Starting phenix.real_space_refine on Thu Jul 2 05:28:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21cn_67573/07_2026/21cn_67573.cif Found real_map, /net/cci-nas-00/data/ceres_data/21cn_67573/07_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_67573/07_2026/21cn_67573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21cn_67573/07_2026/21cn_67573.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21cn_67573/07_2026/21cn_67573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21cn_67573/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' CA': 2} Chain breaks: 2 Time building chain proxies: 1.82, per 1000 atoms: 0.27 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: 0.60 Conformation dependent library (CDL) restraints added in 397.9 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: 1.11 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: 1.34 Time building geometry restraints manager: 0.80 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 3.250 nonbonded pdb=" C5' U A 22 " pdb="CA CA D2002 " model vdw 2.003 3.650 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: 1.550 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.290 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.700 ------------------------------------------------------------------------------- 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= 0.340 Angle : 1.011 10.977 9669 Z= 0.574 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 / 0.34 ( 6961) covalent geometry : angle 1.01132 / 0.57 ( 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 : 0.226 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: 0.0917 time to fit residues: 10.9666 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 : 0.224 ------------------------------------------------------------------------------- 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: 0.7980 chunk 38 optimal weight: 0.0870 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 = 0.4992 r_free = 0.4992 target = 0.176413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.162562 restraints weight = 18339.838| |-----------------------------------------------------------------------------| r_work (start): 0.4816 rms_B_bonded: 3.00 r_work: 0.4716 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5488 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6961 Z= 0.180 Angle : 0.752 9.143 9669 Z= 0.404 Chirality : 0.048 0.440 1114 Planarity : 0.006 0.050 1053 Dihedral : 20.855 152.129 1543 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.03 % Allowed : 21.53 % Favored : 75.44 % 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: -3.67 (0.70), residues: 34 loop : -2.62 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 935 TYR 0.031 0.002 TYR D1330 PHE 0.016 0.002 PHE D1677 TRP 0.004 0.001 TRP D1048 HIS 0.010 0.002 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 ( 6961) covalent geometry : angle 0.75207 / 0.40 ( 9669) hydrogen bonds : bond 0.06761 / 4.16 ( 258) hydrogen bonds : angle 5.12521 / 3.59 ( 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 97 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 934 PRO cc_start: 0.6841 (Cg_exo) cc_final: 0.6597 (Cg_endo) REVERT: D 949 ASP cc_start: 0.7174 (t0) cc_final: 0.6930 (t70) REVERT: D 1019 LYS cc_start: 0.8033 (mmmt) cc_final: 0.7745 (mmmt) REVERT: D 1808 MET cc_start: 0.4537 (mmp) cc_final: 0.4231 (mmp) outliers start: 19 outliers final: 5 residues processed: 92 average time/residue: 0.0820 time to fit residues: 10.2323 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 : 0.233 ------------------------------------------------------------------------------- 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: 1.9990 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.4956 r_free = 0.4956 target = 0.173448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.159222 restraints weight = 18122.674| |-----------------------------------------------------------------------------| r_work (start): 0.4767 rms_B_bonded: 2.98 r_work: 0.4669 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.4669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5620 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6961 Z= 0.202 Angle : 0.765 12.208 9669 Z= 0.402 Chirality : 0.050 0.404 1114 Planarity : 0.005 0.041 1053 Dihedral : 20.583 154.996 1532 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.19 % Allowed : 22.49 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.31), residues: 691 helix: 0.46 (0.30), residues: 298 sheet: -3.04 (0.89), residues: 28 loop : -2.63 (0.30), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 758 TYR 0.029 0.003 TYR D1330 PHE 0.016 0.002 PHE D 896 TRP 0.010 0.002 TRP D1024 HIS 0.010 0.002 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.20 ( 6961) covalent geometry : angle 0.76516 / 0.40 ( 9669) hydrogen bonds : bond 0.06875 / 4.31 ( 258) hydrogen bonds : angle 5.13740 / 3.60 ( 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 98 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 949 ASP cc_start: 0.7442 (t0) cc_final: 0.7240 (t70) REVERT: D 1320 ASP cc_start: 0.6497 (t0) cc_final: 0.6283 (t0) REVERT: D 1758 PHE cc_start: 0.2931 (OUTLIER) cc_final: 0.2345 (p90) outliers start: 20 outliers final: 12 residues processed: 94 average time/residue: 0.0838 time to fit residues: 10.5815 Evaluate side-chains 87 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 899 ASP Chi-restraints excluded: chain D residue 966 GLU Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1065 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 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: 0.9990 chunk 9 