Starting phenix.real_space_refine on Tue Aug 4 22:10:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v42_64764/08_2026/9v42_64764.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v42_64764/08_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_64764/08_2026/9v42_64764.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v42_64764/08_2026/9v42_64764.map" model { file = "/net/cci-nas-00/data/ceres_data/9v42_64764/08_2026/9v42_64764.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v42_64764/08_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.30, per 1000 atoms: 0.19 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: 0.53 Conformation dependent library (CDL) restraints added in 246.8 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: 0.94 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: 1.25 Time building geometry restraints manager: 0.68 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=" P A R 38 " pdb=" O5' A R 38 " ideal model delta sigma weight residual 1.593 1.620 -0.027 1.00e-02 1.00e+04 7.22e+00 ... (remaining 7147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 9352 2.09 - 4.17: 514 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=" C3' G R 1 " pdb=" C2' G R 1 " pdb=" C1' G R 1 " ideal model delta sigma weight residual 101.30 104.54 -3.24 7.00e-01 2.04e+00 2.14e+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=" O5' A R 55 " pdb=" C5' A R 55 " pdb=" C4' A R 55 " ideal model delta sigma weight residual 109.40 112.55 -3.15 8.00e-01 1.56e+00 1.55e+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: 1074 0.110 - 0.219: 65 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 2.510 nonbonded pdb=" OE2 GLU D1705 " pdb="CA CA D2002 " model vdw 1.775 2.510 nonbonded pdb=" OP1 A R 43 " pdb="CA CA D2001 " model vdw 1.821 2.510 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.300 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.700 ------------------------------------------------------------------------------- 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= 0.397 Angle : 1.018 10.429 9948 Z= 0.660 Chirality : 0.073 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 0.00638 / 0.40 ( 7152) covalent geometry : angle 1.01790 / 0.66 ( 9948) hydrogen bonds : bond 0.17536 / 19.16 ( 265) hydrogen bonds : angle 6.41623 / 8.10 ( 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 : 0.216 Fit side-chains revert: symmetry clash 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: 0.2502 (pp) REVERT: D 1315 LEU cc_start: 0.5459 (mp) cc_final: 0.5188 (mp) outliers start: 12 outliers final: 5 residues processed: 107 average time/residue: 0.1060 time to fit residues: 14.2986 Evaluate side-chains 94 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4971 r_free = 0.4971 target = 0.174709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.158865 restraints weight = 18310.267| |-----------------------------------------------------------------------------| r_work (start): 0.4745 rms_B_bonded: 3.15 r_work: 0.4626 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.4626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7152 Z= 0.216 Angle : 0.800 11.408 9948 Z= 0.416 Chirality : 0.046 0.182 1151 Planarity : 0.008 0.087 1072 Dihedral : 18.744 123.037 1624 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 5.66 % Allowed : 22.64 % 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: 0.12 (0.28), residues: 284 sheet: -3.42 (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 0.026 0.003 TYR D1345 PHE 0.012 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 0.00486 / 0.22 ( 7152) covalent geometry : angle 0.79978 / 0.42 ( 9948) hydrogen bonds : bond 0.07535 / 7.73 ( 265) hydrogen bonds : angle 5.74005 / 7.37 ( 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 131 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 95 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 802 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.5348 (m-80) REVERT: D 943 HIS cc_start: 0.2459 (OUTLIER) cc_final: 0.1841 (m170) REVERT: D 946 TYR cc_start: 0.4260 (p90) cc_final: 0.3774 (p90) REVERT: D 997 LEU cc_start: 0.0707 (OUTLIER) cc_final: 0.0309 (tt) REVERT: D 1299 GLN cc_start: 0.6375 (OUTLIER) cc_final: 0.6174 (pt0) REVERT: D 1315 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5425 (mp) outliers start: 36 outliers final: 13 residues processed: 122 average time/residue: 0.0773 time