Starting phenix.real_space_refine on Tue Aug 4 21:37:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21cn_67573/08_2026/21cn_67573.cif Found real_map, /net/cci-nas-00/data/ceres_data/21cn_67573/08_2026/21cn_67573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21cn_67573/08_2026/21cn_67573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21cn_67573/08_2026/21cn_67573.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21cn_67573/08_2026/21cn_67573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21cn_67573/08_2026/21cn_67573.map" } resolution = 3.21 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 49 5.49 5 S 29 5.16 5 C 4106 2.51 5 N 1138 2.21 5 O 1377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6701 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 5655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5655 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 48, 'TRANS': 652} Chain breaks: 4 Chain: "A" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 1044 Classifications: {'RNA': 49} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 22, 'rna3p_pyr': 22} Link IDs: {'rna2p': 4, 'rna3p': 44} Chain breaks: 1 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: 1.27, per 1000 atoms: 0.19 Number of scatterers: 6701 At special positions: 0 Unit cell: (60.958, 75.672, 132.426, 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 49 15.00 O 1377 8.00 N 1138 7.00 C 4106 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: 0.39 Conformation dependent library (CDL) restraints added in 210.1 milliseconds 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1344 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 47.4% alpha, 1.3% beta 18 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'D' and resid 754 through 758 removed outlier: 3.686A pdb=" N ARG D 758 " --> pdb=" O GLU D 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 856 Processing helix chain 'D' and resid 893 through 903 removed outlier: 3.520A pdb=" N MET D 897 " --> pdb=" O ASP D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 975 Processing helix chain 'D' and resid 1012 through 1028 removed outlier: 3.514A pdb=" N LYS D1019 " --> pdb=" O SER D1015 " (cutoff:3.500A) Processing helix chain 'D' and resid 1053 through 1074 Processing helix chain 'D' and resid 1293 through 1302 Processing helix chain 'D' and resid 1312 through 1335 removed outlier: 3.602A pdb=" N GLU D1316 " --> pdb=" O LEU D1312 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET D1317 " --> pdb=" O GLU D1313 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D1318 " --> pdb=" O ARG D1314 " (cutoff:3.500A) Processing helix chain 'D' and resid 1342 through 1354 removed outlier: 3.973A pdb=" N MET D1346 " --> pdb=" O ARG D1342 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N CYS D1354 " --> pdb=" O LYS D1350 " (cutoff:3.500A) Processing helix chain 'D' and resid 1354 through 1364 removed outlier: 3.930A pdb=" N LYS D1362 " --> pdb=" O ARG D1358 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS D1363 " --> pdb=" O LEU D1359 " (cutoff:3.500A) Processing helix chain 'D' and resid 1375 through 1380 removed outlier: 3.642A pdb=" N TRP D1380 " --> pdb=" O PRO D1376 " (cutoff:3.500A) Processing helix chain 'D' and resid 1555 through 1575 removed outlier: 3.781A pdb=" N GLY D1575 " --> pdb=" O LEU D1571 " (cutoff:3.500A) Processing helix chain 'D' and resid 1575 through 1587 Processing helix chain 'D' and resid 1661 through 1673 removed outlier: 3.933A pdb=" N ASN D1668 " --> pdb=" O SER D1664 " (cutoff:3.500A) Processing helix chain 'D' and resid 1683 through 1688 Processing helix chain 'D' and resid 1701 through 1722 Processing helix chain 'D' and resid 1723 through 1727 Processing helix chain 'D' and resid 1728 through 1741 Processing helix chain 'D' and resid 1741 through 1751 Processing helix chain 'D' and resid 1762 through 1776 removed outlier: 4.065A pdb=" N PHE D1766 " --> pdb=" O SER D1762 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN D1774 " --> pdb=" O ASP D1770 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE D1775 " --> pdb=" O ASP D1771 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN D1776 " --> pdb=" O PHE D1772 " (cutoff:3.500A) Processing helix chain 'D' and resid 1805 through 1823 Processing