Starting phenix.real_space_refine on Thu Jul 2 02:31:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ran_19020/07_2026/8ran_19020.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ran_19020/07_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_19020/07_2026/8ran_19020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ran_19020/07_2026/8ran_19020.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ran_19020/07_2026/8ran_19020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ran_19020/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 1.10, per 1000 atoms: 0.19 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: 0.32 Conformation dependent library (CDL) restraints added in 245.1 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: 0.49 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: 0.79 Time building geometry restraints manager: 0.42 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=" N3 C P 11 " pdb=" C4 C P 11 " ideal model delta sigma weight residual 1.335 1.331 0.004 7.00e-03 2.04e+04 3.19e-01 bond pdb=" NE ARG O1813 " pdb=" CZ ARG O1813 " ideal model delta sigma weight residual 1.326 1.332 -0.006 1.10e-02 8.26e+03 2.92e-01 bond pdb=" NE ARG O1610 " pdb=" CZ ARG O1610 " ideal model delta sigma weight residual 1.326 1.332 -0.006 1.10e-02 8.26e+03 2.51e-01 bond pdb=" NE ARG O1760 " pdb=" CZ ARG O1760 " ideal model delta sigma weight residual 1.326 1.331 -0.005 1.10e-02 8.26e+03 2.47e-01 bond pdb=" NE ARG O1841 " pdb=" CZ ARG O1841 " ideal model delta sigma weight residual 1.326 1.331 -0.005 1.10e-02 8.26e+03 2.37e-01 ... (remaining 5927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.85: 7865 0.85 - 1.71: 158 1.71 - 2.56: 5 2.56 - 3.41: 14 3.41 - 4.26: 14 Bond angle restraints: 8056 Sorted by residual: angle pdb=" C2 C P 4 " pdb=" N1 C P 4 " pdb=" C6 C P 4 " ideal model delta sigma weight residual 120.30 119.57 0.73 4.00e-01 6.25e+00 3.32e+00 angle pdb=" C2 C P 11 " pdb=" N1 C P 11 " pdb=" C6 C P 11 " ideal model delta sigma weight residual 120.30 119.60 0.70 4.00e-01 6.25e+00 3.08e+00 angle pdb=" C1' U P 12 " pdb=" N1 U P 12 " pdb=" C6 U P 12 " ideal model delta sigma weight residual 121.20 123.44 -2.24 1.40e+00 5.10e-01 2.56e+00 angle pdb=" CA TRP O1688 " pdb=" CB TRP O1688 " pdb=" CG TRP O1688 " ideal model delta sigma weight residual 113.60 116.28 -2.68 1.90e+00 2.77e-01 1.99e+00 angle pdb=" C1' U P 12 " pdb=" N1 U P 12 " pdb=" C2 U P 12 " ideal model delta sigma weight residual 117.70 116.02 1.68 1.20e+00 6.94e-01 1.97e+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: 596 0.026 - 0.052: 185 0.052 - 0.077: 51 0.077 - 0.103: 37 0.103 - 0.129: 31 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.450 Find NCS groups from input model: 0.010 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.690 ------------------------------------------------------------------------------- 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 : 0.001 0.015 5932 Z= 0.084 Angle : 0.352 4.264 8056 Z= 0.203 Chirality : 0.037 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 0.00149 / 0.08 ( 5932) covalent geometry : angle 0.35203 / 0.20 ( 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 : 0.194 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: 0.0854 time to fit residues: 12.1791 Evaluate side-chains 51 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O1710 ASN O1815 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.098568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.065795 restraints weight = 18818.923| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.80 r_work: 0.3020 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5932 Z= 0.139 Angle : 0.546 7.408 8056 Z= 0.281 Chirality : 0.041 0.141 900 Planarity : 0.004 0.036 993 Dihedral : 13.231 106.043 964 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.14 % Allowed : 8.13 % 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: 2.49 (0.33), residues: 684 helix: 2.96 (0.29), residues: 325 sheet: 0.46 (0.47), residues: 118 loop : 0.51 (0.42), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG O1820 TYR 0.011 0.001 TYR O1855 PHE 0.028 0.002 PHE O1783 TRP 0.032 0.003 TRP O1688 HIS 0.004 0.001 HIS O1433 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 