Starting phenix.real_space_refine on Thu Jul 2 06:03:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v42_64764/07_2026/9v42_64764.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v42_64764/07_2026/9v42_64764.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v42_64764/07_2026/9v42_64764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v42_64764/07_2026/9v42_64764.map" model { file = "/net/cci-nas-00/data/ceres_data/9v42_64764/07_2026/9v42_64764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v42_64764/07_2026/9v42_64764.cif" } resolution = 3.37 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= 0.002 sd= 0.036 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: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 54 5.49 5 S 29 5.16 5 C 4202 2.51 5 N 1166 2.21 5 O 1426 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s 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: 6879 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1144 Classifications: {'RNA': 54} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 25, 'rna3p_pyr': 26} Link IDs: {'rna2p': 3, 'rna3p': 50} Chain breaks: 1 Chain: "D" Number of atoms: 5733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5733 Classifications: {'peptide': 711} Link IDs: {'PTRANS': 49, 'TRANS': 661} Chain breaks: 4 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 1.60, per 1000 atoms: 0.23 Number of scatterers: 6879 At special positions: 0 Unit cell: (62.54, 71.02, 131.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 29 16.00 P 54 15.00 O 1426 8.00 N 1166 7.00 C 4202 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: 0.49 Conformation dependent library (CDL) restraints added in 281.9 milliseconds 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1362 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 3 sheets defined 48.2% alpha, 2.1% beta 20 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'D' and resid 839 through 857 Processing helix chain 'D' and resid 893 through 903 removed outlier: 4.309A pdb=" N GLU D 901 " --> pdb=" O MET D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 917 removed outlier: 4.041A pdb=" N LYS D 916 " --> pdb=" O THR D 912 " (cutoff:3.500A) Processing helix chain 'D' and resid 969 through 976 Processing helix chain 'D' and resid 994 through 998 removed outlier: 3.617A pdb=" N LEU D 997 " --> pdb=" O SER D 994 " (cutoff:3.500A) Processing helix chain 'D' and resid 1017 through 1027 Processing helix chain 'D' and resid 1034 through 1039 removed outlier: 4.064A pdb=" N ALA D1039 " --> pdb=" O PRO D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1044 through 1052 removed outlier: 5.005A pdb=" N LYS D1050 " --> pdb=" O SER D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1053 through 1074 removed outlier: 3.828A pdb=" N THR D1066 " --> pdb=" O HIS D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1293 through 1302 removed outlier: 4.274A pdb=" N GLN D1299 " --> pdb=" O GLY D1295 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ALA D1300 " --> pdb=" O LEU D1296 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU D1301 " --> pdb=" O ILE D1297 " (cutoff:3.500A) Processing helix chain 'D' and resid 1303 through 1307 Processing helix chain 'D' and resid 1313 through 1335 Processing helix chain 'D' and resid 1342 through 1353 removed outlier: 3.858A pdb=" N ARG D1347 " --> pdb=" O LEU D1343 " (cutoff:3.500A) Processing helix chain 'D' and resid 1355 through 1364 removed outlier: 3.752A pdb=" N LEU D1359 " --> pdb=" O ASN D1355 " (cutoff:3.500A) Processing helix chain 'D' and resid 1547 through 1551 removed outlier: 3.535A pdb=" N THR D1550 " --> pdb=" O ASP D1547 " (cutoff:3.500A) Processing helix chain 'D' and resid 1556 through 1574 Processing helix chain 'D' and resid 1575 through 1586 Processing helix chain 'D' and resid 1663 through 1674 removed outlier: 3.973A pdb=" N ASN D1668 " --> pdb=" O SER D1664 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE D1673 " --> pdb=" O PHE D1669 " (cutoff:3.500A) Processing helix chain 'D' and resid 1679 through 1686 removed outlier: 3.705A pdb=" N LEU D1683 " --> pdb=" O ASN D1679 " (cutoff:3.500A) Processing helix chain 'D' and resid 1701 through 1723 removed outlier: 3.620A pdb=" N LEU D1707 " --> pdb=" O ARG D1703 " (cutoff:3.500A) Processing helix chain 'D' and resid 1728 through 1741 Processing helix chain 'D' and resid 1741 through 1752 Processing helix chain 'D' and resid 1766 through 1776 Processing helix chain 'D' and resid 1805 through 1823 Processing helix chain 'D' and resid 1826 through 1838 Proline residue: D1836 - end of helix Processing helix chain 'D' and resid 1838 through 1847 removed outlier: 4.388A pdb=" N ALA D1847 " --> pdb=" O GLU D1843 " (cutoff:3.500A) Processing helix chain 'D' and resid 1852 through 1860 removed outlier: 5.005A pdb=" N LEU D1858 " --> pdb=" O VAL D1854 " (cutoff:3.500A) Processing helix chain 'D' and resid 1896 through 1912 removed outlier: 3.767A pdb=" N ALA D1900 " --> pdb=" O SER D1896 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 802 through 805 removed outlier: 3.522A pdb=" N LEU D 879 " --> pdb=" O GLY D 803 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N CYS D 877 " --> pdb=" O LEU D 805 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 816 through 817 removed outlier: 3.792A pdb=" N PHE D 816 " --> pdb=" O ILE D 827 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 931 through 932 219 hydrogen bonds defined for protein. 