Starting phenix.real_space_refine on Fri Mar 6 18:15:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u5l_26354/03_2026/7u5l_26354.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u5l_26354/03_2026/7u5l_26354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u5l_26354/03_2026/7u5l_26354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u5l_26354/03_2026/7u5l_26354.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u5l_26354/03_2026/7u5l_26354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u5l_26354/03_2026/7u5l_26354.map" } resolution = 2.67 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= 0.000 sd= 0.133 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: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 192 5.16 5 C 21288 2.51 5 N 6048 2.21 5 O 6552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34104 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 2.91, per 1000 atoms: 0.09 Number of scatterers: 34104 At special positions: 0 Unit cell: (129.47, 129.47, 129.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 24 26.01 S 192 16.00 O 6552 8.00 N 6048 7.00 C 21288 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: 2.85 Conformation dependent library (CDL) restraints added in 1.5 seconds 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 14 through 42 Processing helix chain 'A' and resid 49 through 77 Processing helix chain 'A' and resid 96 through 125 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 138 through 160 Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 42 Processing helix chain 'B' and resid 49 through 77 Processing helix chain 'B' and resid 96 through 125 Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 138 through 160 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 42 Processing helix chain 'C' and resid 49 through 77 Processing helix chain 'C' and resid 96 through 125 Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 138 through 160 Processing helix chain 'C' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 42 Processing helix chain 'D' and resid 49 through 77 Processing helix chain 'D' and resid 96 through 125 Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 138 through 160 Processing helix chain 'D' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 42 Processing helix chain 'E' and resid 49 through 77 Processing helix chain 'E' and resid 96 through 125 Processing helix chain 'E' and resid 127 through 138 Processing helix chain 'E' and resid 138 through 160 Processing helix chain 'E' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 42 Processing helix chain 'F' and resid 49 through 77 Processing helix chain 'F' and resid 96 through 125 Processing helix chain 'F' and resid 127 through 138 Processing helix chain 'F' and resid 138 through 160 Processing helix chain 'F' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU F 168 " --> pdb=" O SER F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 42 Processing helix chain 'G' and resid 49 through 77 Processing helix chain 'G' and resid 96 through 125 Processing helix chain 'G' and resid 127 through 138 Processing helix chain 'G' and resid 138 through 160 Processing helix chain 'G' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU G 168 " --> pdb=" O SER G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 42 Processing helix chain 'H' and resid 49 through 77 Processing helix chain 'H' and resid 96 through 125 Processing helix chain 'H' and resid 127 through 138 Processing helix chain 'H' and resid 138 through 160 Processing helix chain 'H' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU H 168 " --> pdb=" O SER H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 42 Processing helix chain 'I' and resid 49 through 77 Processing helix chain 'I' and resid 96 through 125 Processing helix chain 'I' and resid 127 through 138 Processing helix chain 'I' and resid 138 through 160 Processing helix chain 'I' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU I 168 " --> pdb=" O SER I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 42 Processing helix chain 'J' and resid 49 through 77 Processing helix chain 'J' and resid 96 through 125 Processing helix chain 'J' and resid 127 through 138 Processing helix chain 'J' and resid 138 through 160 Processing helix chain 'J' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU J 168 " --> pdb=" O SER J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 42 Processing helix chain 'K' and resid 49 through 77 Processing helix chain 'K' and resid 96 through 125 Processing helix chain 'K' and resid 127 through 138 Processing helix chain 'K' and resid 138 through 160 Processing helix chain 'K' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU K 168 " --> pdb=" O SER K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 42 Processing helix chain 'L' and resid 49 through 77 Processing helix chain 'L' and resid 96 through 125 Processing helix chain 'L' and resid 127 through 138 Processing helix chain 'L' and resid 138 through 160 Processing helix chain 'L' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU L 168 " --> pdb=" O SER L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 42 Processing helix chain 'M' and resid 49 through 77 Processing helix chain 'M' and resid 96 through 125 Processing helix chain 'M' and resid 127 through 138 Processing helix chain 'M' and resid 138 through 160 Processing helix chain 'M' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU M 168 " --> pdb=" O SER M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 42 Processing helix chain 'N' and resid 49 through 77 Processing helix chain 'N' and resid 96 through 125 Processing helix chain 'N' and resid 127 through 138 Processing helix chain 'N' and resid 138 through 160 Processing helix chain 'N' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU N 168 " --> pdb=" O SER N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 42 Processing helix chain 'O' and resid 49 through 77 Processing helix chain 'O' and resid 96 through 125 Processing helix chain 'O' and resid 127 through 138 Processing helix chain 'O' and resid 138 through 160 Processing helix chain 'O' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 42 Processing helix chain 'P' and resid 49 through 77 Processing helix chain 'P' and resid 96 through 125 Processing helix chain 'P' and resid 127 through 138 Processing helix chain 'P' and resid 138 through 160 Processing helix chain 'P' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU P 168 " --> pdb=" O SER P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 42 Processing helix chain 'Q' and resid 49 through 77 Processing helix chain 'Q' and resid 96 through 125 Processing helix chain 'Q' and resid 127 through 138 Processing helix chain 'Q' and resid 138 through 160 Processing helix chain 'Q' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 42 Processing helix chain 'R' and resid 49 through 77 Processing helix chain 'R' and resid 96 through 125 Processing helix chain 'R' and resid 127 through 138 Processing helix chain 'R' and resid 138 through 160 Processing helix chain 'R' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU R 168 " --> pdb=" O SER R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 42 Processing helix chain 'S' and resid 49 through 77 Processing helix chain 'S' and resid 96 through 125 Processing helix chain 'S' and resid 127 through 138 Processing helix chain 'S' and resid 138 through 160 Processing helix chain 'S' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU S 168 " --> pdb=" O SER S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 42 Processing helix chain 'T' and resid 49 through 77 Processing helix chain 'T' and resid 96 through 125 Processing helix chain 'T' and resid 127 through 138 Processing helix chain 'T' and resid 138 through 160 Processing helix chain 'T' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU T 168 " --> pdb=" O SER T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 42 Processing helix chain 'U' and resid 49 through 77 Processing helix chain 'U' and resid 96 through 125 Processing helix chain 'U' and resid 127 through 138 Processing helix chain 'U' and resid 138 through 160 Processing helix chain 'U' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU U 168 " --> pdb=" O SER U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 42 Processing helix chain 'V' and resid 49 through 77 Processing helix chain 'V' and resid 96 through 125 Processing helix chain 'V' and resid 127 through 138 Processing helix chain 'V' and resid 138 through 160 Processing helix chain 'V' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU V 168 " --> pdb=" O SER V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 42 Processing helix chain 'W' and resid 49 through 77 Processing helix chain 'W' and resid 96 through 125 Processing helix chain 'W' and resid 127 through 138 Processing helix chain 'W' and resid 138 through 160 Processing helix chain 'W' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 42 Processing helix chain 'X' and resid 49 through 77 Processing helix chain 'X' and resid 96 through 125 Processing helix chain 'X' and resid 127 through 138 Processing helix chain 'X' and resid 138 through 160 Processing helix chain 'X' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU X 168 " --> pdb=" O SER X 164 " (cutoff:3.500A) 2640 hydrogen bonds defined for protein. 7920 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.32 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7053 1.32 - 1.44: 8486 1.44 - 1.57: 18925 1.57 - 1.69: 0 1.69 - 1.81: 312 Bond restraints: 34776 Sorted by residual: bond pdb=" CA ALA O 67 " pdb=" C ALA O 67 " ideal model delta sigma weight residual 1.524 1.482 0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" CA ALA V 67 " pdb=" C ALA V 67 " ideal model delta sigma weight residual 1.524 1.482 0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" CA ALA D 67 " pdb=" C ALA D 67 " ideal model delta sigma weight residual 1.524 1.482 0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" CA ALA C 67 " pdb=" C ALA C 67 " ideal model delta sigma weight residual 1.524 1.482 0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" CA ALA Q 67 " pdb=" C ALA Q 67 " ideal model delta sigma weight residual 1.524 1.483 0.040 1.29e-02 6.01e+03 9.77e+00 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 45360 1.41 - 2.82: 1211 2.82 - 4.23: 157 4.23 - 5.64: 72 5.64 - 7.05: 24 Bond angle restraints: 46824 Sorted by residual: angle pdb=" N VAL C 143 " pdb=" CA VAL C 143 " pdb=" C VAL C 143 " ideal model delta sigma weight residual 111.00 106.80 4.20 1.09e+00 8.42e-01 1.49e+01 angle pdb=" N VAL M 143 " pdb=" CA VAL M 143 " pdb=" C VAL M 143 " ideal model delta sigma weight residual 111.00 106.82 4.18 1.09e+00 8.42e-01 1.47e+01 angle pdb=" N VAL U 143 " pdb=" CA VAL U 143 " pdb=" C VAL U 143 " ideal model delta sigma weight residual 111.00 106.83 4.17 1.09e+00 8.42e-01 1.46e+01 angle pdb=" N VAL L 143 " pdb=" CA VAL L 143 " pdb=" C VAL L 143 " ideal model delta sigma weight residual 111.00 106.83 4.17 1.09e+00 8.42e-01 1.46e+01 angle pdb=" N VAL Q 143 " pdb=" CA VAL Q 143 " pdb=" C VAL Q 143 " ideal model delta sigma weight residual 111.00 106.84 4.16 1.09e+00 8.42e-01 1.45e+01 ... (remaining 46819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.69: 19416 14.69 - 29.39: 1176 29.39 - 44.08: 336 44.08 - 58.78: 48 58.78 - 73.47: 120 Dihedral angle restraints: 21096 sinusoidal: 8832 harmonic: 12264 Sorted by residual: dihedral pdb=" CA ASP J 172 " pdb=" CB ASP J 172 " pdb=" CG ASP J 172 " pdb=" OD1 ASP J 172 " ideal model delta sinusoidal sigma weight residual -30.00 -89.94 59.94 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP E 172 " pdb=" CB ASP E 172 " pdb=" CG ASP E 172 " pdb=" OD1 ASP E 172 " ideal model delta sinusoidal sigma weight residual -30.00 -89.93 59.93 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP T 172 " pdb=" CB ASP T 172 " pdb=" CG ASP T 172 " pdb=" OD1 ASP T 172 " ideal model delta sinusoidal sigma weight residual -30.00 -89.92 59.92 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 21093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4206 0.062 - 0.124: 459 0.124 - 0.185: 87 0.185 - 0.247: 72 0.247 - 0.309: 48 Chirality restraints: 4872 Sorted by residual: chirality pdb=" CA GLN G 142 " pdb=" N GLN G 142 " pdb=" C GLN G 142 " pdb=" CB GLN G 142 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA GLN V 142 " pdb=" N GLN V 142 " pdb=" C GLN V 142 " pdb=" CB GLN V 142 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA GLN O 142 " pdb=" N GLN O 142 " pdb=" C GLN O 142 " pdb=" CB GLN O 142 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 4869 not shown) Planarity restraints: 6216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN T 140 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ASN T 140 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN T 140 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU T 141 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN K 140 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ASN K 140 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN K 140 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU K 141 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN I 140 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ASN I 140 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN I 140 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU I 141 " 0.012 2.00e-02 2.50e+03 ... (remaining 6213 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 96 2.37 - 3.00: 17766 3.00 - 3.63: 56434 3.63 - 4.27: 89980 4.27 - 4.90: 141307 Nonbonded interactions: 305583 Sorted by model distance: nonbonded pdb=" ND1 HIS V 66 " pdb="FE FE V 201 " model vdw 1.737 2.340 nonbonded pdb=" ND1 HIS D 66 " pdb="FE FE D 201 " model vdw 1.737 2.340 nonbonded pdb=" ND1 HIS O 66 " pdb="FE FE O 201 " model vdw 1.737 2.340 nonbonded pdb=" ND1 HIS G 66 " pdb="FE FE G 201 " model vdw 1.737 2.340 nonbonded pdb=" ND1 HIS A 66 " pdb="FE FE A 201 " model vdw 1.737 2.340 ... (remaining 305578 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 25.150 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 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:8.