Starting phenix.real_space_refine on Tue Aug 4 18:20:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ran_19020/08_2026/8ran_19020.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ran_19020/08_2026/8ran_19020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ran_19020/08_2026/8ran_19020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ran_19020/08_2026/8ran_19020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ran_19020/08_2026/8ran_19020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ran_19020/08_2026/8ran_19020.map" } resolution = 3.25 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: 5 Type Number sf(0) Gaussians P 13 5.49 5 S 31 5.16 5 C 3614 2.51 5 N 1010 2.21 5 O 1131 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s 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: 5799 Number of models: 1 Model: "" Number of chains: 2 Chain: "O" Number of atoms: 5523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5523 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 28, 'TRANS': 661} Chain breaks: 2 Chain: "P" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 276 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 3, 'rna3p_pyr': 2} Link IDs: {'rna2p': 7, 'rna3p': 5} Time building chain proxies: 1.29, per 1000 atoms: 0.22 Number of scatterers: 5799 At special positions: 0 Unit cell: (75.6, 99.75, 96.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 31 16.00 P 13 15.00 O 1131 8.00 N 1010 7.00 C 3614 6.00 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: 0.35 Conformation dependent library (CDL) restraints added in 366.0 milliseconds 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1306 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 5 sheets defined 52.0% alpha, 15.9% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'O' and resid 1095 through 1110 Processing helix chain 'O' and resid 1113 through 1122 removed outlier: 3.545A pdb=" N GLN O1122 " --> pdb=" O GLU O1118 " (cutoff:3.500A) Processing helix chain 'O' and resid 1136 through 1140 Processing helix chain 'O' and resid 1149 through 1176 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: 3.616A 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 1304 No H-bonds generated for 'chain 'O' and resid 1302 through 1304' Processing helix chain 'O' and resid 1306 through 1313 Processing helix chain 'O' and resid 1322 through 1334 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: 3.704A pdb=" N SER O1425 " --> pdb=" O LEU O1421 " (cutoff:3.500A) Processing helix chain 'O' and resid 1449 through 1453 Processing helix chain 'O' and resid 1456 through 1466 Processing helix chain 'O' and resid 1535 through 1562 Processing helix chain 'O' and resid 1570 through 1573 Processing helix chain 'O' and resid 1574 through 1581 Processing helix chain 'O' and resid 1591 through 1595 removed outlier: 3.819A pdb=" N CYS O1595 " --> pdb=" O ALA O1592 " (cutoff:3.500A) Processing helix chain 'O' and resid 1596 through 1602 Processing helix chain 'O' and resid 1603 through 1606 removed outlier: 3.616A 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 removed outlier: 3.544A pdb=" N ARG O1641 " --> pdb=" O SER O1637 " (cutoff:3.500A) Processing helix chain 'O' and resid 1658 through 1668 removed outlier: 4.271A pdb=" N PHE O1664 " --> pdb=" O SER O1660 " (cutoff:3.500A) Proline residue: O1665 - end of helix Processing helix chain 'O' and resid 1719 through 1736 Processing helix chain 'O' and resid 1752 through 1767 Processing helix chain 'O' and resid 1768 through 1773 removed outlier: 3.654A pdb=" N ILE O1771 " --> pdb=" O GLY O1768 " (cutoff:3.500A) Processing helix chain 'O' and resid 1779 through 1784 Processing helix chain 'O' and resid 1805 through 1809 removed outlier: 4.273A pdb=" N LEU O1808 " --> pdb=" O VAL O1805 " (cutoff:3.500A) Processing helix chain 'O' and resid 1810 through 1820 removed outlier: 3.638A pdb=" N MET O1814 " --> pdb=" O ASP O1810 " (cutoff:3.500A) Processing helix chain 'O' and resid 1831 through 1837 removed outlier: 4.061A pdb=" N