642 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1854 1.34 - 1.46: 1542 1.46 - 1.58: 3607 1.58 - 1.69: 107 1.69 - 1.81: 42 Bond restraints: 7152 Sorted by residual: bond pdb=" N ASN D1355 " pdb=" CA ASN D1355 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.23e-02 6.61e+03 9.82e+00 bond pdb=" N VAL D1351 " pdb=" CA VAL D1351 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.19e-02 7.06e+03 8.25e+00 bond pdb=" N ILE D1811 " pdb=" CA ILE D1811 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.30e-02 5.92e+03 7.88e+00 bond pdb=" N TYR D 976 " pdb=" CA TYR D 976 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.20e-02 6.94e+03 7.45e+00 bond pdb=" N ASN D1742 " pdb=" CA ASN D1742 " ideal model delta sigma weight residual 1.459 1.491 -0.031 1.20e-02 6.94e+03 6.87e+00 ... (remaining 7147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 9396 2.09 - 4.17: 470 4.17 - 6.26: 70 6.26 - 8.34: 10 8.34 - 10.43: 2 Bond angle restraints: 9948 Sorted by residual: angle pdb=" N TYR D 965 " pdb=" CA TYR D 965 " pdb=" C TYR D 965 " ideal model delta sigma weight residual 113.17 107.25 5.92 1.26e+00 6.30e-01 2.20e+01 angle pdb=" C4' A R 22 " pdb=" C3' A R 22 " pdb=" C2' A R 22 " ideal model delta sigma weight residual 102.60 98.39 4.21 1.00e+00 1.00e+00 1.77e+01 angle pdb=" C ILE D 753 " pdb=" CA ILE D 753 " pdb=" CB ILE D 753 " ideal model delta sigma weight residual 109.33 113.24 -3.91 9.80e-01 1.04e+00 1.60e+01 angle pdb=" CA ILE D 753 " pdb=" C ILE D 753 " pdb=" N PRO D 754 " ideal model delta sigma weight residual 116.57 120.39 -3.82 9.80e-01 1.04e+00 1.52e+01 angle pdb=" N LEU D1356 " pdb=" CA LEU D1356 " pdb=" C LEU D1356 " ideal model delta sigma weight residual 112.54 107.97 4.57 1.22e+00 6.72e-01 1.40e+01 ... (remaining 9943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.73: 3842 22.73 - 45.46: 403 45.46 - 68.19: 131 68.19 - 90.92: 28 90.92 - 113.64: 3 Dihedral angle restraints: 4407 sinusoidal: 2300 harmonic: 2107 Sorted by residual: dihedral pdb=" O4' G R 1 " pdb=" C2' G R 1 " pdb=" C1' G R 1 " pdb=" C3' G R 1 " ideal model delta sinusoidal sigma weight residual 25.00 -18.32 43.32 1 8.00e+00 1.56e-02 4.09e+01 dihedral pdb=" C4' G R 1 " pdb=" C3' G R 1 " pdb=" C2' G R 1 " pdb=" C1' G R 1 " ideal model delta sinusoidal sigma weight residual 36.00 -1.20 37.20 1 8.00e+00 1.56e-02 3.05e+01 dihedral pdb=" CA ASP D 989 " pdb=" C ASP D 989 " pdb=" N VAL D 990 " pdb=" CA VAL D 990 " ideal model delta harmonic sigma weight residual 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 4404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1081 0.110 - 0.219: 58 0.219 - 0.329: 0 0.329 - 0.439: 1 0.439 - 0.548: 11 Chirality restraints: 1151 Sorted by residual: chirality pdb=" P G R 1 " pdb=" OP1 G R 1 " pdb=" OP2 G R 1 " pdb=" O5' G R 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.51e+00 chirality pdb=" P C R 37 " pdb=" OP1 C R 37 " pdb=" OP2 C R 37 " pdb=" O5' C R 37 " both_signs ideal model delta sigma weight residual True 2.41 2.95 -0.54 2.00e-01 2.50e+01 7.39e+00 chirality pdb=" P G R 42 " pdb=" OP1 G R 42 " pdb=" OP2 G R 42 " pdb=" O5' G R 42 " both_signs ideal model delta sigma weight residual True 2.41 -2.95 -0.54 2.00e-01 2.50e+01 7.25e+00 ... (remaining 1148 not shown) Planarity restraints: 1072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D1001 " 0.068 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO D1002 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO D1002 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D1002 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1907 " -0.255 9.50e-02 1.11e+02 1.14e-01 8.02e+00 pdb=" NE ARG D1907 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D1907 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D1907 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D1907 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO D1382 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO D1383 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO D1383 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D1383 " 0.034 5.00e-02 4.00e+02 ... (remaining 1069 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 22 2.33 - 2.98: 3660 2.98 - 3.62: 11845 3.62 - 4.26: 18044 4.26 - 4.90: 27973 Nonbonded interactions: 61544 Sorted by