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.005 0.041 34776 Z= 0.357 Angle : 0.579 7.048 46824 Z= 0.358 Chirality : 0.057 0.309 4872 Planarity : 0.003 0.021 6216 Dihedral : 12.292 73.471 13176 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.39 (0.13), residues: 4104 helix: 3.40 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : 0.75 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 109 TYR 0.011 0.001 TYR L 40 PHE 0.012 0.001 PHE K 133 TRP 0.002 0.001 TRP U 94 HIS 0.003 0.001 HIS F 66 Details of bonding type rmsd covalent geometry : bond 0.00482 (34776) covalent geometry : angle 0.57892 (46824) hydrogen bonds : bond 0.09518 ( 2640) hydrogen bonds : angle 3.99911 ( 7920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1425 time to evaluate : 1.230 Fit side-chains REVERT: A 18 GLU cc_start: 0.8333 (tt0) cc_final: 0.8057 (tt0) REVERT: A 63 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6781 (mm-30) REVERT: A 64 ARG cc_start: 0.8099 (tpp80) cc_final: 0.7311 (ttp-170) REVERT: A 68 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8135 (mt-10) REVERT: A 91 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7943 (mtp85) REVERT: A 93 ASP cc_start: 0.7910 (t0) cc_final: 0.7669 (t70) REVERT: A 113 GLN cc_start: 0.8718 (tp40) cc_final: 0.8438 (tp40) REVERT: A 125 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8641 (mmtm) REVERT: A 135 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7325 (mt-10) REVERT: A 148 GLU cc_start: 0.8333 (tt0) cc_final: 0.8118 (tt0) REVERT: A 173 LYS cc_start: 0.8679 (mptp) cc_final: 0.8367 (mptp) REVERT: B 16 ASP cc_start: 0.8858 (m-30) cc_final: 0.8549 (m-30) REVERT: B 18 GLU cc_start: 0.8314 (tt0) cc_final: 0.8037 (tt0) REVERT: B 63 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6784 (mm-30) REVERT: B 91 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7939 (mtp85) REVERT: B 93 ASP cc_start: 0.7878 (t0) cc_final: 0.7632 (t70) REVERT: B 113 GLN cc_start: 0.8701 (tp40) cc_final: 0.8411 (tp40) REVERT: B 125 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8599 (mmtm) REVERT: B 135 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7276 (mt-10) REVERT: B 141 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7533 (tm-30) REVERT: B 148 GLU cc_start: 0.8340 (tt0) cc_final: 0.7930 (tt0) REVERT: C 18 GLU cc_start: 0.8293 (tt0) cc_final: 0.8007 (tt0) REVERT: C 63 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6765 (mm-30) REVERT: C 64 ARG cc_start: 0.8074 (tpp80) cc_final: 0.7236 (ttp-170) REVERT: C 91 ARG cc_start: 0.8238 (mtp85) cc_final: 0.7930 (mtp85) REVERT: C 93 ASP cc_start: 0.7897 (t0) cc_final: 0.7644 (t70) REVERT: C 113 GLN cc_start: 0.8706 (tp40) cc_final: 0.8418 (tp40) REVERT: C 125 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8645 (mmtm) REVERT: C 135 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7279 (mt-10) REVERT: C 141 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7477 (tm-30) REVERT: C 148 GLU cc_start: 0.8275 (tt0) cc_final: 0.8045 (tt0) REVERT: D 18 GLU cc_start: 0.8291 (tt0) cc_final: 0.8009 (tt0) REVERT: D 63 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6773 (mm-30) REVERT: D 91 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7931 (mtp85) REVERT: D 93 ASP cc_start: 0.7897 (t0) cc_final: 0.7646 (t70) REVERT: D 113 GLN cc_start: 0.8709 (tp40) cc_final: 0.8425 (tp40) REVERT: D 125 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8646 (mmtm) REVERT: D 135 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7282 (mt-10) REVERT: D 141 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7477 (tm-30) REVERT: D 148 GLU cc_start: 0.8287 (tt0) cc_final: 0.8058 (tt0) REVERT: E 16 ASP cc_start: 0.8850 (m-30) cc_final: 0.8531 (m-30) REVERT: E 18 GLU cc_start: 0.8317 (tt0) cc_final: 0.8042 (tt0) REVERT: E 63 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6776 (mm-30) REVERT: E 64 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7226 (ttp-170) REVERT: E 91 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7932 (mtp85) REVERT: E 93 ASP cc_start: 0.7892 (t0) cc_final: 0.7656 (t70) REVERT: E 113 GLN cc_start: 0.8702 (tp40) cc_final: 0.8407 (tp40) REVERT: E 125 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8598 (mmtm) REVERT: E 135 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7285 (mt-10) REVERT: E 148 GLU cc_start: 0.8363 (tt0) cc_final: 0.8118 (tt0) REVERT: E 173 LYS cc_start: 0.8706 (mptp) cc_final: 0.8374 (mptp) REVERT: F 18 GLU cc_start: 0.8317 (tt0) cc_final: 0.8045 (tt0) REVERT: F 63 GLU cc_start: 0.7593 (mm-30) cc_final: 0.6782 (mm-30) REVERT: F 64 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7238 (ttp-170) REVERT: F 91 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7931 (mtp85) REVERT: F 93 ASP cc_start: 0.7901 (t0) cc_final: 0.7663 (t70) REVERT: F 113 GLN cc_start: 0.8727 (tp40) cc_final: 0.8443 (tp40) REVERT: F 120 LYS cc_start: 0.8553 (tttm) cc_final: 0.8216 (ttpt) REVERT: F 125 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8641 (mmtm) REVERT: F 135 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7281 (mt-10) REVERT: F 141 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7495 (tm-30) REVERT: F 148 GLU cc_start: 0.8336 (tt0) cc_final: 0.8117 (tt0) REVERT: F 173 LYS cc_start: 0.8686 (mptp) cc_final: 0.8374 (mptp) REVERT: G 64 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7229 (ttp-170) REVERT: G 68 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8193 (mt-10) REVERT: G 91 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7899 (mtp85) REVERT: G 93 ASP cc_start: 0.7901 (t0) cc_final: 0.7638 (t70) REVERT: G 120 LYS cc_start: 0.8532 (tttm) cc_final: 0.8175 (ttmp) REVERT: G 124 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7746 (tm-30) REVERT: G 125 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8623 (mmtm) REVERT: G 141 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7254 (mp0) REVERT: G 148 GLU cc_start: 0.8280 (tt0) cc_final: 0.8041 (tt0) REVERT: G 173 LYS cc_start: 0.8711 (mptp) cc_final: 0.8396 (mptp) REVERT: H 16 ASP cc_start: 0.8856 (m-30) cc_final: 0.8536 (m-30) REVERT: H 18 GLU cc_start: 0.8335 (tt0) cc_final: 0.8055 (tt0) REVERT: H 63 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6789 (mm-30) REVERT: H 91 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7955 (mtp85) REVERT: H 93 ASP cc_start: 0.7867 (t0) cc_final: 0.7641 (t70) REVERT: H 113 GLN cc_start: 0.8712 (tp40) cc_final: 0.8434 (tp40) REVERT: H 125 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8596 (mmtm) REVERT: H 135 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7280 (mt-10) REVERT: H 148 GLU cc_start: 0.8380 (tt0) cc_final: 0.8162 (tt0) REVERT: I 18 GLU cc_start: 0.8314 (tt0) cc_final: 0.8036 (tt0) REVERT: I 63 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6768 (mm-30) REVERT: I 64 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7228 (ttp-170) REVERT: I 91 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7930 (mtp85) REVERT: I 93 ASP cc_start: 0.7890 (t0) cc_final: 0.7618 (t70) REVERT: I 113 GLN cc_start: 0.8722 (tp40) cc_final: 0.8437 (tp40) REVERT: I 125 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8641 (mmtm) REVERT: I 135 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7277 (mt-10) REVERT: I 148 GLU cc_start: 0.8278 (tt0) cc_final: 0.8037 (tt0) REVERT: J 18 GLU cc_start: 0.8312 (tt0) cc_final: 0.8035 (tt0) REVERT: J 63 GLU cc_start: 0.7590 (mm-30) cc_final: 0.6780 (mm-30) REVERT: J 91 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7939 (mtp85) REVERT: J 93 ASP cc_start: 0.7893 (t0) cc_final: 0.7621 (t70) REVERT: J 113 GLN cc_start: 0.8725 (tp40) cc_final: 0.8443 (tp40) REVERT: J 125 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8641 (mmtm) REVERT: J 135 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7276 (mt-10) REVERT: J 148 GLU cc_start: 0.8281 (tt0) cc_final: 0.8043 (tt0) REVERT: K 16 ASP cc_start: 0.8821 (m-30) cc_final: 0.8502 (m-30) REVERT: K 18 GLU cc_start: 0.8318 (tt0) cc_final: 0.8032 (tt0) REVERT: K 63 GLU cc_start: 0.7590 (mm-30) cc_final: 0.6777 (mm-30) REVERT: K 64 ARG cc_start: 0.8083 (tpp80) cc_final: 0.7236 (ttp-170) REVERT: K 91 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7908 (mtp85) REVERT: K 93 ASP cc_start: 0.7882 (t0) cc_final: 0.7643 (t70) REVERT: K 95 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7592 (mm-30) REVERT: K 113 GLN cc_start: 0.8721 (tp40) cc_final: 0.8430 (tp40) REVERT: K 117 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7855 (mm-30) REVERT: K 125 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8612 (mmtm) REVERT: K 135 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7283 (mt-10) REVERT: K 141 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7256 (mp0) REVERT: K 148 GLU cc_start: 0.8349 (tt0) cc_final: 0.7930 (tt0) REVERT: L 64 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7229 (ttp-170) REVERT: L 68 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8202 (mt-10) REVERT: L 91 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7901 (mtp85) REVERT: L 93 ASP cc_start: 0.7896 (t0) cc_final: 0.7633 (t70) REVERT: L 113 GLN cc_start: 0.8721 (tp40) cc_final: 0.8436 (tp40) REVERT: L 120 LYS cc_start: 0.8531 (tttm) cc_final: 0.8176 (ttmp) REVERT: L 124 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7743 (tm-30) REVERT: L 125 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8622 (mmtm) REVERT: L 141 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7256 (mp0) REVERT: L 148 GLU cc_start: 0.8279 (tt0) cc_final: 0.8040 (tt0) REVERT: L 173 LYS cc_start: 0.8707 (mptp) cc_final: 0.8391 (mptp) REVERT: M 16 ASP cc_start: 0.8844 (m-30) cc_final: 0.8516 (m-30) REVERT: M 18 GLU cc_start: 0.8315 (tt0) cc_final: 0.8041 (tt0) REVERT: M 63 GLU cc_start: 0.7588 (mm-30) cc_final: 0.6771 (mm-30) REVERT: M 64 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7324 (ttp-170) REVERT: M 68 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8145 (mt-10) REVERT: M 91 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7913 (mtp85) REVERT: M 93 ASP cc_start: 0.7897 (t0) cc_final: 0.7663 (t70) REVERT: M 113 GLN cc_start: 0.8706 (tp40) cc_final: 0.8422 (tp40) REVERT: M 120 LYS cc_start: 0.8516 (tttm) cc_final: 0.8233 (tttp) REVERT: M 125 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8605 (mmtm) REVERT: M 135 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7319 (mt-10) REVERT: M 141 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7506 (tm-30) REVERT: M 148 GLU cc_start: 0.8316 (tt0) cc_final: 0.8080 (tt0) REVERT: N 16 ASP cc_start: 0.8852 (m-30) cc_final: 0.8532 (m-30) REVERT: N 18 GLU cc_start: 0.8317 (tt0) cc_final: 0.8043 (tt0) REVERT: N 63 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6779 (mm-30) REVERT: N 91 ARG cc_start: 0.8247 (mtp85) cc_final: 0.7936 (mtp85) REVERT: N 93 ASP cc_start: 0.7892 (t0) cc_final: 0.7654 (t70) REVERT: N 113 GLN cc_start: 0.8701 (tp40) cc_final: 0.8408 (tp40) REVERT: N 125 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8593 (mmtm) REVERT: N 135 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7283 (mt-10) REVERT: N 148 GLU cc_start: 0.8361 (tt0) cc_final: 0.8123 (tt0) REVERT: N 173 LYS cc_start: 0.8707 (mptp) cc_final: 0.8384 (mptp) REVERT: O 18 GLU cc_start: 0.8312 (tt0) cc_final: 0.8035 (tt0) REVERT: O 63 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6770 (mm-30) REVERT: O 64 ARG cc_start: 0.8090 (tpp80) cc_final: 0.7228 (ttp-170) REVERT: O 91 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7927 (mtp85) REVERT: O 93 ASP cc_start: 0.7882 (t0) cc_final: 0.7641 (t70) REVERT: O 113 GLN cc_start: 0.8721 (tp40) cc_final: 0.8434 (tp40) REVERT: O 120 LYS cc_start: 0.8496 (tttm) cc_final: 0.8119 (ttmt) REVERT: O 125 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8640 (mmtm) REVERT: O 135 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7282 (mt-10) REVERT: O 148 GLU cc_start: 0.8299 (tt0) cc_final: 0.8071 (tt0) REVERT: P 18 GLU cc_start: 0.8312 (tt0) cc_final: 0.8035 (tt0) REVERT: P 63 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6779 (mm-30) REVERT: P 91 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7931 (mtp85) REVERT: P 93 ASP cc_start: 0.7876 (t0) cc_final: 0.7648 (t70) REVERT: P 113 GLN cc_start: 0.8709 (tp40) cc_final: 0.8433 (tp40) REVERT: P 125 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8598 (mmtm) REVERT: P 135 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7277 (mt-10) REVERT: P 141 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7509 (tm-30) REVERT: P 148 GLU cc_start: 0.8313 (tt0) cc_final: 0.8017 (tt0) REVERT: Q 16 ASP cc_start: 0.8855 (m-30) cc_final: 0.8549 (m-30) REVERT: Q 18 GLU cc_start: 0.8311 (tt0) cc_final: 0.8034 (tt0) REVERT: Q 63 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6784 (mm-30) REVERT: Q 91 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7935 (mtp85) REVERT: Q 93 ASP cc_start: 0.7882 (t0) cc_final: 0.7639 (t70) REVERT: Q 113 GLN cc_start: 0.8702 (tp40) cc_final: 0.8410 (tp40) REVERT: Q 125 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8600 (mmtm) REVERT: Q 135 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7281 (mt-10) REVERT: Q 141 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7531 (tm-30) REVERT: Q 148 GLU cc_start: 0.8340 (tt0) cc_final: 0.7918 (tt0) REVERT: R 16 ASP cc_start: 0.8848 (m-30) cc_final: 0.8525 (m-30) REVERT: R 18 GLU cc_start: 0.8312 (tt0) cc_final: 0.8040 (tt0) REVERT: R 63 GLU cc_start: 0.7588 (mm-30) cc_final: 0.6786 (mm-30) REVERT: R 68 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8152 (mt-10) REVERT: R 91 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7917 (mtp85) REVERT: R 93 ASP cc_start: 0.7894 (t0) cc_final: 0.7670 (t70) REVERT: R 113 GLN cc_start: 0.8710 (tp40) cc_final: 0.8424 (tp40) REVERT: R 125 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8593 (mmtm) REVERT: R 135 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7274 (mt-10) REVERT: R 141 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7505 (tm-30) REVERT: R 148 GLU cc_start: 0.8319 (tt0) cc_final: 0.8095 (tt0) REVERT: R 173 LYS cc_start: 0.8695 (mptp) cc_final: 0.8369 (mptp) REVERT: S 16 ASP cc_start: 0.8844 (m-30) cc_final: 0.8525 (m-30) REVERT: S 18 GLU cc_start: 0.8321 (tt0) cc_final: 0.8045 (tt0) REVERT: S 63 GLU cc_start: 0.7592 (mm-30) cc_final: 0.6783 (mm-30) REVERT: S 64 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7316 (ttp-170) REVERT: S 68 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8145 (mt-10) REVERT: S 91 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7920 (mtp85) REVERT: S 93 ASP cc_start: 0.7897 (t0) cc_final: 0.7669 (t70) REVERT: S 113 GLN cc_start: 0.8707 (tp40) cc_final: 0.8428 (tp40) REVERT: S 125 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8593 (mmtm) REVERT: S 135 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7271 (mt-10) REVERT: S 141 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7498 (tm-30) REVERT: S 148 GLU cc_start: 0.8313 (tt0) cc_final: 0.8086 (tt0) REVERT: S 173 LYS cc_start: 0.8697 (mptp) cc_final: 0.8377 (mptp) REVERT: T 16 ASP cc_start: 0.8828 (m-30) cc_final: 0.8510 (m-30) REVERT: T 18 GLU cc_start: 0.8324 (tt0) cc_final: 0.8041 (tt0) REVERT: T 63 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6783 (mm-30) REVERT: T 91 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7904 (mtp85) REVERT: T 93 ASP cc_start: 0.7879 (t0) cc_final: 0.7637 (t70) REVERT: T 95 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7591 (mm-30) REVERT: T 113 GLN cc_start: 0.8719 (tp40) cc_final: 0.8432 (tp40) REVERT: T 117 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7857 (mm-30) REVERT: T 125 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8614 (mmtm) REVERT: T 135 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7283 (mt-10) REVERT: T 141 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7261 (mp0) REVERT: T 148 GLU cc_start: 0.8349 (tt0) cc_final: 0.7927 (tt0) REVERT: U 18 GLU cc_start: 0.8312 (tt0) cc_final: 0.8033 (tt0) REVERT: U 63 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6768 (mm-30) REVERT: U 64 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7237 (ttp-170) REVERT: U 91 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7932 (mtp85) REVERT: U 93 ASP cc_start: 0.7875 (t0) cc_final: 0.7644 (t70) REVERT: U 113 GLN cc_start: 0.8707 (tp40) cc_final: 0.8427 (tp40) REVERT: U 125 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8595 (mmtm) REVERT: U 135 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7274 (mt-10) REVERT: U 141 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7506 (tm-30) REVERT: U 148 GLU cc_start: 0.8311 (tt0) cc_final: 0.8013 (tt0) REVERT: V 18 GLU cc_start: 0.8308 (tt0) cc_final: 0.8032 (tt0) REVERT: V 63 GLU cc_start: 0.7583 (mm-30) cc_final: 0.6777 (mm-30) REVERT: V 91 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7934 (mtp85) REVERT: V 93 ASP cc_start: 0.7886 (t0) cc_final: 0.7648 (t70) REVERT: V 113 GLN cc_start: 0.8722 (tp40) cc_final: 0.8439 (tp40) REVERT: V 120 LYS cc_start: 0.8505 (tttm) cc_final: 0.8127 (ttmt) REVERT: V 125 