (tp) cc_final: 0.4434 (tp) REVERT: O 1566 CYS cc_start: 0.9572 (m) cc_final: 0.9255 (p) REVERT: O 1582 ILE cc_start: 0.8955 (pt) cc_final: 0.7624 (pt) REVERT: O 1584 PHE cc_start: 0.9071 (m-80) cc_final: 0.8681 (m-80) REVERT: O 1613 MET cc_start: 0.9669 (mtm) cc_final: 0.9242 (mtp) REVERT: O 1783 PHE cc_start: 0.9209 (t80) cc_final: 0.8630 (t80) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.0859 time to fit residues: 14.2034 Evaluate side-chains 82 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1104 HIS O1139 ASN O1555 GLN O1757 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.050949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.036626 restraints weight = 39441.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.037950 restraints weight = 25249.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.038847 restraints weight = 18460.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.039545 restraints weight = 14791.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.039950 restraints weight = 12595.305| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5904 Z= 0.152 Angle : 0.595 7.258 8002 Z= 0.302 Chirality : 0.043 0.277 887 Planarity : 0.004 0.043 997 Dihedral : 12.952 110.126 925 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.33), residues: 688 helix: 2.50 (0.30), residues: 339 sheet: 0.71 (0.43), residues: 130 loop : -0.03 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O1610 TYR 0.009 0.001 TYR O1117 PHE 0.031 0.002 PHE O1763 TRP 0.008 0.002 TRP O1166 HIS 0.002 0.001 HIS O1268 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 5904) covalent geometry : angle 0.59504 / 0.30 ( 8002) hydrogen bonds : bond 0.03821 / 2.52 ( 256) hydrogen bonds : angle 4.35670 / 3.24 ( 735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1105 MET cc_start: 0.9363 (tpt) cc_final: 0.8906 (tpt) REVERT: O 1157 MET cc_start: 0.8882 (mmm) cc_final: 0.8502 (mmm) REVERT: O 1216 LEU cc_start: 0.8960 (tp) cc_final: 0.8728 (tt) REVERT: O 1288 MET cc_start: 0.9476 (mmp) cc_final: 0.9230 (mmm) REVERT: O 1294 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9094 (mt-10) REVERT: O 1418 GLU cc_start: 0.8994 (tt0) cc_final: 0.8685 (mt-10) REVERT: O 1566 CYS cc_start: 0.9519 (m) cc_final: 0.9260 (p) REVERT: O 1584 PHE cc_start: 0.8678 (m-80) cc_final: 0.8433 (m-80) REVERT: O 1613 MET cc_start: 0.9578 (mtm) cc_final: 0.8615 (mtm) REVERT: O 1657 MET cc_start: 0.8147 (mmp) cc_final: 0.7800 (mmp) REVERT: O 1776 ASP cc_start: 0.8773 (t0) cc_final: 0.8101 (m-30) REVERT: O 1783 PHE cc_start: 0.9085 (t80) cc_final: 0.8343 (t80) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.0666 time to fit residues: 8.7670 Evaluate side-chains 70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 67 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1241 HIS O1267 ASN O1312 GLN O1757 GLN O1831 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.048547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.034296 restraints weight = 40917.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.035485 restraints weight = 26447.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.036302 restraints weight = 19604.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.036915 restraints weight = 15898.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.037310 restraints weight = 13691.511| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 5904 Z= 0.199 Angle : 0.587 8.425 8002 Z= 0.300 Chirality : 0.041 0.181 887 Planarity : 0.005 0.083 997 Dihedral : 13.117 118.616 925 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.33), residues: 688 helix: 2.18 (0.29), residues: 338 sheet: 0.73 (0.43), residues: 132 loop : 0.07 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O1175 TYR 0.016 0.001 TYR O1195 PHE 0.019 0.002 PHE O1777 TRP 0.027 0.003 TRP O1840 HIS 0.004 0.001 HIS O1574 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 ( 5904) covalent geometry : angle 0.58662 / 0.30 ( 8002) hydrogen bonds : bond 0.03356 / 2.19 ( 256) hydrogen bonds : angle 