5932) covalent geometry : angle 0.54552 / 0.28 ( 8056) hydrogen bonds : bond 0.03677 / 2.47 ( 256) hydrogen bonds : angle 4.29364 / 2.94 ( 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: 7 poor density : 56 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 1117 TYR cc_start: 0.7973 (m-10) cc_final: 0.7559 (m-10) REVERT: O 1373 TYR cc_start: 0.9424 (t80) cc_final: 0.9220 (t80) REVERT: O 1536 MET cc_start: 0.5121 (ppp) cc_final: 0.4803 (ppp) REVERT: O 1564 ILE cc_start: 0.9115 (mt) cc_final: 0.8632 (pt) REVERT: O 1602 ILE cc_start: 0.9516 (mt) cc_final: 0.9190 (mp) REVERT: O 1756 MET cc_start: 0.8647 (tmm) cc_final: 0.8307 (tmm) REVERT: O 1855 TYR cc_start: 0.8730 (m-10) cc_final: 0.8440 (m-10) outliers start: 7 outliers final: 3 residues processed: 59 average time/residue: 0.0886 time to fit residues: 6.8838 Evaluate side-chains 51 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1433 HIS Chi-restraints excluded: chain O residue 1749 ILE 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: 0.9990 chunk 30 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3938 r_free = 0.3938 target = 0.096013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.062660 restraints weight = 18168.770| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.64 r_work: 0.2945 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5932 Z= 0.157 Angle : 0.517 7.481 8056 Z= 0.265 Chirality : 0.040 0.128 900 Planarity : 0.004 0.039 993 Dihedral : 13.217 105.881 964 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.63 % Allowed : 9.76 % Favored : 88.62 % 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: 2.08 (0.33), residues: 684 helix: 2.51 (0.29), residues: 325 sheet: 0.51 (0.49), residues: 108 loop : 0.35 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O1765 TYR 0.010 0.001 TYR O1766 PHE 0.020 0.002 PHE O1783 TRP 0.023 0.004 TRP O1688 HIS 0.003 0.001 HIS O1268 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 5932) covalent geometry : angle 0.51667 / 0.27 ( 8056) hydrogen bonds : bond 0.03081 / 2.07 ( 256) hydrogen bonds : angle 4.10171 / 2.80 ( 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 60 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: O 1148 ASN cc_start: 0.8845 (m-40) cc_final: 0.8572 (t0) REVERT: O 1355 ILE cc_start: 0.9649 (mt) cc_final: 0.9403 (mm) REVERT: O 1564 ILE cc_start: 0.9096 (mt) cc_final: 0.8595 (pt) REVERT: O 1591 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8614 (tp30) REVERT: O 1783 PHE cc_start: 0.9106 (t80) cc_final: 0.8880 (t80) REVERT: O 1792 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9185 (tt) outliers start: 10 outliers final: 4 residues processed: 58 average time/residue: 0.0717 time to fit residues: 5.7221 Evaluate side-chains 49 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 1749 ILE Chi-restraints excluded: chain O residue 1792 LEU 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: 1.9990 chunk 51 optimal weight: 2.9990 chunk 32 optimal weight: 0.0040 chunk 29 optimal weight: 0.0670 chunk 25 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 22 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.4532 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.095714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.062185 restraints weight = 18359.541| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.64 r_work: 0.2932 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2931 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= 0.112 Angle : 0.491 8.812 8056 Z= 0.249 Chirality : 0.040 0.209 900 Planarity : 0.004 0.045 993 Dihedral : 13.145 105.205 964 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.81 % Allowed : 11.71 % Favored : 87.48 % 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: 1.99 (0.33), residues: 684 helix: 2.33 (0.29), residues: 324 sheet: 0.73 (0.49), residues: 110 loop : 0.32 (0.41), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O1706 TYR 0.009 0.001 TYR O1153 PHE 0.013 0.001 PHE O1783 TRP 0.031 0.003 TRP O1826 HIS 0.003 0.001 HIS O1433 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 5932) covalent geometry : angle 0.49134 / 0.25 ( 8056) hydrogen bonds : bond 0.02739 / 1.87 ( 256) hydrogen bonds : angle 4.02077 / 2.75 ( 