Starting phenix.real_space_refine on Tue Aug 4 21:52:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21cq_67575/08_2026/21cq_67575.cif Found real_map, /net/cci-nas-00/data/ceres_data/21cq_67575/08_2026/21cq_67575.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21cq_67575/08_2026/21cq_67575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21cq_67575/08_2026/21cq_67575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21cq_67575/08_2026/21cq_67575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21cq_67575/08_2026/21cq_67575.map" } resolution = 3.29 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 54 5.49 5 S 29 5.16 5 C 4144 2.51 5 N 1146 2.21 5 O 1408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6783 Number of models: 1 Model: "" Number of chains: 4 Chain: "R" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 1144 Classifications: {'RNA': 54} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 26, 'rna3p_pyr': 27} Link IDs: {'rna2p': 1, 'rna3p': 52} Chain breaks: 1 Chain: "D" Number of atoms: 5637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5637 Classifications: {'peptide': 700} Link IDs: {'PTRANS': 48, 'TRANS': 651} Chain breaks: 4 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.50, per 1000 atoms: 0.22 Number of scatterers: 6783 At special positions: 0 Unit cell: (63.06, 71.468, 131.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 2 19.99 S 29 16.00 P 54 15.00 O 1408 8.00 N 1146 7.00 C 4144 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: 0.54 Conformation dependent library (CDL) restraints added in 373.4 milliseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1340 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 4 sheets defined 49.6% alpha, 2.4% beta 19 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'D' and resid 781 through 785 removed outlier: 4.399A pdb=" N LEU D 785 " --> pdb=" O PRO D 782 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 857 Processing helix chain 'D' and resid 893 through 903 removed outlier: 3.948A pdb=" N MET D 897 " --> pdb=" O ASP D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 914 removed outlier: 3.553A pdb=" N TYR D 914 " --> pdb=" O SER D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 929 removed outlier: 4.020A pdb=" N GLN D 928 " --> pdb=" O LEU D 924 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP D 929 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 968 through 976 Processing helix chain 'D' and resid 997 through 1001 Processing helix chain 'D' and resid 1018 through 1028 Processing helix chain 'D' and resid 1034 through 1039 Processing helix chain 'D' and resid 1044 through 1052 removed outlier: 4.594A pdb=" N LYS D1050 " --> pdb=" O SER D1046 " (cutoff:3.500A) Processing helix chain 'D' and resid 1053 through 1074 Processing helix chain 'D' and resid 1293 through 1302 removed outlier: 3.978A pdb=" N ALA D1300 " --> pdb=" O LEU D1296 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR D1302 " --> pdb=" O LEU D1298 " (cutoff:3.500A) Processing helix chain 'D' and resid 1303 through 1307 Processing helix chain 'D' and resid 1313 through 1335 Processing helix chain 'D' and resid 1341 through 1354 Processing helix chain 'D' and resid 1356 through 1361 Processing helix chain 'D' and resid 1555 through 1574 removed outlier: 3.993A pdb=" N ALA D1560 " --> pdb=" O ASP D1556 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASP D1561 " --> pdb=" O LYS D1557 " (cutoff:3.500A) Processing helix chain 'D' and resid 1575 through 1586 removed outlier: 3.713A pdb=" N ALA D1579 " --> pdb=" O GLY D1575 " (cutoff:3.500A) Processing helix chain 'D' and resid 1660 through 1662 No H-bonds generated for 'chain 'D' and resid 1660 through 1662' Processing helix chain 'D' and resid 1663 through 1674 removed outlier: 3.621A pdb=" N GLU D1667 " --> pdb=" O ILE D1663 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN D1668 " --> pdb=" O SER D1664 " (cutoff:3.500A) Processing helix chain 'D' and resid 1679 through 1687 removed outlier: 3.717A pdb=" N LEU D1683 " --> pdb=" O ASN D1679 " (cutoff:3.500A) Processing helix chain 'D' and resid 1701 through 1723 Processing helix chain 'D' and resid 1728 through 1741 Processing helix