optimal weight: 0.2980 chunk 66 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4961 r_free = 0.4961 target = 0.173787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4773 r_free = 0.4773 target = 0.159609 restraints weight = 18188.321| |-----------------------------------------------------------------------------| r_work (start): 0.4753 rms_B_bonded: 2.99 r_work: 0.4652 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5591 moved from start: 0.2099 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= 0.173 Angle : 0.728 11.495 9669 Z= 0.383 Chirality : 0.048 0.398 1114 Planarity : 0.005 0.046 1053 Dihedral : 20.464 152.121 1532 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.51 % Allowed : 24.24 % 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: -1.78 (0.31), residues: 691 helix: 0.49 (0.30), residues: 293 sheet: -2.98 (0.89), residues: 28 loop : -2.57 (0.30), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 790 TYR 0.048 0.002 TYR D1330 PHE 0.029 0.002 PHE D 896 TRP 0.010 0.002 TRP D1024 HIS 0.009 0.002 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 ( 6961) covalent geometry : angle 0.72846 / 0.38 ( 9669) hydrogen bonds : bond 0.06099 / 3.84 ( 258) hydrogen bonds : angle 4.95949 / 3.48 ( 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 97 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 949 ASP cc_start: 0.7063 (t0) cc_final: 0.6785 (t70) REVERT: D 1320 ASP cc_start: 0.6638 (t0) cc_final: 0.6310 (t0) outliers start: 22 outliers final: 15 residues processed: 91 average time/residue: 0.0797 time to fit residues: 9.9040 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 : 0.213 ------------------------------------------------------------------------------- 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 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 1552 GLN 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 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: 4.9990 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1379 ASN ** D1549 HIS ** 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 = 0.4941 r_free = 0.4941 target = 0.172775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.159884 restraints weight = 17714.360| |-----------------------------------------------------------------------------| r_work (start): 0.4759 rms_B_bonded: 2.78 r_work: 0.4659 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5663 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6961 Z= 0.200 Angle : 0.771 13.752 9669 Z= 0.398 Chirality : 0.049 0.368 1114 Planarity : 0.006 0.046 1053 Dihedral : 20.427 153.139 1532 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.31 % Allowed : 23.76 % 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: -1.83 (0.31), residues: 691 helix: 0.41 (0.30), residues: 296 sheet: -3.25 (1.09), residues: 18 loop : -2.60 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1060 TYR 0.053 0.003 TYR D 936 PHE 0.026 0.002 PHE D 896 TRP 0.013 0.002 TRP D1024 HIS 0.010 0.002 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 6961) covalent geometry : angle 0.77058 / 0.40 ( 9669) hydrogen bonds : bond 0.06197 / 3.91 ( 258) hydrogen bonds : angle 4.96833 / 3.49 ( 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 105 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.4469 (mpp) cc_final: 0.3917 (mpp) REVERT: D 968 PHE cc_start: 0.5223 (OUTLIER) cc_final: 0.4843 (p90) REVERT: D 1020 ARG cc_start: 0.6361 (tmm160) cc_final: 0.5810 (ptm-80) REVERT: D 1320 ASP cc_start: 0.6973 (t0) cc_final: 0.6598 (t0) REVERT: D 1345 TYR cc_start: 0.5357 (m-80) cc_final: 0.4914 (m-10) REVERT: D 1758 PHE cc_start: 0.3268 (OUTLIER) cc_final: 0.2555 (p90) outliers start: 27 outliers final: 16 residues processed: 97 average time/residue: 0.0928 time to fit residues: 11.5890 Evaluate side-chains 87 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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 968 PHE Chi-restraints excluded: chain D residue 1003 ARG 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 0.0370 chunk 68 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 64 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.4953 r_free = 0.4953 target = 0.173720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.161061 restraints weight = 17681.622| |-----------------------------------------------------------------------------| r_work (start): 0.4774 rms_B_bonded: 2.77 r_work: 0.4674 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5612 moved from start: 0.2632 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= 0.163 Angle : 0.740 11.343 9669 Z= 0.382 Chirality : 0.047 0.350 1114 Planarity : 0.006 0.055 1053 Dihedral : 20.340 149.301 1532 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 22.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.67 % Allowed : 25.04 % 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: -1.66 (0.31), residues: 691 helix: 0.60 (0.31), residues: 296 sheet: -3.20 (1.09), residues: 18 loop : -2.55 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 821 TYR 0.038 0.003 TYR D 976 PHE 0.025 0.002 PHE D1374 TRP 0.007 0.001 TRP D1048 HIS 0.009 0.002 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 6961) covalent geometry : angle 0.73996 / 0.38 ( 9669) hydrogen bonds : bond 0.05696 / 3.58 ( 258) hydrogen bonds : angle 4.82279 / 3.39 ( 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 93 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.4491 (mpp) cc_final: 0.3192 (ptp) REVERT: D 959 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7231 (ptpp) REVERT: D 1320 ASP cc_start: 0.6895 (t0) cc_final: 0.6511 (t0) REVERT: D 1345 TYR cc_start: 0.5270 (m-80) cc_final: 0.4872 (m-80) outliers start: 23 outliers final: 18 residues processed: 88 average time/residue: 0.0944 time to fit residues: 10.9324 Evaluate side-chains 85 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 968 PHE Chi-restraints excluded: chain D residue 1003 ARG 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 1573 SER Chi-restraints excluded: chain D residue 1712 LEU 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: 2.9990 chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 66 optimal weight: 0.0050 chunk 15 optimal weight: 1.