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8643 (mmtm) REVERT: V 135 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7281 (mt-10) REVERT: V 148 GLU cc_start: 0.8304 (tt0) cc_final: 0.8080 (tt0) REVERT: W 16 ASP cc_start: 0.8853 (m-30) cc_final: 0.8533 (m-30) REVERT: W 18 GLU cc_start: 0.8328 (tt0) cc_final: 0.8050 (tt0) REVERT: W 63 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6792 (mm-30) REVERT: W 91 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7955 (mtp85) REVERT: W 93 ASP cc_start: 0.7866 (t0) cc_final: 0.7645 (t70) REVERT: W 113 GLN cc_start: 0.8712 (tp40) cc_final: 0.8436 (tp40) REVERT: W 125 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8597 (mmtm) REVERT: W 135 GLU cc_start: 0.7575 (mt-10) cc_final: 0.7281 (mt-10) REVERT: W 148 GLU cc_start: 0.8380 (tt0) cc_final: 0.8156 (tt0) REVERT: W 173 LYS cc_start: 0.8705 (mptp) cc_final: 0.8386 (mptp) REVERT: X 16 ASP cc_start: 0.8847 (m-30) cc_final: 0.8518 (m-30) REVERT: X 18 GLU cc_start: 0.8311 (tt0) cc_final: 0.8041 (tt0) REVERT: X 63 GLU cc_start: 0.7585 (mm-30) cc_final: 0.6776 (mm-30) REVERT: X 68 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8151 (mt-10) REVERT: X 91 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7915 (mtp85) REVERT: X 93 ASP cc_start: 0.7894 (t0) cc_final: 0.7660 (t70) REVERT: X 113 GLN cc_start: 0.8709 (tp40) cc_final: 0.8421 (tp40) REVERT: X 120 LYS cc_start: 0.8514 (tttm) cc_final: 0.8230 (tttp) REVERT: X 125 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8610 (mmtm) REVERT: X 135 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7282 (mt-10) REVERT: X 141 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7508 (tm-30) REVERT: X 148 GLU cc_start: 0.8316 (tt0) cc_final: 0.8081 (tt0) outliers start: 0 outliers final: 12 residues processed: 1425 average time/residue: 0.8735 time to fit residues: 1432.5177 Evaluate side-chains 1122 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1110 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain M residue 46 ASP Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain X residue 46 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 26 ASN A 84 GLN A 112 ASN A 137 HIS B 12 ASN B 26 ASN B 61 HIS B 84 GLN B 112 ASN B 137 HIS C 12 ASN C 84 GLN C 112 ASN C 137 HIS D 12 ASN D 84 GLN D 112 ASN D 137 HIS E 12 ASN E 26 ASN E 61 HIS E 84 GLN E 112 ASN E 137 HIS F 12 ASN F 26 ASN F 84 GLN F 112 ASN F 137 HIS G 12 ASN G 26 ASN G 84 GLN G 112 ASN G 137 HIS H 12 ASN H 26 ASN H 61 HIS H 84 GLN H 112 ASN H 137 HIS I 12 ASN I 26 ASN I 84 GLN I 112 ASN I 137 HIS J 12 ASN J 84 GLN J 112 ASN J 137 HIS K 12 ASN K 61 HIS K 84 GLN K 112 ASN K 137 HIS L 12 ASN L 26 ASN L 84 GLN L 112 ASN L 137 HIS M 12 ASN M 26 ASN M 84 GLN M 112 ASN M 137 HIS N 12 ASN N 26 ASN N 61 HIS N 84 GLN N 112 ASN N 137 HIS O 12 ASN O 84 GLN O 112 ASN O 137 HIS P 12 ASN P 84 GLN P 112 ASN P 137 HIS Q 12 ASN Q 26 ASN Q 84 GLN Q 112 ASN Q 137 HIS R 12 ASN R 84 GLN R 112 ASN R 137 HIS S 12 ASN S 84 GLN S 112 ASN S 137 HIS T 12 ASN T 61 HIS T 84 GLN T 112 ASN T 137 HIS U 12 ASN U 84 GLN U 112 ASN U 137 HIS V 12 ASN V 84 GLN V 112 ASN V 137 HIS W 12 ASN W 26 ASN W 61 HIS W 84 GLN W 112 ASN W 137 HIS X 12 ASN X 26 ASN X 84 GLN X 112 ASN X 137 HIS Total number of N/Q/H flips: 116 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.106200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.098629 restraints weight = 43304.295| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.33 r_work: 0.2931 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34776 Z= 0.145 Angle : 0.494 5.275 46824 Z= 0.259 Chirality : 0.036 0.131 4872 Planarity : 0.003 0.028 6216 Dihedral : 3.941 15.240 4608 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.36 % Allowed : 11.14 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.93 (0.13), residues: 4104 helix: 3.82 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.71 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 157 TYR 0.011 0.002 TYR F 138 PHE 0.012 0.002 PHE C 133 TRP 0.003 0.001 TRP R 94 HIS 0.002 0.001 HIS G 119 Details of bonding type rmsd covalent geometry : bond 0.00325 (34776) covalent geometry : angle 0.49413 (46824) hydrogen bonds : bond 0.03902 ( 2640) hydrogen bonds : angle 3.18743 ( 7920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1167 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 1117 time to evaluate : 1.424 Fit side-chains REVERT: A 64 ARG cc_start: 0.8508 (tpp80) cc_final: 0.7495 (ttp-170) REVERT: A 91 ARG cc_start: 0.8468 (mtp85) cc_final: 0.8265 (mtp85) REVERT: A 113 GLN cc_start: 0.9015 (tp40) cc_final: 0.8738 (tp40) REVERT: A 124 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8233 (tm-30) REVERT: A 125 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8700 (mmtm) REVERT: A 148 GLU cc_start: 0.8885 (tt0) cc_final: 0.8674 (tt0) REVERT: B 16 ASP cc_start: 0.9134 (m-30) cc_final: 0.8885 (m-30) REVERT: B 93 ASP cc_start: 0.8220 (t0) cc_final: 0.7945 (t70) REVERT: B 113 GLN cc_start: 0.9012 (tp40) cc_final: 0.8736 (tp40) REVERT: B 141 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7732 (tm-30) REVERT: B 148 GLU cc_start: 0.8879 (tt0) cc_final: 0.8560 (tt0) REVERT: C 64 ARG cc_start: 0.8489 (tpp80) cc_final: 0.7573 (ttp-170) REVERT: C 91 ARG cc_start: 0.8463 (mtp85) cc_final: 0.8255 (mtp85) REVERT: C 93 ASP cc_start: 0.8236 (t0) cc_final: 0.7942 (t70) REVERT: C 113 GLN cc_start: 0.9030 (tp40) cc_final: 0.8762 (tp40) REVERT: C 125 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8723 (mmtm) REVERT: C 141 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7773 (tm-30) REVERT: D 91 ARG cc_start: 0.8464 (mtp85) cc_final: 0.8254 (mtp85) REVERT: D 93 ASP cc_start: 0.8234 (t0) cc_final: 0.7941 (t70) REVERT: D 113 GLN cc_start: 0.9018 (tp40) cc_final: 0.8748 (tp40) REVERT: D 125 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8726 (mmtm) REVERT: D 141 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7770 (tm-30) REVERT: E 16 ASP cc_start: 0.9129 (m-30) cc_final: 0.8839 (m-30) REVERT: E 62 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7924 (mm-30) REVERT: E 64 ARG cc_start: 0.8478 (tpp80) cc_final: 0.7504 (ttp-170) REVERT: E 91 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8270 (mtp85) REVERT: E 93 ASP cc_start: 0.8232 (t0) cc_final: 0.7960 (t70) REVERT: E 113 GLN cc_start: 0.9016 (tp40) cc_final: 0.8737 (tp40) REVERT: E 124 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8223 (tm-30) REVERT: E 125 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8654 (mmtm) REVERT: E 148 GLU cc_start: 0.8882 (tt0) cc_final: 0.8668 (tt0) REVERT: F 64 ARG cc_start: 0.8486 (tpp80) cc_final: 0.7528 (ttp-170) REVERT: F 91 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8255 (mtp85) REVERT: F 113 GLN cc_start: 0.9030 (tp40) cc_final: 0.8751 (tp40) REVERT: F 124 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8219 (tm-30) REVERT: F 125 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8694 (mmtm) REVERT: F 141 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7824 (mp0) REVERT: F 148 GLU cc_start: 0.8882 (tt0) cc_final: 0.8668 (tt0) REVERT: G 16 ASP cc_start: 0.9149 (m-30) cc_final: 0.8836 (m-30) REVERT: G 64 ARG cc_start: 0.8522 (tpp80) cc_final: 0.7499 (ttp-170) REVERT: G 93 ASP cc_start: 0.8236 (t0) cc_final: 0.7954 (t70) REVERT: G 120 LYS cc_start: 0.8866 (tttm) cc_final: 0.8518 (ttmp) REVERT: G 124 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8240 (tm-30) REVERT: G 125 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8659 (mmtm) REVERT: G 141 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7842 (mp0) REVERT: G 148 GLU cc_start: 0.8843 (tt0) cc_final: 0.8639 (tt0) REVERT: H 16 ASP cc_start: 0.9136 (m-30) cc_final: 0.8850 (m-30) REVERT: H 93 ASP cc_start: 0.8218 (t0) cc_final: 0.7949 (t70) REVERT: H 113 GLN cc_start: 0.9025 (tp40) cc_final: 0.8746 (tp40) REVERT: H 124 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8246 (tm-30) REVERT: H 125 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8687 (mmtm) REVERT: H 148 GLU cc_start: 0.8912 (tt0) cc_final: 0.8700 (tt0) REVERT: I 62 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7977 (mm-30) REVERT: I 64 ARG cc_start: 0.8493 (tpp80) cc_final: 0.7500 (ttp-170) REVERT: I 93 ASP cc_start: 0.8183 (t0) cc_final: 0.7927 (t70) REVERT: I 113 GLN cc_start: 0.9034 (tp40) cc_final: 0.8754 (tp40) REVERT: I 124 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8231 (tm-30) REVERT: I 125 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8700 (mmtm) REVERT: I 148 GLU cc_start: 0.8820 (tt0) cc_final: 0.8603 (tt0) REVERT: J 62 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7981 (mm-30) REVERT: J 93 ASP cc_start: 0.8183 (t0) cc_final: 0.7928 (t70) REVERT: J 113 GLN cc_start: 0.9019 (tp40) cc_final: 0.8738 (tp40) REVERT: J 124 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8246 (tm-30) REVERT: J 125 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8712 (mmtm) REVERT: J 148 GLU cc_start: 0.8834 (tt0) cc_final: 0.8620 (tt0) REVERT: K 16 ASP cc_start: 0.9118 (m-30) cc_final: 0.8815 (m-30) REVERT: K 64 ARG cc_start: 0.8487 (tpp80) cc_final: 0.7494 (ttp-170) REVERT: K 91 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8235 (mtp85) REVERT: K 93 ASP cc_start: 0.8205 (t0) cc_final: 0.7941 (t70) REVERT: K 113 GLN cc_start: 0.9049 (tp40) cc_final: 0.8761 (tp40) REVERT: K 124 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8231 (tm-30) REVERT: K 125 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8700 (mmtm) REVERT: K 141 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7832 (mp0) REVERT: K 148 GLU cc_start: 0.8869 (tt0) cc_final: 0.8563 (tt0) REVERT: L 16 ASP cc_start: 0.9144 (m-30) cc_final: 0.8840 (m-30) REVERT: L 64 ARG cc_start: 0.8511 (tpp80) cc_final: 0.7501 (ttp-170) REVERT: L 93 ASP cc_start: 0.8247 (t0) cc_final: 0.7970 (t70) REVERT: L 120 LYS cc_start: 0.8907 (tttm) cc_final: 0.8558 (ttmp) REVERT: L 124 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8235 (tm-30) REVERT: L 125 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8653 (mmtm) REVERT: L 141 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7836 (mp0) REVERT: M 64 ARG cc_start: 0.8511 (tpp80) cc_final: 0.7495 (ttp-170) REVERT: M 91 ARG cc_start: 0.8438 (mtp85) cc_final: 0.8232 (mtp85) REVERT: M 93 ASP cc_start: 0.8214 (t0) cc_final: 0.7954 (t70) REVERT: M 120 LYS cc_start: 0.8852 (tttm) cc_final: 0.8524 (tttp) REVERT: M 124 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8245 (tm-30) REVERT: M 125 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8685 (mmtm) REVERT: M 141 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7817 (mp0) REVERT: M 148 GLU cc_start: 0.8886 (tt0) cc_final: 0.8661 (tt0) REVERT: N 16 ASP cc_start: 0.9143 (m-30) cc_final: 0.8851 (m-30) REVERT: N 62 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7944 (mm-30) REVERT: N 93 ASP cc_start: 0.8241 (t0) cc_final: 0.7948 (t70) REVERT: N 113 GLN cc_start: 0.9022 (tp40) cc_final: 0.8744 (tp40) REVERT: N 124 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8224 (tm-30) REVERT: N 125 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8650 (mmtm) REVERT: N 148 GLU cc_start: 0.8891 (tt0) cc_final: 0.8673 (tt0) REVERT: O 64 ARG cc_start: 0.8502 (tpp80) cc_final: 0.7492 (ttp-170) REVERT: O 93 ASP cc_start: 0.8221 (t0) cc_final: 0.7948 (t70) REVERT: O 113 GLN cc_start: 0.9038 (tp40) cc_final: 0.8764 (tp40) REVERT: O 120 LYS cc_start: 0.8839 (tttm) cc_final: 0.8416 (ttmt) REVERT: O 124 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8213 (tm-30) REVERT: O 125 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8711 (mmtm) REVERT: O 148 GLU cc_start: 0.8865 (tt0) cc_final: 0.8657 (tt0) REVERT: P 91 ARG cc_start: 0.8478 (mtp85) cc_final: 0.8271 (mtp85) REVERT: P 93 ASP cc_start: 0.8211 (t0) cc_final: 0.7931 (t70) REVERT: P 124 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8289 (tm-30) REVERT: P 125 LYS cc_start: 0.8946 (mmtt) cc_final: 0.8741 (mmtm) REVERT: P 141 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7835 (mp0) REVERT: Q 16 ASP cc_start: 0.9116 (m-30) cc_final: 0.8869 (m-30) REVERT: Q 91 ARG cc_start: 0.8459 (mtp85) cc_final: 0.8254 (mtp85) REVERT: Q 93 ASP cc_start: 0.8237 (t0) cc_final: 0.7949 (t70) REVERT: Q 113 GLN cc_start: 0.9021 (tp40) cc_final: 0.8749 (tp40) REVERT: Q 141 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7743 (tm-30) REVERT: Q 148 GLU cc_start: 0.8875 (tt0) cc_final: 0.8561 (tt0) REVERT: R 93 ASP cc_start: 0.8223 (t0) cc_final: 0.7969 (t70) REVERT: R 113 GLN cc_start: 0.9021 (tp40) cc_final: 0.8754 (tp40) REVERT: R 124 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8242 (tm-30) REVERT: R 125 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8658 (mmtm) REVERT: R 141 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7827 (mp0) REVERT: R 148 GLU cc_start: 0.8852 (tt0) cc_final: 0.8646 (tt0) REVERT: S 64 ARG cc_start: 0.8517 (tpp80) cc_final: 0.7495 (ttp-170) REVERT: S 93 ASP cc_start: 0.8217 (t0) cc_final: 0.7964 (t70) REVERT: S 113 GLN cc_start: 0.9015 (tp40) cc_final: 0.8748 (tp40) REVERT: S 124 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8223 (tm-30) REVERT: S 125 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8666 (mmtm) REVERT: S 141 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7850 (mp0) REVERT: S 148 GLU cc_start: 0.8847 (tt0) cc_final: 0.8642 (tt0) REVERT: T 16 ASP cc_start: 0.9123 (m-30) cc_final: 0.8816 (m-30) REVERT: T 91 ARG cc_start: 0.8447 (mtp85) cc_final: 0.8240 (mtp85) REVERT: T 93 ASP cc_start: 0.8203 (t0) cc_final: 0.7937 (t70) REVERT: T 113 GLN cc_start: 0.9041 (tp40) cc_final: 0.8753 (tp40) REVERT: T 125 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8694 (mmtm) REVERT: T 141 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7830 (mp0) REVERT: T 148 GLU cc_start: 0.8880 (tt0) cc_final: 0.8573 (tt0) REVERT: U 64 ARG cc_start: 0.8494 (tpp80) cc_final: 0.7506 (ttp-170) REVERT: U 91 ARG cc_start: 0.8457 (mtp85) cc_final: 0.8249 (mtp85) REVERT: U 93 ASP cc_start: 0.8205 (t0) cc_final: 0.7941 (t70) REVERT: U 124 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8266 (tm-30) REVERT: U 125 LYS cc_start: 0.8941 (mmtt) cc_final: 0.8739 (mmtm) REVERT: U 141 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7826 (mp0) REVERT: V 93 ASP cc_start: 0.8222 (t0) cc_final: 0.7946 (t70) REVERT: V 113 GLN cc_start: 0.9035 (tp40) cc_final: 0.8763 (tp40) REVERT: V 120 LYS cc_start: 0.8832 (tttm) cc_final: 0.8410 (ttmt) REVERT: V 124 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8231 (tm-30) REVERT: V 125 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8704 (mmtm) REVERT: V 148 GLU cc_start: 0.8862 (tt0) cc_final: 0.8654 (tt0) REVERT: W 16 ASP cc_start: 0.9135 (m-30) cc_final: 0.8851 (m-30) REVERT: W 93 ASP cc_start: 0.8217 (t0) cc_final: 0.7944 (t70) REVERT: W 113 GLN cc_start: 0.9025 (tp40) cc_final: 0.8748 (tp40) REVERT: W 125 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8702 (mmtm) REVERT: W 148 GLU cc_start: 0.8909 (tt0) cc_final: 0.8698 (tt0) REVERT: X 93 ASP cc_start: 0.8241 (t0) cc_final: 0.7968 (t70) REVERT: X 120 LYS cc_start: 0.8843 (tttm) cc_final: 0.8493 (ttmp) REVERT: X 124 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8247 (tm-30) REVERT: X 125 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8672 (mmtm) REVERT: X 141 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7809 (mp0) REVERT: X 148 GLU cc_start: 0.8889 (tt0) cc_final: 0.8662 (tt0) outliers start: 50 outliers final: 50 residues processed: 1141 average time/residue: 0.8441 time to fit residues: 1117.2697 Evaluate side-chains 1111 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 1061 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 