to fit residues: 12.2197 Evaluate side-chains 103 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 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 1315 LEU 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: 0.3980 chunk 18 optimal weight: 0.7980 chunk 56 optimal weight: 0.0870 chunk 20 optimal weight: 0.4980 chunk 27 optimal weight: 0.0870 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 69 optimal weight: 0.3980 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 0.2936 ------------------------------------------------------------------------------- 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 = 0.4982 r_free = 0.4982 target = 0.176108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.161058 restraints weight = 18343.415| |-----------------------------------------------------------------------------| r_work (start): 0.4776 rms_B_bonded: 3.01 r_work: 0.4663 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5624 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7152 Z= 0.164 Angle : 0.732 9.236 9948 Z= 0.374 Chirality : 0.044 0.328 1151 Planarity : 0.007 0.099 1072 Dihedral : 18.516 114.155 1617 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 5.03 % Allowed : 25.16 % 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: -1.73 (0.30), residues: 701 helix: 0.08 (0.29), residues: 272 sheet: -2.66 (1.31), residues: 12 loop : -2.05 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 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 0.00365 / 0.16 ( 7152) covalent geometry : angle 0.73192 / 0.37 ( 9948) hydrogen bonds : bond 0.06378 / 6.62 ( 265) hydrogen bonds : angle 5.54165 / 7.01 ( 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 123 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.249 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: 0.4637 (pp30) cc_final: 0.4040 (pp30) REVERT: D 802 PHE cc_start: 0.5812 (OUTLIER) cc_final: 0.5286 (m-80) REVERT: D 943 HIS cc_start: 0.2037 (OUTLIER) cc_final: 0.1454 (m170) REVERT: D 1369 MET cc_start: 0.4732 (mpp) cc_final: 0.4515 (mpp) REVERT: D 1838 MET cc_start: 0.5330 (mpp) cc_final: 0.4357 (mtm) outliers start: 32 outliers final: 18 residues processed: 114 average time/residue: 0.0983 time to fit residues: 14.4297 Evaluate side-chains 100 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 801 CYS 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 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: 2.9990 chunk 64 optimal weight: 0.1980 chunk 2 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 7 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1299 GLN D1580 GLN ** D1695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.175634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.160093 restraints weight = 19006.601| |-----------------------------------------------------------------------------| r_work (start): 0.4745 rms_B_bonded: 3.15 r_work: 0.4629 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5684 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7152 Z= 0.163 Angle : 0.725 10.807 9948 Z= 0.367 Chirality : 0.045 0.275 1151 Planarity : 0.007 0.059 1072 Dihedral : 18.462 110.889 1617 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.56 % Allowed : 26.26 % 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: -1.71 (0.30), residues: 701 helix: 0.17 (0.30), residues: 272 sheet: -2.88 (1.24), residues: 12 loop : -2.09 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1703 TYR 0.022 0.002 TYR D1330 PHE 0.011 0.002 PHE D1582 TRP 0.006 0.001 TRP D1048 HIS 0.007 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 7152) covalent geometry : angle 0.72537 / 0.37 ( 9948) hydrogen bonds : bond 0.06042 / 6.23 ( 265) hydrogen bonds : angle 5.49852 / 6.86 ( 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 118 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.219 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: 0.4785 (pp30) cc_final: 0.4186 (pp30) REVERT: D 802 PHE cc_start: 0.5896 (OUTLIER) cc_final: 0.5341 (m-80) REVERT: D 943 HIS cc_start: 0.2274 (OUTLIER) cc_final: 0.1669 (m170) REVERT: D 976 TYR cc_start: 0.3712 (OUTLIER) cc_final: 0.3190 (m-80) REVERT: D 1735 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5594 (mm) REVERT: D 1813 GLU cc_start: 0.6913 (pt0) cc_final: 0.6527 (pt0) outliers start: 29 outliers final: 17 residues processed: 110 average time/residue: 0.0838 time to fit residues: 