Starting phenix.real_space_refine on Tue Jan 14 06:30:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ran_19020/01_2025/8ran_19020.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ran_19020/01_2025/8ran_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8ran_19020/01_2025/8ran_19020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ran_19020/01_2025/8ran_19020.map" model { file = "/net/cci-nas-00/data/ceres_data/8ran_19020/01_2025/8ran_19020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ran_19020/01_2025/8ran_19020.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 4.88, per 1000 atoms: 0.84 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: 1.59 Conformation dependent library (CDL) restraints added in 809.1 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: 1.87 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: 1.97 Time building geometry restraints manager: 1.82 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=" 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 bond pdb=" NE ARG O1673 " pdb=" CZ ARG O1673 " ideal model delta sigma weight residual 1.326 1.331 -0.005 1.10e-02 8.26e+03 2.20e-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=" 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=" C ILE O1602 " pdb=" CA ILE O1602 " pdb=" CB ILE O1602 " ideal model delta sigma weight residual 113.70 112.52 1.18 9.50e-01 1.11e+00 1.55e+00 angle pdb=" NE ARG O1753 " pdb=" CZ ARG O1753 " pdb=" NH1 ARG O1753 " ideal model delta sigma weight residual 121.50 120.26 1.24 1.00e+00 1.00e+00 1.55e+00 angle pdb=" NE ARG O1173 " pdb=" CZ ARG O1173 " pdb=" NH1 ARG O1173 " ideal model delta sigma weight residual 121.50 120.28 1.22 1.00e+00 1.00e+00 1.49e+00 angle pdb=" NE ARG O1605 " pdb=" CZ ARG O1605 " pdb=" NH1 ARG O1605 " ideal model delta sigma weight residual 121.50 120.28 1.22 1.00e+00 1.00e+00 1.49e+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: 3.390 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.690 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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= 0.094 Angle : 0.352 4.264 8056 Z= 0.193 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP O1688 HIS 0.001 0.000 HIS O1658 PHE 0.004 0.001 PHE O1374 TYR 0.004 0.000 TYR O1195 ARG 0.002 0.000 ARG O1537 *********************** 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 : 0.665 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: 0.2536 time to fit residues: 35.5878 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 : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 29 optimal weight: 0.0270 chunk 18 optimal weight: 0.7980 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O1710 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.097425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.064173 restraints weight = 18474.524| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 3.75 r_work: 0.2976 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5932 Z= 0.226 Angle : 0.534 7.712 8056 Z= 0.272 Chirality : 0.041 0.131 900 Planarity : 0.005 0.059 993 Dihedral : 13.271 105.819 964 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.33), residues: 684 helix: 2.93 (0.29), residues: 325 sheet: 0.54 (0.49), residues: 108 loop : 0.44 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP O1688 HIS 0.003 0.001 HIS O1268 PHE 0.026 0.002 PHE O1783 TYR 0.008 0.001 TYR O1855 ARG 0.011 0.001 ARG O1760 *********************** 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 64 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: O 1117 TYR cc_start: 0.8045 (m-10) cc_final: 0.7820 (m-10) REVERT: O 1148 ASN cc_start: 0.8850 (m-40) cc_final: 0.8562 (t0) REVERT: O 1564 ILE cc_start: 0.9082 (mt) cc_final: 0.8598 (pt) REVERT: O 1657 MET cc_start: 0.7444 (tpp) cc_final: 0.7204 (tpp) REVERT: O 1826 TRP cc_start: 0.8627 (m-10) cc_final: 0.7982 (m-10) REVERT: O 1855 TYR cc_start: 0.8684 (m-10) cc_final: 0.8427 (m-10) outliers start: 6 outliers final: 1 residues processed: 61 average time/residue: 0.2251 time to fit residues: 18.0098 Evaluate side-chains 48 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1816 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O1287 GLN O1815 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.092118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.057253 restraints weight = 18170.190| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 3.53 r_work: 0.2795 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5932 Z= 0.319 Angle : 0.558 8.256 8056 Z= 0.291 Chirality : 0.042 0.129 900 Planarity : 0.005 0.052 993 Dihedral : 13.288 105.210 964 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.14 % Allowed : 10.57 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.33), residues: 