26 optimal weight: 0.8980 chunk 370 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 151 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 376 optimal weight: 4.9990 chunk 346 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 8 GLN C 8 GLN C 26 ASN D 26 ASN E 8 GLN I 8 GLN J 8 GLN J 26 ASN K 26 ASN M 8 GLN O 26 ASN P 8 GLN P 26 ASN Q 8 GLN R 26 ASN S 26 ASN T 26 ASN U 26 ASN V 26 ASN X 8 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.107207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.099629 restraints weight = 43129.326| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.35 r_work: 0.2971 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 34776 Z= 0.103 Angle : 0.454 5.088 46824 Z= 0.239 Chirality : 0.034 0.115 4872 Planarity : 0.003 0.022 6216 Dihedral : 3.772 16.315 4584 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.87 % Allowed : 12.66 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.41 (0.13), residues: 4104 helix: 4.18 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.82 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 157 TYR 0.009 0.001 TYR A 138 PHE 0.011 0.002 PHE C 133 TRP 0.003 0.001 TRP D 94 HIS 0.002 0.000 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00222 (34776) covalent geometry : angle 0.45378 (46824) hydrogen bonds : bond 0.03339 ( 2640) hydrogen bonds : angle 2.95286 ( 7920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1169 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 1137 time to evaluate : 1.281 Fit side-chains REVERT: A 64 ARG cc_start: 0.8470 (tpp80) cc_final: 0.7475 (ttp-170) REVERT: A 113 GLN cc_start: 0.9025 (tp40) cc_final: 0.8735 (tp40) REVERT: A 124 GLU cc_start: 0.8404 (tm-30) cc_final: 0.8183 (tm-30) REVERT: A 125 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8696 (mmtm) REVERT: A 148 GLU cc_start: 0.8882 (tt0) cc_final: 0.8666 (tt0) REVERT: B 63 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 93 ASP cc_start: 0.8131 (t0) cc_final: 0.7886 (t70) REVERT: B 113 GLN cc_start: 0.9016 (tp40) cc_final: 0.8721 (tp40) REVERT: B 124 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 141 GLU cc_start: 0.8425 (mm-30) cc_final: 0.7842 (mp0) REVERT: B 148 GLU cc_start: 0.8881 (tt0) cc_final: 0.8646 (tt0) REVERT: C 64 ARG cc_start: 0.8501 (tpp80) cc_final: 0.7544 (ttp-170) REVERT: C 93 ASP cc_start: 0.8190 (t0) cc_final: 0.7924 (t70) REVERT: C 124 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8224 (tm-30) REVERT: C 125 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8701 (mmtm) REVERT: C 141 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7870 (mp0) REVERT: D 93 ASP cc_start: 0.8132 (t0) cc_final: 0.7881 (t70) REVERT: D 141 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7865 (mp0) REVERT: E 16 ASP cc_start: 0.9110 (m-30) cc_final: 0.8824 (m-30) REVERT: E 18 GLU cc_start: 0.8599 (tt0) cc_final: 0.8319 (tt0) REVERT: E 64 ARG cc_start: 0.8458 (tpp80) cc_final: 0.7457 (ttp-170) REVERT: E 93 ASP cc_start: 0.8184 (t0) cc_final: 0.7929 (t70) REVERT: E 113 GLN cc_start: 0.9017 (tp40) cc_final: 0.8720 (tp40) REVERT: E 125 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8648 (mmtm) REVERT: E 148 GLU cc_start: 0.8881 (tt0) cc_final: 0.8654 (tt0) REVERT: F 18 GLU cc_start: 0.8599 (tt0) cc_final: 0.8322 (tt0) REVERT: F 64 ARG cc_start: 0.8456 (tpp80) cc_final: 0.7470 (ttp-170) REVERT: F 113 GLN cc_start: 0.9032 (tp40) cc_final: 0.8739 (tp40) REVERT: F 124 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8214 (tm-30) REVERT: F 125 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8681 (mmtm) REVERT: F 141 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7871 (mp0) REVERT: F 148 GLU cc_start: 0.8880 (tt0) cc_final: 0.8665 (tt0) REVERT: G 16 ASP cc_start: 0.9097 (m-30) cc_final: 0.8788 (m-30) REVERT: G 18 GLU cc_start: 0.8618 (tt0) cc_final: 0.8346 (tt0) REVERT: G 64 ARG cc_start: 0.8479 (tpp80) cc_final: 0.7475 (ttp-170) REVERT: G 93 ASP cc_start: 0.8173 (t0) cc_final: 0.7908 (t70) REVERT: G 120 LYS cc_start: 0.8879 (tttm) cc_final: 0.8537 (ttmp) REVERT: G 124 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8216 (tm-30) REVERT: G 125 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8639 (mmtm) REVERT: G 141 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7843 (mp0) REVERT: G 148 GLU cc_start: 0.8847 (tt0) cc_final: 0.8643 (tt0) REVERT: G 158 LYS cc_start: 0.8369 (mttt) cc_final: 0.8132 (mtmt) REVERT: H 16 ASP cc_start: 0.9108 (m-30) cc_final: 0.8819 (m-30) REVERT: H 93 ASP cc_start: 0.8173 (t0) cc_final: 0.7927 (t70) REVERT: H 113 GLN cc_start: 0.9019 (tp40) cc_final: 0.8730 (tp40) REVERT: H 124 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8202 (tm-30) REVERT: H 125 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8641 (mmtm) REVERT: H 148 GLU cc_start: 0.8913 (tt0) cc_final: 0.8698 (tt0) REVERT: I 18 GLU cc_start: 0.8586 (tt0) cc_final: 0.8299 (tt0) REVERT: I 64 ARG cc_start: 0.8460 (tpp80) cc_final: 0.7473 (ttp-170) REVERT: I 93 ASP cc_start: 0.8187 (t0) cc_final: 0.7909 (t70) REVERT: I 113 GLN cc_start: 0.9035 (tp40) cc_final: 0.8744 (tp40) REVERT: I 125 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8692 (mmtm) REVERT: J 18 GLU cc_start: 0.8598 (tt0) cc_final: 0.8315 (tt0) REVERT: J 93 ASP cc_start: 0.8193 (t0) cc_final: 0.7915 (t70) REVERT: J 113 GLN cc_start: 0.9029 (tp40) cc_final: 0.8741 (tp40) REVERT: J 125 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8699 (mmtm) REVERT: K 64 ARG cc_start: 0.8455 (tpp80) cc_final: 0.7453 (ttp-170) REVERT: K 93 ASP cc_start: 0.8174 (t0) cc_final: 0.7926 (t70) REVERT: K 113 GLN cc_start: 0.9031 (tp40) cc_final: 0.8734 (tp40) REVERT: K 124 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8208 (tm-30) REVERT: K 125 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8686 (mmtm) REVERT: K 141 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7855 (mp0) REVERT: K 148 GLU cc_start: 0.8872 (tt0) cc_final: 0.8536 (tt0) REVERT: L 16 ASP cc_start: 0.9096 (m-30) cc_final: 0.8833 (m-30) REVERT: L 64 ARG cc_start: 0.8472 (tpp80) cc_final: 0.7486 (ttp-170) REVERT: L 93 ASP cc_start: 0.8188 (t0) cc_final: 0.7924 (t70) REVERT: L 120 LYS cc_start: 0.8892 (tttm) cc_final: 0.8543 (ttmp) REVERT: L 124 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8223 (tm-30) REVERT: L 125 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8694 (mmtm) REVERT: L 141 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7852 (mp0) REVERT: L 158 LYS cc_start: 0.8366 (mttt) cc_final: 0.8130 (mtmt) REVERT: M 16 ASP cc_start: 0.9041 (m-30) cc_final: 0.8793 (m-30) REVERT: M 62 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7929 (mm-30) REVERT: M 64 ARG cc_start: 0.8469 (tpp80) cc_final: 0.7489 (ttp-170) REVERT: M 93 ASP cc_start: 0.8149 (t0) cc_final: 0.7921 (t70) REVERT: M 120 LYS cc_start: 0.8874 (tttm) cc_final: 0.8534 (ttmp) REVERT: M 124 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8228 (tm-30) REVERT: M 125 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8697 (mmtm) REVERT: M 141 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7859 (mp0) REVERT: M 148 GLU cc_start: 0.8879 (tt0) cc_final: 0.8665 (tt0) REVERT: N 16 ASP cc_start: 0.9112 (m-30) cc_final: 0.8824 (m-30) REVERT: N 18 GLU cc_start: 0.8611 (tt0) cc_final: 0.8335 (tt0) REVERT: N 93 ASP cc_start: 0.8174 (t0) cc_final: 0.7916 (t70) REVERT: N 113 GLN cc_start: 0.9019 (tp40) cc_final: 0.8724 (tp40) REVERT: N 125 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8650 (mmtm) REVERT: N 148 GLU cc_start: 0.8889 (tt0) cc_final: 0.8663 (tt0) REVERT: O 18 GLU cc_start: 0.8593 (tt0) cc_final: 0.8319 (tt0) REVERT: O 64 ARG cc_start: 0.8472 (tpp80) cc_final: 0.7478 (ttp-170) REVERT: O 93 ASP cc_start: 0.8181 (t0) cc_final: 0.7927 (t70) REVERT: O 113 GLN cc_start: 0.9035 (tp40) cc_final: 0.8746 (tp40) REVERT: O 120 LYS cc_start: 0.8824 (tttm) cc_final: 0.8425 (ttmt) REVERT: O 125 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8731 (mmtm) REVERT: O 148 GLU cc_start: 0.8832 (tt0) cc_final: 0.8628 (tt0) REVERT: P 18 GLU cc_start: 0.8603 (tt0) cc_final: 0.8328 (tt0) REVERT: P 93 ASP cc_start: 0.8168 (t0) cc_final: 0.7916 (t70) REVERT: P 124 GLU cc_start: 0.8472 (tm-30) cc_final: 0.8261 (tm-30) REVERT: P 125 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8648 (mmtm) REVERT: P 141 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7873 (mp0) REVERT: Q 63 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7591 (mm-30) REVERT: Q 93 ASP cc_start: 0.8177 (t0) cc_final: 0.7918 (t70) REVERT: Q 113 GLN cc_start: 0.9014 (tp40) cc_final: 0.8721 (tp40) REVERT: Q 124 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8186 (tm-30) REVERT: Q 141 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7850 (mp0) REVERT: Q 148 GLU cc_start: 0.8880 (tt0) cc_final: 0.8647 (tt0) REVERT: R 18 GLU cc_start: 0.8618 (tt0) cc_final: 0.8355 (tt0) REVERT: R 93 ASP cc_start: 0.8187 (t0) cc_final: 0.7943 (t70) REVERT: R 124 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8232 (tm-30) REVERT: R 125 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8665 (mmtm) REVERT: R 141 GLU cc_start: 0.8440 (mm-30) cc_final: 0.7864 (mp0) REVERT: S 18 GLU cc_start: 0.8610 (tt0) cc_final: 0.8343 (tt0) REVERT: S 64 ARG cc_start: 0.8469 (tpp80) cc_final: 0.7457 (ttp-170) REVERT: S 93 ASP cc_start: 0.8193 (t0) cc_final: 0.7950 (t70) REVERT: S 124 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8221 (tm-30) REVERT: S 125 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8672 (mmtm) REVERT: S 141 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7862 (mp0) REVERT: S 148 GLU cc_start: 0.8867 (tt0) cc_final: 0.8656 (tt0) REVERT: T 63 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7590 (mm-30) REVERT: T 93 ASP cc_start: 0.8159 (t0) cc_final: 0.7908 (t70) REVERT: T 113 GLN cc_start: 0.9040 (tp40) cc_final: 0.8745 (tp40) REVERT: T 124 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8173 (tm-30) REVERT: T 125 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8672 (mmtm) REVERT: T 141 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7863 (mp0) REVERT: T 148 GLU cc_start: 0.8888 (tt0) cc_final: 0.8554 (tt0) REVERT: U 63 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7564 (mm-30) REVERT: U 64 ARG cc_start: 0.8456 (tpp80) cc_final: 0.7549 (ttp-170) REVERT: U 93 ASP cc_start: 0.8144 (t0) cc_final: 0.7913 (t70) REVERT: U 141 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7748 (tm-30) REVERT: V 18 GLU cc_start: 0.8598 (tt0) cc_final: 0.8321 (tt0) REVERT: V 93 ASP cc_start: 0.8175 (t0) cc_final: 0.7922 (t70) REVERT: V 113 GLN cc_start: 0.9016 (tp40) cc_final: 0.8726 (tp40) REVERT: V 120 LYS cc_start: 0.8829 (tttm) cc_final: 0.8431 (ttmt) REVERT: V 148 GLU cc_start: 0.8837 (tt0) cc_final: 0.8630 (tt0) REVERT: V 158 LYS cc_start: 0.8369 (mttt) cc_final: 0.8150 (tppp) REVERT: W 93 ASP cc_start: 0.8111 (t0) cc_final: 0.7878 (t70) REVERT: W 113 GLN cc_start: 0.9012 (tp40) cc_final: 0.8722 (tp40) REVERT: W 125 LYS cc_start: 0.8968 (mmtt) cc_final: 0.8663 (mmtm) REVERT: W 148 GLU cc_start: 0.8909 (tt0) cc_final: 0.8691 (tt0) REVERT: X 16 ASP cc_start: 0.9032 (m-30) cc_final: 0.8787 (m-30) REVERT: X 62 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7922 (mm-30) REVERT: X 93 ASP cc_start: 0.8195 (t0) cc_final: 0.7944 (t70) REVERT: X 120 LYS cc_start: 0.8873 (tttm) cc_final: 0.8531 (ttmp) REVERT: X 124 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8216 (tm-30) REVERT: X 125 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8700 (mmtm) REVERT: X 141 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7862 (mp0) REVERT: X 148 GLU cc_start: 0.8879 (tt0) cc_final: 0.8665 (tt0) outliers start: 32 outliers final: 28 residues processed: 1161 average time/residue: 0.8690 time to fit residues: 1167.1921 Evaluate side-chains 1038 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 1010 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain X residue 7 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 270 optimal weight: 0.8980 chunk 343 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 309 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 304 optimal weight: 2.9990 chunk 282 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 8 GLN C 8 GLN E 8 GLN F 8 GLN G 8 GLN H 8 GLN I 8 GLN J 8 GLN K 8 GLN N 8 GLN O 8 GLN P 8 GLN Q 8 GLN R 8 GLN S 8 GLN U 8 GLN V 8 GLN V 61 HIS W 8 GLN X 8 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.104731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.097145 restraints weight = 42928.769| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.34 r_work: 0.2921 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 34776 Z= 0.156 Angle : 0.504 5.256 46824 Z= 0.263 Chirality : 0.036 0.123 4872 Planarity : 0.003 0.024 6216 Dihedral : 3.908 15.532 4584 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.04 % Allowed : 12.09 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.23 (0.13), residues: 4104 helix: 4.06 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.72 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 157 TYR 0.011 0.002 TYR K 138 PHE 0.012 0.002 PHE U 133 TRP 0.005 0.001 TRP R 94 HIS 0.002 0.001 HIS R 119 Details of bonding type rmsd covalent geometry : bond 0.00353 (34776) covalent geometry : angle 0.50408 (46824) hydrogen bonds : bond 0.03901 ( 2640) hydrogen bonds : angle 3.17411 ( 7920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 999 time to evaluate : 1.213 Fit side-chains REVERT: A 64 ARG cc_start: 0.8492 (tpp80) cc_final: 0.7503 (ttp-170) REVERT: A 113 GLN cc_start: 0.9053 (tp40) cc_final: 0.8758 (tp40) REVERT: A 125 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8729 (mmtm) REVERT: A 148 GLU cc_start: 0.8894 (tt0) cc_final: 0.8682 (tt0) REVERT: B 62 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7913 (mm-30) REVERT: B 93 ASP cc_start: 0.8250 (t0) cc_final: 0.8000 (t70) REVERT: B 113 GLN cc_start: 0.9041 (tp40) cc_final: 0.8795 (tp40) REVERT: B 141 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7852 (mp0) REVERT: B 148 GLU cc_start: 0.8885 (tt0) cc_final: 0.8562 (tt0) REVERT: C 64 ARG cc_start: 0.8513 (tpp80) cc_final: 0.7482 (ttp-170) REVERT: C 93 ASP cc_start: 0.8272 (t0) cc_final: 0.8005 (t70) REVERT: C 125 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8576 (mmtm) REVERT: C 141 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7861 (mp0) REVERT: D 93 ASP cc_start: 0.8269 (t0) cc_final: 0.8001 (t70) REVERT: D 141 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7871 (mp0) REVERT: E 62 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7991 (mm-30) REVERT: E 64 ARG cc_start: 0.8470 (tpp80) cc_final: 0.7506 (ttp-170) REVERT: E 93 ASP cc_start: 0.8246 (t0) cc_final: 0.8007 (t70) REVERT: E 113 GLN cc_start: 0.9051 (tp40) cc_final: 0.8745 (tp40) REVERT: E 125 LYS cc_start: 0.8944 (mmtt) cc_final: 0.8694 (mmtm) REVERT: E 148 GLU cc_start: 0.8889 (tt0) cc_final: 0.8674 (tt0) REVERT: F 64 ARG cc_start: 0.8469 (tpp80) cc_final: 0.7516 (ttp-170) REVERT: F 113 GLN cc_start: 0.9069 (tp40) cc_final: 0.8771 (tp40) REVERT: F 125 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8728 (mmtm) REVERT: F 141 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7861 (mp0) REVERT: F 148 GLU cc_start: 0.8891 (tt0) cc_final: 0.8672 (tt0) REVERT: G 64 ARG cc_start: 0.8483 (tpp80) cc_final: 0.7489 (ttp-170) REVERT: G 93 ASP cc_start: 0.8278 (t0) cc_final: 0.8023 (t70) REVERT: G 120 LYS cc_start: 0.8910 (tttm) cc_final: 0.8551 (ttmp) REVERT: G 125 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8731 (mmtm) REVERT: G 141 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7847 (mp0) REVERT: H 93 ASP cc_start: 0.8269 (t0) cc_final: 