Starting phenix.real_space_refine on Mon Oct 13 11:21:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u5l_26354/10_2025/7u5l_26354.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u5l_26354/10_2025/7u5l_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_26354/10_2025/7u5l_26354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u5l_26354/10_2025/7u5l_26354.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u5l_26354/10_2025/7u5l_26354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u5l_26354/10_2025/7u5l_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-2.0-5842/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: 2.92, 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: 3.31 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.66 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: 6.40 Time building geometry restraints manager: 4.18 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: 0.13 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: 1.390 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: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 25.130 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:5.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.610 ------------------------------------------------------------------------------- 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 aren 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 : 1.406 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: 0.7942 (mtp85) REVERT: A 93 ASP cc_start: 0.7911 (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: 0.8334 (tt0) cc_final: 0.8118 (tt0) REVERT: A 173 LYS cc_start: 0.8678 (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: 0.8038 (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: 0.8412 (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: 0.7532 (tm-30) REVERT: B 148 GLU cc_start: 0.8339 (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: 0.7929 (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: 0.7570 (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: 0.8708 (tp40) cc_final: 0.8425 (tp40) REVERT: D 125 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8645 (mmtm) REVERT: D 135 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7281 (mt-10) REVERT: D 141 GLU cc_start: 0.7706 (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: 0.8043 (tt0) REVERT: E 63 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6775 (mm-30) REVERT: E 64 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7226 (ttp-170) REVERT: E 91 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7933 (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: 0.8117 (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: 0.7932 (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: 0.7727 (mm-30) cc_final: 0.7495 (tm-30) REVERT: F 148 GLU cc_start: 0.8336 (tt0) cc_final: 0.8116 (tt0) REVERT: F 173 LYS cc_start: 0.8686 (mptp) cc_final: 0.8374 (mptp) REVERT: G 64 ARG cc_start: 0.8071 (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: 0.8850 (mmtt) cc_final: 0.8623 (mmtm) REVERT: G 141 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7254 (mp0) REVERT: G 148 GLU cc_start: 0.8280 (tt0) cc_final: 0.8040 (tt0) REVERT: G 173 LYS cc_start: 0.8710 (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: 0.6790 (mm-30) REVERT: H 91 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7954 (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: 0.8863 (mmtt) cc_final: 0.8596 (mmtm) REVERT: H 135 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7279 (mt-10) REVERT: H 148 GLU cc_start: 0.8380 (tt0) cc_final: 0.8161 (tt0) REVERT: I 18 GLU cc_start: 0.8314 (tt0) cc_final: 0.8036 (tt0) REVERT: I 63 GLU cc_start: 0.7587 (mm-30) cc_final: 0.6768 (mm-30) REVERT: I 64 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7228 (ttp-170) REVERT: I 91 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7929 (mtp85) REVERT: I 93 ASP cc_start: 0.7891 (t0) cc_final: 0.7619 (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: 0.8279 (tt0) cc_final: 0.8036 (tt0) REVERT: J 18 GLU cc_start: 0.8311 (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: 0.8238 (mtp85) cc_final: 0.7938 (mtp85) REVERT: J 93 ASP cc_start: 0.7892 (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: 0.8642 (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: 0.8503 (m-30) REVERT: K 18 GLU cc_start: 0.8319 (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: 0.7881 (t0) cc_final: 0.7643 (t70) REVERT: K 95 GLU cc_start: 0.7794 (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: 0.8072 (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: 0.7688 (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: 0.8404 (mt-10) cc_final: 0.8201 (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: 0.8177 (ttmp) REVERT: L 124 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7742 (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: 0.8517 (m-30) REVERT: M 18 GLU cc_start: 0.8314 (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: 