SER O1837 " --> pdb=" O SER O1833 " (cutoff:3.500A) Processing helix chain 'O' and resid 1837 through 1850 Processing helix chain 'O' and resid 1865 through 1876 removed outlier: 3.715A 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: 6.756A pdb=" N ASN O1257 " --> pdb=" O ASN O1252 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN O1252 " --> pdb=" O ASN O1257 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ASP O1259 " --> pdb=" O LEU O1250 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU O1250 " --> pdb=" O ASP O1259 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N THR O1261 " --> pdb=" O ARG O1248 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N HIS O1265 " --> pdb=" O LEU O1244 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N LEU O1244 " --> pdb=" O HIS O1265 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ASP O1215 " --> pdb=" O VAL O1247 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET O1286 " --> pdb=" O LEU O1216 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N VAL O1218 " --> pdb=" O LYS O1284 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LYS O1284 " --> pdb=" O VAL O1218 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ALA O1220 " --> pdb=" O CYS O1282 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N CYS O1282 " --> pdb=" O ALA O1220 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N SER O1182 " --> pdb=" O ALA O1202 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ALA O1202 " --> pdb=" O SER O1182 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE O1184 " --> pdb=" O SER O1200 " (cutoff:3.500A) removed outlier: 3.613A 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: 6.469A pdb=" N ILE O1406 " --> pdb=" O ILE O1565 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N SER O1567 " --> pdb=" O ILE O1406 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE O1408 " --> pdb=" O SER O1567 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL O1587 " --> pdb=" O ILE O1612 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N VAL O1614 " --> pdb=" O VAL O1587 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ILE O1589 " --> pdb=" O VAL O1614 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N SER O1353 " --> pdb=" O MET O1613 " (cutoff:3.500A) removed outlier: 9.935A pdb=" N TYR O1649 " --> pdb=" O PHE O1352 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LEU O1354 " --> pdb=" O TYR O1649 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 1653 through 1654 removed outlier: 3.542A pdb=" N GLN O1654 " --> pdb=" O LYS O1675 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'O' and resid 1775 through 1777 removed outlier: 6.511A pdb=" N GLU O1789 " --> pdb=" O SER O1824 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N TRP O1826 " --> pdb=" O GLU O1789 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE O1791 " --> pdb=" O TRP O1826 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU O1828 " --> pdb=" O ILE O1791 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE O1793 " --> pdb=" O LEU O1828 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N HIS O1830 " --> pdb=" O ILE O1793 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY O1829 " --> pdb=" O PHE O1700 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ALA O1854 " --> pdb=" O TYR O1697 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE O1699 " --> pdb=" O ALA O1854 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ALA O1856 " --> pdb=" O PHE O1699 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ASP O1701 " --> pdb=" O ALA O1856 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'O' and resid 1707 through 1709 256 hydrogen bonds defined for protein. 