chain 'D' and resid 1741 through 1752 Processing helix chain 'D' and resid 1766 through 1775 removed outlier: 3.870A pdb=" N PHE D1772 " --> pdb=" O VAL D1768 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D1773 " --> pdb=" O ILE D1769 " (cutoff:3.500A) Processing helix chain 'D' and resid 1805 through 1823 Processing helix chain 'D' and resid 1826 through 1835 Processing helix chain 'D' and resid 1838 through 1846 Processing helix chain 'D' and resid 1852 through 1861 removed outlier: 3.593A pdb=" N LEU D1857 " --> pdb=" O PRO D1853 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU D1858 " --> pdb=" O VAL D1854 " (cutoff:3.500A) Processing helix chain 'D' and resid 1896 through 1912 removed outlier: 3.544A pdb=" N ALA D1900 " --> pdb=" O SER D1896 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 803 through 805 Processing sheet with id=AA2, first strand: chain 'D' and resid 819 through 820 Processing sheet with id=AA3, first strand: chain 'D' and resid 881 through 883 Processing sheet with id=AA4, first strand: chain 'D' and resid 931 through 932 227 hydrogen bonds defined for protein. 648 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 82 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 1.13 Time building geometry restraints manager: 0.73 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: 1787 1.34 - 1.45: 1509 1.45 - 1.57: 3608 1.57 - 1.69: 107 1.69 - 1.81: 42 Bond restraints: 7053 Sorted by residual: bond pdb=" N VAL D1849 " pdb=" CA VAL D1849 " ideal model delta sigma weight residual 1.460 1.495 -0.035 9.30e-03 1.16e+04 1.44e+01 bond pdb=" P U R 62 " pdb=" O5' U R 62 " ideal model delta sigma weight residual 1.593 1.624 -0.031 1.00e-02 1.00e+04 9.62e+00 bond pdb=" N VAL D1854 " pdb=" CA VAL D1854 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.06e+00 bond pdb=" P U R 18 " pdb=" O5' U R 18 " ideal model delta sigma weight residual 1.593 1.621 -0.028 1.00e-02 1.00e+04 7.61e+00 bond pdb=" N SER D1852 " pdb=" CA SER D1852 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.13e-02 7.83e+03 7.59e+00 ... (remaining 7048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 9600 3.12 - 6.23: 196 6.23 - 9.35: 16 9.35 - 12.47: 1 12.47 - 15.58: 1 Bond angle restraints: 9814 Sorted by residual: angle pdb=" C3' U R 62 " pdb=" C2' U R 62 " pdb=" C1' U R 62 " ideal model delta sigma weight residual 101.30 105.28 -3.98 7.00e-01 2.04e+00 3.23e+01 angle pdb=" CB PRO D 817 " pdb=" CG PRO D 817 " pdb=" CD PRO D 817 " ideal model delta sigma weight residual 106.10 90.52 15.58 3.20e+00 9.77e-02 2.37e+01 angle pdb=" N1 U R 63 " pdb=" C2 U R 63 " pdb=" O2 U R 63 " ideal model delta sigma weight residual 122.80 126.18 -3.38 7.00e-01 2.04e+00 2.34e+01 angle pdb=" O4' A R 43 " pdb=" C1' A R 43 " pdb=" C2' A R 43 " ideal model delta sigma weight residual 107.60 103.27 4.33 9.00e-01 1.23e+00 2.32e+01 angle pdb=" C3' U R 41 " pdb=" C2' U R 41 " pdb=" C1' U R 41 " ideal model delta sigma weight residual 101.30 104.58 -3.28 7.00e-01 2.04e+00 2.20e+01 ... (remaining 9809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.93: 3996 29.93 - 59.85: 285 59.85 - 89.78: 57 89.78 - 119.70: 6 119.70 - 149.63: 1 Dihedral angle restraints: 4345 sinusoidal: 2271 harmonic: 2074 Sorted by residual: dihedral pdb=" O4' U R 62 " pdb=" C4' U R 62 " pdb=" C3' U R 62 " pdb=" C2' U R 62 " ideal model delta sinusoidal sigma weight residual -35.00 20.30 -55.30 1 8.00e+00 1.56e-02 6.46e+01 dihedral pdb=" C5' U R 62 " pdb=" C4' U R 62 " pdb=" C3' U R 62 " pdb=" O3' U R 62 " ideal model delta sinusoidal sigma weight residual 82.00 136.26 -54.26 1 8.00e+00 1.56e-02 6.24e+01 dihedral pdb=" O4' U R 63 " pdb=" C1' U R 63 " pdb=" N1 U R 63 " pdb=" C2 U R 63 " ideal model delta sinusoidal sigma weight residual 232.00 82.37 149.63 1 1.70e+01 3.46e-03 6.19e+01 ... (remaining 4342 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 1057 0.113 - 0.227: 52 0.227 - 0.340: 2 0.340 - 0.454: 8 0.454 - 0.567: 19 Chirality restraints: 1138 Sorted by residual: chirality pdb=" P G R 1 " pdb=" OP1 G R 1 " pdb=" OP2 G R 1 " pdb=" O5' G R 1 " both_signs ideal model delta sigma weight residual True 2.41 2.98 -0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" P U R 18 " pdb=" OP1 U R 18 " pdb=" OP2 U R 18 " pdb=" O5' U R 18 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" P U R 62 " pdb=" OP1 U R 62 " pdb=" OP2 U R 62 " pdb=" O5' U R 62 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.54 2.00e-01 2.50e+01 7.42e+00 ... (remaining 1135 not shown) Planarity restraints: 1053 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D1839 " -0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO D1840 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D1840 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D1840 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D1804 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO D1805 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO D1805 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D1805 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR D 749 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.60e+00 pdb=" N PRO D 750 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 750 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 750 " -0.030 5.00e-02 4.00e+02 ... (remaining 1050 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 4 2.10 - 2.80: 1801 2.80 - 3.50: 10383 3.50 - 4.20: 18132 4.20 - 4.90: 29605 Nonbonded interactions: 59925 Sorted by model distance: nonbonded pdb=" OP1 A R 43 " pdb="CA CA R2001 " model vdw 1.398 2.510 nonbonded pdb=" O LEU D1684 " pdb=" OG1 THR D1688 " model vdw 2.018 3.040 nonbonded pdb=" OG SER D1823 " pdb=" OG SER D1826 " model vdw 2.085 3.040 nonbonded pdb=" O SER D1348 " pdb=" OG SER D1352 " model vdw 2.091 3.040 nonbonded pdb=" OG SER D1826 " pdb=" OG1 THR D1829 " model vdw 2.102 3.040 ... (remaining 59920 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: 1.180 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 8.150 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5353 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 0.115 7053 Z= 0.349 Angle : 0.984 15.583 9814 Z= 0.575 Chirality : 0.090 0.567 1138 Planarity : 0.006 0.060 1053 Dihedral : 20.087 149.630 3005 Min Nonbonded Distance : 1.398 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.96 % Allowed : 23.68 % Favored : 75.36 % 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: -1.59 (0.32), residues: 690 helix: -0.02 (0.30), residues: 277 sheet: -3.37 (0.87), residues: 25 loop : -1.72 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1314 TYR 0.025 0.002 TYR D 971 PHE 0.033 0.002 PHE D1758 TRP 0.006 0.002 TRP D1380 HIS 0.006 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.35 ( 7053) covalent geometry : angle 0.98446 / 0.58 ( 9814) hydrogen bonds : bond 0.16308 / 18.52 ( 272) hydrogen bonds : angle 7.12308 / 8.35 ( 730) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 800 ARG cc_start: 0.4271 (OUTLIER) cc_final: 0.3664 (mtp180) REVERT: D 971 TYR cc_start: 0.2119 (OUTLIER) cc_final: 0.0037 (p90) REVERT: D 1299 GLN cc_start: 0.5597 (tp-100) cc_final: 0.5343 (mm110) REVERT: D 1358 ARG cc_start: 0.3630 (tmm160) cc_final: 0.2813 (tmm160) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.0938 time to fit residues: 10.6069 Evaluate side-chains 86 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 800 ARG Chi-restraints excluded: chain D residue 802 PHE Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 944 ARG Chi-restraints excluded: chain D residue 971 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.0770 chunk 74 optimal weight: 8.9990 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1685 GLN D1695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4937 r_free = 0.4937 target = 0.176124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.161933 restraints weight = 17655.110| |-----------------------------------------------------------------------------| r_work (start): 0.4754 rms_B_bonded: 3.02 r_work: 0.4641 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.4641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5469 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 7053 Z= 0.188 Angle : 0.748 10.910 9814 Z= 0.400 Chirality : 0.047 0.490 1138 Planarity : 0.006 0.062 1053 Dihedral : 18.715 157.680 1609 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.00 % Allowed : 22.40 