model distance: nonbonded pdb=" OE2 GLU D1316 " pdb="CA CA D2001 " model vdw 1.693 3.250 nonbonded pdb=" OE2 GLU D1705 " pdb="CA CA D2002 " model vdw 1.775 3.250 nonbonded pdb=" OP1 A R 43 " pdb="CA CA D2001 " model vdw 1.821 3.250 nonbonded pdb=" O2' U R 62 " pdb=" O5' A R 64 " model vdw 2.009 3.040 nonbonded pdb=" OG SER D1826 " pdb=" OG1 THR D1829 " model vdw 2.032 3.040 ... (remaining 61539 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=0.00 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: 1.130 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.740 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5488 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 : 0.006 0.056 7152 Z= 0.385 Angle : 0.996 10.429 9948 Z= 0.626 Chirality : 0.071 0.548 1151 Planarity : 0.009 0.114 1072 Dihedral : 19.978 113.645 3045 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 1.89 % Allowed : 24.37 % Favored : 73.74 % 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: -1.61 (0.32), residues: 701 helix: 0.30 (0.30), residues: 281 sheet: -2.40 (1.43), residues: 12 loop : -2.14 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D1725 TYR 0.022 0.002 TYR D1330 PHE 0.013 0.002 PHE D 802 TRP 0.007 0.001 TRP D1048 HIS 0.006 0.001 HIS D1755 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.39 ( 7152) covalent geometry : angle 0.99589 / 0.63 ( 9948) hydrogen bonds : bond 0.17536 / 18.02 ( 265) hydrogen bonds : angle 6.41623 / 7.81 ( 730) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 980 LEU cc_start: 0.1882 (OUTLIER) cc_final: 0.1320 (pt) REVERT: D 1014 LEU cc_start: 0.2791 (OUTLIER) cc_final: 0.2530 (pp) REVERT: D 1315 LEU cc_start: 0.5459 (mp) cc_final: 0.5187 (mp) outliers start: 12 outliers final: 5 residues processed: 107 average time/residue: 0.0932 time to fit residues: 12.4483 Evaluate side-chains 93 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 790 ARG Chi-restraints excluded: chain D residue 816 PHE Chi-restraints excluded: chain D residue 976 TYR Chi-restraints excluded: chain D residue 980 LEU Chi-restraints excluded: chain D residue 1014 LEU Chi-restraints excluded: chain D residue 1860 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1073 GLN D1353 ASN D1695 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4975 r_free = 0.4975 target = 0.175078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.159299 restraints weight = 18267.141| |-----------------------------------------------------------------------------| r_work (start): 0.4755 rms_B_bonded: 3.14 r_work: 0.4635 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5686 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7152 Z= 0.207 Angle : 0.786 11.397 9948 Z= 0.411 Chirality : 0.045 0.205 1151 Planarity : 0.008 0.092 1072 Dihedral : 18.792 124.843 1624 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 5.50 % Allowed : 22.80 % Favored : 71.70 % 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: -1.82 (0.31), residues: 701 helix: 0.11 (0.28), residues: 284 sheet: -3.39 (0.82), residues: 22 loop : -2.18 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1049 TYR 0.025 0.002 TYR D1345 PHE 0.011 0.002 PHE D 867 TRP 0.014 0.003 TRP D1048 HIS 0.006 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 ( 7152) covalent geometry : angle 0.78570 / 0.41 ( 9948) hydrogen bonds : bond 0.07461 / 7.03 ( 265) hydrogen bonds : angle 5.73723 / 7.10 ( 730) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 802 PHE cc_start: 0.5893 (OUTLIER) cc_final: 0.5346 (m-80) REVERT: D 943 HIS cc_start: 0.2355 (OUTLIER) cc_final: 0.1757 (m170) REVERT: D 946 TYR cc_start: 0.4219 (p90) cc_final: 0.3736 (p90) REVERT: D 997 LEU cc_start: 0.0616 (OUTLIER) cc_final: 0.0168 (tt) REVERT: D 1299 GLN cc_start: 0.6368 (OUTLIER) cc_final: 0.6167 (pt0) outliers start: 35 outliers final: 12 residues processed: 119 average time/residue: 0.0870 time to fit residues: 13.1957 Evaluate side-chains 102 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 790 ARG Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 816 PHE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 943 HIS Chi-restraints excluded: chain D residue 976 TYR Chi-restraints excluded: chain D residue 977 ASN Chi-restraints excluded: chain D residue 997 LEU Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1070 LEU Chi-restraints excluded: chain D residue 1299 GLN Chi-restraints excluded: chain D residue 1562 CYS Chi-restraints excluded: chain D residue 1734 ASP Chi-restraints excluded: chain D residue 1802 ILE Chi-restraints excluded: chain D residue 1842 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 20.0000 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 20 optimal weight: 0.0270 chunk 27 optimal weight: 0.0980 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.4978 r_free = 0.4978 target = 0.175701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.160630 