Starting phenix.real_space_refine on Thu Jul 2 05:46:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21cq_67575/07_2026/21cq_67575.cif Found real_map, /net/cci-nas-00/data/ceres_data/21cq_67575/07_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_67575/07_2026/21cq_67575.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21cq_67575/07_2026/21cq_67575.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21cq_67575/07_2026/21cq_67575.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21cq_67575/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 1.21, per 1000 atoms: 0.18 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: 0.41 Conformation dependent library (CDL) restraints added in 217.2 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: 0.59 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: 0.87 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 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=" 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=" 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 bond pdb=" N ASN D1848 " pdb=" CA ASN D1848 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.31e-02 5.83e+03 6.10e+00 bond pdb=" N ALA D1847 " pdb=" CA ALA D1847 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.18e-02 7.18e+03 5.70e+00 ... (remaining 7048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 9598 3.12 - 6.23: 198 6.23 - 9.35: 16 9.35 - 12.47: 1 12.47 - 15.58: 1 Bond angle restraints: 9814 Sorted by residual: 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=" O3' C R 61 " pdb=" P U R 62 " pdb=" O5' U R 62 " ideal model delta sigma weight residual 104.00 110.99 -6.99 1.50e+00 4.44e-01 2.17e+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 1.00e+00 1.00e+00 1.88e+01 angle pdb=" C4' G R 1 " pdb=" C3' G R 1 " pdb=" O3' G R 1 " ideal model delta sigma weight residual 113.00 106.93 6.07 1.50e+00 4.44e-01 1.64e+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: 1046 0.113 - 0.227: 63 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 3.250 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: 0.990 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.260 Find NCS groups from input model: 0.010 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.250 ------------------------------------------------------------------------------- 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= 0.328 Angle : 0.983 15.583 9814 Z= 0.556 Chirality : 0.091 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 / 0.33 ( 7053) covalent geometry : angle 0.98346 / 0.56 ( 9814) hydrogen bonds : bond 0.16308 / 17.82 ( 272) hydrogen bonds : angle 7.12308 / 7.83 ( 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 : 0.187 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: 0.3657 (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: 0.2808 (tmm160) outliers start: 6 outliers final: 3 residues processed: 89 average time/residue: 0.0905 time to fit residues: 10.1573 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 : 0.189 ------------------------------------------------------------------------------- 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: 0.5980 chunk 53 optimal weight: 0.0970 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.4980 chunk 74 optimal weight: 8.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1685 GLN D1695 ASN D1742 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.176031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4751 r_free = 0.4751 target = 0.161773 restraints weight = 17619.404| |-----------------------------------------------------------------------------| r_work (start): 0.4735 rms_B_bonded: 3.02 r_work: 0.4623 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.4623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 7053 Z= 0.192 Angle : 0.744 10.977 9814 Z= 0.399 Chirality : 0.047 0.527 1138 Planarity : 0.007 0.060 1053 Dihedral : 18.724 158.803 1609 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.16 % Allowed : 22.24 % 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: -1.61 (0.31), residues: 690 helix: -0.02 (0.29), residues: 281 sheet: -3.44 (0.78), residues: 25 loop : -1.76 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1358 TYR 0.030 0.002 TYR D 976 PHE 0.023 0.002 PHE D1332 TRP 0.044 0.003 TRP D1048 HIS 0.007 0.001 HIS D 856 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 ( 7053) covalent geometry : angle 0.74442 / 0.40 ( 9814) hydrogen bonds : bond 0.07486 / 7.03 ( 272) hydrogen bonds : angle 6.12995 / 6.87 ( 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 114 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.171 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: 0.4210 (OUTLIER) cc_final: 0.3929 (mtp180) REVERT: D 971 TYR cc_start: 0.1864 (OUTLIER) cc_final: -0.0577 (p90) REVERT: D 1320 ASP cc_start: 0.4705 (t0) cc_final: 0.4464 (t0) REVERT: D 1358 ARG cc_start: 0.3205 (tmm160) cc_final: 0.2981 (tmm160) REVERT: D 1722 GLU cc_start: 0.4907 (OUTLIER) cc_final: 0.4604 (mp0) REVERT: D 1831 TRP cc_start: 0.5494 (t-100) cc_final: 0.5047 (t-100) REVERT: D 1837 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.4836 (mpp) outliers start: 26 outliers final: 12 residues processed: 103 average time/residue: 0.0786 time to fit residues: 10.5602 Evaluate side-chains 97 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 1346 MET 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: 4.9990 chunk 24 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 68 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4930 r_free = 0.4930 target = 0.175508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.161349 restraints weight = 17631.312| |-----------------------------------------------------------------------------| r_work (start): 0.4730 rms_B_bonded: 3.04 r_work: 0.4620 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5501 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7053 Z= 0.172 Angle : 0.695 10.809 9814 Z= 0.374 Chirality : 0.046 0.542 1138 Planarity : 0.006 0.046 1053 Dihedral : 18.610 164.461 1607 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.80 % Allowed : 23.68 % Favored : 71.52 % 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: 690 helix: 0.13 (0.29), residues: 278 sheet: -3.42 (0.82), residues: 25 loop : -1.76 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 944 TYR 0.020 0.002 TYR D 965 PHE 0.023 0.002 PHE D1332 TRP 0.039 0.004 TRP D1048 HIS 0.007 0.001 HIS D 856 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 ( 7053) covalent geometry : angle 0.69484 / 0.37 ( 9814) hydrogen bonds : bond 0.06687 / 6.23 ( 272) hydrogen bonds : angle 6.05914 / 6.82 ( 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 112 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.146 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: 0.4301 (OUTLIER) cc_final: 0.3752 (mtp180) REVERT: D 971 TYR cc_start: 0.2200 (OUTLIER) cc_final: -0.0655 (p90) REVERT: D 1064 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5675 (tt) REVERT: D 1362 LYS cc_start: 0.4523 (pttp) cc_final: 0.4135 (tmtt) REVERT: D 1831 TRP cc_start: 0.5823 (t-100) cc_final: 0.5396 (t-100) REVERT: D 1837 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5126 (mpp) REVERT: D 1909 LEU cc_start: 0.6696 (mp) cc_final: 0.6013 (tp) outliers start: 30 outliers final: 15 residues processed: 100 average time/residue: 0.0751 time to fit residues: 9.7934 Evaluate side-chains 98 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.157 ------------------------------------------------------------------------------- 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 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 1064 LEU Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain D residue 1317 MET Chi-restraints excluded: chain D residue 1554 ILE 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: 0.8980 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4916 r_free = 0.4916 target = 0.174492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.160021 restraints weight = 17585.076| |-----------------------------------------------------------------------------| r_work (start): 0.4701 rms_B_bonded: 3.05 r_work: 0.4586 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5554 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7053 Z= 0.181 Angle : 0.704 10.043 9814 Z= 0.373 Chirality : 0.047 0.551 1138 Planarity : 0.006 0.045 1053 Dihedral : 18.542 166.870 1607 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.96 % Allowed : 24.00 % 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: -1.48 (0.31), residues: 690 helix: 0.10 (0.29), residues: 284 sheet: -2.14 (1.22), residues: 12 loop : -1.83 (0.32), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 789 TYR 0.038 0.003 TYR D 946 PHE 0.022 0.002 PHE D1332 TRP 0.028 0.003 TRP D1048 HIS 0.005 0.001 HIS D 856 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.18 ( 7053) covalent geometry : angle 0.70432 / 0.37 ( 9814) hydrogen bonds : bond 0.06362 / 5.92 ( 272) hydrogen bonds : angle 6.01721 / 6.84 ( 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: 31 poor density : 80 time to evaluate : 0.