helix chain 'D' and resid 1826 through 1845 removed outlier: 3.552A pdb=" N VAL D1830 " --> pdb=" O SER D1826 " (cutoff:3.500A) Proline residue: D1836 - end of helix Proline residue: D1840 - end of helix Processing helix chain 'D' and resid 1851 through 1860 removed outlier: 3.660A pdb=" N ARG D1855 " --> pdb=" O ARG D1851 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N LEU D1858 " --> pdb=" O VAL D1854 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET D1860 " --> pdb=" O GLU D1856 " (cutoff:3.500A) Processing helix chain 'D' and resid 1896 through 1912 Processing sheet with id=AA1, first strand: chain 'D' and resid 802 through 805 removed outlier: 4.148A pdb=" N CYS D 877 " --> pdb=" O LEU D 805 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 947 through 949 removed outlier: 6.747A pdb=" N LEU D 988 " --> pdb=" O ALA D 948 " (cutoff:3.500A) 215 hydrogen bonds defined for protein. 636 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 0.83 Time building geometry restraints manager: 0.50 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: 1772 1.34 - 1.45: 1495 1.45 - 1.57: 3556 1.57 - 1.69: 96 1.69 - 1.81: 42 Bond restraints: 6961 Sorted by residual: bond pdb=" N ILE D 810 " pdb=" CA ILE D 810 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.30e-03 1.88e+04 2.06e+01 bond pdb=" P G A 1 " pdb=" O5' G A 1 " ideal model delta sigma weight residual 1.593 1.630 -0.037 1.00e-02 1.00e+04 1.40e+01 bond pdb=" N ILE D 932 " pdb=" CA ILE D 932 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.23e-02 6.61e+03 1.18e+01 bond pdb=" N ILE D 813 " pdb=" CA ILE D 813 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.23e-02 6.61e+03 8.46e+00 bond pdb=" N TYR D 936 " pdb=" CA TYR D 936 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.20e-02 6.94e+03 8.02e+00 ... (remaining 6956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 9243 2.20 - 4.39: 332 4.39 - 6.59: 76 6.59 - 8.78: 15 8.78 - 10.98: 3 Bond angle restraints: 9669 Sorted by residual: angle pdb=" C4' G A 23 " pdb=" O4' G A 23 " pdb=" C1' G A 23 " ideal model delta sigma weight residual 109.70 105.31 4.39 7.00e-01 2.04e+00 3.93e+01 angle pdb=" C4' G A 1 " pdb=" O4' G A 1 " pdb=" C1' G A 1 " ideal model delta sigma weight residual 109.70 105.31 4.39 7.00e-01 2.04e+00 3.93e+01 angle pdb=" C3' G A 1 " pdb=" C2' G A 1 " pdb=" C1' G A 1 " ideal model delta sigma weight residual 101.50 96.99 4.51 8.00e-01 1.56e+00 3.18e+01 angle pdb=" C3' U A 22 " pdb=" C2' U A 22 " pdb=" C1' U A 22 " ideal model delta sigma weight residual 101.30 104.98 -3.68 7.00e-01 2.04e+00 2.77e+01 angle pdb=" C3' G A 1 " pdb=" O3' G A 1 " pdb=" P C A 2 " ideal model delta sigma weight residual 119.70 125.80 -6.10 1.20e+00 6.94e-01 2.58e+01 ... (remaining 9664 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.14: 3880 29.14 - 58.29: 326 58.29 - 87.43: 76 87.43 - 116.57: 7 116.57 - 145.72: 1 Dihedral angle restraints: 4290 sinusoidal: 2211 harmonic: 2079 Sorted by residual: dihedral pdb=" O4' U A 22 " pdb=" C2' U A 22 " pdb=" C1' U A 22 " pdb=" C3' U A 22 " ideal model delta sinusoidal sigma weight residual 25.00 -26.10 51.10 1 8.00e+00 1.56e-02 5.58e+01 dihedral pdb=" C4' U A 22 " pdb=" C3' U A 22 " pdb=" C2' U A 22 " pdb=" C1' U A 22 " ideal model delta sinusoidal sigma weight residual 36.00 -13.27 49.27 1 8.00e+00 1.56e-02 5.21e+01 dihedral pdb=" C5' G A 23 " pdb=" C4' G A 23 " pdb=" C3' G A 23 " pdb=" O3' G A 23 " ideal model delta sinusoidal sigma weight residual 147.00 97.95 49.05 1 8.00e+00 1.56e-02 5.17e+01 ... (remaining 4287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1066 0.123 - 0.246: 26 0.246 - 0.369: 0 0.369 - 0.492: 8 0.492 - 0.615: 14 Chirality restraints: 1114 Sorted by residual: chirality pdb=" P G A 1 " pdb=" OP1 G A 1 " pdb=" OP2 G A 1 " pdb=" O5' G A 1 " both_signs ideal model delta sigma weight residual True 2.41 -3.03 -0.62 2.00e-01 2.50e+01 9.46e+00 chirality pdb=" P A A 37 " pdb=" OP1 A A 37 " pdb=" OP2 A A 37 " pdb=" O5' A A 37 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.53e+00 chirality pdb=" P U A 52 " pdb=" OP1 U A 52 " pdb=" OP2 U A 52 " pdb=" O5' U A 52 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.50e+00 ... (remaining 1111 not shown) Planarity restraints: 1053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN D 985 " -0.041 5.00e-02 4.00e+02 6.18e-02 6.10e+00 pdb=" N PRO D 986 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO D 986 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 986 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 781 " -0.033 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO D 782 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 782 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 782 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 971 " 0.018 2.00e-02 2.50e+03 1.43e-02 4.09e+00 pdb=" CG TYR D 971 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TYR D 971 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR D 971 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 971 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 971 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 971 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 971 " 0.003 2.00e-02 2.50e+03 ... (remaining 1050 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 10 2.24 - 2.90: 2716 2.90 - 3.57: 10993 3.57 - 4.23: 17418 4.23 - 4.90: 28192 Nonbonded interactions: 59329 Sorted by model distance: nonbonded pdb=" OE1 GLU D1316 " pdb="CA CA D2001 " model vdw 1.572 2.510 nonbonded pdb=" C5' U A 22 " pdb="CA CA D2002 " model vdw 2.003 2.910 nonbonded pdb=" O CYS D1063 " pdb=" OG1 THR D1066 " model vdw 2.097 3.040 nonbonded pdb=" OD1 ASN D1305 " pdb=" OG SER D1372 " model vdw 2.137 3.040 nonbonded pdb=" OG SER D1823 " pdb=" OG SER D1826 " model vdw 2.203 3.040 ... (remaining 59324 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.430 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.810 Find NCS groups from input model: 0.010 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5497 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 0.055 6961 Z= 0.361 Angle : 1.017 10.977 9669 Z= 0.605 Chirality : 0.086 0.615 1114 Planarity : 0.006 0.062 1053 Dihedral : 21.069 145.716 2946 Min Nonbonded Distance : 1.572 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.12 % Allowed : 22.65 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.31), residues: 691 helix: 0.41 (0.30), residues: 300 sheet: -3.78 (0.68), residues: 34 loop : -2.78 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 944 TYR 0.035 0.002 TYR D 971 PHE 0.015 0.002 PHE D 867 TRP 0.007 0.002 TRP D1024 HIS 0.008 0.002 HIS D1041 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.36 ( 6961) covalent geometry : angle 1.01740 / 0.61 ( 9669) hydrogen bonds : bond 0.16332 / 9.11 ( 258) hydrogen bonds : angle 7.01963 / 5.16 ( 710) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 934 PRO cc_start: 0.6791 (Cg_exo) cc_final: 0.6408 (Cg_endo) REVERT: D 957 LEU cc_start: 0.4827 (tt) cc_final: 0.4534 (tt) REVERT: D 1019 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7851 (mmmt) REVERT: D 1832 GLN cc_start: 0.5926 (tp-100) cc_final: 0.5716 (pt0) outliers start: 7 outliers final: 5 residues processed: 90 average time/residue: 0.0770 time to fit residues: 9.2545 Evaluate side-chains 78 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 820 THR Chi-restraints excluded: chain D residue 944 ARG Chi-restraints excluded: chain D residue 1024 TRP Chi-restraints excluded: chain D residue 1316 GLU Chi-restraints excluded: chain D residue 1852 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.0020 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 812 GLN ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1305 ASN ** D1549 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 = 0.4990 r_free = 0.4990 target = 0.176568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4828 r_free = 0.4828 target = 0.164325 restraints weight = 17581.320| |-----------------------------------------------------------------------------| r_work (start): 0.4807 rms_B_bonded: 2.73 r_work: 0.4706 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6961 Z= 0.173 Angle : 0.755 9.143 9669 Z= 0.400 Chirality : 0.048 0.403 1114 Planarity : 0.006 0.050 1053 Dihedral : 20.718 148.739 1543 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.03 % Allowed : 21.37 % Favored : 75.60 % 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: -1.89 (0.31), residues: 691 helix: 0.41 (0.30), residues: 303 sheet: -3.68 (0.70), residues: 34 loop : -2.62 