12.0789 Evaluate side-chains 106 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.166 ------------------------------------------------------------------------------- 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 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 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 1034 VAL Chi-restraints excluded: chain D residue 1315 LEU Chi-restraints excluded: chain D residue 1349 LYS 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 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: 0.6980 chunk 21 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 71 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1695 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.172439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.156553 restraints weight = 18419.188| |-----------------------------------------------------------------------------| r_work (start): 0.4708 rms_B_bonded: 3.07 r_work: 0.4593 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.4593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5774 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7152 Z= 0.184 Angle : 0.731 7.496 9948 Z= 0.376 Chirality : 0.045 0.230 1151 Planarity : 0.007 0.059 1072 Dihedral : 18.438 110.484 1615 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 5.82 % Allowed : 26.10 % Favored : 68.08 % 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: -1.71 (0.31), residues: 701 helix: 0.01 (0.30), residues: 277 sheet: -2.53 (1.38), residues: 12 loop : -2.00 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D1895 TYR 0.021 0.002 TYR D1330 PHE 0.010 0.002 PHE D1772 TRP 0.006 0.002 TRP D1831 HIS 0.006 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 ( 7152) covalent geometry : angle 0.73062 / 0.38 ( 9948) hydrogen bonds : bond 0.06102 / 6.21 ( 265) hydrogen bonds : angle 5.59094 / 6.92 ( 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 130 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 746 ARG cc_start: 0.3445 (OUTLIER) cc_final: 0.3145 (tmt-80) REVERT: D 747 GLN cc_start: 0.5088 (pp30) cc_final: 0.4370 (pp30) REVERT: D 802 PHE cc_start: 0.6113 (OUTLIER) cc_final: 0.5635 (m-80) REVERT: D 805 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7528 (mt) REVERT: D 844 GLU cc_start: 0.7040 (tm-30) cc_final: 0.6806 (tm-30) REVERT: D 943 HIS cc_start: 0.2409 (OUTLIER) cc_final: 0.1844 (m170) REVERT: D 1735 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5494 (mm) REVERT: D 1756 LYS cc_start: 0.7450 (mttp) cc_final: 0.6893 (mmtt) outliers start: 37 outliers final: 21 residues processed: 120 average time/residue: 0.0960 time to fit residues: 14.8847 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 : 0.155 ------------------------------------------------------------------------------- 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 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 997 LEU 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 1362 LYS Chi-restraints excluded: chain D residue 1562 CYS Chi-restraints excluded: chain D residue 1571 LEU Chi-restraints excluded: chain D residue 1735 LEU Chi-restraints excluded: chain D residue 1750 VAL 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 1881 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 0.0270 chunk 24 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.4944 r_free = 0.4944 target = 0.173372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.157474 restraints weight = 19225.630| |-----------------------------------------------------------------------------| r_work (start): 0.4706 rms_B_bonded: 3.17 r_work: 0.4586 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5773 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7152 Z= 0.162 Angle : 0.704 7.126 9948 Z= 0.364 Chirality : 0.042 0.159 1151 Planarity : 0.007 0.083 1072 Dihedral : 18.361 110.776 1613 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 5.35 % Allowed : 27.36 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.31), residues: 701 helix: 0.00 (0.29), residues: 278 sheet: -2.38 (1.38), residues: 12 loop : -2.02 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 935 TYR 0.024 0.002 TYR D 819 PHE 0.014 0.001 PHE D 922 TRP 0.006 0.001 TRP D1831 HIS 0.006 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 7152) covalent geometry : angle 0.70407 / 0.36 ( 9948) hydrogen bonds : bond 0.05866 / 5.93 ( 265) hydrogen