684 helix: 2.23 (0.29), residues: 323 sheet: 0.32 (0.47), residues: 115 loop : 0.33 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O1688 HIS 0.007 0.002 HIS O1265 PHE 0.018 0.002 PHE O1783 TYR 0.011 0.002 TYR O1670 ARG 0.008 0.001 ARG O1108 *********************** 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: 7 poor density : 53 time to evaluate : 0.747 Fit side-chains revert: symmetry clash REVERT: O 1564 ILE cc_start: 0.9124 (mt) cc_final: 0.8670 (pt) REVERT: O 1591 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8569 (tp30) REVERT: O 1657 MET cc_start: 0.7989 (tpp) cc_final: 0.7773 (tpp) REVERT: O 1826 TRP cc_start: 0.8848 (m-10) cc_final: 0.8330 (m-10) REVERT: O 1846 ASP cc_start: 0.9440 (OUTLIER) cc_final: 0.9230 (t0) REVERT: O 1855 TYR cc_start: 0.8881 (m-10) cc_final: 0.8610 (m-10) outliers start: 7 outliers final: 2 residues processed: 60 average time/residue: 0.2054 time to fit residues: 16.4548 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 : 0.712 ------------------------------------------------------------------------------- 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 1846 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 51 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.092483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057455 restraints weight = 18450.185| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.64 r_work: 0.2815 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3765 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= 0.185 Angle : 0.503 7.899 8056 Z= 0.254 Chirality : 0.040 0.147 900 Planarity : 0.004 0.042 993 Dihedral : 13.209 104.806 964 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.98 % Allowed : 12.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.33), residues: 684 helix: 2.10 (0.30), residues: 326 sheet: 0.44 (0.48), residues: 115 loop : 0.29 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O1688 HIS 0.004 0.001 HIS O1265 PHE 0.015 0.001 PHE O1783 TYR 0.008 0.001 TYR O1195 ARG 0.006 0.001 ARG O1734 *********************** 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 51 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.663 Fit side-chains REVERT: O 1117 TYR cc_start: 0.8473 (m-10) cc_final: 0.8157 (m-10) REVERT: O 1591 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8744 (tp30) REVERT: O 1657 MET cc_start: 0.7948 (tpp) cc_final: 0.7645 (tpp) REVERT: O 1714 MET cc_start: 0.8691 (mmm) cc_final: 0.8235 (mmp) REVERT: O 1756 MET cc_start: 0.8721 (tmm) cc_final: 0.8434 (tmm) REVERT: O 1826 TRP cc_start: 0.8877 (m-10) cc_final: 0.8334 (m-10) REVERT: O 1855 TYR cc_start: 0.8888 (m-10) cc_final: 0.8621 (m-10) outliers start: 6 outliers final: 2 residues processed: 50 average time/residue: 0.1757 time to fit residues: 12.3729 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 : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1171 SER Chi-restraints excluded: chain O residue 1647 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O1287 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.091720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.057292 restraints weight = 18224.981| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 3.52 r_work: 0.2806 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4040 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= 0.217 Angle : 0.512 7.761 8056 Z= 0.256 Chirality : 0.041 0.199 900 Planarity : 0.004 0.042 993 Dihedral : 13.194 105.201 964 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.46 % Allowed : 12.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.33), residues: 684 helix: 2.12 (0.30), residues: 325 sheet: 0.33 (0.45), residues: 125 loop : 0.35 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O1688 HIS 0.004 0.001 HIS O1265 PHE 0.018 0.001 PHE O1783 TYR 0.007 0.001 TYR O1117 ARG 0.006 0.000 ARG O1175 *********************** 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 50 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.698 Fit side-chains REVERT: O 1117 TYR cc_start: 0.8128 (m-10) cc_final: 0.7831 (m-10) REVERT: O 1591 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8526 (tp30) REVERT: O 1657 MET cc_start: 0.8022 (tpp) cc_final: 0.7687 (tpp) REVERT: O 1714 MET cc_start: 0.8753 (mmm) cc_final: 0.8297 (mmp) REVERT: O 1756 MET cc_start: 0.8738 (tmm) cc_final: 0.8400 (tmm) REVERT: O 1826 TRP cc_start: 0.8964 (m-10) cc_final: 0.8405 (m-10) REVERT: O 1846 ASP cc_start: 0.9439 (OUTLIER) cc_final: 0.9184 (t0) outliers start: 9 outliers final: 4 residues processed: 47 average time/residue: 0.1606 time to fit residues: 10.8849 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 : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 1171 SER Chi-restraints excluded: chain O residue 1406 