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 935 TYR 0.030 0.002 TYR D1330 PHE 0.016 0.002 PHE D1374 TRP 0.004 0.001 TRP D1048 HIS 0.010 0.002 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 6961) covalent geometry : angle 0.75488 / 0.40 ( 9669) hydrogen bonds : bond 0.06806 / 4.21 ( 258) hydrogen bonds : angle 5.05728 / 3.54 ( 710) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 934 PRO cc_start: 0.6827 (Cg_exo) cc_final: 0.6574 (Cg_endo) REVERT: D 949 ASP cc_start: 0.7175 (t0) cc_final: 0.6945 (t70) REVERT: D 1019 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7762 (mmmt) REVERT: D 1808 MET cc_start: 0.4688 (mmp) cc_final: 0.4396 (mmp) outliers start: 19 outliers final: 5 residues processed: 91 average time/residue: 0.0671 time to fit residues: 8.3507 Evaluate side-chains 75 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1332 PHE Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1871 GLU Chi-restraints excluded: chain D residue 1909 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 5 optimal weight: 0.0040 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1549 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 = 0.4965 r_free = 0.4965 target = 0.174064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.159941 restraints weight = 18185.582| |-----------------------------------------------------------------------------| r_work (start): 0.4779 rms_B_bonded: 3.01 r_work: 0.4679 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6961 Z= 0.188 Angle : 0.749 12.149 9669 Z= 0.390 Chirality : 0.048 0.389 1114 Planarity : 0.005 0.050 1053 Dihedral : 20.418 152.691 1532 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.87 % Allowed : 22.33 % Favored : 74.80 % 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: -1.78 (0.31), residues: 691 helix: 0.53 (0.30), residues: 298 sheet: -3.09 (0.87), residues: 28 loop : -2.63 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 790 TYR 0.028 0.002 TYR D1330 PHE 0.015 0.002 PHE D1687 TRP 0.010 0.002 TRP D1024 HIS 0.009 0.002 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 6961) covalent geometry : angle 0.74892 / 0.39 ( 9669) hydrogen bonds : bond 0.06736 / 4.21 ( 258) hydrogen bonds : angle 5.01695 / 3.51 ( 710) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1036 GLU cc_start: 0.1906 (OUTLIER) cc_final: -0.0186 (mm-30) REVERT: D 1320 ASP cc_start: 0.6521 (t0) cc_final: 0.6268 (t0) outliers start: 18 outliers final: 10 residues processed: 90 average time/residue: 0.0684 time to fit residues: 8.3703 Evaluate side-chains 82 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 899 ASP Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1332 PHE Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1563 VAL Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1573 SER Chi-restraints excluded: chain D residue 1712 LEU Chi-restraints excluded: chain D residue 1871 GLU Chi-restraints excluded: chain D residue 1909 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1549 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 = 0.4960 r_free = 0.4960 target = 0.173894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.159716 restraints weight = 18178.375| |-----------------------------------------------------------------------------| r_work (start): 0.4754 rms_B_bonded: 2.99 r_work: 0.4652 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5586 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6961 Z= 0.178 Angle : 0.742 12.177 9669 Z= 0.384 Chirality : 0.049 0.331 1114 Planarity : 0.006 0.054 1053 Dihedral : 20.320 152.024 1532 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.67 % Allowed : 23.60 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.31), residues: 691 helix: 0.47 (0.30), residues: 293 sheet: -3.25 (1.11), residues: 18 loop : -2.57 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D1020 TYR 0.048 0.002 TYR D1330 PHE 0.024 0.002 PHE D1374 TRP 0.012 0.002 TRP D1024 HIS 0.007 0.002 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 ( 6961) covalent geometry : angle 0.74179 / 0.38 ( 9669) hydrogen bonds : bond 0.06082 / 3.80 ( 258) hydrogen bonds : angle 4.89382 / 3.42 ( 710) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1020 ARG cc_start: 0.6326 (tmm160) cc_final: 0.5881 (tmm160) REVERT: D 