restraints weight = 18736.478| |-----------------------------------------------------------------------------| r_work (start): 0.4767 rms_B_bonded: 3.09 r_work: 0.4652 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5662 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7152 Z= 0.171 Angle : 0.734 9.087 9948 Z= 0.377 Chirality : 0.045 0.360 1151 Planarity : 0.007 0.098 1072 Dihedral : 18.615 119.870 1617 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 5.35 % Allowed : 24.84 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.30), residues: 701 helix: -0.01 (0.29), residues: 270 sheet: -1.77 (1.49), residues: 10 loop : -2.14 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1879 TYR 0.025 0.002 TYR D1330 PHE 0.022 0.002 PHE D 867 TRP 0.012 0.002 TRP D1048 HIS 0.007 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 7152) covalent geometry : angle 0.73424 / 0.38 ( 9948) hydrogen bonds : bond 0.06364 / 6.09 ( 265) hydrogen bonds : angle 5.57497 / 6.80 ( 730) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 93 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 747 GLN cc_start: 0.4610 (pp30) cc_final: 0.4010 (pp30) REVERT: D 802 PHE cc_start: 0.5851 (OUTLIER) cc_final: 0.5317 (m-80) REVERT: D 943 HIS cc_start: 0.2073 (OUTLIER) cc_final: 0.1463 (m170) REVERT: D 1369 MET cc_start: 0.4746 (mpp) cc_final: 0.4536 (mpp) outliers start: 34 outliers final: 20 residues processed: 118 average time/residue: 0.0791 time to fit residues: 12.0951 Evaluate side-chains 105 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 790 ARG Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 816 PHE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 834 SER Chi-restraints excluded: chain D residue 879 LEU Chi-restraints excluded: chain D residue 943 HIS Chi-restraints excluded: chain D residue 976 TYR Chi-restraints excluded: chain D residue 997 LEU Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1349 LYS Chi-restraints excluded: chain D residue 1663 ILE Chi-restraints excluded: chain D residue 1731 VAL Chi-restraints excluded: chain D residue 1750 VAL Chi-restraints excluded: chain D residue 1802 ILE Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1884 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 7 optimal weight: 0.0010 chunk 35 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1580 GLN ** D1695 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 = 0.4929 r_free = 0.4929 target = 0.172010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4711 r_free = 0.4711 target = 0.155883 restraints weight = 18140.235| |-----------------------------------------------------------------------------| r_work (start): 0.4701 rms_B_bonded: 3.11 r_work: 0.4584 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.4584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5799 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7152 Z= 0.203 Angle : 0.765 9.740 9948 Z= 0.390 Chirality : 0.046 0.290 1151 Planarity : 0.007 0.068 1072 Dihedral : 18.674 118.835 1617 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 23.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 5.50 % Allowed : 25.00 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.31), residues: 701 helix: 0.05 (0.30), residues: 271 sheet: -2.41 (1.31), residues: 10 loop : -2.12 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1703 TYR 0.021 0.002 TYR D1330 PHE 0.011 0.002 PHE D1687 TRP 0.007 0.002 TRP D1380 HIS 0.006 0.002 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 ( 7152) covalent geometry : angle 0.76540 / 0.39 ( 9948) hydrogen bonds : bond 0.06351 / 5.89 ( 265) hydrogen bonds : angle 5.65449 / 6.91 ( 730) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 746 ARG cc_start: 0.3479 (OUTLIER) cc_final: 0.2079 (tmt170) REVERT: D 747 GLN cc_start: 0.4573 (pp30) cc_final: 0.3385 (pp30) REVERT: D 802 PHE cc_start: 0.5994 (OUTLIER) cc_final: 0.5495 (m-80) REVERT: D 942 PRO cc_start: 0.5741 (Cg_exo) cc_final: 0.5517 (Cg_exo) REVERT: D 943 HIS cc_start: 0.2566 (OUTLIER) cc_final: 0.2044 (m170) REVERT: D 1038 CYS cc_start: 0.7549 (p) cc_final: 0.7171 (p) REVERT: D 1299 GLN cc_start: 0.6340 (pt0) cc_final: 0.6059 (pt0) REVERT: D 1735 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5686 (mm) outliers start: 35 outliers final: 20 residues processed: 122 average time/residue: 0.0740 time to fit residues: 11.7259 Evaluate side-chains 111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 773 ILE Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 790 ARG Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 801 CYS Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 879 LEU Chi-restraints excluded: chain D residue 896 PHE Chi-restraints excluded: chain D residue 943 HIS Chi-restraints excluded: chain D residue 976 TYR Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1034 VAL Chi-restraints