4.43943 / 3.24 ( 735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1105 MET cc_start: 0.9300 (tpt) cc_final: 0.8857 (tpt) REVERT: O 1162 LEU cc_start: 0.9775 (mm) cc_final: 0.9420 (pp) REVERT: O 1286 MET cc_start: 0.8925 (ptp) cc_final: 0.8503 (ptp) REVERT: O 1288 MET cc_start: 0.9516 (mmp) cc_final: 0.9208 (mmm) REVERT: O 1294 GLU cc_start: 0.9293 (mt-10) cc_final: 0.9066 (mt-10) REVERT: O 1421 LEU cc_start: 0.9540 (tp) cc_final: 0.9228 (pp) REVERT: O 1566 CYS cc_start: 0.9501 (m) cc_final: 0.9034 (p) REVERT: O 1584 PHE cc_start: 0.9065 (m-80) cc_final: 0.8448 (m-80) REVERT: O 1613 MET cc_start: 0.9541 (mtm) cc_final: 0.8152 (mtm) REVERT: O 1642 MET cc_start: 0.9512 (mmp) cc_final: 0.8791 (mmm) REVERT: O 1657 MET cc_start: 0.8435 (mmp) cc_final: 0.8104 (mmp) REVERT: O 1680 MET cc_start: 0.8363 (mmm) cc_final: 0.8042 (mmm) REVERT: O 1776 ASP cc_start: 0.8674 (t0) cc_final: 0.7935 (m-30) REVERT: O 1783 PHE cc_start: 0.9079 (t80) cc_final: 0.8356 (t80) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0688 time to fit residues: 7.6129 Evaluate side-chains 64 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1241 HIS O1267 ASN O1309 GLN O1757 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.047445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.033254 restraints weight = 41350.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.034424 restraints weight = 26471.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.035257 restraints weight = 19549.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.035806 restraints weight = 15799.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.036166 restraints weight = 13658.079| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5904 Z= 0.186 Angle : 0.565 8.804 8002 Z= 0.285 Chirality : 0.041 0.177 887 Planarity : 0.005 0.104 997 Dihedral : 13.050 125.465 925 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.32), residues: 688 helix: 2.12 (0.29), residues: 332 sheet: 0.81 (0.43), residues: 132 loop : 0.06 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG O1175 TYR 0.027 0.001 TYR O1140 PHE 0.015 0.001 PHE O1777 TRP 0.009 0.002 TRP O1840 HIS 0.004 0.001 HIS O1574 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 ( 5904) covalent geometry : angle 0.56512 / 0.28 ( 8002) hydrogen bonds : bond 0.03074 / 1.99 ( 256) hydrogen bonds : angle 4.48374 / 3.27 ( 735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1105 MET cc_start: 0.9296 (tpt) cc_final: 0.8829 (tpt) REVERT: O 1157 MET cc_start: 0.8943 (mmm) cc_final: 0.8513 (mmm) REVERT: O 1162 LEU cc_start: 0.9792 (mm) cc_final: 0.9430 (pp) REVERT: O 1166 TRP cc_start: 0.8934 (t-100) cc_final: 0.8649 (t-100) REVERT: O 1288 MET cc_start: 0.9498 (mmp) cc_final: 0.9203 (mmm) REVERT: O 1294 GLU cc_start: 0.9264 (mt-10) cc_final: 0.9021 (mt-10) REVERT: O 1421 LEU cc_start: 0.9608 (tp) cc_final: 0.9289 (pp) REVERT: O 1566 CYS cc_start: 0.9504 (m) cc_final: 0.8994 (p) REVERT: O 1584 PHE cc_start: 0.9192 (m-80) cc_final: 0.8542 (m-80) REVERT: O 1613 MET cc_start: 0.9561 (mtm) cc_final: 0.9346 (mpp) REVERT: O 1638 LEU cc_start: 0.9663 (mt) cc_final: 0.9383 (mt) REVERT: O 1642 MET cc_start: 0.9397 (mmp) cc_final: 0.8969 (mmm) REVERT: O 1657 MET cc_start: 0.8559 (mmp) cc_final: 0.8246 (mmp) REVERT: O 1776 ASP cc_start: 0.8739 (t0) cc_final: 0.8047 (m-30) REVERT: O 1783 PHE cc_start: 0.9180 (t80) cc_final: 0.8506 (t80) REVERT: O 1814 MET cc_start: 0.9636 (mtt) cc_final: 0.8864 (mmm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0642 time to fit residues: 6.7163 Evaluate side-chains 67 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 3 optimal weight: 0.0020 chunk 34 optimal weight: 0.0870 chunk 62 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.4366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1654 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.048173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.033965 restraints weight = 41199.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.035220 restraints weight = 26061.