0.8040 (t70) REVERT: H 125 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8719 (mmtm) REVERT: H 148 GLU cc_start: 0.8904 (tt0) cc_final: 0.8700 (tt0) REVERT: I 50 LYS cc_start: 0.8597 (mttp) cc_final: 0.8064 (mmpt) REVERT: I 62 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7864 (mm-30) REVERT: I 64 ARG cc_start: 0.8485 (tpp80) cc_final: 0.7505 (ttp-170) REVERT: I 93 ASP cc_start: 0.8278 (t0) cc_final: 0.8006 (t70) REVERT: I 113 GLN cc_start: 0.9063 (tp40) cc_final: 0.8766 (tp40) REVERT: I 125 LYS cc_start: 0.8963 (mmtt) cc_final: 0.8737 (mmtm) REVERT: J 50 LYS cc_start: 0.8615 (mttp) cc_final: 0.8073 (mmpt) REVERT: J 62 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7871 (mm-30) REVERT: J 93 ASP cc_start: 0.8279 (t0) cc_final: 0.8006 (t70) REVERT: J 113 GLN cc_start: 0.9052 (tp40) cc_final: 0.8756 (tp40) REVERT: J 125 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8741 (mmtm) REVERT: K 62 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7958 (mm-30) REVERT: K 64 ARG cc_start: 0.8467 (tpp80) cc_final: 0.7497 (ttp-170) REVERT: K 93 ASP cc_start: 0.8269 (t0) cc_final: 0.7994 (t70) REVERT: K 113 GLN cc_start: 0.9056 (tp40) cc_final: 0.8797 (tp40) REVERT: K 125 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8724 (mmtm) REVERT: K 141 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7860 (mp0) REVERT: K 148 GLU cc_start: 0.8878 (tt0) cc_final: 0.8570 (tt0) REVERT: L 64 ARG cc_start: 0.8482 (tpp80) cc_final: 0.7494 (ttp-170) REVERT: L 93 ASP cc_start: 0.8282 (t0) cc_final: 0.8026 (t70) REVERT: L 120 LYS cc_start: 0.8912 (tttm) cc_final: 0.8548 (ttmp) REVERT: L 125 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8722 (mmtm) REVERT: L 141 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7846 (mp0) REVERT: M 62 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7894 (mm-30) REVERT: M 64 ARG cc_start: 0.8488 (tpp80) cc_final: 0.7512 (ttp-170) REVERT: M 93 ASP cc_start: 0.8282 (t0) cc_final: 0.8045 (t70) REVERT: M 120 LYS cc_start: 0.8864 (tttm) cc_final: 0.8507 (ttmp) REVERT: M 124 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8225 (tm-30) REVERT: M 125 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8718 (mmtm) REVERT: M 141 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7849 (mp0) REVERT: M 148 GLU cc_start: 0.8855 (tt0) cc_final: 0.8619 (tt0) REVERT: N 93 ASP cc_start: 0.8263 (t0) cc_final: 0.8029 (t70) REVERT: N 113 GLN cc_start: 0.9050 (tp40) cc_final: 0.8744 (tp40) REVERT: N 125 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8696 (mmtm) REVERT: N 148 GLU cc_start: 0.8879 (tt0) cc_final: 0.8664 (tt0) REVERT: O 64 ARG cc_start: 0.8480 (tpp80) cc_final: 0.7498 (ttp-170) REVERT: O 93 ASP cc_start: 0.8273 (t0) cc_final: 0.8029 (t70) REVERT: O 113 GLN cc_start: 0.9066 (tp40) cc_final: 0.8825 (tp40) REVERT: O 125 LYS cc_start: 0.8973 (mmtt) cc_final: 0.8753 (mmtm) REVERT: P 62 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7940 (mm-30) REVERT: P 93 ASP cc_start: 0.8251 (t0) cc_final: 0.8007 (t70) REVERT: P 124 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8204 (tm-30) REVERT: P 125 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8678 (mmtm) REVERT: P 141 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7872 (mp0) REVERT: Q 93 ASP cc_start: 0.8242 (t0) cc_final: 0.7994 (t70) REVERT: Q 113 GLN cc_start: 0.9040 (tp40) cc_final: 0.8747 (tp40) REVERT: Q 124 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8197 (tm-30) REVERT: Q 141 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7835 (mp0) REVERT: Q 148 GLU cc_start: 0.8884 (tt0) cc_final: 0.8564 (tt0) REVERT: R 93 ASP cc_start: 0.8306 (t0) cc_final: 0.8037 (t70) REVERT: R 141 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7871 (mp0) REVERT: S 64 ARG cc_start: 0.8471 (tpp80) cc_final: 0.7480 (ttp-170) REVERT: S 93 ASP cc_start: 0.8302 (t0) cc_final: 0.8034 (t70) REVERT: S 124 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8233 (tm-30) REVERT: S 141 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7874 (mp0) REVERT: S 148 GLU cc_start: 0.8863 (tt0) cc_final: 0.8662 (tt0) REVERT: T 62 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7950 (mm-30) REVERT: T 113 GLN cc_start: 0.9064 (tp40) cc_final: 0.8807 (tp40) REVERT: T 125 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8749 (mmtm) REVERT: T 141 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7849 (mp0) REVERT: T 148 GLU cc_start: 0.8890 (tt0) cc_final: 0.8582 (tt0) REVERT: U 64 ARG cc_start: 0.8493 (tpp80) cc_final: 0.7540 (ttp-170) REVERT: U 93 ASP cc_start: 0.8258 (t0) cc_final: 0.8014 (t70) REVERT: U 124 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8226 (tm-30) REVERT: U 141 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7851 (mp0) REVERT: V 93 ASP cc_start: 0.8280 (t0) cc_final: 0.8036 (t70) REVERT: V 113 GLN cc_start: 0.9051 (tp40) cc_final: 0.8807 (tp40) REVERT: W 93 ASP cc_start: 0.8260 (t0) cc_final: 0.8025 (t70) REVERT: W 125 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8626 (mmtm) REVERT: W 148 GLU cc_start: 0.8910 (tt0) cc_final: 0.8708 (tt0) REVERT: X 93 ASP cc_start: 0.8280 (t0) cc_final: 0.8044 (t70) REVERT: X 120 LYS cc_start: 0.8861 (tttm) cc_final: 0.8503 (ttmp) REVERT: X 124 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8231 (tm-30) REVERT: X 125 LYS cc_start: 0.8921 (mmtt) cc_final: 0.8718 (mmtm) REVERT: X 141 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7845 (mp0) REVERT: X 148 GLU cc_start: 0.8886 (tt0) cc_final: 0.8654 (tt0) outliers start: 75 outliers final: 72 residues processed: 1025 average time/residue: 0.8289 time to fit residues: 981.5995 Evaluate side-chains 1053 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 981 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 95 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 56 optimal weight: 1.9990 chunk 198 optimal weight: 6.9990 chunk 348 optimal weight: 8.9990 chunk 399 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 chunk 370 optimal weight: 8.9990 chunk 244 optimal weight: 8.9990 chunk 169 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 8 GLN C 8 GLN E 8 GLN F 8 GLN G 8 GLN H 8 GLN I 8 GLN J 8 GLN K 8 GLN N 8 GLN O 8 GLN P 8 GLN Q 8 GLN R 8 GLN S 8 GLN T 8 GLN V 8 GLN W 8 GLN X 8 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.105823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.098341 restraints weight = 43117.552| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.33 r_work: 0.2945 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34776 Z= 0.146 Angle : 0.496 5.163 46824 Z= 0.259 Chirality : 0.036 0.121 4872 Planarity : 0.003 0.025 6216 Dihedral : 3.898 16.160 4584 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.10 % Allowed : 12.50 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.27 (0.13), residues: 4104 helix: 4.10 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.67 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 157 TYR 0.011 0.002 TYR D 138 PHE 0.013 0.002 PHE U 133 TRP 0.004 0.001 TRP W 94 HIS 0.002 0.001 HIS N 66 Details of bonding type rmsd covalent geometry : bond 0.00329 (34776) covalent geometry : angle 0.49643 (46824) hydrogen bonds : bond 0.03788 ( 2640) hydrogen bonds : angle 3.13579 ( 7920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 1008 time to evaluate : 1.282 Fit side-chains REVERT: A 64 ARG cc_start: 0.8482 (tpp80) cc_final: 0.7483 (ttp-170) REVERT: A 113 GLN cc_start: 0.9059 (tp40) cc_final: 0.8767 (tp40) REVERT: A 125 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8755 (mmtm) REVERT: A 148 GLU cc_start: 0.8872 (tt0) cc_final: 0.8658 (tt0) REVERT: B 93 ASP cc_start: 0.8249 (t0) cc_final: 0.7991 (t70) REVERT: B 113 GLN cc_start: 0.9063 (tp40) cc_final: 0.8767 (tp40) REVERT: B 141 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7854 (mp0) REVERT: B 148 GLU cc_start: 0.8879 (tt0) cc_final: 0.8563 (tt0) REVERT: C 64 ARG cc_start: 0.8448 (tpp80) cc_final: 0.7476 (ttp-170) REVERT: C 93 ASP cc_start: 0.8281 (t0) cc_final: 0.8017 (t70) REVERT: C 124 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8106 (tm-30) REVERT: C 141 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7846 (mp0) REVERT: D 93 ASP cc_start: 0.8270 (t0) cc_final: 0.8003 (t70) REVERT: D 141 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7853 (mp0) REVERT: E 62 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7922 (mm-30) REVERT: E 64 ARG cc_start: 0.8488 (tpp80) cc_final: 0.7513 (ttp-170) REVERT: E 93 ASP cc_start: 0.8247 (t0) cc_final: 0.8006 (t70) REVERT: E 113 GLN cc_start: 0.9062 (tp40) cc_final: 0.8762 (tp40) REVERT: E 125 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8685 (mmtm) REVERT: E 148 GLU cc_start: 0.8870 (tt0) cc_final: 0.8654 (tt0) REVERT: F 18 GLU cc_start: 0.8676 (tt0) cc_final: 0.8359 (tt0) REVERT: F 64 ARG cc_start: 0.8484 (tpp80) cc_final: 0.7518 (ttp-170) REVERT: F 113 GLN cc_start: 0.9071 (tp40) cc_final: 0.8775 (tp40) REVERT: F 141 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7857 (mp0) REVERT: F 148 GLU cc_start: 0.8872 (tt0) cc_final: 0.8652 (tt0) REVERT: G 62 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7866 (mm-30) REVERT: G 64 ARG cc_start: 0.8490 (tpp80) cc_final: 0.7493 (ttp-170) REVERT: G 93 ASP cc_start: 0.8287 (t0) cc_final: 0.8024 (t70) REVERT: G 120 LYS cc_start: 0.8920 (tttm) cc_final: 0.8564 (ttmp) REVERT: G 125 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8702 (mmtm) REVERT: G 141 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7860 (mp0) REVERT: H 18 GLU cc_start: 0.8695 (tt0) cc_final: 0.8413 (tt0) REVERT: H 64 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7999 (tpp80) REVERT: H 93 ASP cc_start: 0.8274 (t0) cc_final: 0.8036 (t70) REVERT: H 125 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8625 (mmtm) REVERT: H 148 GLU cc_start: 0.8891 (tt0) cc_final: 0.8575 (tt0) REVERT: I 62 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7853 (mm-30) REVERT: I 64 ARG cc_start: 0.8485 (tpp80) cc_final: 0.7512 (ttp-170) REVERT: I 93 ASP cc_start: 0.8280 (t0) cc_final: 0.8005 (t70) REVERT: I 113 GLN cc_start: 0.9065 (tp40) cc_final: 0.8771 (tp40) REVERT: I 125 LYS cc_start: 0.8894 (mmtt) cc_final: 0.8678 (mmtm) REVERT: J 93 ASP cc_start: 0.8278 (t0) cc_final: 0.8003 (t70) REVERT: J 113 GLN cc_start: 0.9061 (tp40) cc_final: 0.8768 (tp40) REVERT: J 125 LYS cc_start: 0.8898 (mmtt) cc_final: 0.8683 (mmtm) REVERT: K 64 ARG cc_start: 0.8454 (tpp80) cc_final: 0.7489 (ttp-170) REVERT: K 93 ASP cc_start: 0.8251 (t0) cc_final: 0.8014 (t70) REVERT: K 113 GLN cc_start: 0.9062 (tp40) cc_final: 0.8760 (tp40) REVERT: K 125 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8703 (mmtm) REVERT: K 141 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7856 (mp0) REVERT: K 148 GLU cc_start: 0.8872 (tt0) cc_final: 0.8560 (tt0) REVERT: L 62 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7887 (mm-30) REVERT: L 64 ARG cc_start: 0.8483 (tpp80) cc_final: 0.7486 (ttp-170) REVERT: L 93 ASP cc_start: 0.8290 (t0) cc_final: 0.8032 (t70) REVERT: L 120 LYS cc_start: 0.8923 (tttm) cc_final: 0.8563 (ttmp) REVERT: L 125 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8696 (mmtm) REVERT: L 141 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7864 (mp0) REVERT: M 62 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7875 (mm-30) REVERT: M 64 ARG cc_start: 0.8483 (tpp80) cc_final: 0.7513 (ttp-170) REVERT: M 93 ASP cc_start: 0.8266 (t0) cc_final: 0.8035 (t70) REVERT: M 120 LYS cc_start: 0.8871 (tttm) cc_final: 0.8515 (ttmp) REVERT: M 124 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8233 (tm-30) REVERT: M 125 LYS cc_start: 0.8923 (mmtt) cc_final: 0.8713 (mmtm) REVERT: M 141 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7844 (mp0) REVERT: M 148 GLU cc_start: 0.8856 (tt0) cc_final: 0.8621 (tt0) REVERT: N 93 ASP cc_start: 0.8258 (t0) cc_final: 0.8018 (t70) REVERT: N 113 GLN cc_start: 0.9058 (tp40) cc_final: 0.8757 (tp40) REVERT: N 125 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8664 (mmtm) REVERT: N 148 GLU cc_start: 0.8883 (tt0) cc_final: 0.8668 (tt0) REVERT: O 64 ARG cc_start: 0.8497 (tpp80) cc_final: 0.7501 (ttp-170) REVERT: O 93 ASP cc_start: 0.8238 (t0) cc_final: 0.8005 (t70) REVERT: O 113 GLN cc_start: 0.9069 (tp40) cc_final: 0.8773 (tp40) REVERT: O 125 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8701 (mmtm) REVERT: P 59 GLN cc_start: 0.8620 (mm110) cc_final: 0.8410 (mm110) REVERT: P 62 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7922 (mm-30) REVERT: P 93 ASP cc_start: 0.8224 (t0) cc_final: 0.7990 (t70) REVERT: P 124 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8231 (tm-30) REVERT: P 125 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8674 (mmtm) REVERT: P 141 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7881 (mp0) REVERT: Q 62 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7864 (mm-30) REVERT: Q 93 ASP cc_start: 0.8247 (t0) cc_final: 0.7988 (t70) REVERT: Q 113 GLN cc_start: 0.9050 (tp40) cc_final: 0.8755 (tp40) REVERT: Q 141 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7850 (mp0) REVERT: Q 148 GLU cc_start: 0.8878 (tt0) cc_final: 0.8562 (tt0) REVERT: R 62 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7923 (mm-30) REVERT: R 91 ARG cc_start: 0.8376 (mtp85) cc_final: 0.8175 (mtp85) REVERT: R 93 ASP cc_start: 0.8269 (t0) cc_final: 0.8039 (t70) REVERT: R 141 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7866 (mp0) REVERT: S 18 GLU cc_start: 0.8676 (tt0) cc_final: 0.8360 (tt0) REVERT: S 64 ARG cc_start: 0.8467 (tpp80) cc_final: 0.7493 (ttp-170) REVERT: S 93 ASP cc_start: 0.8269 (t0) cc_final: 0.8042 (t70) REVERT: S 124 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8249 (tm-30) REVERT: S 141 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7868 (mp0) REVERT: S 148 GLU cc_start: 0.8849 (tt0) cc_final: 0.8647 (tt0) REVERT: T 62 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7911 (mm-30) REVERT: T 113 GLN cc_start: 0.9064 (tp40) cc_final: 0.8764 (tp40) REVERT: T 125 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8699 (mmtm) REVERT: T 141 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7868 (mp0) REVERT: T 148 GLU cc_start: 0.8884 (tt0) cc_final: 0.8574 (tt0) REVERT: U 64 ARG cc_start: 0.8489 (tpp80) cc_final: 0.7539 (ttp-170) REVERT: U 93 ASP cc_start: 0.8222 (t0) cc_final: 0.7987 (t70) REVERT: U 141 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7854 (mp0) REVERT: V 93 ASP cc_start: 0.8239 (t0) cc_final: 0.7999 (t70) REVERT: V 113 GLN cc_start: 0.9061 (tp40) cc_final: 0.8763 (tp40) REVERT: W 64 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8014 (tpp80) REVERT: W 93 ASP cc_start: 0.8261 (t0) cc_final: 0.8017 (t70) REVERT: W 125 LYS cc_start: 0.8876 (mmtt) cc_final: 0.8657 (mmtm) REVERT: W 148 GLU cc_start: 0.8905 (tt0) cc_final: 0.8594 (tt0) REVERT: X 93 ASP cc_start: 0.8252 (t0) cc_final: 0.8019 (t70) REVERT: X 120 LYS cc_start: 0.8865 (tttm) cc_final: 0.8506 (ttmp) REVERT: X 124 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8236 (tm-30) REVERT: X 125 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8718 (mmtm) REVERT: X 141 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7846 (mp0) REVERT: X 148 GLU cc_start: 0.8875 (tt0) cc_final: 0.8643 (tt0) outliers start: 77 outliers final: 70 residues processed: 1033 average time/residue: 0.8570 time to fit residues: 1021.6788 Evaluate side-chains 1038 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 966 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain W residue 64 ARG Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 95 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 339 optimal weight: 0.9990 chunk 373 optimal weight: 0.8980 chunk 394 