excluded: chain D residue 1315 LEU Chi-restraints excluded: chain D residue 1362 LYS Chi-restraints excluded: chain D residue 1728 SER Chi-restraints excluded: chain D residue 1731 VAL Chi-restraints excluded: chain D residue 1735 LEU Chi-restraints excluded: chain D residue 1750 VAL Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1881 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 1 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 0.0010 chunk 2 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 841 GLN D1695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4951 r_free = 0.4951 target = 0.174105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4741 r_free = 0.4741 target = 0.158469 restraints weight = 18319.908| |-----------------------------------------------------------------------------| r_work (start): 0.4732 rms_B_bonded: 3.04 r_work: 0.4618 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7152 Z= 0.152 Angle : 0.704 9.933 9948 Z= 0.362 Chirality : 0.043 0.192 1151 Planarity : 0.007 0.059 1072 Dihedral : 18.545 115.843 1615 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 5.19 % Allowed : 25.94 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.31), residues: 701 helix: -0.08 (0.29), residues: 282 sheet: -2.74 (1.28), residues: 12 loop : -2.07 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1703 TYR 0.022 0.002 TYR D1330 PHE 0.019 0.002 PHE D1310 TRP 0.007 0.001 TRP D1831 HIS 0.006 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 7152) covalent geometry : angle 0.70435 / 0.36 ( 9948) hydrogen bonds : bond 0.05811 / 5.41 ( 265) hydrogen bonds : angle 5.48616 / 6.58 ( 730) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 746 ARG cc_start: 0.3288 (OUTLIER) cc_final: 0.2491 (tmt170) REVERT: D 747 GLN cc_start: 0.4910 (pp30) cc_final: 0.4584 (pp30) REVERT: D 802 PHE cc_start: 0.6017 (OUTLIER) cc_final: 0.5525 (m-80) REVERT: D 844 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6898 (tm-30) REVERT: D 943 HIS cc_start: 0.2221 (OUTLIER) cc_final: 0.1674 (m170) REVERT: D 976 TYR cc_start: 0.3901 (OUTLIER) cc_final: 0.3322 (m-80) REVERT: D 1038 CYS cc_start: 0.7485 (p) cc_final: 0.7124 (p) REVERT: D 1735 LEU cc_start: 0.5761 (OUTLIER) cc_final: 0.5469 (mm) outliers start: 33 outliers final: 18 residues processed: 111 average time/residue: 0.0804 time to fit residues: 11.4577 Evaluate side-chains 108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 790 ARG Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 801 CYS Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 841 GLN Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 879 LEU Chi-restraints excluded: chain D residue 943 HIS Chi-restraints excluded: chain D residue 976 TYR Chi-restraints excluded: chain D residue 1034 VAL Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1062 HIS Chi-restraints excluded: chain D residue 1315 LEU Chi-restraints excluded: chain D residue 1362 LYS Chi-restraints excluded: chain D residue 1731 VAL Chi-restraints excluded: chain D residue 1735 LEU Chi-restraints excluded: chain D residue 1802 ILE Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1881 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 47 optimal weight: 0.0370 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.173007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4720 r_free = 0.4720 target = 0.157067 restraints weight = 18372.704| |-----------------------------------------------------------------------------| r_work (start): 0.4714 rms_B_bonded: 3.07 r_work: 0.4599 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5754 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7152 Z= 0.165 Angle : 0.707 8.185 9948 Z= 0.364 Chirality : 0.042 0.185 1151 Planarity : 0.007 0.086 1072 Dihedral : 18.485 117.067 1613 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 5.19 % Allowed : 25.63 % Favored : 69.18 % 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: -1.83 (0.31), residues: 701 helix: -0.02 (0.29), residues: 277 sheet: -2.41 (1.37), residues: 12 loop : -2.14 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D1895 TYR 0.021 0.002 TYR D1330 PHE 0.014 0.001 PHE D 922 TRP 0.006 0.001 TRP D1831 HIS 0.005 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 7152) covalent geometry : angle 0.70696 / 0.36 ( 9948) hydrogen bonds : bond 0.05815 / 5.37 ( 265) hydrogen bonds : angle 5.43955 / 6.55 ( 730) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 747 GLN cc_start: 0.5073 (pp30) cc_final: 0.4502 (pp30) REVERT: D 748 CYS cc_start: 0.3590 (OUTLIER) cc_final: 0.2409 (m) REVERT: D 802 PHE cc_start: 0.6041 (OUTLIER) cc_final: 0.5600 (m-80) REVERT: D 805 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7572 (mt) REVERT: D 943 HIS cc_start: 0.2354 (OUTLIER) cc_final: 0.1783 (m170) REVERT: D 976 TYR cc_start: 0.3768 (OUTLIER) cc_final: 0.3203 (m-80) REVERT: D 1038 CYS