1036 GLU cc_start: 0.1901 (OUTLIER) cc_final: -0.0110 (mm-30) REVERT: D 1320 ASP cc_start: 0.6479 (t0) cc_final: 0.6179 (t0) REVERT: D 1758 PHE cc_start: 0.2875 (OUTLIER) cc_final: 0.2308 (p90) outliers start: 23 outliers final: 15 residues processed: 94 average time/residue: 0.0711 time to fit residues: 9.1020 Evaluate side-chains 85 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 899 ASP Chi-restraints excluded: chain D residue 959 LYS Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1036 GLU Chi-restraints excluded: chain D residue 1332 PHE Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1563 VAL Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1573 SER Chi-restraints excluded: chain D residue 1712 LEU Chi-restraints excluded: chain D residue 1758 PHE Chi-restraints excluded: chain D residue 1871 GLU Chi-restraints excluded: chain D residue 1873 THR Chi-restraints excluded: chain D residue 1909 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 21 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 9 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1549 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 = 0.4955 r_free = 0.4955 target = 0.173862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.161073 restraints weight = 17538.908| |-----------------------------------------------------------------------------| r_work (start): 0.4782 rms_B_bonded: 2.78 r_work: 0.4679 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5605 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6961 Z= 0.171 Angle : 0.735 11.454 9669 Z= 0.380 Chirality : 0.047 0.275 1114 Planarity : 0.006 0.047 1053 Dihedral : 20.240 149.947 1532 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.99 % Allowed : 24.08 % Favored : 71.93 % 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: -1.75 (0.31), residues: 691 helix: 0.48 (0.31), residues: 292 sheet: -3.18 (1.09), residues: 18 loop : -2.53 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1049 TYR 0.045 0.003 TYR D 936 PHE 0.016 0.002 PHE D1374 TRP 0.009 0.002 TRP D1024 HIS 0.007 0.002 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 6961) covalent geometry : angle 0.73512 / 0.38 ( 9669) hydrogen bonds : bond 0.05933 / 3.72 ( 258) hydrogen bonds : angle 4.84708 / 3.39 ( 710) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 959 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7255 (ptpp) REVERT: D 1320 ASP cc_start: 0.6649 (t0) cc_final: 0.6288 (t0) REVERT: D 1758 PHE cc_start: 0.3177 (OUTLIER) cc_final: 0.2498 (p90) outliers start: 25 outliers final: 17 residues processed: 95 average time/residue: 0.0892 time to fit residues: 10.9904 Evaluate side-chains 90 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 827 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 899 ASP Chi-restraints excluded: chain D residue 959 LYS Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 1003 ARG Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1332 PHE Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1563 VAL Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1573 SER Chi-restraints excluded: chain D residue 1712 LEU Chi-restraints excluded: chain D residue 1758 PHE Chi-restraints excluded: chain D residue 1835 TYR Chi-restraints excluded: chain D residue 1873 THR Chi-restraints excluded: chain D residue 1909 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1832 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 = 0.172426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.159521 restraints weight = 17617.026| |-----------------------------------------------------------------------------| r_work (start): 0.4754 rms_B_bonded: 2.77 r_work: 0.4653 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5672 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6961 Z= 0.200 Angle : 0.770 14.346 9669 Z= 0.395 Chirality : 0.047 0.254 1114 Planarity : 0.006 0.048 1053 Dihedral : 20.269 151.193 1532 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 3.67 % Allowed : 24.08 % Favored : 72.25 % 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: -1.76 (0.31), residues: 691 helix: 0.49 (0.30), residues: 292 sheet: -3.30 (1.08), residues: 18 loop : -2.54 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 821 TYR 0.046 0.003 TYR D1330 PHE 0.030 