ILE Chi-restraints excluded: chain O residue 1647 SER Chi-restraints excluded: chain O residue 1749 ILE Chi-restraints excluded: chain O residue 1846 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 49 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 52 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.090547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.055846 restraints weight = 18106.641| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.50 r_work: 0.2772 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5932 Z= 0.257 Angle : 0.513 6.911 8056 Z= 0.258 Chirality : 0.041 0.159 900 Planarity : 0.004 0.043 993 Dihedral : 13.261 105.537 964 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.14 % Allowed : 12.20 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.33), residues: 684 helix: 2.03 (0.30), residues: 326 sheet: 0.31 (0.45), residues: 125 loop : 0.29 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O1688 HIS 0.004 0.001 HIS O1265 PHE 0.027 0.001 PHE O1807 TYR 0.007 0.001 TYR O1670 ARG 0.006 0.000 ARG O1175 *********************** 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 49 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.725 Fit side-chains REVERT: O 1591 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8612 (tp30) REVERT: O 1657 MET cc_start: 0.8076 (tpp) cc_final: 0.7754 (tpp) REVERT: O 1714 MET cc_start: 0.8689 (mmm) cc_final: 0.8266 (mmp) REVERT: O 1756 MET cc_start: 0.8737 (tmm) cc_final: 0.8362 (tmm) REVERT: O 1826 TRP cc_start: 0.9019 (m-10) cc_final: 0.8493 (m-10) REVERT: O 1855 TYR cc_start: 0.8884 (m-10) cc_final: 0.8618 (m-10) outliers start: 7 outliers final: 5 residues processed: 46 average time/residue: 0.1691 time to fit residues: 11.0797 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 : 0.691 ------------------------------------------------------------------------------- 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 1647 SER Chi-restraints excluded: chain O residue 1749 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 57 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.090082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.055100 restraints weight = 18313.048| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.52 r_work: 0.2756 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5932 Z= 0.259 Angle : 0.517 8.714 8056 Z= 0.261 Chirality : 0.041 0.169 900 Planarity : 0.004 0.043 993 Dihedral : 13.384 105.923 964 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.30 % Allowed : 12.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.34), residues: 684 helix: 1.97 (0.30), residues: 326 sheet: 0.25 (0.45), residues: 125 loop : 0.25 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O1688 HIS 0.004 0.001 HIS O1265 PHE 0.011 0.001 PHE O1807 TYR 0.010 0.001 TYR O1117 ARG 0.006 0.000 ARG O1175 *********************** 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 48 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.690 Fit side-chains REVERT: O 1591 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8722 (tp30) REVERT: O 1657 MET cc_start: 0.8074 (tpp) cc_final: 0.7788 (tpp) REVERT: O 1714 MET cc_start: 0.8722 (mmm) cc_final: 0.8317 (mmp) REVERT: O 1756 MET cc_start: 0.8750 (tmm) cc_final: 0.8368 (tmm) REVERT: O 1846 ASP cc_start: 0.9456 (OUTLIER) cc_final: 0.9164 (t0) REVERT: O 1855 TYR cc_start: 0.8944 (m-10) cc_final: 0.8689 (m-10) outliers start: 8 outliers final: 5 residues processed: 45 average time/residue: 0.1565 time to fit residues: 10.2501 Evaluate side-chains 44 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 1647 SER Chi-restraints excluded: chain O residue 1749 ILE Chi-restraints excluded: chain O residue 1846 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.089829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.055338 restraints weight = 18100.942| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.46 r_work: 0.2754 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5932 Z= 0.255 Angle : 0.508 8.645 8056 Z= 0.257 Chirality : 0.041 0.161 900 Planarity : 0.004 0.044 993 Dihedral : 13.378 105.968 964 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.98 % Allowed : 12.