cc_start: 0.7482 (p) cc_final: 0.7111 (p) REVERT: D 1735 LEU cc_start: 0.5855 (OUTLIER) cc_final: 0.5501 (mm) outliers start: 33 outliers final: 21 residues processed: 116 average time/residue: 0.0806 time to fit residues: 11.9581 Evaluate side-chains 111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 790 ARG Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 801 CYS Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 805 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 879 LEU Chi-restraints excluded: chain D residue 896 PHE Chi-restraints excluded: chain D residue 943 HIS Chi-restraints excluded: chain D residue 976 TYR Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1034 VAL Chi-restraints excluded: chain D residue 1062 HIS Chi-restraints excluded: chain D residue 1315 LEU Chi-restraints excluded: chain D residue 1362 LYS Chi-restraints excluded: chain D residue 1562 CYS Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1728 SER Chi-restraints excluded: chain D residue 1735 LEU Chi-restraints excluded: chain D residue 1802 ILE Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1880 VAL Chi-restraints excluded: chain D residue 1881 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 3 optimal weight: 8.9990 chunk 43 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.0980 chunk 17 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1755 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.172534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.156849 restraints weight = 18541.760| |-----------------------------------------------------------------------------| r_work (start): 0.4701 rms_B_bonded: 3.09 r_work: 0.4583 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5775 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7152 Z= 0.168 Angle : 0.721 7.541 9948 Z= 0.373 Chirality : 0.043 0.183 1151 Planarity : 0.007 0.070 1072 Dihedral : 18.508 118.153 1613 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 6.29 % Allowed : 25.79 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.31), residues: 701 helix: -0.00 (0.29), residues: 276 sheet: -2.18 (1.45), residues: 12 loop : -2.12 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1703 TYR 0.026 0.002 TYR D1701 PHE 0.014 0.001 PHE D1374 TRP 0.007 0.001 TRP D1831 HIS 0.015 0.002 HIS D1755 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 7152) covalent geometry : angle 0.72053 / 0.37 ( 9948) hydrogen bonds : bond 0.05716 / 5.32 ( 265) hydrogen bonds : angle 5.39714 / 6.50 ( 730) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 84 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 747 GLN cc_start: 0.5038 (OUTLIER) cc_final: 0.4590 (pp30) REVERT: D 748 CYS cc_start: 0.3832 (OUTLIER) cc_final: 0.2591 (m) REVERT: D 802 PHE cc_start: 0.6081 (OUTLIER) cc_final: 0.5616 (m-80) REVERT: D 857 ILE cc_start: 0.5888 (mt) cc_final: 0.5637 (mt) REVERT: D 943 HIS cc_start: 0.2348 (OUTLIER) cc_final: 0.1781 (m170) REVERT: D 976 TYR cc_start: 0.3822 (OUTLIER) cc_final: 0.3293 (m-80) REVERT: D 1037 LEU cc_start: 0.6317 (mm) cc_final: 0.6103 (mm) REVERT: D 1038 CYS cc_start: 0.7483 (p) cc_final: 0.7091 (p) REVERT: D 1735 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5482 (mm) outliers start: 40 outliers final: 23 residues processed: 115 average time/residue: 0.0806 time to fit residues: 11.9535 Evaluate side-chains 114 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 747 GLN Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 790 ARG Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 879 LEU Chi-restraints excluded: chain D residue 896 PHE Chi-restraints excluded: chain D residue 943 HIS Chi-restraints excluded: chain D residue 976 TYR Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1034 VAL Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1062 HIS Chi-restraints excluded: chain D residue 1315 LEU Chi-restraints excluded: chain D residue 1362 LYS Chi-restraints excluded: chain D residue 1562 CYS Chi-restraints excluded: chain D residue 1571 LEU Chi-restraints excluded: chain D residue 1699 ASP Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1728 SER Chi-restraints excluded: chain D residue 1735 LEU Chi-restraints excluded: chain D residue 1802 ILE Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1880 VAL Chi-restraints excluded: chain D residue 1881 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 35 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.172745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.157264 restraints weight = 18690.130| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 3.09 r_work: 0.4589 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5765 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7152 Z= 0.161 Angle : 0.718 7.999 9948 Z= 0.370 Chirality : 0.043 0.196 1151 Planarity : 0.007 0.078 1072 Dihedral : 18.452 118.725 1613 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 22.