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 800 ARG cc_start: 0.4358 (OUTLIER) cc_final: 0.3520 (mtp180) REVERT: D 830 GLU cc_start: 0.5719 (mp0) cc_final: 0.5288 (mp0) REVERT: D 971 TYR cc_start: 0.2484 (OUTLIER) cc_final: -0.0619 (p90) REVERT: D 1320 ASP cc_start: 0.4779 (t0) cc_final: 0.4552 (t0) REVERT: D 1831 TRP cc_start: 0.5923 (t-100) cc_final: 0.5541 (t-100) outliers start: 31 outliers final: 16 residues processed: 99 average time/residue: 0.0702 time to fit residues: 9.1127 Evaluate side-chains 95 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.172 ------------------------------------------------------------------------------- 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 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 993 THR Chi-restraints excluded: chain D residue 1069 GLU Chi-restraints excluded: chain D residue 1317 MET 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 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: 1.9990 chunk 8 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 19 optimal weight: 0.0040 chunk 17 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 856 HIS ** D1552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1679 ASN D1727 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.172658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.157855 restraints weight = 17709.628| |-----------------------------------------------------------------------------| r_work (start): 0.4672 rms_B_bonded: 3.08 r_work: 0.4561 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5652 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 7053 Z= 0.192 Angle : 0.716 6.676 9814 Z= 0.382 Chirality : 0.044 0.207 1138 Planarity : 0.006 0.047 1053 Dihedral : 18.498 167.443 1603 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 5.60 % Allowed : 24.64 % 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: -1.62 (0.31), residues: 690 helix: -0.15 (0.28), residues: 289 sheet: -2.03 (1.19), residues: 12 loop : -1.82 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 944 TYR 0.023 0.002 TYR D 946 PHE 0.023 0.002 PHE D1332 TRP 0.018 0.003 TRP D1048 HIS 0.005 0.001 HIS D1041 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 ( 7053) covalent geometry : angle 0.71638 / 0.38 ( 9814) hydrogen bonds : bond 0.06407 / 5.95 ( 272) hydrogen bonds : angle 6.09680 / 6.91 ( 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 115 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 80 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 830 GLU cc_start: 0.5849 (mp0) cc_final: 0.5557 (mp0) REVERT: D 936 TYR cc_start: 0.5143 (OUTLIER) cc_final: 0.4279 (t80) REVERT: D 971 TYR cc_start: 0.2276 (OUTLIER) cc_final: -0.0998 (p90) REVERT: D 1362 LYS cc_start: 0.4420 (pttp) cc_final: 0.3896 (tmtt) REVERT: D 1831 TRP cc_start: 0.5823 (t-100) cc_final: 0.5448 (t-100) outliers start: 35 outliers final: 21 residues processed: 100 average time/residue: 0.0991 time to fit residues: 12.8877 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 : 0.220 ------------------------------------------------------------------------------- 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 1317 MET 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 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 1767 HIS Chi-restraints excluded: chain D residue 1837 MET Chi-restraints excluded: chain D residue 1857 LEU 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: 0.2980 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 43 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1727 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.173834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.159321 restraints weight = 17738.197| |-----------------------------------------------------------------------------| r_work (start): 0.4694 rms_B_bonded: 3.07 r_work: 0.4584 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5598 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 7053 Z= 0.159 Angle : 0.696 7.957 9814 Z= 0.368 Chirality : 0.043 0.192 1138 Planarity : 0.006 0.046 1053 Dihedral : 18.431 167.915 1599 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 