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 160 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 276 optimal weight: 3.9990 chunk 368 optimal weight: 1.9990 chunk 316 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 8 GLN C 8 GLN E 8 GLN F 8 GLN G 8 GLN I 8 GLN J 8 GLN K 8 GLN N 8 GLN O 8 GLN P 8 GLN Q 8 GLN R 8 GLN S 8 GLN T 8 GLN U 8 GLN V 8 GLN W 8 GLN X 8 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.105526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.097960 restraints weight = 42915.773| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.34 r_work: 0.2950 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 34776 Z= 0.135 Angle : 0.491 5.090 46824 Z= 0.257 Chirality : 0.035 0.120 4872 Planarity : 0.003 0.025 6216 Dihedral : 3.866 16.117 4584 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.55 % Allowed : 13.83 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.35 (0.13), residues: 4104 helix: 4.17 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.65 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 157 TYR 0.011 0.001 TYR Q 138 PHE 0.013 0.002 PHE D 133 TRP 0.003 0.001 TRP R 94 HIS 0.002 0.001 HIS J 66 Details of bonding type rmsd covalent geometry : bond 0.00303 (34776) covalent geometry : angle 0.49127 (46824) hydrogen bonds : bond 0.03675 ( 2640) hydrogen bonds : angle 3.10044 ( 7920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 1011 time to evaluate : 1.354 Fit side-chains REVERT: A 18 GLU cc_start: 0.8677 (tt0) cc_final: 0.8365 (tt0) REVERT: A 64 ARG cc_start: 0.8474 (tpp80) cc_final: 0.7487 (ttp-170) REVERT: A 95 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 113 GLN cc_start: 0.9064 (tp40) cc_final: 0.8769 (tp40) REVERT: A 148 GLU cc_start: 0.8867 (tt0) cc_final: 0.8661 (tt0) REVERT: B 93 ASP cc_start: 0.8205 (t0) cc_final: 0.7955 (t70) REVERT: B 113 GLN cc_start: 0.9053 (tp40) cc_final: 0.8755 (tp40) REVERT: B 141 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7816 (mp0) REVERT: B 148 GLU cc_start: 0.8879 (tt0) cc_final: 0.8572 (tt0) REVERT: C 64 ARG cc_start: 0.8445 (tpp80) cc_final: 0.7476 (ttp-170) REVERT: C 93 ASP cc_start: 0.8263 (t0) cc_final: 0.7993 (t70) REVERT: C 141 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7806 (mp0) REVERT: D 93 ASP cc_start: 0.8261 (t0) cc_final: 0.7989 (t70) REVERT: D 141 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7826 (mp0) REVERT: E 16 ASP cc_start: 0.9125 (m-30) cc_final: 0.8824 (m-30) REVERT: E 62 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7954 (mm-30) REVERT: E 64 ARG cc_start: 0.8464 (tpp80) cc_final: 0.7486 (ttp-170) REVERT: E 93 ASP cc_start: 0.8238 (t0) cc_final: 0.7996 (t70) REVERT: E 113 GLN cc_start: 0.9052 (tp40) cc_final: 0.8750 (tp40) REVERT: E 125 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8658 (mmtm) REVERT: E 148 GLU cc_start: 0.8870 (tt0) cc_final: 0.8651 (tt0) REVERT: F 64 ARG cc_start: 0.8481 (tpp80) cc_final: 0.7512 (ttp-170) REVERT: F 95 GLU cc_start: 0.8305 (mm-30) cc_final: 0.8085 (mm-30) REVERT: F 113 GLN cc_start: 0.9073 (tp40) cc_final: 0.8772 (tp40) REVERT: F 141 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7855 (mp0) REVERT: F 148 GLU cc_start: 0.8859 (tt0) cc_final: 0.8650 (tt0) REVERT: G 62 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7858 (mm-30) REVERT: G 64 ARG cc_start: 0.8483 (tpp80) cc_final: 0.7493 (ttp-170) REVERT: G 93 ASP cc_start: 0.8273 (t0) cc_final: 0.8004 (t70) REVERT: G 120 LYS cc_start: 0.8911 (tttm) cc_final: 0.8550 (ttmp) REVERT: G 125 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8650 (mmtm) REVERT: G 141 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7848 (mp0) REVERT: H 64 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8006 (tpp80) REVERT: H 93 ASP cc_start: 0.8216 (t0) cc_final: 0.7990 (t70) REVERT: H 125 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8610 (mmtm) REVERT: H 148 GLU cc_start: 0.8887 (tt0) cc_final: 0.8577 (tt0) REVERT: I 50 LYS cc_start: 0.8579 (mttp) cc_final: 0.8051 (mmpt) REVERT: I 62 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7886 (mm-30) REVERT: I 64 ARG cc_start: 0.8485 (tpp80) cc_final: 0.7501 (ttp-170) REVERT: I 93 ASP cc_start: 0.8273 (t0) cc_final: 0.7991 (t70) REVERT: I 113 GLN cc_start: 0.9066 (tp40) cc_final: 0.8770 (tp40) REVERT: I 125 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8632 (mmtm) REVERT: J 50 LYS cc_start: 0.8601 (mttp) cc_final: 0.8063 (mmpt) REVERT: J 93 ASP cc_start: 0.8276 (t0) cc_final: 0.7994 (t70) REVERT: J 95 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8065 (mm-30) REVERT: J 113 GLN cc_start: 0.9058 (tp40) cc_final: 0.8762 (tp40) REVERT: J 125 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8635 (mmtm) REVERT: K 64 ARG cc_start: 0.8470 (tpp80) cc_final: 0.7471 (ttp-170) REVERT: K 93 ASP cc_start: 0.8231 (t0) cc_final: 0.7996 (t70) REVERT: K 113 GLN cc_start: 0.9060 (tp40) cc_final: 0.8756 (tp40) REVERT: K 125 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8662 (mmtm) REVERT: K 141 GLU cc_start: 0.8346 (mm-30) cc_final: 0.7809 (mp0) REVERT: K 148 GLU cc_start: 0.8866 (tt0) cc_final: 0.8565 (tt0) REVERT: L 62 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7886 (mm-30) REVERT: L 64 ARG cc_start: 0.8477 (tpp80) cc_final: 0.7491 (ttp-170) REVERT: L 93 ASP cc_start: 0.8273 (t0) cc_final: 0.8005 (t70) REVERT: L 120 LYS cc_start: 0.8924 (tttm) cc_final: 0.8559 (ttmp) REVERT: L 125 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8646 (mmtm) REVERT: L 141 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7858 (mp0) REVERT: M 18 GLU cc_start: 0.8657 (tt0) cc_final: 0.8436 (tt0) REVERT: M 64 ARG cc_start: 0.8468 (tpp80) cc_final: 0.7491 (ttp-170) REVERT: M 93 ASP cc_start: 0.8253 (t0) cc_final: 0.8024 (t70) REVERT: M 120 LYS cc_start: 0.8866 (tttm) cc_final: 0.8509 (ttmp) REVERT: M 141 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7806 (mp0) REVERT: M 148 GLU cc_start: 0.8841 (tt0) cc_final: 0.8614 (tt0) REVERT: N 16 ASP cc_start: 0.9087 (m-30) cc_final: 0.8875 (m-30) REVERT: N 93 ASP cc_start: 0.8243 (t0) cc_final: 0.8002 (t70) REVERT: N 113 GLN cc_start: 0.9053 (tp40) cc_final: 0.8749 (tp40) REVERT: N 125 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8598 (mmtm) REVERT: N 148 GLU cc_start: 0.8882 (tt0) cc_final: 0.8664 (tt0) REVERT: O 64 ARG cc_start: 0.8496 (tpp80) cc_final: 0.7500 (ttp-170) REVERT: O 93 ASP cc_start: 0.8234 (t0) cc_final: 0.8001 (t70) REVERT: O 113 GLN cc_start: 0.9066 (tp40) cc_final: 0.8767 (tp40) REVERT: O 125 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8625 (mmtm) REVERT: P 59 GLN cc_start: 0.8617 (mm110) cc_final: 0.8405 (mm110) REVERT: P 62 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7903 (mm-30) REVERT: P 93 ASP cc_start: 0.8220 (t0) cc_final: 0.7985 (t70) REVERT: P 124 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8227 (tm-30) REVERT: P 125 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8651 (mmtm) REVERT: P 141 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7869 (mp0) REVERT: Q 62 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7873 (mm-30) REVERT: Q 93 ASP cc_start: 0.8205 (t0) cc_final: 0.7959 (t70) REVERT: Q 113 GLN cc_start: 0.9050 (tp40) cc_final: 0.8754 (tp40) REVERT: Q 141 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7836 (mp0) REVERT: Q 148 GLU cc_start: 0.8870 (tt0) cc_final: 0.8564 (tt0) REVERT: R 93 ASP cc_start: 0.8263 (t0) cc_final: 0.8036 (t70) REVERT: R 95 GLU cc_start: 0.8299 (mm-30) cc_final: 0.8076 (mm-30) REVERT: R 141 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7857 (mp0) REVERT: S 62 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7956 (mm-30) REVERT: S 64 ARG cc_start: 0.8463 (tpp80) cc_final: 0.7483 (ttp-170) REVERT: S 93 ASP cc_start: 0.8263 (t0) cc_final: 0.8036 (t70) REVERT: S 95 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8076 (mm-30) REVERT: S 141 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7862 (mp0) REVERT: T 113 GLN cc_start: 0.9067 (tp40) cc_final: 0.8766 (tp40) REVERT: T 125 LYS cc_start: 0.8904 (mmtt) cc_final: 0.8680 (mmtm) REVERT: T 141 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7825 (mp0) REVERT: T 148 GLU cc_start: 0.8883 (tt0) cc_final: 0.8579 (tt0) REVERT: U 59 GLN cc_start: 0.8619 (mm110) cc_final: 0.8403 (mm110) REVERT: U 64 ARG cc_start: 0.8491 (tpp80) cc_final: 0.7539 (ttp-170) REVERT: U 93 ASP cc_start: 0.8211 (t0) cc_final: 0.7976 (t70) REVERT: U 141 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7840 (mp0) REVERT: V 62 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7825 (mm-30) REVERT: V 93 ASP cc_start: 0.8230 (t0) cc_final: 0.7990 (t70) REVERT: V 113 GLN cc_start: 0.9056 (tp40) cc_final: 0.8759 (tp40) REVERT: V 124 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7915 (pp20) REVERT: W 93 ASP cc_start: 0.8215 (t0) cc_final: 0.7990 (t70) REVERT: W 125 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8620 (mmtm) REVERT: W 148 GLU cc_start: 0.8892 (tt0) cc_final: 0.8681 (tt0) REVERT: X 18 GLU cc_start: 0.8650 (tt0) cc_final: 0.8424 (tt0) REVERT: X 93 ASP cc_start: 0.8248 (t0) cc_final: 0.8017 (t70) REVERT: X 120 LYS cc_start: 0.8863 (tttm) cc_final: 0.8506 (ttmp) REVERT: X 141 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7815 (mp0) REVERT: X 148 GLU cc_start: 0.8859 (tt0) cc_final: 0.8650 (tt0) outliers start: 57 outliers final: 56 residues processed: 1035 average time/residue: 0.8521 time to fit residues: 1017.3279 Evaluate side-chains 1030 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 973 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 60 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 212 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 336 optimal weight: 0.6980 chunk 398 optimal weight: 5.9990 chunk 231 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 316 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 8 GLN C 8 GLN D 8 GLN E 8 GLN F 8 GLN G 8 GLN H 8 GLN I 8 GLN J 8 GLN K 8 GLN N 8 GLN O 8 GLN P 8 GLN Q 8 GLN R 8 GLN S 8 GLN T 8 GLN U 8 GLN V 8 GLN W 8 GLN X 8 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.104534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.096979 restraints weight = 43115.643| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.33 r_work: 0.2934 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 34776 Z= 0.167 Angle : 0.523 5.291 46824 Z= 0.272 Chirality : 0.037 0.122 4872 Planarity : 0.003 0.026 6216 Dihedral : 3.931 15.398 4584 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.12 % Allowed : 12.88 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.17 (0.13), residues: 4104 helix: 4.04 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.55 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG V 157 TYR 0.012 0.002 TYR O 40 PHE 0.013 0.002 PHE I 133 TRP 0.005 0.001 TRP X 94 HIS 0.002 0.001 HIS J 66 Details of bonding type rmsd covalent geometry : bond 0.00379 (34776) covalent geometry : angle 0.52345 (46824) hydrogen bonds : bond 0.03980 ( 2640) hydrogen bonds : angle 3.21054 ( 7920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 985 time to evaluate : 1.241 Fit side-chains REVERT: A 64 ARG cc_start: 0.8468 (tpp80) cc_final: 0.7501 (ttp-170) REVERT: A 95 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8100 (mm-30) REVERT: A 113 GLN cc_start: 0.9072 (tp40) cc_final: 0.8781 (tp40) REVERT: A 148 GLU cc_start: 0.8856 (tt0) cc_final: 0.8642 (tt0) REVERT: B 93 ASP cc_start: 0.8311 (t0) cc_final: 0.8009 (t70) REVERT: B 113 GLN cc_start: 0.9064 (tp40) cc_final: 0.8764 (tp40) REVERT: B 141 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7839 (mp0) REVERT: B 148 GLU cc_start: 0.8874 (tt0) cc_final: 0.8559 (tt0) REVERT: C 62 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7881 (mm-30) REVERT: C 64 ARG cc_start: 0.8428 (tpp80) cc_final: 0.7483 (ttp-170) REVERT: C 93 ASP cc_start: 0.8345 (t0) cc_final: 0.8032 (t70) REVERT: C 124 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8133 (pp20) REVERT: C 141 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7838 (mp0) REVERT: D 93 ASP cc_start: 0.8333 (t0) cc_final: 0.8018 (t70) REVERT: D 124 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8114 (pp20) REVERT: D 141 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7840 (mp0) REVERT: E 62 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7924 (mm-30) REVERT: E 64 ARG cc_start: 0.8464 (tpp80) cc_final: 0.7494 (ttp-170) REVERT: E 93 ASP cc_start: 0.8338 (t0) cc_final: 0.8044 (t70) REVERT: E 113 GLN cc_start: 0.9059 (tp40) cc_final: 0.8763 (tp40) REVERT: E 125 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8624 (mmtm) REVERT: E 148 GLU cc_start: 0.8878 (tt0) cc_final: 0.8659 (tt0) REVERT: F 62 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7948 (mm-30) REVERT: F 64 ARG cc_start: 0.8453 (tpp80) cc_final: 0.7496 (ttp-170) REVERT: F 95 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8084 (mm-30) REVERT: F 113 GLN cc_start: 0.9077 (tp40) cc_final: 0.8783 (tp40) REVERT: F 141 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7868 (mp0) REVERT: F 148 GLU cc_start: 0.8855 (tt0) cc_final: 0.8636 (tt0) REVERT: G 62 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7892 (mm-30) REVERT: G 64 ARG cc_start: 0.8464 (tpp80) cc_final: 0.7482 (ttp-170) REVERT: G 93 ASP cc_start: 0.8342 (t0) cc_final: 0.8038 (t70) REVERT: G 120 LYS cc_start: 0.8928 (tttm) cc_final: 0.8559 (ttmp) REVERT: G 125 LYS cc_start: 0.8877 (mmtt) cc_final: 0.8657 (mmtm) REVERT: G 141 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7861 (mp0) REVERT: H 93 ASP cc_start: 0.8334 (t0) cc_final: 0.8053 (t70) REVERT: H 125 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8628 (mmtm) REVERT: H 148 GLU cc_start: 0.8889 (tt0) cc_final: 0.8576 (tt0) REVERT: I 50 LYS cc_start: 0.8604 (mttp) cc_final: 0.8094 (mmpt) REVERT: I 62 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7927 (mm-30) REVERT: I 64 ARG cc_start: 0.8462 (tpp80) cc_final: 0.7484 (ttp-170) REVERT: I 93 ASP cc_start: 0.8340 (t0) cc_final: 0.8011 (t70) REVERT: I 113 GLN cc_start: 0.9073 (tp40) cc_final: 0.8835 (tp40) REVERT: I 125 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8639 (mmtm) REVERT: J 50 LYS cc_start: 0.8615 (mttp) cc_final: 0.8109 (mmpt) REVERT: J 64 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.8013 (tpp80) REVERT: J 93 ASP cc_start: 0.8353 (t0) cc_final: 0.8024 (t70) REVERT: J 95 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8071 (mm-30) REVERT: J 113 GLN cc_start: 0.9061 (tp40) cc_final: 0.8769 (tp40) REVERT: J 125 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8646 (mmtm) REVERT: K 64 ARG cc_start: 0.8460 (tpp80) cc_final: 0.7491 (ttp-170) REVERT: K 93 ASP cc_start: 0.8297 (t0) cc_final: 0.8025 (t70) REVERT: K 113 GLN cc_start: 0.9067 (tp40) cc_final: 0.8767 (tp40) REVERT: K 125 LYS cc_start: 0.8873 (mmtt) cc_final: 0.8643 (mmtm) REVERT: K 141 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7853 (mp0) REVERT: K 148 GLU cc_start: 0.8849 (tt0) cc_final: 0.8535 (tt0) REVERT: L 62 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7856 (mm-30) REVERT: L 64 ARG cc_start: 0.8455 (tpp80) cc_final: 0.7486 (ttp-170) REVERT: L 93 ASP cc_start: 0.8356 (t0) cc_final: 0.8053 (t70) REVERT: L 120 LYS cc_start: 0.8939 (tttm) cc_final: 0.8566 (ttmp) REVERT: L 125 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8650 (mmtm) REVERT: L 141 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7862 (mp0) REVERT: M 64 ARG cc_start: 0.8453 (tpp80) cc_final: 0.7467 (ttp-170) REVERT: M 93 ASP cc_start: 0.8343 (t0) cc_final: 0.8062 (t70) REVERT: M 120 LYS cc_start: 0.8924 (tttm) cc_final: 0.8567 (ttmp) REVERT: M 141 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7849 (mp0) REVERT: M 148 