723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 0.71 Time building geometry restraints manager: 0.49 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: 1844 1.34 - 1.45: 785 1.45 - 1.57: 3229 1.57 - 1.69: 25 1.69 - 1.81: 49 Bond restraints: 5932 Sorted by residual: bond pdb=" C1' C P 11 " pdb=" N1 C P 11 " ideal model delta sigma weight residual 1.464 1.474 -0.010 1.40e-02 5.10e+03 5.22e-01 bond pdb=" C1' U P 3 " pdb=" N1 U P 3 " ideal model delta sigma weight residual 1.464 1.474 -0.010 1.40e-02 5.10e+03 5.13e-01 bond pdb=" C1' C P 4 " pdb=" N1 C P 4 " ideal model delta sigma weight residual 1.464 1.473 -0.009 1.40e-02 5.10e+03 4.04e-01 bond pdb=" C1' U P 12 " pdb=" N1 U P 12 " ideal model delta sigma weight residual 1.464 1.473 -0.009 1.40e-02 5.10e+03 3.91e-01 bond pdb=" C1' G P 5 " pdb=" N9 G P 5 " ideal model delta sigma weight residual 1.483 1.474 0.009 1.50e-02 4.44e+03 3.35e-01 ... (remaining 5927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 7825 0.85 - 1.71: 179 1.71 - 2.56: 23 2.56 - 3.41: 15 3.41 - 4.26: 14 Bond angle restraints: 8056 Sorted by residual: angle pdb=" O5' C P 4 " pdb=" C5' C P 4 " pdb=" C4' C P 4 " ideal model delta sigma weight residual 109.40 112.47 -3.07 8.00e-01 1.56e+00 1.47e+01 angle pdb=" O5' C P 11 " pdb=" C5' C P 11 " pdb=" C4' C P 11 " ideal model delta sigma weight residual 109.40 111.96 -2.56 8.00e-01 1.56e+00 1.02e+01 angle pdb=" O5' U P 10 " pdb=" C5' U P 10 " pdb=" C4' U P 10 " ideal model delta sigma weight residual 109.40 111.86 -2.46 8.00e-01 1.56e+00 9.46e+00 angle pdb=" O5' G P 2 " pdb=" C5' G P 2 " pdb=" C4' G P 2 " ideal model delta sigma weight residual 109.40 111.85 -2.45 8.00e-01 1.56e+00 9.40e+00 angle pdb=" O5' A P 13 " pdb=" C5' A P 13 " pdb=" C4' A P 13 " ideal model delta sigma weight residual 109.40 111.80 -2.40 8.00e-01 1.56e+00 9.01e+00 ... (remaining 8051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.70: 3568 21.70 - 43.39: 66 43.39 - 65.09: 27 65.09 - 86.78: 5 86.78 - 108.48: 2 Dihedral angle restraints: 3668 sinusoidal: 1647 harmonic: 2021 Sorted by residual: dihedral pdb=" O4' U P 12 " pdb=" C1' U P 12 " pdb=" N1 U P 12 " pdb=" C2 U P 12 " ideal model delta sinusoidal sigma weight residual -128.00 -73.98 -54.02 1 1.70e+01 3.46e-03 1.37e+01 dihedral pdb=" P U P 10 " pdb=" O5' U P 10 " pdb=" C5' U P 10 " pdb=" C4' U P 10 " ideal model delta sinusoidal sigma weight residual 170.00 -81.52 -108.48 1 4.00e+01 6.25e-04 7.90e+00 dihedral pdb=" O5' C P 4 " pdb=" C5' C P 4 " pdb=" C4' C P 4 " pdb=" C3' C P 4 " ideal model delta sinusoidal sigma weight residual -65.00 -21.76 -43.24 3 1.50e+01 4.44e-03 7.77e+00 ... (remaining 3665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 587 0.026 - 0.052: 182 0.052 - 0.077: 50 0.077 - 0.103: 46 0.103 - 0.129: 35 Chirality restraints: 900 Sorted by residual: chirality pdb=" CA VAL O1191 " pdb=" N VAL O1191 " pdb=" C VAL O1191 " pdb=" CB VAL O1191 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE O1184 " pdb=" N ILE O1184 " pdb=" C ILE O1184 " pdb=" CB ILE O1184 " 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=" CA ILE O1408 " pdb=" N ILE O1408 " pdb=" C ILE O1408 " pdb=" CB ILE O1408 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 897 not shown) Planarity restraints: 993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER O1647 " 0.017 5.00e-02 4.00e+02 2.63e-02 1.11e+00 pdb=" N PRO O1648 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO O1648 " 0.013 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 GLY O1357 " 0.016 5.00e-02 4.00e+02 2.46e-02 9.68e-01 pdb=" N PRO O1358 " -0.043 5.00e-02 4.00e+02 pdb=" CA PRO O1358 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO O1358 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O1179 " -0.016 5.00e-02 4.00e+02 2.34e-02 8.75e-01 pdb=" N PRO O1180 " 0.040 5.00e-02 4.00e+02 pdb=" CA PRO O1180 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO O1180 " -0.013 5.00e-02 4.00e+02 ... (remaining 990 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 82 2.64 - 3.21: 5573 3.21 - 3.77: 8885 3.77 - 4.34: 12514 4.34 - 4.90: 20306 Nonbonded interactions: 47360 Sorted by model distance: nonbonded pdb=" OG1 THR O1717 " pdb=" OE1 GLU O1754 " model vdw 2.076 3.040 nonbonded pdb=" NZ LYS O1246 " pdb=" OE2 GLU O1292 " model vdw 2.144 3.120 nonbonded pdb=" OD1 ASN O1345 " pdb=" OH TYR O1649 " model vdw 2.155 3.040 nonbonded pdb=" O TYR O1125 " pdb=" NH1 ARG O1173 " model vdw 2.216 3.120 nonbonded pdb=" OE1 GLU O1720 " pdb=" NH2 ARG O1723 " model vdw 2.250 3.120 ... (remaining 47355 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 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: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.860 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 0.015 5932 Z= 0.087 Angle : 0.376 4.264 8056 Z= 0.239 Chirality : 0.039 0.129 900 Planarity : 0.002 0.026 993 Dihedral : 10.557 108.479 2362 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % 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: 3.22 (0.35), residues: 684 helix: 4.09 (0.31), residues: 313 sheet: 0.37 (0.47), residues: 129 loop : 0.50 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O1537 TYR 0.004 0.000 TYR O1195 PHE 0.004 0.001 PHE O1374 TRP 0.006 0.001 TRP O1688 HIS 0.001 0.000 HIS O1658 Details of bonding type rmsd/Z covalent geometry : bond 0.00152 / 0.09 ( 5932) covalent geometry : angle 0.37580 / 0.24 ( 8056) hydrogen bonds : bond 0.13660 / 8.80 ( 256) hydrogen bonds : angle 4.75648 / 3.23 ( 723) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1373 TYR cc_start: 0.9213 (t80) cc_final: 0.8951 (t80) REVERT: O 1564 ILE cc_start: 0.9272 (mt) cc_final: 0.8963 (pt) REVERT: O 1602 ILE cc_start: 0.9255 (mt) cc_final: 0.8946 (mt) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0921 time to fit residues: 12.9403 Evaluate side-chains 52 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.098264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.065681 restraints weight = 18685.648| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.75 r_work: 0.3022 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5932 Z= 0.135 Angle : 0.563 7.049 8056 Z= 0.288 Chirality : 0.042 0.149 900 Planarity : 0.004 0.036 993 Dihedral : 13.071 104.397 964 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.98 % Allowed : 8.29 % Favored : 90.73 % 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: 2.46 (0.33), residues: 684 helix: 2.91 (0.29), residues: 325 sheet: 0.45 (0.47), residues: 118 loop : 0.52 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG O1820 TYR 0.013 0.001 TYR O1855 PHE 0.027 0.002 PHE O1783 TRP 0.035 0.003 TRP O1688 HIS 0.005 0.001 HIS O1433 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 5932) covalent geometry : angle 0.56287 / 0.29 ( 8056) hydrogen bonds : bond 0.03476 / 2.36 ( 256) hydrogen bonds : angle 4.31026 / 2.95 ( 723) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 57 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1117 TYR cc_start: 0.7972 (m-10) cc_final: 0.7566 (m-10) REVERT: O 1373 TYR cc_start: 0.9418 (t80) cc_final: 0.9218 (t80) REVERT: O 1536 MET cc_start: 0.5111 (ppp) cc_final: 0.4812 (ppp) REVERT: O 1564 ILE cc_start: 0.9121 (mt) cc_final: 0.8636 (pt) REVERT: O 1602 ILE cc_start: 0.9521 (mt) cc_final: 0.9197 (mp) REVERT: O 1657 MET cc_start: 0.7506 (tpp) cc_final: 0.7291 (tpp) REVERT: O 1756 MET cc_start: 0.8641 (tmm) cc_final: 0.8360 (tmm) REVERT: O 1783 PHE cc_start: 0.9026 (t80) cc_final: 0.8784 (t80) REVERT: O 1855 TYR cc_start: 0.8811 (m-10) cc_final: 0.8562 (m-10) outliers start: 6 outliers final: 2 residues processed: 60 average time/residue: 0.0720 time to fit residues: 5.7522 Evaluate side-chains 51 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1433 HIS Chi-restraints excluded: chain O residue 1792 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.4980 chunk 63 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.093233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058979 restraints weight = 18127.218| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 3.57 r_work: 0.2849 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 5932 Z= 0.232 Angle : 0.581 7.756 8056 Z= 0.297 Chirality : 0.042 0.138 900 Planarity : 0.004 0.037 993 Dihedral : 13.234 104.211 964 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.63 % Allowed : 9.59 % Favored : 88.78 % 