Starting phenix.real_space_refine on Sun Apr 5 01:22:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21cn_67573/04_2026/21cn_67573.cif Found real_map, /net/cci-nas-00/data/ceres_data/21cn_67573/04_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/21cn_67573/04_2026/21cn_67573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21cn_67573/04_2026/21cn_67573.map" model { file = "/net/cci-nas-00/data/ceres_data/21cn_67573/04_2026/21cn_67573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21cn_67573/04_2026/21cn_67573.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/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: 1.61, per 1000 atoms: 0.24 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: 0.64 Conformation dependent library (CDL) restraints added in 197.1 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: 0.91 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: 1.14 Time building geometry restraints manager: 0.81 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=" 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 bond pdb=" N ILE D 933 " pdb=" CA ILE D 933 " ideal model delta sigma weight residual 1.461 1.496 -0.034 1.23e-02 6.61e+03 7.80e+00 ... (remaining 6956 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 9233 2.20 - 4.39: 345 4.39 - 6.59: 73 6.59 - 8.78: 15 8.78 - 10.98: 3 Bond angle restraints: 9669 Sorted by residual: angle pdb=" C4' G A 1 " pdb=" C3' G A 1 " pdb=" O3' G A 1 " ideal model delta sigma weight residual 109.40 102.19 7.21 1.50e+00 4.44e-01 2.31e+01 angle pdb=" O3' C A 21 " pdb=" C3' C A 21 " pdb=" C2' C A 21 " ideal model delta sigma weight residual 113.70 106.76 6.94 1.50e+00 4.44e-01 2.14e+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 1.00e+00 1.00e+00 2.03e+01 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 1.00e+00 1.00e+00 1.93e+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 1.00e+00 1.00e+00 1.93e+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: 1056 0.123 - 0.246: 36 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.450 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5397 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= 0.327 Angle : 1.011 10.977 9669 Z= 0.544 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 covalent geometry : bond 0.00612 ( 6961) covalent geometry : angle 1.01130 ( 9669) hydrogen bonds : bond 0.16332 ( 258) hydrogen bonds : angle 7.01963 ( 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 : 0.166 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: 0.1007 time to fit residues: 11.8194 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 : 0.158 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: D 812 GLN ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1305 ASN D1549 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5004 r_free = 0.5004 target = 0.177664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.165493 restraints weight = 17990.012| |-----------------------------------------------------------------------------| r_work (start): 0.4838 rms_B_bonded: 2.77 r_work: 0.4739 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5352 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6961 Z= 0.156 Angle : 0.737 8.085 9669 Z= 0.370 Chirality : 0.045 0.330 1114 Planarity : 0.005 0.049 1053 Dihedral : 20.644 145.555 1543 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.51 % Allowed : 20.10 % Favored : 76.40 % 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: -1.70 (0.31), residues: 691 helix: 0.58 (0.30), residues: 303 sheet: -3.62 (0.70), residues: 34 loop : -2.53 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 937 TYR 0.031 0.002 TYR D1330 PHE 0.019 0.002 PHE D1374 TRP 0.004 0.001 TRP D1380 HIS 0.007 0.001 HIS D 992 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6961) covalent geometry : angle 0.73716 ( 9669) hydrogen bonds : bond 0.05974 ( 258) hydrogen bonds : angle 4.67599 ( 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 99 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 934 PRO cc_start: 0.6805 (Cg_exo) cc_final: 0.6505 (Cg_endo) REVERT: D 949 ASP cc_start: 0.7280 (t0) cc_final: 0.7039 (t70) REVERT: D 1019 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7694 (mmmt) REVERT: D 1020 ARG cc_start: 0.6331 (tmm160) cc_final: 0.6130 (tmm160) REVERT: D 1320 ASP cc_start: 0.6513 (t0) cc_final: 0.6286 (t0) REVERT: D 1373 ILE cc_start: 0.6435 (tp) cc_final: 0.6156 (tp) outliers start: 22 outliers final: 5 residues processed: 92 average time/residue: 0.0739 time to fit residues: 9.1639 Evaluate side-chains 77 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 1854 VAL 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: 2.9990 chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.0010 