0.002 PHE D1374 TRP 0.010 0.002 TRP D1024 HIS 0.010 0.002 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 ( 6961) covalent geometry : angle 0.77023 / 0.40 ( 9669) hydrogen bonds : bond 0.06026 / 3.78 ( 258) hydrogen bonds : angle 4.91635 / 3.45 ( 710) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.4970 (mpp) cc_final: 0.3656 (ptp) REVERT: D 959 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7280 (ptpp) REVERT: D 1320 ASP cc_start: 0.6792 (t0) cc_final: 0.6429 (t0) REVERT: D 1345 TYR cc_start: 0.5585 (OUTLIER) cc_final: 0.5291 (t80) REVERT: D 1758 PHE cc_start: 0.3196 (OUTLIER) cc_final: 0.2492 (p90) outliers start: 23 outliers final: 15 residues processed: 89 average time/residue: 0.0842 time to fit residues: 9.7508 Evaluate side-chains 88 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 853 ILE Chi-restraints excluded: chain D residue 899 ASP Chi-restraints excluded: chain D residue 959 LYS Chi-restraints excluded: chain D residue 1003 ARG Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1332 PHE Chi-restraints excluded: chain D residue 1345 TYR Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1563 VAL Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1712 LEU Chi-restraints excluded: chain D residue 1758 PHE Chi-restraints excluded: chain D residue 1835 TYR Chi-restraints excluded: chain D residue 1873 THR Chi-restraints excluded: chain D residue 1909 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 4 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 19 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 0.0070 chunk 15 optimal weight: 1.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1028 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1549 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 = 0.4979 r_free = 0.4979 target = 0.173871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.160434 restraints weight = 18329.686| |-----------------------------------------------------------------------------| r_work (start): 0.4793 rms_B_bonded: 2.88 r_work: 0.4689 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5573 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 6961 Z= 0.160 Angle : 0.782 17.556 9669 Z= 0.393 Chirality : 0.045 0.298 1114 Planarity : 0.006 0.067 1053 Dihedral : 20.160 145.487 1532 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 20.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.67 % Allowed : 25.20 % Favored : 71.13 % 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: -1.58 (0.32), residues: 691 helix: 0.71 (0.31), residues: 286 sheet: -3.16 (1.10), residues: 18 loop : -2.47 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D1020 TYR 0.047 0.003 TYR D 976 PHE 0.032 0.002 PHE D1374 TRP 0.014 0.002 TRP D1048 HIS 0.013 0.002 HIS D1719 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 ( 6961) covalent geometry : angle 0.78176 / 0.39 ( 9669) hydrogen bonds : bond 0.05448 / 3.40 ( 258) hydrogen bonds : angle 4.79508 / 3.38 ( 710) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.4704 (mpp) cc_final: 0.3417 (ptp) REVERT: D 959 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7323 (ptpp) REVERT: D 1320 ASP cc_start: 0.6506 (t0) cc_final: 0.6180 (t0) REVERT: D 1346 MET cc_start: 0.7542 (tpp) cc_final: 0.6893 (tpt) REVERT: D 1860 MET cc_start: 0.4934 (OUTLIER) cc_final: 0.4172 (ptp) outliers start: 23 outliers final: 16 residues processed: 87 average time/residue: 0.0734 time to fit residues: 8.6428 Evaluate side-chains 88 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 70 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 899 ASP Chi-restraints excluded: chain D residue 909 ILE Chi-restraints excluded: chain D residue 959 LYS Chi-restraints excluded: chain D residue 968 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1047 LEU Chi-restraints excluded: chain D residue 1332 PHE Chi-restraints excluded: chain D residue 1345 TYR Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1712 LEU Chi-restraints excluded: chain D residue 1835 TYR Chi-restraints excluded: chain D residue 1860 MET Chi-restraints excluded: chain D residue 1873 THR Chi-restraints excluded: chain D residue 1897 TYR Chi-restraints excluded: chain D residue 1909 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 63 