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: 1.92 (0.33), residues: 684 helix: 2.38 (0.30), residues: 323 sheet: 0.41 (0.46), residues: 117 loop : 0.29 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O1173 TYR 0.010 0.002 TYR O1752 PHE 0.022 0.002 PHE O1783 TRP 0.025 0.005 TRP O1826 HIS 0.006 0.002 HIS O1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 ( 5932) covalent geometry : angle 0.58055 / 0.30 ( 8056) hydrogen bonds : bond 0.03558 / 2.39 ( 256) hydrogen bonds : angle 4.20621 / 2.87 ( 723) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: O 1355 ILE cc_start: 0.9665 (mt) cc_final: 0.9439 (mm) REVERT: O 1564 ILE cc_start: 0.9147 (mt) cc_final: 0.8671 (pt) REVERT: O 1591 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8552 (tp30) REVERT: O 1657 MET cc_start: 0.7705 (tpp) cc_final: 0.7421 (tpp) outliers start: 10 outliers final: 3 residues processed: 60 average time/residue: 0.0673 time to fit residues: 5.2888 Evaluate side-chains 42 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1171 SER Chi-restraints excluded: chain O residue 1647 SER Chi-restraints excluded: chain O residue 1816 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 0.0010 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 29 optimal weight: 0.0570 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 22 optimal weight: 8.9990 chunk 3 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.4304 ------------------------------------------------------------------------------- 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 = 0.3895 r_free = 0.3895 target = 0.093752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059393 restraints weight = 18381.001| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.62 r_work: 0.2871 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5932 Z= 0.121 Angle : 0.521 8.660 8056 Z= 0.265 Chirality : 0.040 0.160 900 Planarity : 0.005 0.082 993 Dihedral : 13.184 103.846 964 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.49 % Allowed : 12.20 % Favored : 87.32 % 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: 1.88 (0.33), residues: 684 helix: 2.32 (0.30), residues: 324 sheet: 0.37 (0.47), residues: 115 loop : 0.32 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O1734 TYR 0.007 0.001 TYR O1766 PHE 0.014 0.001 PHE O1783 TRP 0.022 0.002 TRP O1826 HIS 0.004 0.001 HIS O1433 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 5932) covalent geometry : angle 0.52058 / 0.27 ( 8056) hydrogen bonds : bond 0.02972 / 2.04 ( 256) hydrogen bonds : angle 4.09899 / 2.80 ( 723) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: O 1117 TYR cc_start: 0.8360 (m-10) cc_final: 0.8069 (m-10) REVERT: O 1564 ILE cc_start: 0.9008 (mt) cc_final: 0.8788 (tt) REVERT: O 1591 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8625 (tp30) REVERT: O 1657 MET cc_start: 0.7782 (tpp) cc_final: 0.7577 (tpp) REVERT: O 1756 MET cc_start: 0.8739 (tmm) cc_final: 0.8457 (tmm) outliers start: 3 outliers final: 2 residues processed: 48 average time/residue: 0.0449 time to fit residues: 3.0799 Evaluate side-chains 42 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1162 LEU Chi-restraints excluded: chain O residue 1792 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 29 optimal weight: 0.0570 chunk 7 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 chunk 43 optimal weight: 0.0050 chunk 59 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 overall best weight: 0.3312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.093764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060123 restraints weight = 18509.211| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.66 r_work: 0.2883 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5932 Z= 0.106 Angle : 0.489 8.449 8056 Z= 0.250 Chirality : 0.040 0.201 900 Planarity : 0.004 0.050 993 Dihedral : 13.137 103.505 964 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.98 % Allowed : 11.87 % Favored : 87.15 % 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: 684 helix: 2.30 (0.30), residues: 324 sheet: 0.50 (0.48), residues: 114 loop : 0.25 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O1734 TYR 0.007 0.001 TYR O1752 PHE 0.015 0.001 PHE O1783 TRP 0.028 0.002 TRP O1826 HIS 0.002 0.001 HIS O1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 5932) covalent geometry : angle 0.48897 / 0.25 ( 8056) hydrogen bonds : bond 0.02742 / 1.87 ( 256) hydrogen bonds : angle 4.00636 / 2.73 ( 723) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.211 Fit side-chains REVERT: O 1117 TYR cc_start: 0.8316 (m-10) cc_final: 0.7988 (m-10) REVERT: O 1564 ILE cc_start: 0.8933 (mt) cc_final: 0.8707 (tt) REVERT: O 1591 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8586 (tp30) REVERT: O 1657 MET cc_start: 0.7787 (tpp) cc_final: 0.7543 (tpp) REVERT: O 1756 MET cc_start: 0.8761 (tmm) cc_final: 0.8418 (tmm) outliers start: 6 outliers final: 2 residues processed: 49 average time/residue: 0.0582 time to fit residues: 3.9117 Evaluate side-chains 40 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1171 SER Chi-restraints excluded: chain O residue 1792 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 16 optimal weight: 0.0670 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 0.0060 chunk 25 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 overall best weight: 0.4734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.093669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.059409 restraints weight = 18459.240| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 3.66 r_work: 0.2866 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5932 Z= 0.113 Angle : 0.501 9.187 8056 Z= 0.252 Chirality : 0.041 0.288 900 Planarity : 0.004 0.043 993 Dihedral : 13.090 103.431 964 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.14 % Allowed : 12.36 % Favored : 86.50 % 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: 1.86 (0.33), residues: 684 helix: 2.25 (0.30), residues: 324 sheet: 0.68 (0.47), residues: 116 loop : 0.20 (0.42), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O1175 TYR 0.006 0.001 TYR O1752 PHE 0.016 0.001 PHE O1783 TRP 0.024 0.002 TRP O1826 HIS 0.003 0.001 HIS O1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 5932) covalent geometry : angle 0.50146 / 0.25 ( 8056) hydrogen bonds : bond 0.02756 / 1.88 ( 256) hydrogen bonds : angle 3.97639 / 2.71 ( 723) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.123 Fit side-chains REVERT: O 1117 TYR cc_start: 0.8357 (m-10) cc_final: 0.7980 (m-10) REVERT: O 1564 ILE cc_start: 0.8912 (mt) cc_final: 0.8604 (tt) REVERT: O 1591 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8535 (tp30) REVERT: O 1756 MET cc_start: 0.8774 (tmm) cc_final: 0.8373 (tmm) outliers start: 7 outliers final: 3 residues processed: 46 average time/residue: 0.0465 time to fit residues: 3.1413 Evaluate side-chains 41 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1171 SER Chi-restraints excluded: chain O residue 1319 VAL Chi-restraints excluded: chain O residue 1792 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 chunk 69 optimal weight: 10.0000 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.093109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058448 restraints weight = 18615.423| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.67 r_work: 0.2838 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5932 Z= 0.133 Angle : 0.502 9.604 8056 Z= 0.253 Chirality : 0.040 0.208 900 Planarity : 0.004 0.044 993 Dihedral : 13.069 103.483 964 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.30 % Allowed : 12.52 % Favored : 86.18 % 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: 1.84 (0.34), residues: 684 helix: 2.24 (0.30), residues: 327 sheet: 0.67 (0.48), residues: 117 loop : 0.15 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O1175 TYR 0.005 0.001 TYR O1752 PHE 0.018 0.001 PHE O1783 TRP 0.026 0.002 TRP O1826 HIS 0.004 0.001 HIS O1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 5932) covalent geometry : angle 0.50220 / 0.25 ( 8056) hydrogen bonds : bond 0.02845 / 1.92 ( 256) hydrogen bonds : angle 3.92460 / 2.67 ( 723) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.149 Fit side-chains REVERT: O 1117 TYR cc_start: 0.8187 (m-10) cc_final: 0.7901 (m-10) REVERT: O 1591 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8768 (tp30) REVERT: O 1657 MET cc_start: 0.7741 (tpp) cc_final: 0.7520 (tpp) outliers start: 8 outliers final: 4 residues processed: 48 average time/residue: 0.0541 time to fit residues: 3.7700 Evaluate side-chains 41 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 37 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1171 SER Chi-restraints excluded: chain O residue 1319 VAL Chi-restraints excluded: chain O residue 1749 ILE Chi-restraints excluded: chain O residue 1792 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.0870 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.092330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057792 restraints weight = 18493.427| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.65 r_work: 0.2818 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 5932 Z= 0.148 Angle : 0.551 14.401 8056 Z= 0.268 Chirality : 0.044 0.450 900 Planarity : 0.004 0.044 993 Dihedral : 13.087 103.610 964 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.14 % Allowed : 13.66 % Favored : 85.20 % 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 (0.34), residues: 684 helix: 2.20 (0.30), residues: 327 sheet: 0.73 (0.48), residues: 116 loop : 0.12 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O1175 TYR 0.006 0.001 TYR O1752 PHE 0.024 0.001 PHE O1807 TRP 0.028 0.002 TRP O1826 HIS 0.004 0.001 HIS O1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 5932) covalent geometry : angle 0.55057 / 0.27 ( 8056) hydrogen bonds : bond 0.02883 / 1.94 ( 256) hydrogen bonds : angle 3.99351 / 2.73 ( 723) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.146 Fit side-chains REVERT: O 1117 TYR cc_start: 0.8206 (m-10) cc_final: 0.7927 (m-10) REVERT: O 1591 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8526 (tp30) REVERT: O 1657 MET cc_start: 0.7796 (tpp) cc_final: 0.7554 (tpp) REVERT: O 1714 MET cc_start: 0.8543 (mmm) cc_final: 0.8123 (mmp) REVERT: O 1756 MET cc_start: 0.8782 (tmm) cc_final: 0.8518 (tmm) outliers start: 7 outliers final: 5 residues processed: 44 average time/residue: 0.0590 time to fit residues: 3.7295 Evaluate side-chains 41 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1171 SER Chi-restraints excluded: chain O residue 1319 VAL Chi-restraints excluded: chain O residue 1406 ILE Chi-restraints excluded: chain O residue 1749 ILE Chi-restraints excluded: chain O residue 1792 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 5.9990 chunk 26 optimal weight: 0.0470 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 67 optimal weight: 0.0370 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 49 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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 = 0.3883 r_free = 0.3883 target = 0.092951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.059007 restraints weight = 18473.640| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.64 r_work: 0.2842 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5932 Z= 0.111 Angle : 0.551 13.196 8056 Z= 0.269 Chirality : 0.043 0.357 900 Planarity : 0.004 0.044 993 Dihedral : 13.046 103.673 964 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.98 % Allowed : 13.98 % Favored : 85.04 % 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: 1.73 (0.34), residues: 684 helix: 2.07 (0.30), residues: 327 sheet: 0.54 (0.46), residues: 126 loop : 0.27 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O1175 TYR 0.011 0.001 TYR O1716 PHE 0.019 0.001 PHE O1807 TRP 0.033 0.003 TRP O1826 HIS 0.002 0.001 HIS O1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 5932) covalent geometry : angle 0.55097 / 0.27 ( 8056) hydrogen bonds : bond 0.02785 / 1.89 ( 256) hydrogen bonds : angle 4.02001 / 2.74 ( 723) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.207 