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 55 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: O 1117 TYR cc_start: 0.8092 (m-10) cc_final: 0.7637 (m-10) REVERT: O 1355 ILE cc_start: 0.9644 (mt) cc_final: 0.9401 (mm) REVERT: O 1591 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8626 (tp30) REVERT: O 1756 MET cc_start: 0.8755 (tmm) cc_final: 0.8492 (tmm) REVERT: O 1792 LEU cc_start: 0.9584 (OUTLIER) cc_final: 0.9368 (tp) REVERT: O 1855 TYR cc_start: 0.8769 (m-10) cc_final: 0.8480 (m-10) outliers start: 5 outliers final: 1 residues processed: 54 average time/residue: 0.0652 time to fit residues: 5.0001 Evaluate side-chains 45 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 43 time to evaluate : 0.225 ------------------------------------------------------------------------------- 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: 0.8980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 0.0970 chunk 46 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 61 optimal weight: 0.0770 chunk 43 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.095193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.061960 restraints weight = 18408.055| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.62 r_work: 0.2929 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5932 Z= 0.112 Angle : 0.492 7.424 8056 Z= 0.253 Chirality : 0.043 0.456 900 Planarity : 0.004 0.038 993 Dihedral : 13.121 104.935 964 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.46 % Allowed : 12.36 % 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: 1.90 (0.33), residues: 684 helix: 2.29 (0.30), residues: 324 sheet: 0.58 (0.50), residues: 104 loop : 0.29 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O1706 TYR 0.007 0.001 TYR O1153 PHE 0.024 0.001 PHE O1783 TRP 0.031 0.002 TRP O1826 HIS 0.002 0.001 HIS O1433 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 5932) covalent geometry : angle 0.49248 / 0.25 ( 8056) hydrogen bonds : bond 0.02687 / 1.82 ( 256) hydrogen bonds : angle 3.94242 / 2.67 ( 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 52 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: O 1117 TYR cc_start: 0.8121 (m-10) cc_final: 0.7668 (m-10) REVERT: O 1355 ILE cc_start: 0.9661 (mt) cc_final: 0.9424 (mm) REVERT: O 1591 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8594 (tp30) REVERT: O 1756 MET cc_start: 0.8743 (tmm) cc_final: 0.8411 (tmm) REVERT: O 1826 TRP cc_start: 0.8769 (m100) cc_final: 0.8499 (m100) REVERT: O 1855 TYR cc_start: 0.8759 (m-10) cc_final: 0.8448 (m-10) outliers start: 9 outliers final: 3 residues processed: 50 average time/residue: 0.0665 time to fit residues: 4.7398 Evaluate side-chains 45 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1162 LEU Chi-restraints excluded: chain O residue 1171 SER Chi-restraints excluded: chain O residue 1749 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 16 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 chunk 34 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.094427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.061147 restraints weight = 18226.620| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 3.62 r_work: 0.2903 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5932 Z= 0.118 Angle : 0.485 9.192 8056 Z= 0.245 Chirality : 0.041 0.297 900 Planarity : 0.004 0.037 993 Dihedral : 13.078 104.862 964 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % 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: 1.92 (0.33), residues: 684 helix: 2.30 (0.30), residues: 324 sheet: 0.70 (0.47), residues: 116 loop : 0.23 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O1175 TYR 0.006 0.001 TYR O1752 PHE 0.013 0.001 PHE O1783 TRP 0.022 0.002 TRP O1826 HIS 0.003 0.001 HIS O1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 ( 5932) covalent geometry : angle 0.48543 / 0.25 ( 8056) hydrogen bonds : bond 0.02638 / 1.78 ( 256) hydrogen bonds : angle 3.95627 / 2.69 ( 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 51 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.226 Fit side-chains revert: symmetry clash REVERT: O 1117 TYR cc_start: 0.8223 (m-10) cc_final: 0.7813 (m-10) REVERT: O 1355 ILE cc_start: 0.9658 (mt) cc_final: 0.9457 (mm) REVERT: O 1591 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8586 (tp30) REVERT: O 1855 TYR cc_start: 0.8781 (m-10) cc_final: 0.8477 (m-10) outliers start: 8 outliers final: 3 residues processed: 50 average time/residue: 0.0733 time to fit residues: 5.2335 Evaluate side-chains 44 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3854 r_free = 0.3854 target = 0.091524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.057209 restraints weight = 18483.147| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 3.57 r_work: 0.2795 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 5932 Z= 0.206 Angle : 0.581 10.909 8056 Z= 0.290 Chirality : 0.042 0.247 900 Planarity : 0.004 0.035 993 Dihedral : 13.183 105.075 964 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.30 % Allowed : 11.71 % Favored : 86.99 % 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: 1.69 (0.33), residues: 684 helix: 2.09 (0.30), residues: 327 sheet: 0.67 (0.48), residues: 117 loop : 0.07 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O1175 TYR 0.013 0.001 TYR O1117 PHE 0.017 0.001 PHE O1783 TRP 0.046 0.003 TRP O1826 HIS 0.007 0.002 HIS O1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.21 ( 5932) covalent geometry : angle 0.58080 / 0.29 ( 8056) hydrogen bonds : bond 0.03206 / 2.15 ( 256) hydrogen bonds : angle 4.02633 / 2.74 ( 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 54 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.228 Fit side-chains REVERT: O 1591 GLU cc_start: 0.8994 (mm-30) cc_final: 0.8767 (tp30) REVERT: O 1756 MET cc_start: 0.8812 (tmm) cc_final: 0.8531 (tmm) REVERT: O 1792 LEU cc_start: 0.9597 (mm) cc_final: 0.9284 (mm) REVERT: O 1855 TYR cc_start: 0.8851 (m-10) cc_final: 0.8577 (m-10) outliers start: 8 outliers final: 4 residues processed: 52 average time/residue: 0.0737 time to fit residues: 5.3488 Evaluate side-chains 42 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.092318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.057594 restraints weight = 18432.008| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 3.65 r_work: 0.2808 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5932 Z= 0.137 Angle : 0.553 11.845 8056 Z= 0.274 Chirality : 0.042 0.247 900 Planarity : 0.004 0.036 993 Dihedral : 13.189 105.113 964 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.30 % Allowed : 12.68 % Favored : 86.02 % 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: 1.68 (0.34), residues: 684 helix: 2.07 (0.30), residues: 327 sheet: 0.71 (0.49), residues: 117 loop : 0.08 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O1175 TYR 0.006 0.001 TYR O1125 PHE 0.014 0.001 PHE O1783 TRP 0.039 0.003 TRP O1826 HIS 0.005 0.001 HIS O1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 5932) covalent geometry : angle 0.55261 / 0.27 ( 8056) hydrogen bonds : bond 0.02920 / 1.99 ( 256) hydrogen bonds : angle 3.99551 / 2.72 ( 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: 8 poor density : 38 time to evaluate : 0.270 Fit side-chains REVERT: O 1591 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8608 (tp30) REVERT: O 1792 LEU cc_start: 0.9576 (mm) cc_final: 0.9358 (mm) REVERT: O 1855 TYR cc_start: 0.8908 (m-10) cc_final: 0.8624 (m-10) outliers start: 8 outliers final: 4 residues processed: 44 average time/residue: 0.0722 time to fit residues: 4.5157 Evaluate side-chains 40 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.9980 chunk 26 optimal weight: 0.0770 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 overall best weight: 0.8940 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.091735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.057125 restraints weight = 18500.467| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 3.63 r_work: 0.2795 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5932 Z= 0.160 Angle : 0.563 12.259 8056 Z= 0.277 Chirality : 0.042 0.228 900 Planarity : 0.004 0.037 993 Dihedral : 13.175 105.344 964 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.81 % Allowed : 13.66 % Favored : 85.53 % 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: 1.67 (0.34), residues: 684 helix: 2.03 (0.30), residues: 326 sheet: 0.52 (0.47), residues: 127 loop : 0.21 