bonds : angle 5.45351 / 6.70 ( 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 119 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 746 ARG cc_start: 0.3410 (OUTLIER) cc_final: 0.3073 (tmt170) REVERT: D 802 PHE cc_start: 0.6041 (OUTLIER) cc_final: 0.5544 (m-80) REVERT: D 943 HIS cc_start: 0.2361 (OUTLIER) cc_final: 0.1777 (m170) REVERT: D 997 LEU cc_start: 0.1060 (OUTLIER) cc_final: 0.0820 (tt) REVERT: D 1038 CYS cc_start: 0.7563 (p) cc_final: 0.7174 (p) REVERT: D 1735 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5631 (mm) REVERT: D 1756 LYS cc_start: 0.7565 (mttp) cc_final: 0.7004 (mmtt) outliers start: 34 outliers final: 20 residues processed: 113 average time/residue: 0.0899 time to fit residues: 13.1225 Evaluate side-chains 111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 746 ARG Chi-restraints excluded: chain D residue 748 CYS Chi-restraints excluded: chain D residue 760 SER Chi-restraints excluded: chain D residue 773 ILE 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 943 HIS Chi-restraints excluded: chain D residue 997 LEU 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 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: 10.0000 chunk 43 optimal weight: 0.0770 chunk 28 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 0.0370 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 0.0370 chunk 27 optimal weight: 7.9990 overall best weight: 0.3694 ------------------------------------------------------------------------------- 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 = 0.4964 r_free = 0.4964 target = 0.174706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.158870 restraints weight = 18983.313| |-----------------------------------------------------------------------------| r_work (start): 0.4731 rms_B_bonded: 3.13 r_work: 0.4614 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.4614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.3212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7152 Z= 0.145 Angle : 0.686 7.391 9948 Z= 0.354 Chirality : 0.042 0.161 1151 Planarity : 0.007 0.069 1072 Dihedral : 18.285 110.248 1613 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 5.35 % Allowed : 26.26 % Favored : 68.40 % 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: -1.71 (0.31), residues: 701 helix: -0.00 (0.29), residues: 275 sheet: -2.45 (1.36), residues: 12 loop : -1.99 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1703 TYR 0.022 0.002 TYR D1330 PHE 0.026 0.002 PHE D1758 TRP 0.005 0.001 TRP D1831 HIS 0.005 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 ( 7152) covalent geometry : angle 0.68646 / 0.35 ( 9948) hydrogen bonds : bond 0.05606 / 5.71 ( 265) hydrogen bonds : angle 5.35867 / 6.55 ( 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 122 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 88 time to evaluate : 0.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 746 ARG cc_start: 0.3373 (OUTLIER) cc_final: 0.3117 (tmt170) REVERT: D 758 ARG cc_start: 0.6335 (mmt180) cc_final: 0.5894 (mmt-90) REVERT: D 802 PHE cc_start: 0.5840 (OUTLIER) cc_final: 0.5399 (m-80) REVERT: D 805 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7578 (mt) REVERT: D 857 ILE cc_start: 0.5940 (mt) cc_final: 0.5680 (mt) REVERT: D 943 HIS cc_start: 0.2244 (OUTLIER) cc_final: 0.1707 (m170) REVERT: D 1037 LEU cc_start: 0.6375 (mm) cc_final: 0.6155 (mm) REVERT: D 1038 CYS cc_start: 0.7538 (p) cc_final: 0.7139 (p) REVERT: D 1735 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5575 (mm) REVERT: D 1756 LYS cc_start: 0.7507 (mttp) cc_final: 0.6978 (mmtt) outliers start: 34 outliers final: 20 residues processed: 115 average time/residue: 0.0942 time to fit residues: 14.0762 Evaluate side-chains 109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 802 PHE Chi-restraints excluded: chain D residue 805 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 879 LEU Chi-restraints excluded: chain D residue 943 HIS 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 1362 LYS Chi-restraints excluded: chain D residue 1562 CYS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 0.0050 chunk 75 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 0.3980 chunk 70 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.4963 r_free = 0.4963 target = 0.174655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.158890 restraints weight = 