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.036068 restraints weight = 18997.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.036707 restraints weight = 15302.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.037116 restraints weight = 13085.064| |-----------------------------------------------------------------------------| r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5904 Z= 0.114 Angle : 0.538 9.035 8002 Z= 0.269 Chirality : 0.042 0.170 887 Planarity : 0.004 0.093 997 Dihedral : 13.012 127.373 925 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.33), residues: 688 helix: 2.13 (0.29), residues: 332 sheet: 0.81 (0.43), residues: 133 loop : 0.11 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O1175 TYR 0.012 0.001 TYR O1140 PHE 0.008 0.001 PHE O1763 TRP 0.005 0.001 TRP O1840 HIS 0.002 0.001 HIS O1574 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 ( 5904) covalent geometry : angle 0.53809 / 0.27 ( 8002) hydrogen bonds : bond 0.02805 / 1.84 ( 256) hydrogen bonds : angle 4.31085 / 3.13 ( 735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1105 MET cc_start: 0.9296 (tpt) cc_final: 0.8836 (tpt) REVERT: O 1162 LEU cc_start: 0.9775 (mm) cc_final: 0.9399 (pp) REVERT: O 1166 TRP cc_start: 0.8939 (t-100) cc_final: 0.8529 (t-100) REVERT: O 1234 ASP cc_start: 0.9404 (m-30) cc_final: 0.9069 (p0) REVERT: O 1282 CYS cc_start: 0.9497 (m) cc_final: 0.9074 (m) REVERT: O 1286 MET cc_start: 0.9062 (ptp) cc_final: 0.8573 (ptp) REVERT: O 1288 MET cc_start: 0.9483 (mmp) cc_final: 0.9161 (mmm) REVERT: O 1294 GLU cc_start: 0.9275 (mt-10) cc_final: 0.9024 (mt-10) REVERT: O 1421 LEU cc_start: 0.9600 (tp) cc_final: 0.9259 (pp) REVERT: O 1566 CYS cc_start: 0.9474 (m) cc_final: 0.8956 (p) REVERT: O 1584 PHE cc_start: 0.9175 (m-80) cc_final: 0.8540 (m-80) REVERT: O 1642 MET cc_start: 0.9431 (mmp) cc_final: 0.8838 (mmm) REVERT: O 1657 MET cc_start: 0.8624 (mmp) cc_final: 0.8327 (mmp) REVERT: O 1680 MET cc_start: 0.8283 (mmm) cc_final: 0.8068 (mmm) REVERT: O 1776 ASP cc_start: 0.8723 (t0) cc_final: 0.8043 (m-30) REVERT: O 1783 PHE cc_start: 0.9120 (t80) cc_final: 0.8421 (t80) REVERT: O 1814 MET cc_start: 0.9617 (mtt) cc_final: 0.8856 (mmm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0606 time to fit residues: 6.3871 Evaluate side-chains 68 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 63 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1757 GLN ** O1815 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 = 0.3217 r_free = 0.3217 target = 0.045890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.032158 restraints weight = 42706.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.033304 restraints weight = 27258.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.034096 restraints weight = 20053.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.034685 restraints weight = 16190.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.035054 restraints weight = 13903.655| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5904 Z= 0.225 Angle : 0.593 8.622 8002 Z= 0.299 Chirality : 0.040 0.150 887 Planarity : 0.004 0.048 997 Dihedral : 13.121 130.314 925 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.32), residues: 688 helix: 2.04 (0.29), residues: 333 sheet: 0.86 (0.43), residues: 132 loop : -0.04 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG O1266 TYR 0.025 0.001 TYR O1195 PHE 0.017 0.002 PHE O1669 TRP 0.006 0.002 TRP O1826 HIS 0.004 0.002 HIS O1574 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.23 ( 5904) covalent geometry : angle 0.59294 / 0.30 ( 8002) hydrogen bonds : bond 0.03083 / 2.03 ( 256) hydrogen bonds : angle 4.55445 / 3.29 ( 735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1105 MET cc_start: 0.9288 (tpt) cc_final: 0.8817 (tpt) REVERT: O 1114 ASN cc_start: 0.8766 (m-40) cc_final: 0.8535 (m-40) REVERT: O 1157 MET cc_start: 0.8944 (mmm) cc_final: 0.8488 (mmm) REVERT: O 1162 LEU cc_start: 0.9789 (mm) cc_final: 0.9457 (pp) REVERT: O 1247 VAL cc_start: 0.9385 (t) cc_final: 0.9005 (p) REVERT: O 1286 MET cc_start: 0.9192 (ptp) cc_final: 0.8606 (ptp) REVERT: O 1288 MET cc_start: 0.9591 (mmp) cc_final: 0.9277 (mmm) REVERT: O 1294 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8959 (mt-10) REVERT: O 1421 LEU cc_start: 0.9656 (tp) cc_final: 0.9319 (pp) REVERT: O 1566 CYS cc_start: 0.9518 (m) cc_final: 0.9012 (p) REVERT: O 1584 PHE cc_start: 0.9370 (m-80) cc_final: 0.8723 (m-80) REVERT: O 1613 MET cc_start: 0.8883 (mpp) cc_final: 0.7574 (mpp) REVERT: O 1657 MET cc_start: 0.8635 (mmp) cc_final: 0.8274 (mmp) REVERT: O 1680 MET cc_start: 0.8354 (mmm) cc_final: 0.8013 (mmm) REVERT: O 1783 PHE cc_start: 0.9075 (t80) cc_final: 0.8400 (t80) REVERT: O 1814 MET cc_start: 0.9571 (mtt) cc_final: 0.9000 (mmm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0583 time to fit residues: 5.6227 Evaluate side-chains 58 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 30 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.047103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.033066 restraints weight = 42558.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.034295 restraints weight = 26789.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.035140 restraints weight = 19587.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.035724 restraints weight = 15753.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.036090 restraints weight = 13558.416| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5904 Z= 0.131 Angle : 0.542 7.141 8002 Z= 0.274 Chirality : 0.041 0.141 887 Planarity : 0.004 0.044 997 Dihedral : 13.112 132.189 925 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.33), residues: 688 helix: 2.20 (0.29), residues: 331 sheet: 0.91 (0.43), residues: 133 loop : 0.04 (0.42), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O1175 TYR 0.011 0.001 TYR O1195 PHE 0.009 0.001 PHE O1669 TRP 0.039 0.002 TRP O1826 HIS 0.002 0.001 HIS O1104 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 5904) covalent geometry : angle 0.54183 / 0.27 ( 8002) hydrogen bonds : bond 0.02800 / 1.84 ( 256) hydrogen bonds : angle 4.44647 / 3.17 ( 735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1105 MET cc_start: 0.9294 (tpt) cc_final: 0.8839 (tpt) REVERT: O 1162 LEU cc_start: 0.9778 (mm) cc_final: 0.9392 (pp) REVERT: O 1247 VAL cc_start: 0.9364 (t) cc_final: 0.8998 (p) REVERT: O 1282 CYS cc_start: 0.9423 (m) cc_final: 0.9076 (m) REVERT: O 1286 MET cc_start: 0.9172 (ptp) cc_final: 0.8571 (ptp) REVERT: O 1288 MET cc_start: 0.9510 (mmp) cc_final: 0.9241 (mmm) REVERT: O 1294 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8947 (mt-10) REVERT: O 1566 CYS cc_start: 0.9472 (m) cc_final: 0.8925 (p) REVERT: O 1584 PHE cc_start: 0.9334 (m-80) cc_final: 0.8615 (m-80) REVERT: O 1602 ILE cc_start: 0.9448 (mt) cc_final: 0.9128 (mm) REVERT: O 1657 MET cc_start: 0.8638 (mmp) cc_final: 0.8284 (mmp) REVERT: O 1680 MET cc_start: 0.8310 (mmm) cc_final: 0.7952 (mmm) REVERT: O 1776 ASP cc_start: 0.8860 (t0) cc_final: 0.8115 (m-30) REVERT: O 1783 PHE cc_start: 0.9042 (t80) cc_final: 0.8322 (t80) REVERT: O 1814 MET cc_start: 0.9593 (mtp) cc_final: 0.9276 (mmm) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.0621 time to fit residues: 6.2203 Evaluate side-chains 59 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 61 optimal weight: 9.9990 chunk 68 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O1815 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 = 0.3234 r_free = 0.3234 target = 0.046267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.032408 restraints weight = 41764.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.033565 restraints weight = 26603.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.034239 restraints weight = 19558.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.034919 restraints weight = 16154.