GLU cc_start: 0.8844 (tt0) cc_final: 0.8607 (tt0) REVERT: N 113 GLN cc_start: 0.9062 (tp40) cc_final: 0.8766 (tp40) REVERT: N 125 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8617 (mmtm) REVERT: N 148 GLU cc_start: 0.8880 (tt0) cc_final: 0.8662 (tt0) REVERT: O 64 ARG cc_start: 0.8473 (tpp80) cc_final: 0.7483 (ttp-170) REVERT: O 113 GLN cc_start: 0.9078 (tp40) cc_final: 0.8783 (tp40) REVERT: O 125 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8630 (mmtm) REVERT: P 62 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7945 (mm-30) REVERT: P 93 ASP cc_start: 0.8325 (t0) cc_final: 0.8030 (t70) REVERT: P 125 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8676 (mmtm) REVERT: P 141 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7870 (mp0) REVERT: Q 62 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7868 (mm-30) REVERT: Q 93 ASP cc_start: 0.8310 (t0) cc_final: 0.8006 (t70) REVERT: Q 113 GLN cc_start: 0.9061 (tp40) cc_final: 0.8764 (tp40) REVERT: Q 124 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8164 (pp20) REVERT: Q 141 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7838 (mp0) REVERT: Q 148 GLU cc_start: 0.8866 (tt0) cc_final: 0.8549 (tt0) REVERT: R 62 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7948 (mm-30) REVERT: R 93 ASP cc_start: 0.8312 (t0) cc_final: 0.8044 (t70) REVERT: R 95 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: R 124 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8044 (pp20) REVERT: R 141 GLU cc_start: 0.8451 (mm-30) cc_final: 0.7880 (mp0) REVERT: S 64 ARG cc_start: 0.8482 (tpp80) cc_final: 0.7477 (ttp-170) REVERT: S 93 ASP cc_start: 0.8353 (t0) cc_final: 0.8077 (t70) REVERT: S 141 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7881 (mp0) REVERT: T 62 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7972 (mm-30) REVERT: T 113 GLN cc_start: 0.9078 (tp40) cc_final: 0.8782 (tp40) REVERT: T 125 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8680 (mmtm) REVERT: T 141 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7869 (mp0) REVERT: T 148 GLU cc_start: 0.8880 (tt0) cc_final: 0.8567 (tt0) REVERT: U 64 ARG cc_start: 0.8488 (tpp80) cc_final: 0.7551 (ttp-170) REVERT: U 93 ASP cc_start: 0.8315 (t0) cc_final: 0.8027 (t70) REVERT: U 124 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8158 (pp20) REVERT: U 125 LYS cc_start: 0.9014 (mmtm) cc_final: 0.8785 (mmtm) REVERT: U 141 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7859 (mp0) REVERT: V 113 GLN cc_start: 0.9070 (tp40) cc_final: 0.8774 (tp40) REVERT: W 64 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8078 (tpp80) REVERT: W 93 ASP cc_start: 0.8318 (t0) cc_final: 0.8036 (t70) REVERT: W 125 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8633 (mmtm) REVERT: W 148 GLU cc_start: 0.8891 (tt0) cc_final: 0.8576 (tt0) REVERT: X 93 ASP cc_start: 0.8350 (t0) cc_final: 0.8063 (t70) REVERT: X 120 LYS cc_start: 0.8924 (tttm) cc_final: 0.8565 (ttmp) REVERT: X 141 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7842 (mp0) REVERT: X 148 GLU cc_start: 0.8862 (tt0) cc_final: 0.8625 (tt0) outliers start: 78 outliers final: 71 residues processed: 1009 average time/residue: 0.8556 time to fit residues: 996.5949 Evaluate side-chains 1049 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 972 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 64 ARG Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain W residue 64 ARG Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 95 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 67 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 321 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 384 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 59 GLN B 8 GLN B 59 GLN C 8 GLN C 59 GLN D 8 GLN D 59 GLN E 8 GLN E 59 GLN F 8 GLN F 59 GLN G 8 GLN H 8 GLN I 8 GLN J 8 GLN J 59 GLN K 8 GLN L 8 GLN M 8 GLN N 8 GLN N 59 GLN O 8 GLN O 59 GLN P 8 GLN Q 8 GLN Q 59 GLN R 8 GLN S 8 GLN S 59 GLN T 8 GLN T 59 GLN U 8 GLN V 8 GLN V 59 GLN W 8 GLN X 8 GLN X 59 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.103033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.095446 restraints weight = 42987.419| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.33 r_work: 0.2911 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 34776 Z= 0.206 Angle : 0.567 5.746 46824 Z= 0.293 Chirality : 0.039 0.126 4872 Planarity : 0.004 0.027 6216 Dihedral : 4.031 15.033 4584 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.15 % Allowed : 13.70 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.88 (0.13), residues: 4104 helix: 3.92 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.22 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 157 TYR 0.013 0.002 TYR B 40 PHE 0.014 0.002 PHE C 133 TRP 0.005 0.002 TRP R 94 HIS 0.002 0.001 HIS X 119 Details of bonding type rmsd covalent geometry : bond 0.00472 (34776) covalent geometry : angle 0.56673 (46824) hydrogen bonds : bond 0.04296 ( 2640) hydrogen bonds : angle 3.32951 ( 7920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1065 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 986 time to evaluate : 1.151 Fit side-chains REVERT: A 64 ARG cc_start: 0.8453 (tpp80) cc_final: 0.7491 (ttp-170) REVERT: A 95 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8106 (mm-30) REVERT: A 113 GLN cc_start: 0.9076 (tp40) cc_final: 0.8851 (tp40) REVERT: A 124 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8214 (pp20) REVERT: A 148 GLU cc_start: 0.8858 (tt0) cc_final: 0.8652 (tt0) REVERT: B 93 ASP cc_start: 0.8364 (t0) cc_final: 0.8065 (t70) REVERT: B 113 GLN cc_start: 0.9067 (tp40) cc_final: 0.8833 (tp40) REVERT: B 124 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8117 (pp20) REVERT: B 141 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7861 (mp0) REVERT: B 148 GLU cc_start: 0.8887 (tt0) cc_final: 0.8593 (tt0) REVERT: C 62 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7866 (mm-30) REVERT: C 64 ARG cc_start: 0.8442 (tpp80) cc_final: 0.7492 (ttp-170) REVERT: C 124 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8127 (pp20) REVERT: C 141 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7867 (mp0) REVERT: D 141 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7855 (mp0) REVERT: E 62 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7985 (mm-30) REVERT: E 64 ARG cc_start: 0.8478 (tpp80) cc_final: 0.7502 (ttp-170) REVERT: E 113 GLN cc_start: 0.9071 (tp40) cc_final: 0.8789 (tp40) REVERT: E 125 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8630 (mmtm) REVERT: E 148 GLU cc_start: 0.8890 (tt0) cc_final: 0.8682 (tt0) REVERT: F 64 ARG cc_start: 0.8470 (tpp80) cc_final: 0.7516 (ttp-170) REVERT: F 95 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8087 (mm-30) REVERT: F 113 GLN cc_start: 0.9084 (tp40) cc_final: 0.8856 (tp40) REVERT: F 124 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8218 (pp20) REVERT: F 141 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7901 (mp0) REVERT: F 148 GLU cc_start: 0.8867 (tt0) cc_final: 0.8662 (tt0) REVERT: G 62 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7950 (mm-30) REVERT: G 64 ARG cc_start: 0.8478 (tpp80) cc_final: 0.7518 (ttp-170) REVERT: G 120 LYS cc_start: 0.8943 (tttm) cc_final: 0.8562 (ttmp) REVERT: G 125 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8631 (mmtm) REVERT: G 141 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7902 (mp0) REVERT: H 93 ASP cc_start: 0.8372 (t0) cc_final: 0.8100 (t70) REVERT: H 125 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8636 (mmtm) REVERT: H 148 GLU cc_start: 0.8932 (tt0) cc_final: 0.8624 (tt0) REVERT: I 62 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7948 (mm-30) REVERT: I 64 ARG cc_start: 0.8475 (tpp80) cc_final: 0.7510 (ttp-170) REVERT: I 113 GLN cc_start: 0.9080 (tp40) cc_final: 0.8850 (tp40) REVERT: I 125 LYS cc_start: 0.8849 (mmtt) cc_final: 0.8633 (mmtm) REVERT: J 113 GLN cc_start: 0.9069 (tp40) cc_final: 0.8842 (tp40) REVERT: J 125 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8638 (mmtm) REVERT: K 64 ARG cc_start: 0.8475 (tpp80) cc_final: 0.7509 (ttp-170) REVERT: K 113 GLN cc_start: 0.9063 (tp40) cc_final: 0.8827 (tp40) REVERT: K 125 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8659 (mmtm) REVERT: K 141 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7874 (mp0) REVERT: K 148 GLU cc_start: 0.8887 (tt0) cc_final: 0.8595 (tt0) REVERT: L 64 ARG cc_start: 0.8471 (tpp80) cc_final: 0.7507 (ttp-170) REVERT: L 120 LYS cc_start: 0.8944 (tttm) cc_final: 0.8558 (ttmp) REVERT: L 125 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8627 (mmtm) REVERT: L 141 GLU cc_start: 0.8458 (mm-30) cc_final: 0.7890 (mp0) REVERT: M 64 ARG cc_start: 0.8469 (tpp80) cc_final: 0.7490 (ttp-170) REVERT: M 93 ASP cc_start: 0.8398 (t0) cc_final: 0.8118 (t70) REVERT: M 120 LYS cc_start: 0.8903 (tttm) cc_final: 0.8531 (ttmp) REVERT: M 141 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7886 (mp0) REVERT: M 148 GLU cc_start: 0.8856 (tt0) cc_final: 0.8626 (tt0) REVERT: N 113 GLN cc_start: 0.9080 (tp40) cc_final: 0.8799 (tp40) REVERT: N 125 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8618 (mmtm) REVERT: N 148 GLU cc_start: 0.8882 (tt0) cc_final: 0.8675 (tt0) REVERT: O 62 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7877 (mm-30) REVERT: O 64 ARG cc_start: 0.8473 (tpp80) cc_final: 0.7505 (ttp-170) REVERT: O 113 GLN cc_start: 0.9086 (tp40) cc_final: 0.8854 (tp40) REVERT: O 125 LYS cc_start: 0.8844 (mmtt) cc_final: 0.8639 (mmtm) REVERT: P 62 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7945 (mm-30) REVERT: P 93 ASP cc_start: 0.8377 (t0) cc_final: 0.8093 (t70) REVERT: P 125 LYS cc_start: 0.8925 (mmtt) cc_final: 0.8660 (mmtm) REVERT: P 141 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7887 (mp0) REVERT: Q 62 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7914 (mm-30) REVERT: Q 93 ASP cc_start: 0.8359 (t0) cc_final: 0.8059 (t70) REVERT: Q 113 GLN cc_start: 0.9068 (tp40) cc_final: 0.8835 (tp40) REVERT: Q 141 GLU cc_start: 0.8428 (mm-30) cc_final: 0.7856 (mp0) REVERT: Q 148 GLU cc_start: 0.8884 (tt0) cc_final: 0.8587 (tt0) REVERT: R 93 ASP cc_start: 0.8427 (t0) cc_final: 0.8158 (t70) REVERT: R 95 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8118 (mm-30) REVERT: R 141 GLU cc_start: 0.8486 (mm-30) cc_final: 0.7915 (mp0) REVERT: S 64 ARG cc_start: 0.8483 (tpp80) cc_final: 0.7484 (ttp-170) REVERT: S 93 ASP cc_start: 0.8399 (t0) cc_final: 0.8131 (t70) REVERT: S 124 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8154 (pp20) REVERT: S 125 LYS cc_start: 0.8988 (mmtm) cc_final: 0.8779 (mmtm) REVERT: S 141 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7918 (mp0) REVERT: T 62 GLU cc_start: 0.8226 (mm-30) cc_final: 0.8001 (mm-30) REVERT: T 113 GLN cc_start: 0.9073 (tp40) cc_final: 0.8838 (tp40) REVERT: T 125 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8633 (mmtm) REVERT: T 141 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7882 (mp0) REVERT: T 148 GLU cc_start: 0.8910 (tt0) cc_final: 0.8618 (tt0) REVERT: U 64 ARG cc_start: 0.8474 (tpp80) cc_final: 0.7538 (ttp-170) REVERT: U 93 ASP cc_start: 0.8372 (t0) cc_final: 0.8080 (t70) REVERT: U 141 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7886 (mp0) REVERT: V 113 GLN cc_start: 0.9078 (tp40) cc_final: 0.8847 (tp40) REVERT: V 124 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8167 (pp20) REVERT: W 93 ASP cc_start: 0.8361 (t0) cc_final: 0.8081 (t70) REVERT: W 125 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8637 (mmtm) REVERT: W 148 GLU cc_start: 0.8928 (tt0) cc_final: 0.8620 (tt0) REVERT: X 93 ASP cc_start: 0.8397 (t0) cc_final: 0.8123 (t70) REVERT: X 120 LYS cc_start: 0.8897 (tttm) cc_final: 0.8526 (ttmp) REVERT: X 141 GLU cc_start: 0.8438 (mm-30) cc_final: 0.7877 (mp0) REVERT: X 148 GLU cc_start: 0.8879 (tt0) cc_final: 0.8654 (tt0) outliers start: 79 outliers final: 73 residues processed: 1010 average time/residue: 0.8670 time to fit residues: 1011.3360 Evaluate side-chains 1025 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 949 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain R residue 110 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 95 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 307 optimal weight: 4.9990 chunk 158 optimal weight: 0.9990 chunk 345 optimal weight: 4.9990 chunk 268 optimal weight: 3.9990 chunk 182 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 356 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 385 optimal weight: 0.9980 chunk 377 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 GLN I 8 GLN M 8 GLN N 8 GLN P 8 GLN R 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.106550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.098980 restraints weight = 42801.334| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.35 r_work: 0.2945 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34776 Z= 0.116 Angle : 0.486 5.935 46824 Z= 0.256 Chirality : 0.034 0.114 4872 Planarity : 0.003 0.024 6216 Dihedral : 3.828 16.401 4584 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.61 % Allowed : 14.62 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.39 (0.13), residues: 4104 helix: 4.21 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.56 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 157 TYR 0.011 0.001 TYR O 40 PHE 0.013 0.002 PHE U 133 TRP 0.003 0.001 TRP U 94 HIS 0.003 0.001 HIS V 137 Details of bonding type rmsd covalent geometry : bond 0.00259 (34776) covalent geometry : angle 0.48641 (46824) hydrogen bonds : bond 0.03479 ( 2640) hydrogen bonds : angle 3.04258 ( 7920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 994 time to evaluate : 1.318 Fit side-chains REVERT: A 64 ARG cc_start: 0.8445 (tpp80) cc_final: 0.7470 (ttp-170) REVERT: A 95 GLU cc_start: 0.8315 (mm-30) cc_final: 0.8083 (mm-30) REVERT: A 113 GLN cc_start: 0.9050 (tp40) cc_final: 0.8772 (tp40) REVERT: A 124 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8109 (pp20) REVERT: A 148 GLU cc_start: 0.8851 (tt0) cc_final: 0.8634 (tt0) REVERT: B 62 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7907 (mm-30) REVERT: B 93 ASP cc_start: 0.8211 (t0) cc_final: 0.7974 (t70) REVERT: B 113 GLN cc_start: 0.9039 (tp40) cc_final: 0.8744 (tp40) REVERT: B 124 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8122 (pp20) REVERT: B 125 LYS cc_start: 0.8998 (mmtm) cc_final: 0.8790 (mmtm) REVERT: B 141 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7805 (mp0) REVERT: B 148 GLU cc_start: 0.8871 (tt0) cc_final: 0.8566 (tt0) REVERT: C 62 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7852 (mm-30) REVERT: C 64 ARG cc_start: 0.8432 (tpp80) cc_final: 0.7462 (ttp-170) REVERT: C 124 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8061 (pp20) REVERT: C 141 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7801 (mp0) REVERT: D 141 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7794 (mp0) REVERT: E 62 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7946 (mm-30) REVERT: E 64 ARG cc_start: 0.8471 (tpp80) cc_final: 0.7478 (ttp-170) REVERT: E 113 GLN cc_start: 0.9040 (tp40) cc_final: 0.8743 (tp40) REVERT: E 125 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8582 (mmtm) REVERT: E 148 GLU cc_start: 0.8864 (tt0) cc_final: 0.8648 (tt0) REVERT: F 62 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7909 (mm-30) REVERT: F 64 ARG cc_start: 0.8437 (tpp80) cc_final: 0.7476 (ttp-170) REVERT: F 95 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8104 (mm-30) REVERT: F 113 GLN cc_start: 0.9061 (tp40) cc_final: 0.8779 (tp40) REVERT: F 124 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8193 (pp20) REVERT: F 141 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7811 (mp0) REVERT: F 148 GLU cc_start: 0.8849 (tt0) cc_final: 0.8631 (tt0) REVERT: G 64 ARG cc_start: 0.8440 (tpp80) cc_final: 0.7475 (ttp-170) REVERT: G 120 LYS cc_start: 0.8918 (tttm) cc_final: 0.8554 (ttmp) REVERT: G 125 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8614 (mmtm) REVERT: G 141 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7818 (mp0) REVERT: H 64 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8019 (tpp80) REVERT: H 93 ASP cc_start: 0.8215 (t0) cc_final: 0.8003 (t70) REVERT: H 125 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8599 (mmtm) REVERT: H 148 GLU cc_start: 0.8894 (tt0) cc_final: 0.8673 (tt0) REVERT: I 64 ARG cc_start: 0.8473 (tpp80) cc_final: 0.7468 (ttp-170) REVERT: I 113 GLN cc_start: 0.9061 (tp40) cc_final: 0.8774 (tp40) REVERT: J 113 GLN cc_start: 0.9051 (tp40) cc_final: 0.8765 (tp40) REVERT: K 59 GLN cc_start: 0.8605 (mm110) cc_final: 0.8388 (mm110) REVERT: K 64 ARG cc_start: 0.8477 (tpp80) cc_final: 0.7448 (ttp-170) REVERT: K 113 GLN cc_start: 0.9052 (tp40) cc_final: 0.8757 (tp40) REVERT: K 141 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7799 (mp0) REVERT: K 148 GLU cc_start: 0.8871 (tt0) cc_final: 0.8557 (tt0) REVERT: L 64 ARG cc_start: 0.8428 (tpp80) cc_final: 0.7467 (ttp-170) REVERT: L 120 LYS cc_start: 0.8918 (tttm) cc_final: 0.8551 (ttmp) REVERT: L 125 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8612 (mmtm) REVERT: L 141 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7842 (mp0) REVERT: M 64 ARG cc_start: 0.8449 (tpp80) cc_final: 0.7524 (ttp-170) REVERT: M 93 ASP cc_start: 0.8253 (t0) cc_final: 0.8035 (t70) REVERT: M 120 LYS cc_start: 0.8859 (tttm) cc_final: 0.8459 (ttmp) REVERT: M 141 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7795 (mp0) REVERT: M 148 GLU cc_start: 0.8858 (tt0) cc_final: 0.8643 (tt0) REVERT: N 16 ASP cc_start: 0.9097 (m-30) cc_final: 0.8860 (m-30) REVERT: N 113 GLN cc_start: 0.9042 (tp40) cc_final: 0.8745 (tp40) REVERT: N 125 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8576 (mmtm) REVERT: N 148 GLU cc_start: 0.8870 (tt0) cc_final: 0.8654 (tt0) REVERT: O 62 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7901 (mm-30) REVERT: O 64 ARG cc_start: 0.8483 (tpp80) cc_final: 0.7470 (ttp-170) REVERT: O 113 GLN cc_start: 0.9063 (tp40) cc_final: 0.8774 (tp40) REVERT: P 59 GLN cc_start: 0.8615 (mm110) cc_final: 0.8413 (mm110) REVERT: P 62 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7914 (mm-30) REVERT: P 93 ASP cc_start: 0.8221 (t0) cc_final: 0.7994 (t70) REVERT: P 125 LYS cc_start: 0.8871 (mmtt) cc_final: 0.8628 (mmtm) REVERT: P 141 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7818 (mp0) REVERT: Q 93 ASP cc_start: 0.8203 (t0) cc_final: 0.7965 (t70) REVERT: Q 113 GLN cc_start: 0.9036 (tp40) cc_final: 0.8743 (tp40) REVERT: Q 124 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8184 (pp20) REVERT: Q 141 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7795 (mp0) REVERT: Q 148 GLU cc_start: 0.8861 (tt0) cc_final: 0.8556 (tt0) REVERT: R 93 ASP cc_start: 0.8250 (t0) cc_final: 0.8039 (t70) REVERT: R 95 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8144 (mm-30) REVERT: R 124 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8210 (pp20) REVERT: R 141 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7820 (mp0) REVERT: S 62 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7943 (mm-30) REVERT: S 64 ARG cc_start: 0.8444 (tpp80) cc_final: 0.7462 (ttp-170) REVERT: S 93 ASP cc_start: 0.8248 (t0) cc_final: 0.8041 (t70) REVERT: S 95 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8132 (mm-30) REVERT: S 124 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8047 (pp20) REVERT: S 125 LYS cc_start: 0.8973 (mmtm) cc_final: 0.8762 (mmtm) REVERT: S 141 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7860 (mp0) REVERT: T 62 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7960 (mm-30) REVERT: T 113 GLN cc_start: 0.9062 (tp40) cc_final: 0.8762 (tp40) REVERT: T 125 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8615 (mmtm) REVERT: T 141 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7806 (mp0) REVERT: T 148 GLU cc_start: 0.8886 (tt0) cc_final: 0.8582 (tt0) REVERT: U 62 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7838 (mm-30) REVERT: U 64 ARG cc_start: 0.8492 (tpp80) cc_final: 0.7530 (ttp-170) REVERT: U 93 ASP cc_start: 0.8212 (t0) cc_final: 0.7986 (t70) REVERT: U 124 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8210 (pp20) REVERT: U 141 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7836 (mp0) REVERT: V 62 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7889 (mm-30) REVERT: V 113 GLN cc_start: 0.9049 (tp40) cc_final: 0.8765 (tp40) REVERT: V 124 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8018 (pp20) REVERT: W 64 ARG cc_start: 0.8430 (OUTLIER) cc_final: 0.8035 (tpp80) REVERT: W 93 ASP cc_start: 0.8213 (t0) cc_final: 0.7999 (t70) REVERT: W 148 GLU cc_start: 0.8892 (tt0) cc_final: 0.8675 (tt0) REVERT: X 93 ASP cc_start: 0.8238 (t0) cc_final: 0.8016 (t70) REVERT: X 120 LYS cc_start: 0.8851 (tttm) cc_final: 0.8449 (ttmp) REVERT: X 141 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7792 (mp0) REVERT: X 148 GLU cc_start: 0.8862 (tt0) cc_final: 0.8646 (tt0) outliers start: 59 outliers final: 49 residues processed: 1018 average time/residue: 0.8642 time to fit residues: 1017.8524 Evaluate side-chains 1030 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 979 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 64 ARG Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 64 ARG Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 60 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 254 optimal weight: 2.9990 chunk 144 optimal weight: 0.4980 chunk 361 optimal weight: 7.9990 chunk 402 optimal weight: 0.9990 chunk 352 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 166 optimal weight: 0.0070 chunk 219 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 337 optimal weight: 7.9990 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 59 GLN C 59 GLN D 59 GLN E 8 GLN E 59 GLN F 59 GLN G 59 GLN H 59 GLN I 59 GLN J 59 GLN K 8 GLN L 8 GLN L 59 GLN M 8 GLN M 59 GLN N 8 GLN N 59 GLN O 59 GLN P 8 GLN Q 59 GLN R 59 GLN S 59 GLN T 8 GLN T 59 GLN U 8 GLN V 59 GLN W 59 GLN X 59 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.108142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.100549 restraints weight = 43054.733| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.35 r_work: 0.2994 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 34776 Z= 0.098 Angle : 0.471 6.295 46824 Z= 0.249 Chirality : 0.033 0.114 4872 Planarity : 0.003 0.022 6216 Dihedral : 3.662 16.544 4584 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.82 % Allowed : 15.41 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.72 (0.13), residues: 4104 helix: 4.43 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.75 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 157 TYR 0.010 0.001 TYR D 138 PHE 0.012 0.002 PHE D 133 TRP 0.004 0.001 TRP H 94 HIS 0.002 0.000 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.00215 (34776) covalent geometry : angle 0.47055 (46824) hydrogen bonds : bond 0.03051 ( 2640) hydrogen bonds : angle 2.89772 ( 7920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1097 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 1067 time to evaluate : 1.350 Fit side-chains REVERT: A 64 ARG cc_start: 0.8445 (tpp80) cc_final: 0.7540 (ttp-170) REVERT: A 113 GLN cc_start: 0.9045 (tp40) cc_final: 0.8751 (tp40) REVERT: A 124 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8093 (pp20) REVERT: A 148 GLU cc_start: 0.8867 (tt0) cc_final: 0.8633 (tt0) REVERT: B 93 ASP cc_start: 0.8167 (t0) cc_final: 0.7923 (t70) REVERT: B 113 GLN cc_start: 0.9014 (tp40) cc_final: 0.8724 (tp40) REVERT: B 124 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8115 (pp20) REVERT: B 125 LYS cc_start: 0.8972 (mmtm) cc_final: 0.8757 (mmtm) REVERT: B 141 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7783 (mp0) REVERT: B 148 GLU cc_start: 0.8885 (tt0) cc_final: 0.8572 (tt0) REVERT: C 62 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7838 (mm-30) REVERT: C 64 ARG cc_start: 0.8464 (tpp80) cc_final: 0.7550 (ttp-170) REVERT: C 124 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8142 (pp20) REVERT: C 141 GLU cc_start: 0.8374 (mm-30) cc_final: 0.7794 (mp0) REVERT: D 141 GLU cc_start: 0.8390 (mm-30) cc_final: 0.7808 (mp0) REVERT: E 62 GLU cc_start: 0.8215 (mm-30) cc_final: 0.8013 (mm-30) REVERT: E 64 ARG cc_start: 0.8445 (tpp80) cc_final: 0.7467 (ttp-170) REVERT: E 113 GLN cc_start: 0.9030 (tp40) cc_final: 0.8729 (tp40) REVERT: E 125 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8605 (mmtm) REVERT: E 148 GLU cc_start: 0.8871 (tt0) cc_final: 0.8632 (tt0) REVERT: F 62 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7990 (mm-30) REVERT: F 64 ARG cc_start: 0.8451 (tpp80) cc_final: 0.7531 (ttp-170) REVERT: F 113 GLN cc_start: 0.9048 (tp40) cc_final: 0.8752 (tp40) REVERT: F 141 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7804 (mp0) REVERT: F 148 GLU cc_start: 0.8863 (tt0) cc_final: 0.8625 (tt0) REVERT: G 64 ARG cc_start: 0.8470 (tpp80) cc_final: 0.7476 (ttp-170) REVERT: G 120 LYS cc_start: 0.8872 (tttm) cc_final: 0.8538 (ttmp) REVERT: G 125 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8595 (mmtm) REVERT: G 141 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7785 (mp0) REVERT: H 93 ASP cc_start: 0.8107 (t0) cc_final: 0.7895 (t70) REVERT: H 148 GLU cc_start: 0.8907 (tt0) cc_final: 0.8682 (tt0) REVERT: I 64 ARG cc_start: 0.8495 (tpp80) cc_final: 0.7546 (ttp-170) REVERT: I 113 GLN cc_start: 0.9049 (tp40) cc_final: 0.8756 (tp40) REVERT: J 113 GLN cc_start: 0.9035 (tp40) cc_final: 0.8740 (tp40) REVERT: K 59 GLN cc_start: 0.8545 (mm110) cc_final: 0.8328 (mm110) REVERT: K 64 ARG cc_start: 0.8451 (tpp80) cc_final: 0.7515 (ttp-170) REVERT: K 113 GLN cc_start: 0.9038 (tp40) cc_final: 0.8733 (tp40) REVERT: K 141 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7787 (mp0) REVERT: K 148 GLU cc_start: 0.8877 (tt0) cc_final: 0.8570 (tt0) REVERT: L 62 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7940 (mm-30) REVERT: L 64 ARG cc_start: 0.8454 (tpp80) cc_final: 0.7475 (ttp-170) REVERT: L 120 LYS cc_start: 0.8834 (tttm) cc_final: 0.8493 (ttmp) REVERT: L 141 GLU cc_start: 0.8373 (mm-30) cc_final: 0.7803 (mp0) REVERT: M 64 ARG cc_start: 0.8486 (tpp80) cc_final: 0.7529 (ttp-170) REVERT: M 93 ASP cc_start: 0.8207 (t0) cc_final: 0.7997 (t70) REVERT: M 120 LYS cc_start: 0.8816 (tttm) cc_final: 0.8436 (ttmp) REVERT: M 124 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8169 (pp20) REVERT: M 141 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7790 (mp0) REVERT: M 148 GLU cc_start: 0.8868 (tt0) cc_final: 0.8630 (tt0) REVERT: N 113 GLN cc_start: 0.9032 (tp40) cc_final: 0.8733 (tp40) REVERT: N 125 LYS cc_start: 0.8797 (mmtt) cc_final: 0.8577 (mmtm) REVERT: N 148 GLU cc_start: 0.8874 (tt0) cc_final: 0.8637 (tt0) REVERT: O 62 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7922 (mm-30) REVERT: O 64 ARG cc_start: 0.8452 (tpp80) cc_final: 0.7525 (ttp-170) REVERT: O 113 GLN cc_start: 0.9046 (tp40) cc_final: 0.8758 (tp40) REVERT: P 59 GLN cc_start: 0.8586 (mm110) cc_final: 0.8378 (mm110) REVERT: P 93 ASP cc_start: 0.8138 (t0) cc_final: 0.7920 (t70) REVERT: P 125 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8603 (mmtm) REVERT: P 141 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7817 (mp0) REVERT: Q 93 ASP cc_start: 0.8162 (t0) cc_final: 0.7923 (t70) REVERT: Q 113 GLN cc_start: 0.9015 (tp40) cc_final: 0.8726 (tp40) REVERT: Q 141 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7785 (mp0) REVERT: Q 148 GLU cc_start: 0.8861 (tt0) cc_final: 0.8548 (tt0) REVERT: R 62 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7963 (mm-30) REVERT: R 93 ASP cc_start: 0.8151 (t0) cc_final: 0.7943 (t70) REVERT: R 124 GLU cc_start: 0.8437 (tm-30) cc_final: 0.8111 (pp20) REVERT: R 141 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7806 (mp0) REVERT: S 62 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7964 (mm-30) REVERT: S 64 ARG cc_start: 0.8474 (tpp80) cc_final: 0.7522 (ttp-170) REVERT: S 93 ASP cc_start: 0.8163 (t0) cc_final: 0.7954 (t70) REVERT: S 124 GLU cc_start: 0.8396 (tm-30) cc_final: 0.8038 (pp20) REVERT: S 125 LYS cc_start: 0.8942 (mmtm) cc_final: 0.8721 (mmtm) REVERT: S 141 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7813 (mp0) REVERT: T 113 GLN cc_start: 0.9047 (tp40) cc_final: 0.8747 (tp40) REVERT: T 125 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8591 (mmtm) REVERT: T 141 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7781 (mp0) REVERT: T 148 GLU cc_start: 0.8894 (tt0) cc_final: 0.8586 (tt0) REVERT: U 59 GLN cc_start: 0.8589 (mm110) cc_final: 0.8367 (mm110) REVERT: U 62 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7881 (mm-30) REVERT: U 64 ARG cc_start: 0.8477 (tpp80) cc_final: 0.7498 (ttp-170) REVERT: U 93 ASP cc_start: 0.8153 (t0) cc_final: 0.7922 (t70) REVERT: U 141 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7789 (mp0) REVERT: V 62 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7891 (mm-30) REVERT: V 113 GLN cc_start: 0.9041 (tp40) cc_final: 0.8756 (tp40) REVERT: V 120 LYS cc_start: 0.8816 (tttm) cc_final: 0.8556 (ttpt) REVERT: W 93 ASP cc_start: 0.8111 (t0) cc_final: 0.7892 (t70) REVERT: W 124 GLU cc_start: 0.8390 (tm-30) cc_final: 0.8104 (pp20) REVERT: W 148 GLU cc_start: 0.8908 (tt0) cc_final: 0.8685 (tt0) REVERT: X 93 ASP cc_start: 0.8196 (t0) cc_final: 0.7967 (t70) REVERT: X 120 LYS cc_start: 0.8810 (tttm) cc_final: 0.8437 (ttmp) REVERT: X 141 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7791 (mp0) REVERT: X 148 GLU cc_start: 0.8852 (tt0) cc_final: 0.8615 (tt0) outliers start: 30 outliers final: 27 residues processed: 1091 average time/residue: 0.8618 time to fit residues: 1089.8761 Evaluate side-chains 1022 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 995 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain X residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 287 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 252 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 382 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 8 GLN E 8 GLN E 137 HIS F 8 GLN G 8 GLN H 8 GLN I 8 GLN I 137 HIS J 8 GLN J 137 HIS K 8 GLN L 8 GLN N 8 GLN N 137 HIS O 8 GLN O 137 HIS P 8 GLN P 137 HIS R 8 GLN R 61 HIS R 137 HIS S 8 GLN S 137 HIS T 8 GLN U 8 GLN U 137 HIS V 8 GLN V 137 HIS W 8 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.104503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.096882 restraints weight = 43062.476| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.34 r_work: 0.2927 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34776 Z= 0.173 Angle : 0.543 6.253 46824 Z= 0.283 Chirality : 0.037 0.118 4872 Planarity : 0.003 0.027 6216 Dihedral : 3.886 14.934 4584 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.14 % Allowed : 15.31 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.15 (0.13), residues: 4104 helix: 4.05 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.47 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 91 TYR 0.012 0.002 TYR B 138 PHE 0.014 0.002 PHE I 133 TRP 0.006 0.002 TRP E 94 HIS 0.002 0.001 HIS L 137 Details of bonding type rmsd covalent geometry : bond 0.00396 (34776) covalent geometry : angle 0.54311 (46824) hydrogen bonds : bond 0.03963 ( 2640) hydrogen bonds : angle 3.22097 ( 7920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16227.42 seconds wall clock time: 276 minutes 15.16 seconds (16575.16 seconds total)