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 14 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 998 ASN D1028 GLN ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1549 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 = 0.4974 r_free = 0.4974 target = 0.174290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.161720 restraints weight = 17945.806| |-----------------------------------------------------------------------------| r_work (start): 0.4773 rms_B_bonded: 2.80 r_work: 0.4661 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5600 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6961 Z= 0.163 Angle : 0.765 14.687 9669 Z= 0.386 Chirality : 0.046 0.346 1114 Planarity : 0.006 0.047 1053 Dihedral : 20.129 144.468 1532 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.67 % Allowed : 25.36 % Favored : 70.97 % 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 (0.31), residues: 691 helix: 0.68 (0.31), residues: 288 sheet: -3.20 (1.07), residues: 18 loop : -2.49 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1003 TYR 0.031 0.003 TYR D1330 PHE 0.024 0.002 PHE D1374 TRP 0.008 0.001 TRP D1024 HIS 0.010 0.002 HIS D1719 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 6961) covalent geometry : angle 0.76454 / 0.39 ( 9669) hydrogen bonds : bond 0.05442 / 3.40 ( 258) hydrogen bonds : angle 4.79852 / 3.37 ( 710) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.4799 (mpp) cc_final: 0.3469 (ptp) REVERT: D 792 LEU cc_start: 0.6010 (OUTLIER) cc_final: 0.5795 (mt) REVERT: D 959 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7362 (ptpp) REVERT: D 968 PHE cc_start: 0.5152 (OUTLIER) cc_final: 0.4764 (p90) REVERT: D 1320 ASP cc_start: 0.6717 (t0) cc_final: 0.6379 (t0) outliers start: 23 outliers final: 16 residues processed: 86 average time/residue: 0.0686 time to fit residues: 7.9703 Evaluate side-chains 90 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 899 ASP Chi-restraints excluded: chain D residue 959 LYS Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 968 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1047 LEU Chi-restraints excluded: chain D residue 1332 PHE Chi-restraints excluded: chain D residue 1345 TYR Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1563 VAL Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1573 SER Chi-restraints excluded: chain D residue 1835 TYR Chi-restraints excluded: chain D residue 1873 THR Chi-restraints excluded: chain D residue 1909 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.2980 chunk 55 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 33 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1549 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 = 0.4985 r_free = 0.4985 target = 0.174458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.161081 restraints weight = 18562.365| |-----------------------------------------------------------------------------| r_work (start): 0.4786 rms_B_bonded: 2.90 r_work: 0.4689 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5536 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 6961 Z= 0.157 Angle : 0.772 18.018 9669 Z= 0.386 Chirality : 0.043 0.205 1114 Planarity : 0.006 0.049 1053 Dihedral : 20.110 142.319 1532 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.87 % Allowed : 26.16 % Favored : 70.97 % 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: -1.47 (0.32), residues: 691 helix: 0.79 (0.32), residues: 287 sheet: None (None), residues: 0 loop : -2.48 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 821 TYR 0.029 0.002 TYR D1330 PHE 0.017 0.002 PHE D1374 TRP 0.008 0.002 TRP D1024 HIS 0.010 0.002 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 ( 6961) covalent geometry : angle 0.77204 / 0.39 ( 9669) hydrogen bonds : bond 0.05204 / 3.26 ( 258) hydrogen bonds : angle 4.69827 / 3.29 ( 710) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.4869 (mpp) cc_final: 0.3198 (ptp) REVERT: D 792 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5516 (mt) REVERT: D 927 TYR cc_start: 0.3411 (m-10) cc_final: 0.3198 (m-10) REVERT: D 959 LYS cc_start: 0.7578 (OUTLIER) cc_final: 0.7330 (ptpp) REVERT: D 1320 ASP cc_start: 0.6670 (t0) cc_final: 0.6349 (t0) REVERT: D 1838 MET cc_start: 0.5744 (mtp) cc_final: 0.5342 (mtt) outliers start: 18 outliers final: 13 residues