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.31), residues: 690 helix: 0.04 (0.29), residues: 281 sheet: -3.47 (0.77), residues: 25 loop : -1.76 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 859 TYR 0.032 0.002 TYR D 976 PHE 0.023 0.002 PHE D1332 TRP 0.041 0.003 TRP D1048 HIS 0.009 0.002 HIS D 943 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.19 ( 7053) covalent geometry : angle 0.74799 / 0.40 ( 9814) hydrogen bonds : bond 0.07660 / 7.58 ( 272) hydrogen bonds : angle 6.11947 / 7.22 ( 730) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 800 ARG cc_start: 0.4241 (OUTLIER) cc_final: 0.3954 (mtp180) REVERT: D 971 TYR cc_start: 0.1857 (OUTLIER) cc_final: -0.0512 (p90) REVERT: D 1320 ASP cc_start: 0.4600 (t0) cc_final: 0.4383 (t0) REVERT: D 1722 GLU cc_start: 0.4888 (OUTLIER) cc_final: 0.4588 (mp0) REVERT: D 1831 TRP cc_start: 0.5416 (t-100) cc_final: 0.4975 (t-100) REVERT: D 1837 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.4815 (mpp) outliers start: 25 outliers final: 11 residues processed: 103 average time/residue: 0.0796 time to fit residues: 10.6205 Evaluate side-chains 94 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 800 ARG Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 944 ARG Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1705 GLU Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1837 MET Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1668 ASN D1727 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.174676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.160396 restraints weight = 17674.189| |-----------------------------------------------------------------------------| r_work (start): 0.4719 rms_B_bonded: 3.07 r_work: 0.4605 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5535 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 7053 Z= 0.179 Angle : 0.700 11.814 9814 Z= 0.371 Chirality : 0.046 0.534 1138 Planarity : 0.006 0.048 1053 Dihedral : 18.617 165.219 1607 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 5.44 % Allowed : 23.52 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.31), residues: 690 helix: 0.01 (0.29), residues: 287 sheet: -3.46 (0.81), residues: 25 loop : -1.76 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 996 TYR 0.022 0.002 TYR D 965 PHE 0.023 0.002 PHE D1332 TRP 0.039 0.003 TRP D1048 HIS 0.007 0.001 HIS D 856 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 ( 7053) covalent geometry : angle 0.69954 / 0.37 ( 9814) hydrogen bonds : bond 0.06708 / 6.64 ( 272) hydrogen bonds : angle 6.02197 / 7.19 ( 730) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 800 ARG cc_start: 0.4456 (OUTLIER) cc_final: 0.4025 (mtp180) REVERT: D 894 PHE cc_start: 0.5288 (OUTLIER) cc_final: 0.4838 (m-80) REVERT: D 971 TYR cc_start: 0.2128 (OUTLIER) cc_final: -0.0754 (p90) REVERT: D 1320 ASP cc_start: 0.4899 (t0) cc_final: 0.4666 (t0) REVERT: D 1831 TRP cc_start: 0.5816 (t-100) cc_final: 0.5388 (t-100) outliers start: 34 outliers final: 18 residues processed: 103 average time/residue: 0.0771 time to fit residues: 10.4353 Evaluate side-chains 99 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 800 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 845 LEU Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain D residue 1352 SER Chi-restraints excluded: chain D residue 1365 LEU Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1705 GLU Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1837 MET Chi-restraints excluded: chain D residue 1890 PHE Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 856 HIS D1727 HIS 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 = 0.174721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4738 r_free = 0.4738 target = 0.160377 restraints weight = 17603.349| |-----------------------------------------------------------------------------| r_work (start): 0.4711 rms_B_bonded: 3.07 r_work: 0.4601 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5556 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7053 Z= 0.166 Angle : 0.689 6.685 9814 Z= 0.365 Chirality : 0.044 0.379 1138 Planarity : 0.006 0.044 1053 Dihedral : 18.516 167.097 1603 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.48 % Allowed : 24.32 % Favored : 71.20 % 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: -1.54 (0.31), residues: 690 helix: 0.08 (0.29), residues: 284 sheet: -2.17 (1.24), residues: 12 loop : -1.90 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 944 TYR 0.034 0.002 TYR D 946 PHE 0.022 0.002 PHE D1332 TRP 0.029 0.003 TRP D1048 HIS 0.006 0.001 HIS D 856 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 ( 7053) covalent geometry : angle 0.68922 / 0.36 ( 9814) hydrogen bonds : bond 0.06485 / 6.32 ( 272) hydrogen bonds : angle 5.92879 / 7.07 ( 730) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 800 ARG cc_start: 0.4326 (OUTLIER) cc_final: 0.3355 (mtp180) REVERT: D 830 GLU cc_start: 0.5911 (mp0) cc_final: 0.4992 (mp0) REVERT: D 894 PHE cc_start: 0.5420 (OUTLIER) cc_final: 0.4910 (m-80) REVERT: D 971 TYR cc_start: 0.2390 (OUTLIER) cc_final: -0.0729 (p90) REVERT: D 1362 LYS cc_start: 0.4377 (pttp) cc_final: 0.4031 (tmtt) REVERT: D 1831 TRP cc_start: 0.5922 (t-100) cc_final: 0.5559 (t-100) outliers start: 28 outliers final: 14 residues processed: 99 average time/residue: 0.0840 time to fit residues: 10.9583 Evaluate side-chains 98 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 800 ARG Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain D residue 1352 SER Chi-restraints excluded: chain D residue 1359 LEU Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1837 MET Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 17 optimal weight: 0.0040 chunk 73 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 overall best weight: 0.5150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1727 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.174998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4737 r_free = 0.4737 target = 0.160492 restraints weight = 17790.433| |-----------------------------------------------------------------------------| r_work (start): 0.4718 rms_B_bonded: 3.08 r_work: 0.4606 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5541 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 7053 Z= 0.158 Angle : 0.679 7.668 9814 Z= 0.358 Chirality : 0.043 0.266 1138 Planarity : 0.005 0.048 1053 Dihedral : 18.463 167.763 1603 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.64 % Allowed : 24.80 % Favored : 70.56 % 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: -1.52 (0.31), residues: 690 helix: 0.00 (0.29), residues: 286 sheet: -2.07 (1.22), residues: 12 loop : -1.81 (0.32), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 944 TYR 0.033 0.002 TYR D 946 PHE 0.021 0.002 PHE D1332 TRP 0.024 0.003 TRP D1048 HIS 0.005 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 7053) covalent geometry : angle 0.67871 / 0.36 ( 9814) hydrogen bonds : bond 0.06337 / 6.16 ( 272) hydrogen bonds : angle 5.94873 / 7.13 ( 730) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 78 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: D 830 GLU cc_start: 0.5793 (mp0) cc_final: 0.4850 (mp0) REVERT: D 936 TYR cc_start: 0.4804 (OUTLIER) cc_final: 0.4104 (t80) REVERT: D 971 TYR cc_start: 0.2669 (OUTLIER) cc_final: -0.0564 (p90) REVERT: D 1362 LYS cc_start: 0.4435 (pttp) cc_final: 0.4148 (tmtt) REVERT: D 1831 TRP cc_start: 0.5899 (t-100) cc_final: 0.5564 (t-100) outliers start: 29 outliers final: 17 residues processed: 95 average time/residue: 0.0821 time to fit residues: 10.3659 Evaluate side-chains 95 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1556 ASP Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1705 GLU Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1821 MET Chi-restraints excluded: chain D residue 1837 MET Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 0.0870 chunk 48 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 0.0970 chunk 2 optimal weight: 9.