19077.097| |-----------------------------------------------------------------------------| r_work (start): 0.4729 rms_B_bonded: 3.11 r_work: 0.4612 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.4612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5713 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7152 Z= 0.149 Angle : 0.700 9.246 9948 Z= 0.358 Chirality : 0.041 0.159 1151 Planarity : 0.007 0.076 1072 Dihedral : 18.207 110.787 1611 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.25 % Allowed : 27.99 % 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: -1.70 (0.31), residues: 701 helix: 0.10 (0.29), residues: 277 sheet: -2.43 (1.37), residues: 12 loop : -2.07 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1703 TYR 0.022 0.002 TYR D1330 PHE 0.020 0.001 PHE D1758 TRP 0.005 0.001 TRP D1831 HIS 0.005 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 7152) covalent geometry : angle 0.69987 / 0.36 ( 9948) hydrogen bonds : bond 0.05564 / 5.70 ( 265) hydrogen bonds : angle 5.29656 / 6.50 ( 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 117 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 746 ARG cc_start: 0.3314 (OUTLIER) cc_final: 0.3032 (tmt170) REVERT: D 802 PHE cc_start: 0.5846 (OUTLIER) cc_final: 0.5383 (m-80) REVERT: D 805 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7650 (mt) REVERT: D 857 ILE cc_start: 0.5861 (mt) cc_final: 0.5592 (mt) REVERT: D 943 HIS cc_start: 0.2283 (OUTLIER) cc_final: 0.1736 (m170) REVERT: D 1037 LEU cc_start: 0.6285 (mm) cc_final: 0.6049 (mm) REVERT: D 1038 CYS cc_start: 0.7603 (p) cc_final: 0.7192 (p) REVERT: D 1735 LEU cc_start: 0.5912 (OUTLIER) cc_final: 0.5528 (mm) REVERT: D 1756 LYS cc_start: 0.7645 (mttp) cc_final: 0.7014 (mmtt) outliers start: 27 outliers final: 19 residues processed: 111 average time/residue: 0.0873 time to fit residues: 12.5944 Evaluate side-chains 109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 85 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 802 PHE Chi-restraints excluded: chain D residue 805 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 879 LEU Chi-restraints excluded: chain D residue 943 HIS 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 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 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: 0.0980 chunk 73 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1755 HIS ** 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 = 0.4962 r_free = 0.4962 target = 0.174557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.158854 restraints weight = 18930.275| |-----------------------------------------------------------------------------| r_work (start): 0.4735 rms_B_bonded: 3.10 r_work: 0.4617 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5714 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7152 Z= 0.150 Angle : 0.721 11.566 9948 Z= 0.366 Chirality : 0.042 0.217 1151 Planarity : 0.007 0.074 1072 Dihedral : 18.181 111.210 1611 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.25 % Allowed : 28.62 % Favored : 67.14 % 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: -1.71 (0.31), residues: 701 helix: 0.10 (0.30), residues: 277 sheet: -2.53 (1.42), residues: 12 loop : -2.07 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 758 TYR 0.026 0.002 TYR D1692 PHE 0.018 0.001 PHE D1758 TRP 0.005 0.001 TRP D1831 HIS 0.012 0.001 HIS D1755 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 7152) covalent geometry : angle 0.72106 / 0.37 ( 9948) hydrogen bonds : bond 0.05561 / 5.71 ( 265) hydrogen bonds : angle 5.32333 / 6.59 ( 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 113 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 746 ARG cc_start: 0.3408 (OUTLIER) cc_final: 0.3143 (tmt170) REVERT: D 802 PHE cc_start: 0.5874 (OUTLIER) cc_final: 0.5418 (m-80) REVERT: D 805 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7651 (mt) REVERT: D 943 HIS cc_start: 0.2132 (OUTLIER) cc_final: 0.1659 (m170) REVERT: D 1037 LEU cc_start: 0.6358 (mm) cc_final: 0.6107 (mm) REVERT: D 1038 CYS cc_start: 0.7526 (p) cc_final: 0.7124 (p) REVERT: D 1735 LEU cc_start: 0.5921 (OUTLIER) cc_final: 0.5486 (mm) REVERT: D 1756 LYS cc_start: 0.7534 (mttp) cc_final: 0.6989 (mmtt) outliers start: 27 outliers final: 20 residues processed: 107 average time/residue: 0.0893 time to fit residues: 12.3886 Evaluate side-chains 110 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 802 PHE