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.035301 restraints weight = 13733.372| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5904 Z= 0.176 Angle : 0.568 11.238 8002 Z= 0.285 Chirality : 0.041 0.174 887 Planarity : 0.004 0.035 997 Dihedral : 13.160 134.091 925 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.33), residues: 688 helix: 2.09 (0.29), residues: 334 sheet: 0.90 (0.44), residues: 131 loop : 0.07 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O1266 TYR 0.012 0.001 TYR O1198 PHE 0.015 0.001 PHE O1669 TRP 0.049 0.003 TRP O1826 HIS 0.003 0.001 HIS O1574 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 ( 5904) covalent geometry : angle 0.56750 / 0.29 ( 8002) hydrogen bonds : bond 0.02879 / 1.92 ( 256) hydrogen bonds : angle 4.42788 / 3.18 ( 735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1105 MET cc_start: 0.9256 (tpt) cc_final: 0.8799 (tpt) REVERT: O 1162 LEU cc_start: 0.9766 (mm) cc_final: 0.9430 (pp) REVERT: O 1247 VAL cc_start: 0.9369 (t) cc_final: 0.9021 (p) REVERT: O 1286 MET cc_start: 0.9170 (ptp) cc_final: 0.8543 (ptp) REVERT: O 1288 MET cc_start: 0.9510 (mmp) cc_final: 0.9246 (mmm) REVERT: O 1294 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8947 (mt-10) REVERT: O 1566 CYS cc_start: 0.9440 (m) cc_final: 0.8924 (p) REVERT: O 1584 PHE cc_start: 0.9357 (m-80) cc_final: 0.8699 (m-80) REVERT: O 1602 ILE cc_start: 0.9449 (mt) cc_final: 0.9112 (mm) REVERT: O 1613 MET cc_start: 0.8696 (mpp) cc_final: 0.7427 (mpp) REVERT: O 1657 MET cc_start: 0.8716 (mmp) cc_final: 0.8463 (mmp) REVERT: O 1776 ASP cc_start: 0.8942 (t0) cc_final: 0.8190 (m-30) REVERT: O 1783 PHE cc_start: 0.9021 (t80) cc_final: 0.8249 (t80) REVERT: O 1814 MET cc_start: 0.9627 (mtp) cc_final: 0.9183 (mmm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0608 time to fit residues: 5.7160 Evaluate side-chains 54 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 57 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O1815 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 = 0.3249 r_free = 0.3249 target = 0.046845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.032934 restraints weight = 42227.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.034127 restraints weight = 26831.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.034983 restraints weight = 19638.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.035560 restraints weight = 15764.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.035930 restraints weight = 13544.909| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5904 Z= 0.130 Angle : 0.548 12.320 8002 Z= 0.271 Chirality : 0.041 0.133 887 Planarity : 0.003 0.033 997 Dihedral : 13.142 136.425 925 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.33), residues: 688 helix: 1.99 (0.29), residues: 334 sheet: 0.89 (0.44), residues: 131 loop : 0.07 (0.41), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O1850 TYR 0.010 0.001 TYR O1140 PHE 0.011 0.001 PHE O1669 TRP 0.031 0.002 TRP O1826 HIS 0.002 0.001 HIS O1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 5904) covalent geometry : angle 0.54818 / 0.27 ( 8002) hydrogen bonds : bond 0.02653 / 1.76 ( 256) hydrogen bonds : angle 4.30339 / 3.12 ( 735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1105 MET cc_start: 0.9274 (tpt) cc_final: 0.8820 (tpt) REVERT: O 1116 LEU cc_start: 0.9564 (tt) cc_final: 0.9363 (tt) REVERT: O 1162 LEU cc_start: 0.9759 (mm) cc_final: 0.9431 (pp) REVERT: O 1247 VAL cc_start: 0.9349 (t) cc_final: 0.8976 (p) REVERT: O 1286 MET cc_start: 0.9128 (ptp) cc_final: 0.8318 (ptp) REVERT: O 1288 MET cc_start: 0.9510 (mmp) cc_final: 0.9287 (mmm) REVERT: O 1294 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8919 (mt-10) REVERT: O 1566 CYS cc_start: 0.9454 (m) cc_final: 0.8917 (p) REVERT: O 1584 PHE cc_start: 0.9379 (m-80) cc_final: 0.8706 (m-80) REVERT: O 1657 MET cc_start: 0.8743 (mmp) cc_final: 0.8357 (mmp) REVERT: O 1680 MET cc_start: 0.8252 (mmm) cc_final: 0.8037 (mmm) REVERT: O 1776 ASP cc_start: 0.8959 (t0) cc_final: 0.8219 (m-30) REVERT: O 1783 PHE cc_start: 0.8990 (t80) cc_final: 0.8140 (t80) REVERT: O 1814 MET cc_start: 0.9631 (mtp) cc_final: 0.9182 (mmm) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0626 time to fit residues: 5.7786 Evaluate side-chains 57 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 7.