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.174649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.160327 restraints weight = 17760.186| |-----------------------------------------------------------------------------| r_work (start): 0.4714 rms_B_bonded: 3.06 r_work: 0.4603 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5538 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 7053 Z= 0.154 Angle : 0.669 6.793 9814 Z= 0.354 Chirality : 0.043 0.258 1138 Planarity : 0.005 0.047 1053 Dihedral : 18.383 168.122 1599 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.16 % Allowed : 26.08 % Favored : 69.76 % 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: -1.54 (0.31), residues: 690 helix: 0.03 (0.29), residues: 280 sheet: -1.89 (1.27), residues: 12 loop : -1.84 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D1368 TYR 0.029 0.002 TYR D 946 PHE 0.021 0.002 PHE D1332 TRP 0.020 0.003 TRP D1048 HIS 0.005 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 7053) covalent geometry : angle 0.66858 / 0.35 ( 9814) hydrogen bonds : bond 0.06381 / 6.17 ( 272) hydrogen bonds : angle 6.00330 / 7.22 ( 730) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 824 GLU cc_start: 0.5865 (pt0) cc_final: 0.5659 (mt-10) REVERT: D 830 GLU cc_start: 0.5755 (mp0) cc_final: 0.4997 (mp0) REVERT: D 936 TYR cc_start: 0.4836 (OUTLIER) cc_final: 0.4455 (t80) REVERT: D 971 TYR cc_start: 0.2309 (OUTLIER) cc_final: -0.0838 (p90) REVERT: D 1320 ASP cc_start: 0.4970 (t0) cc_final: 0.4672 (t0) REVERT: D 1831 TRP cc_start: 0.5865 (t-100) cc_final: 0.5546 (t-100) REVERT: D 1909 LEU cc_start: 0.6594 (mm) cc_final: 0.6169 (tp) outliers start: 26 outliers final: 17 residues processed: 92 average time/residue: 0.0794 time to fit residues: 9.6996 Evaluate side-chains 92 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1556 ASP Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1662 LEU Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1821 MET Chi-restraints excluded: chain D residue 1837 MET Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 3 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 0.0170 chunk 73 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1679 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.175038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.160832 restraints weight = 17544.966| |-----------------------------------------------------------------------------| r_work (start): 0.4725 rms_B_bonded: 3.02 r_work: 0.4616 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7053 Z= 0.149 Angle : 0.665 6.632 9814 Z= 0.352 Chirality : 0.042 0.246 1138 Planarity : 0.005 0.048 1053 Dihedral : 18.337 168.515 1599 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.48 % Allowed : 25.76 % Favored : 69.76 % 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: -1.50 (0.31), residues: 690 helix: 0.06 (0.30), residues: 280 sheet: -1.88 (1.30), residues: 12 loop : -1.82 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D1368 TYR 0.024 0.002 TYR D 946 PHE 0.020 0.001 PHE D1332 TRP 0.019 0.002 TRP D1048 HIS 0.005 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 7053) covalent geometry : angle 0.66494 / 0.35 ( 9814) hydrogen bonds : bond 0.06469 / 6.23 ( 272) hydrogen bonds : angle 5.92689 / 7.04 ( 730) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 824 GLU cc_start: 0.5891 (pt0) cc_final: 0.5548 (mt-10) REVERT: D 830 GLU cc_start: 0.5528 (mp0) cc_final: 0.4755 (mp0) REVERT: D 936 TYR cc_start: 0.4794 (OUTLIER) cc_final: 0.4430 (t80) REVERT: D 971 TYR cc_start: 0.2372 (OUTLIER) cc_final: -0.0793 (p90) REVERT: D 1831 TRP cc_start: 0.5877 (t-100) cc_final: 0.5587 (t-100) REVERT: D 1909 LEU cc_start: 0.6352 (mm) cc_final: 0.5991 (tp) outliers start: 28 outliers final: 17 residues processed: 94 average time/residue: 0.0964 time to fit residues: 11.6858 Evaluate side-chains 94 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain D residue 1314 ARG Chi-restraints excluded: chain D residue 1357 TYR Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1556 ASP Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1821 MET Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 11 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.0170 chunk 39 optimal weight: 0.5980 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4930 r_free = 0.4930 target = 0.175462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.161165 restraints weight = 17779.025| |-----------------------------------------------------------------------------| r_work (start): 0.4724 rms_B_bonded: 3.05 r_work: 0.4618 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5503 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7053 