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4970 r_free = 0.4970 target = 0.174859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.162323 restraints weight = 17579.045| |-----------------------------------------------------------------------------| r_work (start): 0.4769 rms_B_bonded: 2.74 r_work: 0.4663 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.4663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5476 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6961 Z= 0.165 Angle : 0.757 12.049 9669 Z= 0.368 Chirality : 0.045 0.296 1114 Planarity : 0.005 0.045 1053 Dihedral : 20.357 146.948 1532 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.67 % Allowed : 21.69 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.31), residues: 691 helix: 0.65 (0.31), residues: 298 sheet: -3.18 (0.86), residues: 28 loop : -2.49 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1895 TYR 0.025 0.002 TYR D1330 PHE 0.014 0.002 PHE D 896 TRP 0.009 0.002 TRP D1024 HIS 0.009 0.002 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6961) covalent geometry : angle 0.75712 ( 9669) hydrogen bonds : bond 0.05342 ( 258) hydrogen bonds : angle 4.69234 ( 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 105 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 959 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7162 (ptpp) REVERT: D 1320 ASP cc_start: 0.6728 (t0) cc_final: 0.6445 (t0) REVERT: D 1345 TYR cc_start: 0.5337 (m-80) cc_final: 0.4872 (m-80) REVERT: D 1889 LYS cc_start: 0.8149 (tppt) cc_final: 0.7927 (tppt) outliers start: 23 outliers final: 11 residues processed: 99 average time/residue: 0.0884 time to fit residues: 11.7043 Evaluate side-chains 87 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 825 VAL 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 1332 PHE 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 1873 THR 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: 0.9980 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 43 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4953 r_free = 0.4953 target = 0.172889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.158590 restraints weight = 18322.139| |-----------------------------------------------------------------------------| r_work (start): 0.4741 rms_B_bonded: 3.04 r_work: 0.4639 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.4639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5534 moved from start: 0.2757 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= 0.169 Angle : 0.746 12.039 9669 Z= 0.367 Chirality : 0.044 0.258 1114 Planarity : 0.006 0.056 1053 Dihedral : 20.311 144.751 1532 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 20.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.67 % Allowed : 23.92 % Favored : 72.41 % 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: -1.56 (0.31), residues: 691 helix: 0.66 (0.31), residues: 297 sheet: None (None), residues: 0 loop : -2.55 (0.28), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1895 TYR 0.043 0.003 TYR D 936 PHE 0.026 0.002 PHE D 896 TRP 0.008 0.002 TRP D1024 HIS 0.008 0.002 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 6961) covalent geometry : angle 0.74616 ( 9669) hydrogen bonds : bond 0.05249 ( 258) hydrogen bonds : angle 4.74649 ( 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 103 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: D 959 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7267 (ptpp) REVERT: D 1320 ASP cc_start: 0.6753 (t0) cc_final: 0.6458 (t0) REVERT: D 1838 MET cc_start: 0.6095 (mtp) cc_final: 0.5872 (mtp) outliers start: 23 outliers final: 13 residues processed: 96 average time/residue: 0.0978 time to fit residues: 12.3144 Evaluate side-chains 88 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 959 LYS 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 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 1854 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4931 r_free = 0.4931 target = 0.170395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4756 r_free = 0.4756 target = 0.157118 restraints weight = 17810.645| |-----------------------------------------------------------------------------| r_work (start): 0.4752 rms_B_bonded: 2.71 r_work: 0.4651 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.3200 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= 0.172 Angle : 0.773 13.536 9669 Z= 0.375 Chirality : 0.045 0.243 1114 Planarity : 0.006 0.053 1053 Dihedral : 20.281 144.761 1532 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.99 % Allowed : 23.92 % Favored : 72.09 % 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: -1.49 (0.31), residues: 691 helix: 0.66 (0.31), residues: 297 sheet: None (None), residues: 0 loop : -2.46 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1020 TYR 0.023 0.002 TYR D 876 PHE 0.032 0.002 PHE D1374 TRP 0.009 0.001 TRP D1024 HIS 0.011 0.002 HIS D1719 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6961) covalent geometry : angle 0.77299 ( 9669) hydrogen bonds : bond 0.05251 ( 258) hydrogen bonds : angle 4.76671 ( 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 106 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: D 959 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7428 (ptpp) REVERT: D 1320 ASP cc_start: 0.6903 (t0) cc_final: 0.6596 (t0) REVERT: D 1350 LYS cc_start: 0.7802 (tmmt) cc_final: 0.7584 (ttmm) REVERT: D 1675 TYR cc_start: 0.6148 (OUTLIER) cc_final: 0.4352 (p90) REVERT: D 1889 LYS cc_start: 0.8012 (tppt) cc_final: 0.7765 (tppt) outliers start: 25 outliers final: 15 residues processed: 94 average time/residue: 0.0999 time to fit residues: 12.2311 Evaluate side-chains 92 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 959 LYS Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1047 LEU Chi-restraints excluded: chain D residue 1345 TYR Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1373 ILE Chi-restraints excluded: chain D residue 1563 VAL Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1675 TYR Chi-restraints excluded: chain D residue 1712 LEU Chi-restraints excluded: chain D residue 1835 TYR Chi-restraints excluded: chain D residue 1854 VAL Chi-restraints excluded: chain D residue 1897 TYR 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: 0.5980 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1028 GLN ** 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 = 0.4934 r_free = 0.4934 target = 0.171636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.158465 restraints weight = 17917.631| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 2.79 r_work: 0.4617 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6961 Z= 0.170 Angle : 0.769 12.268 9669 Z= 0.374 Chirality : 0.044 0.232 1114 Planarity : 0.006 0.051 1053 Dihedral : 20.259 143.272 1532 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 4.15 % Allowed : 23.29 % Favored : 72.57 % 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: -1.43 (0.32), residues: 691 helix: 0.71 (0.31), residues: 297 sheet: None (None), residues: 0 loop : -2.43 (0.29), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1003 TYR 0.025 0.002 TYR D 876 PHE 0.028 0.002 PHE D1374 TRP 0.009 0.001 TRP D1024 HIS 0.010 0.002 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6961) covalent geometry : angle 0.76887 ( 9669) hydrogen bonds : bond 0.05221 ( 258) hydrogen bonds : angle 4.75242 ( 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 107 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 1320 ASP cc_start: 0.7059 (t0) cc_final: 0.6797 (t0) REVERT: D 1379 ASN cc_start: 0.4083 (t0) cc_final: 0.3785 (t0) REVERT: D 1675 TYR cc_start: 0.6181 (OUTLIER) cc_final: 0.4359 (p90) REVERT: D 1889 LYS cc_start: 0.8061 (tppt) cc_final: 0.7832 (tppt) outliers start: 26 outliers final: 18 residues processed: 93 average time/residue: 0.1048 time to fit residues: 12.7002 Evaluate side-chains 97 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 966 GLU Chi-restraints excluded: chain D residue 968 PHE Chi-restraints excluded: chain D residue 997 LEU 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 1667 GLU Chi-restraints excluded: chain D residue 1675 TYR Chi-restraints excluded: chain D residue 1835 TYR Chi-restraints excluded: chain D residue 1854 VAL Chi-restraints excluded: chain D residue 1860 MET Chi-restraints excluded: chain D residue 1897 TYR 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: 0.0060 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 998 ASN D1006 ASN D1028 GLN ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4931 r_free = 0.4931 target = 0.171699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.158593 restraints weight = 17676.806| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 2.76 r_work: 0.4622 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5576 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6961 Z= 0.164 Angle : 0.779 14.514 9669 Z= 0.376 Chirality : 0.044 0.201 1114 Planarity : 0.006 0.055 1053 Dihedral : 20.252 146.943 1532 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 4.47 % Allowed : 23.29 % 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: -1.34 (0.32), residues: 691 helix: 0.82 (0.31), residues: 291 sheet: None (None), residues: 0 loop : -2.35 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 906 TYR 0.023 0.002 TYR D 936 PHE 0.021 0.002 PHE D1374 TRP 0.008 0.002 TRP D1024 HIS 0.011 0.002 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6961) covalent