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O1815 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 = 0.3259 r_free = 0.3259 target = 0.047175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.033139 restraints weight = 42579.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.034344 restraints weight = 26989.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.035204 restraints weight = 19829.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.035746 restraints weight = 15921.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.036006 restraints weight = 13777.297| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5904 Z= 0.112 Angle : 0.553 14.769 8002 Z= 0.271 Chirality : 0.042 0.231 887 Planarity : 0.003 0.031 997 Dihedral : 13.143 138.819 925 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.66 (0.33), residues: 688 helix: 1.98 (0.29), residues: 332 sheet: 0.85 (0.44), residues: 131 loop : 0.02 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O1266 TYR 0.009 0.001 TYR O1140 PHE 0.010 0.001 PHE O1669 TRP 0.027 0.002 TRP O1826 HIS 0.005 0.001 HIS O1268 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 5904) covalent geometry : angle 0.55335 / 0.27 ( 8002) hydrogen bonds : bond 0.02533 / 1.71 ( 256) hydrogen bonds : angle 4.27309 / 3.11 ( 735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1376 Ramachandran restraints generated. 688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1105 MET cc_start: 0.9254 (tpt) cc_final: 0.8802 (tpt) REVERT: O 1162 LEU cc_start: 0.9745 (mm) cc_final: 0.9420 (pp) REVERT: O 1247 VAL cc_start: 0.9338 (t) cc_final: 0.8986 (p) REVERT: O 1286 MET cc_start: 0.9081 (ptp) cc_final: 0.8317 (ptp) REVERT: O 1294 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8891 (mt-10) REVERT: O 1566 CYS cc_start: 0.9368 (m) cc_final: 0.8889 (p) REVERT: O 1584 PHE cc_start: 0.9322 (m-80) cc_final: 0.8669 (m-80) REVERT: O 1657 MET cc_start: 0.8583 (mmp) cc_final: 0.8216 (mmp) REVERT: O 1680 MET cc_start: 0.8149 (mmm) cc_final: 0.7898 (mmm) REVERT: O 1776 ASP cc_start: 0.9016 (t0) cc_final: 0.8316 (m-30) REVERT: O 1783 PHE cc_start: 0.8963 (t80) cc_final: 0.8126 (t80) REVERT: O 1814 MET cc_start: 0.9592 (mtp) cc_final: 0.9142 (mmm) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0590 time to fit residues: 5.6112 Evaluate side-chains 56 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 68 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 9.9990 chunk 60 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O1815 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 = 0.3262 r_free = 0.3262 target = 0.047230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.033286 restraints weight = 41201.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.034459 restraints weight = 26346.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.035284 restraints weight = 19442.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.035892 restraints weight = 15745.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.036275 restraints weight = 13486.379| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5904 Z= 0.108 Angle : 0.554 14.084 8002 Z= 0.271 Chirality : 0.042 0.162 887 Planarity : 0.003 0.032 997 Dihedral : 13.203 140.545 925 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.64 (0.33), residues: 688 helix: 1.95 (0.30), residues: 332 sheet: 0.84 (0.45), residues: 131 loop : 0.01 (0.41), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O1266 TYR 0.008 0.001 TYR O1140 PHE 0.010 0.001 PHE O1669 TRP 0.021 0.002 TRP O1826 HIS 0.002 0.001 HIS O1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 ( 5904) covalent geometry : angle 0.55440 / 0.27 ( 8002) hydrogen bonds : bond 0.02527 / 1.70 ( 256) hydrogen bonds : angle 4.23699 / 3.09 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 911.47 seconds wall clock time: 16 minutes 25.42 seconds (985.42 seconds total)