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.72 % Allowed : 26.57 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.31), residues: 701 helix: -0.08 (0.29), residues: 283 sheet: -2.27 (1.42), residues: 12 loop : -2.13 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1703 TYR 0.026 0.002 TYR D1701 PHE 0.012 0.001 PHE D 922 TRP 0.007 0.001 TRP D1831 HIS 0.005 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 7152) covalent geometry : angle 0.71760 / 0.37 ( 9948) hydrogen bonds : bond 0.05631 / 5.28 ( 265) hydrogen bonds : angle 5.29973 / 6.40 ( 730) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 747 GLN cc_start: 0.5313 (OUTLIER) cc_final: 0.4832 (pp30) REVERT: D 748 CYS cc_start: 0.3748 (OUTLIER) cc_final: 0.2652 (m) REVERT: D 802 PHE cc_start: 0.5914 (OUTLIER) cc_final: 0.5544 (m-80) REVERT: D 857 ILE cc_start: 0.5706 (mt) cc_final: 0.5437 (mt) REVERT: D 943 HIS cc_start: 0.2382 (OUTLIER) cc_final: 0.1830 (m170) REVERT: D 1038 CYS cc_start: 0.7482 (p) cc_final: 0.7097 (p) REVERT: D 1735 LEU cc_start: 0.5964 (OUTLIER) cc_final: 0.5560 (mm) REVERT: D 1813 GLU cc_start: 0.6675 (pt0) cc_final: 0.6233 (pt0) outliers start: 30 outliers final: 21 residues processed: 110 average time/residue: 0.0813 time to fit residues: 11.6743 Evaluate side-chains 109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 747 GLN Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 790 ARG Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 879 LEU Chi-restraints excluded: chain D residue 896 PHE Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 943 HIS Chi-restraints excluded: chain D residue 976 TYR Chi-restraints excluded: chain D residue 1034 VAL Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1062 HIS Chi-restraints excluded: chain D residue 1315 LEU Chi-restraints excluded: chain D residue 1562 CYS Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1728 SER Chi-restraints excluded: chain D residue 1735 LEU Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1802 ILE Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1880 VAL Chi-restraints excluded: chain D residue 1881 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.171786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.156139 restraints weight = 18182.506| |-----------------------------------------------------------------------------| r_work (start): 0.4693 rms_B_bonded: 3.05 r_work: 0.4576 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.4576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5794 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7152 Z= 0.172 Angle : 0.746 8.519 9948 Z= 0.383 Chirality : 0.044 0.223 1151 Planarity : 0.007 0.075 1072 Dihedral : 18.456 120.001 1613 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.56 % Allowed : 27.67 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -1.76 (0.31), residues: 701 helix: 0.03 (0.30), residues: 276 sheet: -2.19 (1.45), residues: 12 loop : -2.08 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1879 TYR 0.032 0.002 TYR D1692 PHE 0.010 0.001 PHE D1582 TRP 0.004 0.001 TRP D1380 HIS 0.005 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 7152) covalent geometry : angle 0.74593 / 0.38 ( 9948) hydrogen bonds : bond 0.05771 / 5.43 ( 265) hydrogen bonds : angle 5.33625 / 6.44 ( 730) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 747 GLN cc_start: 0.5367 (OUTLIER) cc_final: 0.4844 (pp30) REVERT: D 748 CYS cc_start: 0.3843 (OUTLIER) cc_final: 0.2673 (m) REVERT: D 802 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.5629 (m-80) REVERT: D 857 ILE cc_start: 0.5723 (mt) cc_final: 0.5439 (mt) REVERT: D 943 HIS cc_start: 0.2215 (OUTLIER) cc_final: 0.1711 (m170) REVERT: D 1038 CYS cc_start: 0.7497 (p) cc_final: 0.7129 (p) REVERT: D 1735 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5518 (mm) outliers start: 29 outliers final: 22 residues processed: 106 average time/residue: 0.0772 time to fit residues: 10.7151 Evaluate side-chains 112 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 747 GLN Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 790 ARG Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 798 THR Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 879 LEU Chi-restraints excluded: chain D residue 896 PHE Chi-restraints excluded: chain D residue 943 HIS Chi-restraints excluded: chain D residue 976 TYR Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1034 VAL Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1315 LEU Chi-restraints excluded: chain D residue 1562 CYS Chi-restraints excluded: chain D residue 1571 LEU Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1728 SER Chi-restraints excluded: chain D residue 1735 LEU Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1802 ILE Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1880 VAL Chi-restraints excluded: chain D