processed: 82 average time/residue: 0.0702 time to fit residues: 7.6575 Evaluate side-chains 82 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 792 LEU Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 899 ASP Chi-restraints excluded: chain D residue 959 LYS Chi-restraints excluded: chain D residue 968 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1332 PHE Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1563 VAL Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1835 TYR Chi-restraints excluded: chain D residue 1873 THR Chi-restraints excluded: chain D residue 1909 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 64 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1073 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 = 0.4958 r_free = 0.4958 target = 0.172466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.158500 restraints weight = 18291.414| |-----------------------------------------------------------------------------| r_work (start): 0.4750 rms_B_bonded: 2.92 r_work: 0.4650 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5638 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6961 Z= 0.180 Angle : 0.811 15.149 9669 Z= 0.403 Chirality : 0.046 0.283 1114 Planarity : 0.006 0.048 1053 Dihedral : 20.151 142.567 1532 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.71 % Allowed : 26.00 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.58 (0.32), residues: 691 helix: 0.63 (0.31), residues: 287 sheet: -3.23 (1.06), residues: 18 loop : -2.39 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1003 TYR 0.031 0.003 TYR D1330 PHE 0.024 0.002 PHE D1374 TRP 0.011 0.002 TRP D1024 HIS 0.015 0.002 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.18 ( 6961) covalent geometry : angle 0.81140 / 0.40 ( 9669) hydrogen bonds : bond 0.05509 / 3.47 ( 258) hydrogen bonds : angle 4.79716 / 3.35 ( 710) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.4747 (mpp) cc_final: 0.3433 (ptp) REVERT: D 959 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7410 (ptpp) REVERT: D 1320 ASP cc_start: 0.6835 (t0) cc_final: 0.6520 (t0) outliers start: 17 outliers final: 14 residues processed: 82 average time/residue: 0.0775 time to fit residues: 8.3629 Evaluate side-chains 87 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 818 VAL Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 899 ASP Chi-restraints excluded: chain D residue 959 LYS Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 968 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1345 TYR Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1563 VAL Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1835 TYR Chi-restraints excluded: chain D residue 1873 THR Chi-restraints excluded: chain D residue 1909 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 8 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 30 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 24 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 998 ASN ** D1073 GLN ** 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 = 0.4966 r_free = 0.4966 target = 0.173528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.161136 restraints weight = 17849.408| |-----------------------------------------------------------------------------| r_work (start): 0.4766 rms_B_bonded: 2.70 r_work: 0.4661 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5562 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6961 Z= 0.157 Angle : 0.797 14.108 9669 Z= 0.394 Chirality : 0.047 0.310 1114 Planarity : 0.006 0.049 1053 Dihedral : 20.153 140.651 1532 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.71 % Allowed : 26.00 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.51 (0.32), residues: 691 helix: 0.71 (0.31), residues: 287 sheet: -3.19 (1.07), residues: 18 loop : -2.38 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 790 TYR 0.034 0.002 TYR D 876 PHE 0.019 0.002 PHE D1374 TRP 0.009 0.001 TRP D1024 HIS 0.014 0.002 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 6961) covalent geometry : angle 0.79713 / 0.39 ( 9669) hydrogen bonds : bond 0.05244 / 3.28 ( 258) hydrogen bonds : angle 4.78223 / 3.35 ( 710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1499.87 seconds wall clock time: 26 minutes 32.36 seconds (1592.36 seconds total)