Z= 0.149 Angle : 0.671 7.006 9814 Z= 0.354 Chirality : 0.043 0.270 1138 Planarity : 0.005 0.048 1053 Dihedral : 18.333 168.905 1599 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 5.12 % Allowed : 24.64 % Favored : 70.24 % 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: -1.42 (0.31), residues: 690 helix: 0.15 (0.30), residues: 283 sheet: -1.96 (1.36), residues: 12 loop : -1.80 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 944 TYR 0.023 0.002 TYR D 946 PHE 0.019 0.002 PHE D1332 TRP 0.019 0.002 TRP D1048 HIS 0.005 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 7053) covalent geometry : angle 0.67100 / 0.35 ( 9814) hydrogen bonds : bond 0.06544 / 6.26 ( 272) hydrogen bonds : angle 5.89447 / 7.01 ( 730) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 830 GLU cc_start: 0.5422 (mp0) cc_final: 0.5002 (mp0) REVERT: D 936 TYR cc_start: 0.4807 (OUTLIER) cc_final: 0.4437 (t80) REVERT: D 971 TYR cc_start: 0.2640 (OUTLIER) cc_final: -0.0686 (p90) REVERT: D 1831 TRP cc_start: 0.5858 (t-100) cc_final: 0.5575 (t-100) REVERT: D 1909 LEU cc_start: 0.6155 (mm) cc_final: 0.5886 (tp) outliers start: 32 outliers final: 23 residues processed: 98 average time/residue: 0.1013 time to fit residues: 13.0080 Evaluate side-chains 101 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain D residue 1314 ARG Chi-restraints excluded: chain D residue 1357 TYR Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1556 ASP Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1662 LEU Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1757 TYR Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1821 MET Chi-restraints excluded: chain D residue 1837 MET Chi-restraints excluded: chain D residue 1839 ARG Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 3 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 56 optimal weight: 0.0980 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1552 GLN 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 = 0.175647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.161457 restraints weight = 17935.359| |-----------------------------------------------------------------------------| r_work (start): 0.4742 rms_B_bonded: 3.06 r_work: 0.4631 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5508 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 7053 Z= 0.159 Angle : 0.714 12.484 9814 Z= 0.368 Chirality : 0.044 0.328 1138 Planarity : 0.005 0.045 1053 Dihedral : 18.363 169.179 1599 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.16 % Allowed : 25.60 % Favored : 70.24 % 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: -1.42 (0.32), residues: 690 helix: 0.18 (0.30), residues: 283 sheet: -1.82 (1.43), residues: 12 loop : -1.84 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 996 TYR 0.022 0.002 TYR D 946 PHE 0.019 0.002 PHE D1332 TRP 0.019 0.002 TRP D1048 HIS 0.004 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 7053) covalent geometry : angle 0.71374 / 0.37 ( 9814) hydrogen bonds : bond 0.06659 / 6.40 ( 272) hydrogen bonds : angle 5.85947 / 7.01 ( 730) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 830 GLU cc_start: 0.5472 (mp0) cc_final: 0.5060 (mp0) REVERT: D 936 TYR cc_start: 0.4967 (OUTLIER) cc_final: 0.4544 (t80) REVERT: D 971 TYR cc_start: 0.2500 (OUTLIER) cc_final: -0.0933 (p90) REVERT: D 1831 TRP cc_start: 0.5824 (t-100) cc_final: 0.5532 (t-100) REVERT: D 1909 LEU cc_start: 0.6220 (mm) cc_final: 0.5922 (tp) outliers start: 26 outliers final: 21 residues processed: 92 average time/residue: 0.0970 time to fit residues: 11.7229 Evaluate side-chains 99 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain D residue 1314 ARG Chi-restraints excluded: chain D residue 1357 TYR Chi-restraints excluded: chain D residue 1371 VAL Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1556 ASP Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1662 LEU Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1821 MET Chi-restraints excluded: chain D residue 1839 ARG Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.0030 chunk 16 optimal weight: 0.1980 chunk 39 optimal weight: 0.0980 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.0030 overall best weight: 0.