geometry : angle 0.77874 ( 9669) hydrogen bonds : bond 0.05102 ( 258) hydrogen bonds : angle 4.72953 ( 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 113 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 773 ILE cc_start: 0.7100 (tp) cc_final: 0.6893 (tp) REVERT: D 1320 ASP cc_start: 0.7104 (t0) cc_final: 0.6831 (t0) REVERT: D 1675 TYR cc_start: 0.6152 (OUTLIER) cc_final: 0.4317 (p90) REVERT: D 1838 MET cc_start: 0.6175 (mtp) cc_final: 0.5781 (mtt) outliers start: 28 outliers final: 19 residues processed: 98 average time/residue: 0.0908 time to fit residues: 11.7841 Evaluate side-chains 101 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.218 ------------------------------------------------------------------------------- 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 827 ILE 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 997 LEU 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 1667 GLU Chi-restraints excluded: chain D residue 1675 TYR Chi-restraints excluded: chain D residue 1835 TYR Chi-restraints excluded: chain D residue 1854 VAL 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: 0.9990 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4940 r_free = 0.4940 target = 0.172358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.159690 restraints weight = 17870.650| |-----------------------------------------------------------------------------| r_work (start): 0.4737 rms_B_bonded: 2.69 r_work: 0.4635 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5545 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6961 Z= 0.158 Angle : 0.780 13.571 9669 Z= 0.374 Chirality : 0.043 0.184 1114 Planarity : 0.006 0.052 1053 Dihedral : 20.204 145.589 1532 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 4.15 % Allowed : 24.08 % Favored : 71.77 % 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: -1.32 (0.32), residues: 691 helix: 0.80 (0.31), residues: 291 sheet: None (None), residues: 0 loop : -2.32 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1003 TYR 0.023 0.002 TYR D 876 PHE 0.018 0.002 PHE D 896 TRP 0.007 0.002 TRP D1380 HIS 0.012 0.002 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 6961) covalent geometry : angle 0.78009 ( 9669) hydrogen bonds : bond 0.05041 ( 258) hydrogen bonds : angle 4.68798 ( 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 118 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.5058 (mpp) cc_final: 0.4521 (mpp) REVERT: D 789 ARG cc_start: 0.6440 (mmm160) cc_final: 0.5657 (mmm160) REVERT: D 909 ILE cc_start: 0.4458 (tp) cc_final: 0.4125 (tp) REVERT: D 1320 ASP cc_start: 0.7065 (t0) cc_final: 0.6787 (t0) REVERT: D 1675 TYR cc_start: 0.6102 (OUTLIER) cc_final: 0.4331 (p90) outliers start: 26 outliers final: 19 residues processed: 104 average time/residue: 0.0964 time to fit residues: 13.0943 Evaluate side-chains 103 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 826 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 899 ASP Chi-restraints excluded: chain D residue 943 HIS 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 997 LEU Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1663 ILE Chi-restraints excluded: chain D residue 1667 GLU Chi-restraints excluded: chain D residue 1675 TYR Chi-restraints excluded: chain D residue 1835 TYR Chi-restraints excluded: chain D residue 1854 VAL Chi-restraints excluded: chain D residue 1897 TYR 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: 0.8980 chunk 37 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 13 optimal weight: 0.0870 chunk 22 optimal weight: 0.0980 chunk 33 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1379 ASN ** 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 = 0.174245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.161910 restraints weight = 17965.122| |-----------------------------------------------------------------------------| r_work (start): 0.4760 rms_B_bonded: 2.65 r_work: 0.4657 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.4657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6961 Z= 0.148 Angle : 0.785 15.087 9669 Z= 0.373 Chirality : 0.043 0.174 1114 Planarity : 0.006 0.052 1053 Dihedral : 20.069 144.237 1532 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 3.67 % Allowed : 24.56 % Favored : 71.77 % 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: -1.26 (0.32), residues: 691 helix: 0.88 (0.31), residues: 290 sheet: None (None), residues: 0 loop : -2.29 (0.30), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D1003 TYR 0.022 0.002 TYR D 876 PHE 0.015 0.002 PHE D 896 TRP 0.006 0.001 TRP D1048 HIS 0.013 0.002 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6961) covalent geometry : angle 0.78461 ( 9669) hydrogen bonds : bond 0.04926 ( 258) hydrogen bonds : angle 4.65847 ( 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 105 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.5132 (mpp) cc_final: 0.4615 (mpp) REVERT: D 1020 ARG cc_start: 0.5868 (ppt170) cc_final: 0.5639 (ppt170) REVERT: D 1320 ASP cc_start: 0.7013 (t0) cc_final: 0.6727 (t0) REVERT: D 1675 TYR cc_start: 0.5910 (OUTLIER) cc_final: 0.4184 (p90) outliers start: 23 outliers final: 17 residues processed: 92 average time/residue: 0.0999 time to fit residues: 11.9771 Evaluate side-chains 101 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 826 THR 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 1371 VAL Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1663 ILE Chi-restraints excluded: chain D residue 1667 GLU Chi-restraints excluded: chain D residue 1675 TYR Chi-restraints excluded: chain D residue 1835 TYR Chi-restraints excluded: chain D residue 1854 VAL Chi-restraints excluded: chain D residue 1897 TYR 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: 2.9990 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 42 optimal weight: 0.0370 chunk 13 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4933 r_free = 0.4933 target = 0.171920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.159242 restraints weight = 17622.541| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 2.70 r_work: 0.4623 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5554 moved from start: 0.4403 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= 0.170 Angle : 0.825 15.015 9669 Z= 0.392 Chirality : 0.045 0.225 1114 Planarity : 0.006 0.056 1053 Dihedral : 20.100 145.254 1532 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 3.67 % Allowed : 24.40 % 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: -1.29 (0.32), residues: 691 helix: 0.82 (0.31), residues: 290 sheet: None (None), residues: 0 loop : -2.29 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1358 TYR 0.043 0.003 TYR D1345 PHE 0.020 0.002 PHE D 896 TRP 0.008 0.002 TRP D1380 HIS 0.014 0.002 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 6961) covalent geometry : angle 0.82455 ( 9669) hydrogen bonds : bond 0.05212 ( 258) hydrogen bonds : angle 4.72989 ( 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 107 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.5263 (mpp) cc_final: 0.4832 (mpp) REVERT: D 789 ARG cc_start: 0.6471 (mmm160) cc_final: 0.5814 (mmm160) REVERT: D 1320 ASP cc_start: 0.7094 (t0) cc_final: 0.6829 (t0) REVERT: D 1675 TYR cc_start: 0.6050 (OUTLIER) cc_final: 0.4208 (p90) outliers start: 23 outliers final: 17 residues processed: 95 average time/residue: 0.0993 time to fit residues: 12.3019 Evaluate side-chains 96 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 826 THR 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 1371 VAL Chi-restraints excluded: chain D residue 1563 VAL Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1663 ILE Chi-restraints excluded: chain D residue 1667 GLU Chi-restraints excluded: chain D residue 1675 TYR Chi-restraints excluded: chain D residue 1835 TYR Chi-restraints excluded: chain D residue 1854 VAL Chi-restraints excluded: chain D residue 1897 TYR 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: 0.6980 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 0.0670 chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1379 ASN ** 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 = 0.4942 r_free = 0.4942 target = 0.172406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4767 r_free = 0.4767 target = 0.159870 restraints weight = 17749.302| |-----------------------------------------------------------------------------| r_work (start): 0.4739 rms_B_bonded: 2.73 r_work: 0.4635 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 moved from start: 0.4530 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= 0.162 Angle : 0.838 14.689 9669 Z= 0.394 Chirality : 0.045 0.198 1114 Planarity : 0.006 0.058 1053 Dihedral : 20.113 143.423 1532 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 23.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.87 % Allowed : 25.68 % Favored : 71.45 % 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: -1.40 (0.31), residues: 691 helix: 0.67 (0.31), residues: 291 sheet: None (None), residues: 0 loop : -2.31 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 745 TYR 0.054 0.003 TYR D1345 PHE 0.018 0.002 PHE D 896 TRP 0.006 0.001 TRP D1024 HIS 0.013 0.002 HIS D 850 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 6961) covalent geometry : angle 0.83816 ( 9669) hydrogen bonds : bond 0.05251 ( 258) hydrogen bonds : angle 4.79671 ( 710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1810.77 seconds wall clock time: 31 minutes 51.14 seconds (1911.14 seconds total)