4.64 % Allowed : 25.28 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.31), residues: 690 helix: -0.04 (0.29), residues: 280 sheet: -2.01 (1.24), residues: 12 loop : -1.86 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 789 TYR 0.028 0.002 TYR D 946 PHE 0.022 0.002 PHE D1332 TRP 0.018 0.002 TRP D1048 HIS 0.005 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 7053) covalent geometry : angle 0.69574 / 0.37 ( 9814) hydrogen bonds : bond 0.06377 / 5.78 ( 272) hydrogen bonds : angle 6.03423 / 6.83 ( 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 111 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.262 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 800 ARG cc_start: 0.4298 (OUTLIER) cc_final: 0.3292 (mtp180) REVERT: D 830 GLU cc_start: 0.5843 (mp0) cc_final: 0.5521 (mp0) REVERT: D 936 TYR cc_start: 0.4964 (OUTLIER) cc_final: 0.4489 (t80) REVERT: D 971 TYR cc_start: 0.2209 (OUTLIER) cc_final: -0.1032 (p90) REVERT: D 1320 ASP cc_start: 0.4905 (t0) cc_final: 0.4653 (t0) REVERT: D 1362 LYS cc_start: 0.4562 (pttp) cc_final: 0.4193 (tmtt) REVERT: D 1831 TRP cc_start: 0.5902 (t-100) cc_final: 0.5544 (t-100) REVERT: D 1909 LEU cc_start: 0.6983 (mp) cc_final: 0.6237 (tp) outliers start: 29 outliers final: 18 residues processed: 99 average time/residue: 0.1051 time to fit residues: 13.3916 Evaluate side-chains 97 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1314 ARG Chi-restraints excluded: chain D residue 1317 MET 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 1893 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 8 optimal weight: 0.0970 chunk 23 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D1552 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.172960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.158475 restraints weight = 17402.160| |-----------------------------------------------------------------------------| r_work (start): 0.4681 rms_B_bonded: 3.01 r_work: 0.4570 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.4570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5634 moved from start: 0.2942 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= 0.169 Angle : 0.710 10.481 9814 Z= 0.375 Chirality : 0.044 0.300 1138 Planarity : 0.006 0.045 1053 Dihedral : 18.430 168.373 1599 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.64 % Allowed : 24.32 % 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: -1.62 (0.31), residues: 690 helix: -0.07 (0.29), residues: 280 sheet: -1.94 (1.34), residues: 12 loop : -1.86 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1314 TYR 0.023 0.002 TYR D 946 PHE 0.021 0.002 PHE D1332 TRP 0.018 0.002 TRP D1048 HIS 0.005 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 7053) covalent geometry : angle 0.70986 / 0.38 ( 9814) hydrogen bonds : bond 0.06427 / 5.83 ( 272) hydrogen bonds : angle 6.05452 / 6.79 ( 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: 29 poor density : 76 time to evaluate : 0.238 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: 0.4335 (OUTLIER) cc_final: 0.3345 (mtp180) REVERT: D 830 GLU cc_start: 0.5895 (mp0) cc_final: 0.5594 (mp0) REVERT: D 936 TYR cc_start: 0.5197 (OUTLIER) cc_final: 0.4848 (t80) REVERT: D 971 TYR cc_start: 0.2460 (OUTLIER) cc_final: -0.1054 (p90) REVERT: D 1320 ASP cc_start: 0.4968 (t0) cc_final: 0.4713 (t0) REVERT: D 1362 LYS cc_start: 0.4471 (pttp) cc_final: 0.4130 (tmtt) REVERT: D 1831 TRP cc_start: 0.5918 (t-100) cc_final: 0.5573 (t-100) REVERT: D 1909 LEU cc_start: 0.6729 (mp) cc_final: 0.5977 (tp) outliers start: 29 outliers final: 19 residues processed: 95 average time/residue: 0.1000 time to fit residues: 12.3417 Evaluate side-chains 95 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.223 ------------------------------------------------------------------------------- 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 932 ILE Chi-restraints excluded: chain D residue 936 TYR Chi-restraints excluded: chain D residue 971 TYR Chi-restraints excluded: chain D residue 1317 MET Chi-restraints excluded: chain D residue 1346 MET Chi-restraints excluded: chain D residue 1357 TYR 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 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 1857 LEU 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: 0.6980 chunk 49 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 34 optimal weight: 0.4980 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 