Chi-restraints excluded: chain D residue 805 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 879 LEU Chi-restraints excluded: chain D residue 943 HIS 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 1362 LYS 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 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 32 optimal weight: 0.0970 chunk 50 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.0370 chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 943 HIS D1031 GLN ** D1755 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.174884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.159110 restraints weight = 19118.041| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 3.12 r_work: 0.4609 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7152 Z= 0.148 Angle : 0.717 12.895 9948 Z= 0.364 Chirality : 0.043 0.286 1151 Planarity : 0.007 0.059 1072 Dihedral : 18.161 111.475 1611 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 3.93 % Allowed : 28.62 % Favored : 67.45 % 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: -1.71 (0.31), residues: 701 helix: 0.12 (0.29), residues: 286 sheet: -2.49 (1.45), residues: 12 loop : -2.13 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1703 TYR 0.032 0.002 TYR D1692 PHE 0.016 0.001 PHE D1758 TRP 0.005 0.001 TRP D1831 HIS 0.013 0.001 HIS D1755 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 7152) covalent geometry : angle 0.71743 / 0.36 ( 9948) hydrogen bonds : bond 0.05507 / 5.66 ( 265) hydrogen bonds : angle 5.32392 / 6.56 ( 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 108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 746 ARG cc_start: 0.3371 (OUTLIER) cc_final: 0.2986 (tmt170) REVERT: D 802 PHE cc_start: 0.5870 (OUTLIER) cc_final: 0.5399 (m-80) REVERT: D 805 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7642 (mt) REVERT: D 943 HIS cc_start: 0.1957 (OUTLIER) cc_final: 0.1145 (m90) REVERT: D 1037 LEU cc_start: 0.6382 (mm) cc_final: 0.6127 (mm) REVERT: D 1049 ARG cc_start: 0.5296 (mmm160) cc_final: 0.4693 (mmp-170) REVERT: D 1735 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5469 (mm) REVERT: D 1756 LYS cc_start: 0.7507 (mttp) cc_final: 0.6873 (mmtt) outliers start: 25 outliers final: 19 residues processed: 101 average time/residue: 0.0828 time to fit residues: 10.9051 Evaluate side-chains 107 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 802 PHE Chi-restraints excluded: chain D residue 805 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 879 LEU Chi-restraints excluded: chain D residue 943 HIS 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 1802 ILE Chi-restraints excluded: chain D residue 1835 TYR Chi-restraints excluded: chain D residue 1838 MET Chi-restraints excluded: chain D residue 1842 ILE 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: 7.9990 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 0.7980 chunk 29 optimal weight: 0.3980 chunk 31 optimal weight: 0.6980 chunk 63 optimal weight: 0.0970 chunk 51 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 0.0970 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 943 HIS D1755 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.175144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.159422 restraints weight = 18898.504| |-----------------------------------------------------------------------------| r_work (start): 0.4741 rms_B_bonded: 3.14 r_work: 0.4620 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5703 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7152 Z= 0.146 Angle : 0.721 12.882 9948 Z= 0.364 Chirality : 0.042 0.207 1151 Planarity : 0.007 0.086 1072 Dihedral : 18.134 111.499 1611 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 4.09 % Allowed : 28.77 % Favored : 67.14 % 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: -1.71 (0.31), residues: 701 helix: 0.09 (0.29), residues: 286 sheet: -2.52 (1.46), residues: 12 loop : -2.11 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1703 TYR 0.024 0.002 TYR D 819 PHE 0.014 0.001 PHE D1758 TRP 0.005 0.001 TRP D1831 HIS 0.012 0.001 HIS D1755 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 7152) covalent geometry : angle 0.72070 / 0.36 ( 9948) hydrogen bonds : bond 0.05474 / 5.62 ( 265) hydrogen bonds : angle 5.27351 / 6.50 ( 730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1558.03 seconds wall clock time: 27 minutes 35.89 seconds (1655.89 seconds total)