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 747 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 = 0.4959 r_free = 0.4959 target = 0.177510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.163561 restraints weight = 17820.477| |-----------------------------------------------------------------------------| r_work (start): 0.4770 rms_B_bonded: 2.99 r_work: 0.4660 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5423 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7053 Z= 0.141 Angle : 0.702 8.931 9814 Z= 0.364 Chirality : 0.044 0.326 1138 Planarity : 0.006 0.086 1053 Dihedral : 18.376 169.317 1599 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.52 % Allowed : 26.72 % Favored : 69.76 % 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: -1.35 (0.32), residues: 690 helix: 0.28 (0.31), residues: 283 sheet: -2.08 (1.25), residues: 12 loop : -1.82 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 996 TYR 0.025 0.002 TYR D 946 PHE 0.019 0.001 PHE D1758 TRP 0.018 0.002 TRP D1048 HIS 0.006 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7053) covalent geometry : angle 0.70208 / 0.36 ( 9814) hydrogen bonds : bond 0.06747 / 6.42 ( 272) hydrogen bonds : angle 5.85373 / 6.91 ( 730) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 830 GLU cc_start: 0.5261 (mp0) cc_final: 0.4817 (mp0) REVERT: D 936 TYR cc_start: 0.4931 (OUTLIER) cc_final: 0.4600 (t80) REVERT: D 971 TYR cc_start: 0.3116 (OUTLIER) cc_final: -0.0400 (p90) REVERT: D 1299 GLN cc_start: 0.5133 (tp-100) cc_final: 0.4918 (mm-40) REVERT: D 1831 TRP cc_start: 0.5848 (t-100) cc_final: 0.5577 (t-100) REVERT: D 1909 LEU cc_start: 0.6120 (mm) cc_final: 0.5855 (tp) outliers start: 22 outliers final: 20 residues processed: 87 average time/residue: 0.0920 time to fit residues: 10.5738 Evaluate side-chains 97 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 777 LEU Chi-restraints excluded: chain D residue 787 PHE Chi-restraints excluded: chain D residue 825 VAL Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 894 PHE Chi-restraints excluded: chain D residue 914 TYR Chi-restraints excluded: chain D residue 932 ILE Chi-restraints excluded: chain D residue 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1064 LEU Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain D residue 1314 ARG Chi-restraints excluded: chain D residue 1554 ILE Chi-restraints excluded: chain D residue 1556 ASP Chi-restraints excluded: chain D residue 1569 CYS Chi-restraints excluded: chain D residue 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1757 TYR Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1821 MET Chi-restraints excluded: chain D residue 1839 ARG Chi-restraints excluded: chain D residue 1893 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 27 optimal weight: 0.8980 chunk 34 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1004 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4942 r_free = 0.4942 target = 0.176354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.162096 restraints weight = 17974.043| |-----------------------------------------------------------------------------| r_work (start): 0.4744 rms_B_bonded: 3.07 r_work: 0.4632 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.4632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5496 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 7053 Z= 0.159 Angle : 0.724 10.707 9814 Z= 0.378 Chirality : 0.044 0.296 1138 Planarity : 0.006 0.079 1053 Dihedral : 18.394 169.360 1599 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.68 % Allowed : 26.72 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.32), residues: 690 helix: 0.28 (0.31), residues: 277 sheet: -1.88 (1.32), residues: 12 loop : -1.87 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 944 TYR 0.022 0.002 TYR D 946 PHE 0.020 0.002 PHE D1332 TRP 0.018 0.002 TRP D1048 HIS 0.010 0.002 HIS D1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 ( 7053) covalent geometry : angle 0.72393 / 0.38 ( 9814) hydrogen bonds : bond 0.06747 / 6.42 ( 272) hydrogen bonds : angle 5.87846 / 6.97 ( 730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1686.48 seconds wall clock time: 29 minutes 49.65 seconds (1789.65 seconds total)