0.8146 (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: 0.7662 (t70) REVERT: M 113 GLN cc_start: 0.8706 (tp40) cc_final: 0.8422 (tp40) REVERT: M 120 LYS cc_start: 0.8517 (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: 0.7604 (mt-10) cc_final: 0.7319 (mt-10) REVERT: M 141 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7506 (tm-30) REVERT: M 148 GLU cc_start: 0.8317 (tt0) cc_final: 0.8081 (tt0) REVERT: N 16 ASP cc_start: 0.8852 (m-30) cc_final: 0.8531 (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: 0.8385 (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: 0.7640 (t70) REVERT: O 113 GLN cc_start: 0.8720 (tp40) cc_final: 0.8434 (tp40) REVERT: O 120 LYS cc_start: 0.8496 (tttm) cc_final: 0.8118 (ttmt) REVERT: O 125 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8640 (mmtm) REVERT: O 135 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7281 (mt-10) REVERT: O 148 GLU cc_start: 0.8299 (tt0) cc_final: 0.8070 (tt0) REVERT: P 18 GLU cc_start: 0.8313 (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: 0.7875 (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: 0.7572 (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: 0.8314 (tt0) cc_final: 0.8016 (tt0) REVERT: Q 16 ASP cc_start: 0.8856 (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: 0.7588 (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: 0.7883 (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: 0.8599 (mmtm) REVERT: Q 135 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7281 (mt-10) REVERT: Q 141 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7530 (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: 0.8153 (mt-10) REVERT: R 91 ARG cc_start: 0.8228 (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: 0.8423 (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: 0.7746 (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: 0.8046 (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: 0.8144 (mt-10) REVERT: S 91 ARG cc_start: 0.8225 (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: 0.7272 (mt-10) REVERT: S 141 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7497 (tm-30) REVERT: S 148 GLU cc_start: 0.8314 (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: 0.8829 (m-30) cc_final: 0.8510 (m-30) REVERT: T 18 GLU cc_start: 0.8324 (tt0) cc_final: 0.8042 (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: 0.7905 (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: 0.8066 (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: 0.8348 (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: 0.7584 (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: 0.7874 (t0) cc_final: 0.7643 (t70) REVERT: U 113 GLN cc_start: 0.8707 (tp40) cc_final: 0.8426 (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: 0.7507 (tm-30) REVERT: U 148 GLU cc_start: 0.8311 (tt0) cc_final: 0.8013 (tt0) REVERT: V 18 GLU cc_start: 0.8307 (tt0) cc_final: 0.8031 (tt0) REVERT: V 63 GLU cc_start: 0.7583 (mm-30) cc_final: 0.6778 (mm-30) REVERT: V 91 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7934 (mtp85) REVERT: V 93 ASP cc_start: 0.7885 (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: 0.8128 (ttmt) REVERT: V 125 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8643 (mmtm) REVERT: V 135 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7281 (mt-10) REVERT: V 148 GLU cc_start: 0.8305 (tt0) cc_final: 0.8081 (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: 0.7574 (mt-10) cc_final: 0.7280 (mt-10) REVERT: W 148 GLU cc_start: 0.8381 (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: 0.8310 (tt0) cc_final: 0.8041 (tt0) REVERT: X 63 GLU cc_start: 0.7584 (mm-30) cc_final: 0.6775 (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: 0.8708 (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: 0.7569 (mt-10) cc_final: 0.7282 (mt-10) REVERT: X 141 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7507 (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: 0.8797 time to fit residues: 1443.6326 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 : 1.211 ------------------------------------------------------------------------------- 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 aren 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 : 1.433 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: 0.8920 (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: 0.8886 (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: 0.8366 (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: 0.8254 (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: 0.8463 (mtp85) cc_final: 0.8254 (mtp85) REVERT: D 93 ASP cc_start: 0.8234 (t0) cc_final: 0.7942 (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: 0.8271 (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: 0.8436 (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: 0.7955 (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: 0.8913 (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: 0.8217 (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: 