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O1175 TYR 0.014 0.001 TYR O1117 PHE 0.010 0.001 PHE O1783 TRP 0.045 0.003 TRP O1826 HIS 0.005 0.001 HIS O1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 5932) covalent geometry : angle 0.56315 / 0.28 ( 8056) hydrogen bonds : bond 0.03001 / 2.04 ( 256) hydrogen bonds : angle 4.08765 / 2.78 ( 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 42 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.234 Fit side-chains REVERT: O 1591 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8580 (tp30) REVERT: O 1756 MET cc_start: 0.8746 (tmm) cc_final: 0.8534 (tmm) REVERT: O 1759 MET cc_start: 0.8796 (mtm) cc_final: 0.8461 (mtm) REVERT: O 1792 LEU cc_start: 0.9593 (mm) cc_final: 0.9354 (mm) REVERT: O 1855 TYR cc_start: 0.8894 (m-10) cc_final: 0.8602 (m-10) outliers start: 5 outliers final: 3 residues processed: 40 average time/residue: 0.0739 time to fit residues: 4.3041 Evaluate side-chains 40 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 26 optimal weight: 0.0670 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 41 optimal weight: 0.0980 chunk 21 optimal weight: 0.7980 overall best weight: 0.3918 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.092309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.058858 restraints weight = 18456.301| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.59 r_work: 0.2825 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5932 Z= 0.113 Angle : 0.551 12.994 8056 Z= 0.269 Chirality : 0.041 0.225 900 Planarity : 0.004 0.037 993 Dihedral : 13.139 105.401 964 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.81 % Allowed : 13.66 % Favored : 85.53 % 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 (0.34), residues: 684 helix: 2.01 (0.30), residues: 326 sheet: 0.50 (0.47), 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 0.007 0.001 TYR O1117 PHE 0.007 0.001 PHE O1807 TRP 0.044 0.003 TRP O1826 HIS 0.004 0.001 HIS O1658 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 5932) covalent geometry : angle 0.55087 / 0.27 ( 8056) hydrogen bonds : bond 0.02805 / 1.92 ( 256) hydrogen bonds : angle 4.05680 / 2.76 ( 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 45 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.166 Fit side-chains REVERT: O 1117 TYR cc_start: 0.8132 (m-10) cc_final: 0.7858 (m-10) REVERT: O 1591 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8580 (tp30) REVERT: O 1792 LEU cc_start: 0.9582 (mm) cc_final: 0.9362 (mm) REVERT: O 1855 TYR cc_start: 0.8889 (m-10) cc_final: 0.8603 (m-10) outliers start: 5 outliers final: 4 residues processed: 43 average time/residue: 0.0627 time to fit residues: 3.9433 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 : 0.198 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 44 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 22 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.0370 chunk 59 optimal weight: 0.0050 chunk 3 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 overall best weight: 0.3672 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.092882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058723 restraints weight = 18264.435| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 3.60 r_work: 0.2833 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4217 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= 0.110 Angle : 0.544 12.494 8056 Z= 0.267 Chirality : 0.041 0.217 900 Planarity : 0.004 0.037 993 Dihedral : 13.107 105.558 964 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.14 % Allowed : 13.50 % Favored : 85.37 % 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: 1.60 (0.34), residues: 684 helix: 2.02 (0.30), residues: 326 sheet: 0.37 (0.46), residues: 127 loop : 0.19 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O1175 TYR 0.005 0.001 TYR O1117 PHE 0.006 0.001 PHE O1807 TRP 0.041 0.003 TRP O1826 HIS 0.003 0.001 HIS O1265 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 ( 5932) covalent geometry : angle 0.54409 / 0.27 ( 8056) hydrogen bonds : bond 0.02754 / 1.90 ( 256) hydrogen bonds : angle 4.08461 / 2.77 ( 723) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1934.84 seconds wall clock time: 33 minutes 52.42 seconds (2032.42 seconds total)