Fit side-chains REVERT: O 1117 TYR cc_start: 0.8077 (m-10) cc_final: 0.7799 (m-10) REVERT: O 1591 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8514 (tp30) REVERT: O 1657 MET cc_start: 0.7851 (tpp) cc_final: 0.7631 (tpp) REVERT: O 1714 MET cc_start: 0.8638 (mmm) cc_final: 0.8199 (mmp) outliers start: 6 outliers final: 5 residues processed: 43 average time/residue: 0.0663 time to fit residues: 4.0739 Evaluate side-chains 42 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1171 SER Chi-restraints excluded: chain O residue 1319 VAL Chi-restraints excluded: chain O residue 1406 ILE Chi-restraints excluded: chain O residue 1749 ILE Chi-restraints excluded: chain O residue 1792 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 0.0170 chunk 20 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.093109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.058771 restraints weight = 18786.636| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.66 r_work: 0.2844 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5932 Z= 0.111 Angle : 0.550 13.418 8056 Z= 0.266 Chirality : 0.043 0.335 900 Planarity : 0.004 0.043 993 Dihedral : 13.004 103.753 964 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.81 % Allowed : 13.98 % Favored : 85.20 % 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 (0.34), residues: 684 helix: 2.07 (0.30), residues: 326 sheet: 0.41 (0.45), residues: 127 loop : 0.21 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O1175 TYR 0.006 0.001 TYR O1195 PHE 0.020 0.001 PHE O1807 TRP 0.036 0.003 TRP O1826 HIS 0.003 0.001 HIS O1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 5932) covalent geometry : angle 0.54952 / 0.27 ( 8056) hydrogen bonds : bond 0.02791 / 1.89 ( 256) hydrogen bonds : angle 4.05119 / 2.77 ( 723) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.174 Fit side-chains REVERT: O 1117 TYR cc_start: 0.8212 (m-10) cc_final: 0.7934 (m-10) REVERT: O 1591 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8524 (tp30) REVERT: O 1657 MET cc_start: 0.7826 (tpp) cc_final: 0.7573 (tpp) REVERT: O 1714 MET cc_start: 0.8686 (mmm) cc_final: 0.8213 (mmp) outliers start: 5 outliers final: 5 residues processed: 41 average time/residue: 0.0595 time to fit residues: 3.4913 Evaluate side-chains 42 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1171 SER Chi-restraints excluded: chain O residue 1319 VAL Chi-restraints excluded: chain O residue 1406 ILE Chi-restraints excluded: chain O residue 1749 ILE Chi-restraints excluded: chain O residue 1792 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 22 optimal weight: 0.0470 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 0.0050 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 0.3980 overall best weight: 0.4492 ------------------------------------------------------------------------------- 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 = 0.3884 r_free = 0.3884 target = 0.093161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.058619 restraints weight = 18254.286| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 3.61 r_work: 0.2846 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5932 Z= 0.111 Angle : 0.548 12.839 8056 Z= 0.266 Chirality : 0.042 0.317 900 Planarity : 0.004 0.043 993 Dihedral : 12.985 103.872 964 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.81 % Allowed : 13.98 % Favored : 85.20 % 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: 1.62 (0.33), residues: 684 helix: 2.03 (0.30), residues: 326 sheet: 0.38 (0.45), residues: 127 loop : 0.20 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O1760 TYR 0.006 0.001 TYR O1752 PHE 0.027 0.001 PHE O1807 TRP 0.037 0.003 TRP O1826 HIS 0.003 0.001 HIS O1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 5932) covalent geometry : angle 0.54796 / 0.27 ( 8056) hydrogen bonds : bond 0.02782 / 1.88 ( 256) hydrogen bonds : angle 4.05294 / 2.76 ( 723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1562.09 seconds wall clock time: 27 minutes 21.16 seconds (1641.16 seconds total)