61 optimal weight: 0.4980 chunk 2 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 40.0000 chunk 39 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1004 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 = 0.4896 r_free = 0.4896 target = 0.172871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.158409 restraints weight = 17665.971| |-----------------------------------------------------------------------------| r_work (start): 0.4688 rms_B_bonded: 3.02 r_work: 0.4576 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5614 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7053 Z= 0.169 Angle : 0.717 11.793 9814 Z= 0.378 Chirality : 0.044 0.211 1138 Planarity : 0.006 0.081 1053 Dihedral : 18.475 168.863 1599 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 4.16 % Allowed : 25.12 % Favored : 70.72 % 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: -1.64 (0.31), residues: 690 helix: -0.10 (0.29), residues: 280 sheet: -1.55 (1.50), residues: 12 loop : -1.88 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D1368 TYR 0.025 0.002 TYR D 946 PHE 0.021 0.002 PHE D1332 TRP 0.016 0.003 TRP D1048 HIS 0.006 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 7053) covalent geometry : angle 0.71686 / 0.38 ( 9814) hydrogen bonds : bond 0.06555 / 5.83 ( 272) hydrogen bonds : angle 6.02216 / 6.77 ( 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 102 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.225 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: 0.4523 (OUTLIER) cc_final: 0.3554 (mtp180) REVERT: D 830 GLU cc_start: 0.5867 (mp0) cc_final: 0.5544 (mp0) REVERT: D 936 TYR cc_start: 0.5171 (OUTLIER) cc_final: 0.4895 (t80) REVERT: D 971 TYR cc_start: 0.2672 (OUTLIER) cc_final: -0.1083 (p90) REVERT: D 1362 LYS cc_start: 0.4294 (pttp) cc_final: 0.3966 (tmtt) REVERT: D 1691 SER cc_start: 0.6039 (p) cc_final: 0.5313 (t) REVERT: D 1831 TRP cc_start: 0.5903 (t-100) cc_final: 0.5576 (t-100) REVERT: D 1909 LEU cc_start: 0.6690 (mp) cc_final: 0.5948 (tp) outliers start: 26 outliers final: 17 residues processed: 94 average time/residue: 0.1087 time to fit residues: 13.2019 Evaluate side-chains 96 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 831 LEU Chi-restraints excluded: chain D residue 894 PHE 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 1317 MET 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 1857 LEU 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: 2.9990 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.2980 chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 747 GLN ** D1004 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 = 0.4876 r_free = 0.4876 target = 0.170826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.156628 restraints weight = 17166.245| |-----------------------------------------------------------------------------| r_work (start): 0.4671 rms_B_bonded: 2.96 r_work: 0.4561 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5646 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 7053 Z= 0.177 Angle : 0.727 11.433 9814 Z= 0.383 Chirality : 0.045 0.284 1138 Planarity : 0.006 0.072 1053 Dihedral : 18.559 169.343 1599 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 3.68 % Allowed : 25.60 % Favored : 70.72 % 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: -1.67 (0.31), residues: 690 helix: -0.08 (0.29), residues: 280 sheet: -2.64 (0.94), residues: 22 loop : -1.86 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1368 TYR 0.023 0.002 TYR D 946 PHE 0.022 0.002 PHE D1332 TRP 0.015 0.003 TRP D1048 HIS 0.004 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 7053) covalent geometry : angle 0.72677 / 0.38 ( 9814) hydrogen bonds : bond 0.06786 / 5.96 ( 272) hydrogen bonds : angle 6.01144 / 6.69 ( 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 98 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.282 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 800 ARG cc_start: 0.4504 (OUTLIER) cc_final: 0.3571 (mtp180) REVERT: D 830 GLU cc_start: 0.5958 (mp0) cc_final: 0.5672 (mp0) REVERT: D 936 TYR cc_start: 0.5136 (OUTLIER) cc_final: 0.4874 (t80) REVERT: D 971 TYR cc_start: 0.2779 (OUTLIER) cc_final: -0.1225 (p90) REVERT: D 1691 SER cc_start: 0.6197 (p) cc_final: 0.5520 (t) REVERT: D 1831 TRP cc_start: 0.5947 (t-100) cc_final: 0.5618 (t-100) REVERT: D 1909 LEU cc_start: 0.6707 (mp) cc_final: 0.5972 (tp) outliers start: 23 outliers final: 17 residues processed: 