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1028 GLN ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1549 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4923 r_free = 0.4923 target = 0.171199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4743 r_free = 0.4743 target = 0.158282 restraints weight = 17302.591| |-----------------------------------------------------------------------------| r_work (start): 0.4742 rms_B_bonded: 2.77 r_work: 0.4640 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.4640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5719 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6961 Z= 0.203 Angle : 0.802 14.541 9669 Z= 0.408 Chirality : 0.048 0.335 1114 Planarity : 0.006 0.047 1053 Dihedral : 20.358 150.148 1532 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 24.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 4.47 % Allowed : 24.56 % 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: -1.65 (0.31), residues: 691 helix: 0.66 (0.31), residues: 296 sheet: -3.29 (1.08), residues: 18 loop : -2.59 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1872 TYR 0.032 0.003 TYR D1330 PHE 0.024 0.002 PHE D 896 TRP 0.009 0.002 TRP D1024 HIS 0.009 0.002 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 ( 6961) covalent geometry : angle 0.80243 / 0.41 ( 9669) hydrogen bonds : bond 0.06066 / 3.86 ( 258) hydrogen bonds : angle 4.93764 / 3.48 ( 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 101 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.5020 (mpp) cc_final: 0.4384 (mpp) REVERT: D 959 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.7318 (ptpp) REVERT: D 1320 ASP cc_start: 0.7093 (t0) cc_final: 0.6706 (t0) REVERT: D 1345 TYR cc_start: 0.5364 (m-80) cc_final: 0.4954 (m-80) REVERT: D 1675 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.4762 (p90) REVERT: D 1832 GLN cc_start: 0.6453 (tp-100) cc_final: 0.5826 (pt0) outliers start: 28 outliers final: 18 residues processed: 93 average time/residue: 0.0893 time to fit residues: 10.8892 Evaluate side-chains 87 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 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 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 1371 VAL Chi-restraints excluded: chain D residue 1379 ASN 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 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: 2.9990 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.0670 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 41 optimal weight: 0.0070 chunk 62 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 overall best weight: 0.4536 ------------------------------------------------------------------------------- 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 = 0.4960 r_free = 0.4960 target = 0.172504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4776 r_free = 0.4776 target = 0.158795 restraints weight = 18496.625| |-----------------------------------------------------------------------------| r_work (start): 0.4756 rms_B_bonded: 2.98 r_work: 0.4654 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5635 moved from start: 0.3049 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= 0.162 Angle : 0.797 14.901 9669 Z= 0.399 Chirality : 0.047 0.314 1114 Planarity : 0.006 0.056 1053 Dihedral : 20.297 146.280 1532 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 3.99 % Allowed : 24.88 % 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: -1.53 (0.31), residues: 691 helix: 0.80 (0.31), residues: 290 sheet: None (None), residues: 0 loop : -2.58 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D1855 TYR 0.026 0.003 TYR D 936 PHE 0.027 0.002 PHE D1374 TRP 0.008 0.001 TRP D1048 HIS 0.009 0.002 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 6961) covalent geometry : angle 0.79730 / 0.40 ( 9669) hydrogen bonds : bond 0.05401 / 3.41 ( 258) hydrogen bonds : angle 4.86276 / 3.43 ( 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 102 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.4906 (mpp) cc_final: 0.3599 (ptp) REVERT: D 906 ARG cc_start: 0.7067 (tmm-80) cc_final: 0.6810 (ttt-90) REVERT: D 959 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7366 (ptpp) REVERT: D 1320 ASP cc_start: 0.6888 (t0) cc_final: 0.6581 (t0) outliers start: 25 outliers final: 16 residues processed: 95 average time/residue: 0.0892 time to fit residues: 11.1993 Evaluate side-chains 87 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 968 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1047 LEU Chi-restraints excluded: chain D residue 1052 VAL Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1563 VAL Chi-restraints excluded: chain D residue 1567 LEU Chi-restraints excluded: chain D residue 1569 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 45 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 22 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4952 r_free = 0.4952 target = 0.172775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.160015 restraints weight = 