residue 1881 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 25 optimal weight: 0.0670 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 22 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1031 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.173489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.158003 restraints weight = 18376.363| |-----------------------------------------------------------------------------| r_work (start): 0.4721 rms_B_bonded: 3.04 r_work: 0.4604 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5724 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7152 Z= 0.150 Angle : 0.732 11.767 9948 Z= 0.374 Chirality : 0.043 0.182 1151 Planarity : 0.007 0.060 1072 Dihedral : 18.401 118.702 1613 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 22.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.40 % Allowed : 27.99 % Favored : 67.61 % 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: -1.77 (0.31), residues: 701 helix: -0.04 (0.29), residues: 282 sheet: -2.35 (1.39), residues: 12 loop : -2.07 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1879 TYR 0.023 0.002 TYR D1701 PHE 0.013 0.001 PHE D1582 TRP 0.004 0.001 TRP D1380 HIS 0.006 0.001 HIS D1755 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 ( 7152) covalent geometry : angle 0.73202 / 0.37 ( 9948) hydrogen bonds : bond 0.05627 / 5.38 ( 265) hydrogen bonds : angle 5.32647 / 6.44 ( 730) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1402 Ramachandran restraints generated. 701 Oldfield, 0 Emsley, 701 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 747 GLN cc_start: 0.5272 (OUTLIER) cc_final: 0.4692 (pp30) REVERT: D 748 CYS cc_start: 0.3560 (OUTLIER) cc_final: 0.2452 (m) REVERT: D 802 PHE cc_start: 0.5799 (OUTLIER) cc_final: 0.5436 (m-80) REVERT: D 837 MET cc_start: 0.5353 (tmm) cc_final: 0.5007 (tmm) REVERT: D 857 ILE cc_start: 0.5841 (mt) cc_final: 0.5575 (mt) REVERT: D 942 PRO cc_start: 0.6070 (Cg_endo) cc_final: 0.5865 (Cg_exo) REVERT: D 943 HIS cc_start: 0.2206 (OUTLIER) cc_final: 0.1688 (m170) REVERT: D 1735 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5495 (mm) outliers start: 28 outliers final: 21 residues processed: 105 average time/residue: 0.0722 time to fit residues: 9.8529 Evaluate side-chains 108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 747 GLN Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 776 VAL Chi-restraints excluded: chain D residue 790 ARG Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 879 LEU Chi-restraints excluded: chain D residue 896 PHE Chi-restraints excluded: chain D residue 943 HIS Chi-restraints excluded: chain D residue 976 TYR Chi-restraints excluded: chain D residue 1034 VAL Chi-restraints excluded: chain D residue 1053 CYS Chi-restraints excluded: chain D residue 1062 HIS Chi-restraints excluded: chain D residue 1315 LEU Chi-restraints excluded: chain D residue 1562 CYS Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1728 SER Chi-restraints excluded: chain D residue 1735 LEU Chi-restraints excluded: chain D residue 1802 ILE Chi-restraints excluded: chain D residue 1838 MET Chi-restraints excluded: chain D residue 1842 ILE Chi-restraints excluded: chain D residue 1880 VAL Chi-restraints excluded: chain D residue 1881 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.0370 chunk 31 optimal weight: 0.9980 chunk 63 optimal weight: 0.0000 chunk 51 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 0.0070 overall best weight: 0.3280 ------------------------------------------------------------------------------- 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 = 0.4947 r_free = 0.4947 target = 0.174076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.158600 restraints weight = 18194.242| |-----------------------------------------------------------------------------| r_work (start): 0.4730 rms_B_bonded: 3.03 r_work: 0.4611 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5712 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7152 Z= 0.147 Angle : 0.727 11.424 9948 Z= 0.371 Chirality : 0.043 0.318 1151 Planarity : 0.007 0.060 1072 Dihedral : 18.348 118.326 1613 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.09 % Allowed : 28.14 % Favored : 67.77 % 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 (0.31), residues: 701 helix: 0.09 (0.29), residues: 283 sheet: -2.16 (1.38), residues: 12 loop : -2.06 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1879 TYR 0.023 0.002 TYR D1330 PHE 0.012 0.001 PHE D1582 TRP 0.004 0.001 TRP D1380 HIS 0.009 0.001 HIS D1755 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 7152) covalent geometry : angle 0.72657 / 0.37 ( 9948) hydrogen bonds : bond 0.05499 / 5.23 ( 265) hydrogen bonds : angle 5.25165 / 6.30 ( 730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1516.32 seconds wall clock time: 26 minutes 56.03 seconds (1616.03 seconds total)