90 average time/residue: 0.0929 time to fit residues: 11.2248 Evaluate side-chains 95 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 800 ARG Chi-restraints excluded: chain D residue 831 LEU Chi-restraints excluded: chain D residue 894 PHE 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 1317 MET 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 1857 LEU 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: 1.9990 chunk 32 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 15 optimal weight: 0.0470 chunk 8 optimal weight: 0.9980 chunk 55 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1004 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 = 0.4901 r_free = 0.4901 target = 0.173223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.158884 restraints weight = 17532.604| |-----------------------------------------------------------------------------| r_work (start): 0.4691 rms_B_bonded: 3.01 r_work: 0.4580 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5592 moved from start: 0.3490 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= 0.154 Angle : 0.722 11.093 9814 Z= 0.376 Chirality : 0.045 0.363 1138 Planarity : 0.006 0.069 1053 Dihedral : 18.561 169.460 1599 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.84 % Allowed : 25.60 % 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: -1.62 (0.31), residues: 690 helix: 0.06 (0.30), residues: 280 sheet: -3.06 (0.84), residues: 22 loop : -1.89 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1368 TYR 0.027 0.002 TYR D 946 PHE 0.023 0.002 PHE D1758 TRP 0.014 0.002 TRP D1048 HIS 0.005 0.001 HIS D1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 7053) covalent geometry : angle 0.72247 / 0.38 ( 9814) hydrogen bonds : bond 0.06726 / 5.83 ( 272) hydrogen bonds : angle 5.95594 / 6.64 ( 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 107 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.210 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: 0.4568 (OUTLIER) cc_final: 0.3735 (mtp180) REVERT: D 830 GLU cc_start: 0.5815 (mp0) cc_final: 0.5534 (mp0) REVERT: D 936 TYR cc_start: 0.5097 (OUTLIER) cc_final: 0.4836 (t80) REVERT: D 971 TYR cc_start: 0.2804 (OUTLIER) cc_final: -0.1261 (p90) REVERT: D 1691 SER cc_start: 0.6088 (p) cc_final: 0.5411 (t) REVERT: D 1831 TRP cc_start: 0.5859 (t-100) cc_final: 0.5555 (t-100) REVERT: D 1909 LEU cc_start: 0.6548 (mp) cc_final: 0.5821 (tp) outliers start: 24 outliers final: 16 residues processed: 99 average time/residue: 0.1024 time to fit residues: 13.2077 Evaluate side-chains 96 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.176 ------------------------------------------------------------------------------- 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 800 ARG 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 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 1701 TYR Chi-restraints excluded: chain D residue 1722 GLU Chi-restraints excluded: chain D residue 1761 VAL Chi-restraints excluded: chain D residue 1857 LEU 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: 0.5980 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D1004 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 = 0.4886 r_free = 0.4886 target = 0.171815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.157865 restraints weight = 17053.255| |-----------------------------------------------------------------------------| r_work (start): 0.4694 rms_B_bonded: 2.90 r_work: 0.4584 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5588 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7053 Z= 0.162 Angle : 0.725 11.092 9814 Z= 0.379 Chirality : 0.044 0.275 1138 Planarity : 0.006 0.068 1053 Dihedral : 18.586 169.451 1599 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 3.52 % Allowed : 25.76 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.31), residues: 690 helix: -0.03 (0.29), residues: 281 sheet: -3.34 (0.80), residues: 22 loop : -1.89 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1906 TYR 0.026 0.002 TYR D 946 PHE 0.020 0.002 PHE D1332 TRP 0.013 0.002 TRP D1048 HIS 0.006 0.001 HIS D1041 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 7053) covalent geometry : angle 0.72512 / 0.38 ( 9814) hydrogen bonds : bond 0.06781 / 5.88 ( 272) hydrogen bonds : angle 5.96585 / 6.58 ( 730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1630.17 seconds wall clock time: 28 minutes 51.07 seconds (1731.07 seconds total)