17972.809| |-----------------------------------------------------------------------------| r_work (start): 0.4772 rms_B_bonded: 2.84 r_work: 0.4668 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5659 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6961 Z= 0.181 Angle : 0.833 15.903 9669 Z= 0.411 Chirality : 0.047 0.310 1114 Planarity : 0.006 0.052 1053 Dihedral : 20.316 145.951 1532 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.67 % Allowed : 25.52 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.32), residues: 691 helix: 0.81 (0.31), residues: 291 sheet: None (None), residues: 0 loop : -2.61 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 790 TYR 0.032 0.003 TYR D1345 PHE 0.024 0.002 PHE D1374 TRP 0.008 0.001 TRP D1024 HIS 0.010 0.002 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 6961) covalent geometry : angle 0.83305 / 0.41 ( 9669) hydrogen bonds : bond 0.05540 / 3.51 ( 258) hydrogen bonds : angle 4.92849 / 3.46 ( 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 96 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.4994 (mpp) cc_final: 0.3731 (ptp) REVERT: D 959 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7452 (ptpp) REVERT: D 1320 ASP cc_start: 0.7054 (t0) cc_final: 0.6721 (t0) REVERT: D 1675 TYR cc_start: 0.6303 (OUTLIER) cc_final: 0.4454 (p90) outliers start: 23 outliers final: 18 residues processed: 88 average time/residue: 0.0887 time to fit residues: 10.1191 Evaluate side-chains 91 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 968 PHE Chi-restraints excluded: chain D residue 1033 LEU Chi-restraints excluded: chain D residue 1052 VAL Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1379 ASN 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 1663 ILE Chi-restraints excluded: chain D residue 1675 TYR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1004 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 = 0.4936 r_free = 0.4936 target = 0.171779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.158793 restraints weight = 17514.413| |-----------------------------------------------------------------------------| r_work (start): 0.4727 rms_B_bonded: 2.75 r_work: 0.4618 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5706 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 6961 Z= 0.214 Angle : 0.877 18.412 9669 Z= 0.433 Chirality : 0.050 0.296 1114 Planarity : 0.007 0.090 1053 Dihedral : 20.455 146.973 1532 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 26.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 3.51 % Allowed : 26.00 % Favored : 70.49 % 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: -1.65 (0.31), residues: 691 helix: 0.61 (0.31), residues: 294 sheet: None (None), residues: 0 loop : -2.61 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D1020 TYR 0.049 0.003 TYR D1345 PHE 0.028 0.003 PHE D1374 TRP 0.016 0.002 TRP D1024 HIS 0.015 0.002 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 ( 6961) covalent geometry : angle 0.87732 / 0.43 ( 9669) hydrogen bonds : bond 0.05753 / 3.75 ( 258) hydrogen bonds : angle 5.07410 / 3.53 ( 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 97 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 775 MET cc_start: 0.5171 (mpp) cc_final: 0.4541 (mpp) REVERT: D 876 TYR cc_start: 0.3531 (m-10) cc_final: 0.3314 (m-10) REVERT: D 1320 ASP cc_start: 0.7081 (t0) cc_final: 0.6770 (t0) REVERT: D 1379 ASN cc_start: 0.4634 (OUTLIER) cc_final: 0.4181 (t160) REVERT: D 1675 TYR cc_start: 0.6442 (OUTLIER) cc_final: 0.4640 (p90) outliers start: 22 outliers final: 16 residues processed: 88 average time/residue: 0.0966 time to fit residues: 10.9312 Evaluate side-chains 92 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.134 ------------------------------------------------------------------------------- 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 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 1379 ASN 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 1873 THR 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 8 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 30 optimal weight: 0.0470 chunk 50 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 856 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1004 HIS ** D1073 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1549 HIS ** 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 = 0.4951 r_free = 0.4951 target = 0.171812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.158157 restraints weight = 18339.054| |-----------------------------------------------------------------------------| r_work (start): 0.4747 rms_B_bonded: 2.88 r_work: 0.4651 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5656 moved from start: 0.3523 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= 0.177 Angle : 0.849 16.623 9669 Z= 0.415 Chirality : 0.049 0.387 1114 Planarity : 0.006 0.052 1053 Dihedral : 20.409 144.268 1532 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 24.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 2.71 % Allowed : 27.27 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.62 (0.31), residues: 691 helix: 0.66 (0.31), residues: 291 sheet: None (None), residues: 0 loop : -2.58 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D1020 TYR 0.031 0.003 TYR D 936 PHE 0.021 0.002 PHE D1374 TRP 0.010 0.002 TRP D1024 HIS 0.015 0.002 HIS D 850 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 6961) covalent geometry : angle 0.84941 / 0.41 ( 9669) hydrogen bonds : bond 0.05362 / 3.45 ( 258) hydrogen bonds : angle 4.98612 / 3.50 ( 710) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1689.33 seconds wall clock time: 29 minutes 54.14 seconds (1794.14 seconds total)