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.34), residues: 684 helix: 1.96 (0.30), residues: 326 sheet: 0.05 (0.45), residues: 127 loop : 0.22 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP O1826 HIS 0.005 0.001 HIS O1265 PHE 0.006 0.001 PHE O1639 TYR 0.009 0.001 TYR O1117 ARG 0.006 0.000 ARG O1175 *********************** 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 44 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.639 Fit side-chains REVERT: O 1117 TYR cc_start: 0.8476 (m-10) cc_final: 0.8188 (m-10) REVERT: O 1591 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8691 (tp30) REVERT: O 1657 MET cc_start: 0.8071 (tpp) cc_final: 0.7805 (tpp) REVERT: O 1714 MET cc_start: 0.8784 (mmm) cc_final: 0.8386 (mmp) REVERT: O 1756 MET cc_start: 0.8740 (tmm) cc_final: 0.8411 (tmm) REVERT: O 1759 MET cc_start: 0.8918 (ttm) cc_final: 0.8605 (mtt) REVERT: O 1792 LEU cc_start: 0.9516 (mt) cc_final: 0.8911 (mm) REVERT: O 1846 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.9176 (t0) outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.1639 time to fit residues: 10.1777 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 : 0.688 ------------------------------------------------------------------------------- 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 1647 SER Chi-restraints excluded: chain O residue 1846 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 0.0870 chunk 68 optimal weight: 10.0000 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.090326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.056077 restraints weight = 18200.085| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.46 r_work: 0.2777 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5932 Z= 0.200 Angle : 0.507 9.846 8056 Z= 0.254 Chirality : 0.041 0.161 900 Planarity : 0.004 0.044 993 Dihedral : 13.354 105.981 964 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.81 % Allowed : 12.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.33), residues: 684 helix: 1.93 (0.30), residues: 326 sheet: -0.03 (0.45), residues: 127 loop : 0.22 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP O1826 HIS 0.003 0.001 HIS O1265 PHE 0.008 0.001 PHE O1669 TYR 0.009 0.001 TYR O1117 ARG 0.006 0.000 ARG O1175 *********************** 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: 5 poor density : 40 time to evaluate : 0.641 Fit side-chains REVERT: O 1591 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8689 (tp30) REVERT: O 1657 MET cc_start: 0.8017 (tpp) cc_final: 0.7788 (tpp) REVERT: O 1756 MET cc_start: 0.8755 (tmm) cc_final: 0.8436 (tmm) REVERT: O 1759 MET cc_start: 0.8907 (ttm) cc_final: 0.8581 (mtt) REVERT: O 1846 ASP cc_start: 0.9457 (OUTLIER) cc_final: 0.9165 (t0) outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 0.1543 time to fit residues: 9.8534 Evaluate side-chains 39 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 1846 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.089564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.054101 restraints weight = 18408.272| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.53 r_work: 0.2736 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5932 Z= 0.265 Angle : 0.545 11.518 8056 Z= 0.272 Chirality : 0.041 0.160 900 Planarity : 0.004 0.043 993 Dihedral : 13.464 106.109 964 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.65 % Allowed : 13.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.34), residues: 684 helix: 1.90 (0.30), residues: 326 sheet: 0.06 (0.45), residues: 129 loop : 0.16 (0.44), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP O1826 HIS 0.005 0.001 HIS O1265 PHE 0.009 0.001 PHE O1181 TYR 0.010 0.001 TYR O1117 ARG 0.006 0.000 ARG O1175 ********************** 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 39 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.950 Fit side-chains REVERT: O 1714 MET cc_start: 0.8453 (mmm) cc_final: 0.7792 (tpp) REVERT: O 1756 MET cc_start: 0.8769 (tmm) cc_final: 0.8431 (tmm) REVERT: O 1846 ASP cc_start: 0.9463 (OUTLIER) cc_final: 0.9172 (t0) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.2119 time to fit residues: 12.1750 Evaluate side-chains 38 residues out of total 615 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 1846 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 6 optimal weight: 0.2980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O1287 GLN ** O1336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.090236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.054810 restraints weight = 18557.370| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 3.57 r_work: 0.2757 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5932 Z= 0.194 Angle : 0.521 11.575 8056 Z= 0.260 Chirality : 0.040 0.158 900 Planarity : 0.004 0.043 993 Dihedral : 13.446 106.080 964 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.81 % Allowed : 13.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.33), residues: 684 helix: 1.88 (0.30), residues: 326 sheet: 0.05 (0.45), residues: 129 loop : 0.15 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP O1826 HIS 0.003 0.001 HIS O1265 PHE 0.009 0.001 PHE O1807 TYR 0.012 0.001 TYR O1117 ARG 0.008 0.000 ARG O1175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3584.73 seconds wall clock time: 64 minutes 56.26 seconds (3896.26 seconds total)