0.8459 (tm-30) cc_final: 0.8246 (tm-30) REVERT: H 125 LYS cc_start: 0.8941 (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: 0.8494 (tpp80) cc_final: 0.7502 (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: 0.8184 (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: 0.8929 (mmtt) cc_final: 0.8713 (mmtm) REVERT: J 148 GLU cc_start: 0.8834 (tt0) cc_final: 0.8619 (tt0) REVERT: K 16 ASP cc_start: 0.9118 (m-30) cc_final: 0.8815 (m-30) REVERT: K 64 ARG cc_start: 0.8488 (tpp80) cc_final: 0.7495 (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: 0.7940 (t70) REVERT: K 113 GLN cc_start: 0.9049 (tp40) cc_final: 0.8761 (tp40) REVERT: K 124 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8231 (tm-30) REVERT: K 125 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8701 (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: 0.8562 (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: 0.7502 (ttp-170) REVERT: L 93 ASP cc_start: 0.8246 (t0) cc_final: 0.7969 (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: 0.8391 (mm-30) cc_final: 0.7836 (mp0) REVERT: M 64 ARG cc_start: 0.8512 (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: 0.7953 (t70) REVERT: M 120 LYS cc_start: 0.8852 (tttm) cc_final: 0.8523 (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: 0.7818 (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: 0.8890 (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: 0.8866 (tt0) cc_final: 0.8658 (tt0) REVERT: P 91 ARG cc_start: 0.8478 (mtp85) cc_final: 0.8271 (mtp85) REVERT: P 93 ASP cc_start: 0.8212 (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: 0.8360 (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: 0.8236 (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: 0.8224 (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: 0.8241 (tm-30) REVERT: R 125 LYS cc_start: 0.8914 (mmtt) cc_final: 0.8657 (mmtm) REVERT: R 141 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7826 (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: 0.8239 (mtp85) REVERT: T 93 ASP cc_start: 0.8203 (t0) cc_final: 0.7937 (t70) REVERT: T 113 GLN cc_start: 0.9042 (tp40) cc_final: 0.8754 (tp40) REVERT: T 125 LYS cc_start: 0.8947 (mmtt) cc_final: 0.8694 (mmtm) REVERT: T 141 GLU cc_start: 0.8336 (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: 0.7505 (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: 0.7940 (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: 0.8740 (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: 0.8663 (tt0) outliers start: 50 outliers final: 50 residues processed: 1141 average time/residue: 0.8495 time to fit residues: 1124.5110 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 : 1.466 ------------------------------------------------------------------------------- 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 aren 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 : 1.357 Fit side-chains REVERT: A 64 ARG cc_start: 0.8471 (tpp80) cc_final: 0.7476 (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: 0.8182 (tm-30) REVERT: A 125 LYS cc_start: 0.8921 (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: 0.8132 (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: 0.7843 (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: 0.8441 (tm-30) cc_final: 0.8223 (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: 0.7871 (mp0) REVERT: D 93 ASP cc_start: 0.8133 (t0) cc_final: 0.7881 (t70) REVERT: D 141 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7865 (mp0) REVERT: E 16 ASP cc_start: 0.9110 (m-30) cc_final: 0.8823 (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: 0.7930 (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: 0.7469 (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: 0.8213 (tm-30) REVERT: F 125 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8681 (mmtm) REVERT: F 141 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7871 (mp0) REVERT: F 148 GLU cc_start: 0.8879 (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: 0.7907 (t70) REVERT: G 120 LYS cc_start: 0.8879 (tttm) cc_final: 0.8537 (ttmp) REVERT: G 124 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8217 (tm-30) REVERT: G 125 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8639 (mmtm) REVERT: G 141 GLU cc_start: 0.8402 (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: 0.8731 (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: 0.8914 (tt0) cc_final: 0.8698 (tt0) REVERT: I 18 GLU cc_start: 0.8586 (tt0) cc_final: 0.8298 (tt0) REVERT: I 64 ARG cc_start: 0.8460 (tpp80) cc_final: 0.7473 (ttp-170) REVERT: I 93 ASP cc_start: 0.8186 (t0) cc_final: 0.7908 (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: 0.8316 (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: 0.8175 (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: 0.8955 (mmtt) cc_final: 0.8686 (mmtm) REVERT: K 141 GLU cc_start: 0.8391 (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: 0.7923 (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: 0.8913 (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: 0.7920 (t70) REVERT: M 120 LYS cc_start: 0.8874 (tttm) cc_final: 0.8534 (ttmp) REVERT: M 124 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8228 (tm-30) REVERT: M 125 LYS cc_start: 0.8907 (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: 0.9111 (m-30) cc_final: 0.8823 (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: 0.7915 (t70) REVERT: N 113 GLN cc_start: 0.9020 (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: 0.8890 (tt0) cc_final: 0.8664 (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: 0.8260 (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: 0.8313 (mm-30) cc_final: 0.7591 (mm-30) REVERT: Q 93 ASP cc_start: 0.8176 (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: 0.8435 (mm-30) cc_final: 0.7850 (mp0) REVERT: Q 148 GLU cc_start: 0.8880 (tt0) cc_final: 0.8648 (tt0) REVERT: R 18 GLU cc_start: 0.8618 (tt0) cc_final: 0.8356 (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: 0.8441 (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: 0.8468 (tpp80) cc_final: 0.7456 (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: 0.8866 (tt0) cc_final: 0.8656 (tt0) REVERT: T 63 GLU cc_start: 0.8309 (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: 0.8744 (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: 0.8176 (t0) cc_final: 0.7923 (t70) REVERT: V 113 GLN cc_start: 0.9015 (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: 0.7879 (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: 0.8910 (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: 0.8881 (tt0) cc_final: 0.8667 (tt0) outliers start: 32 outliers final: 28 residues processed: 1161 average time/residue: 0.8936 time to fit residues: 1199.2077 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 : 1.396 ------------------------------------------------------------------------------- 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 aren 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 : 1.449 Fit side-chains REVERT: A 64 ARG cc_start: 0.8491 (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: 0.8730 (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: 0.8514 (tpp80) cc_final: 0.7482 (ttp-170) REVERT: C 93 ASP cc_start: 0.8273 (t0) cc_final: 0.8006 (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: 0.7860 (mp0) REVERT: D 93 ASP cc_start: 0.8270 (t0) cc_final: 0.8001 (t70) REVERT: D 141 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7871 (mp0) REVERT: E 64 ARG cc_start: 0.8470 (tpp80) cc_final: 0.7506 (ttp-170) REVERT: E 93 ASP cc_start: 0.8247 (t0) cc_final: 0.8007 (t70) REVERT: E 113 GLN cc_start: 0.9051 (tp40) cc_final: 0.8746 (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: 0.8770 (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: 0.8022 (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: 0.8270 (t0) cc_final: 0.8040 (t70) REVERT: H 125 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8719 (mmtm) REVERT: H 148 GLU cc_start: 0.8904 (tt0) cc_final: 0.8699 (tt0) REVERT: I 50 LYS cc_start: 0.8597 (mttp) cc_final: 0.8064 (mmpt) REVERT: I 62 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7865 (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: 0.9053 (tp40) cc_final: 0.8757 (tp40) REVERT: J 125 LYS cc_start: 0.8967 (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: 0.9055 (tp40) cc_final: 0.8797 (tp40) REVERT: K 125 LYS cc_start: 0.8952 (mmtt) cc_final: 0.8725 (mmtm) REVERT: K 141 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7860 (mp0) REVERT: K 148 GLU cc_start: 0.8877 (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: 0.8027 (t70) REVERT: L 120 LYS cc_start: 0.8911 (tttm) cc_final: 0.8547 (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: 0.8487 (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: 0.8444 (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: 0.8396 (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: 0.8243 (t0) cc_final: 0.7995 (t70) REVERT: Q 113 GLN cc_start: 0.9040 (tp40) cc_final: 0.8746 (tp40) REVERT: Q 124 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8197 (tm-30) REVERT: Q 141 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7836 (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: 0.8038 (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: 0.8035 (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: 0.8158 (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: 0.8494 (tpp80) cc_final: 0.7541 (ttp-170) REVERT: U 93 ASP cc_start: 0.8258 (t0) cc_final: 0.8015 (t70) REVERT: U 124 GLU cc_start: 0.8441 (tm-30) cc_final: 0.8226 (tm-30) REVERT: U 141 GLU cc_start: 0.8397 (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: 0.9050 (tp40) cc_final: 0.8806 (tp40) REVERT: W 93 ASP cc_start: 0.8260 (t0) cc_final: 0.8026 (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: 0.8230 (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: 0.8878 time to fit residues: 1049.7281 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 : 1.136 ------------------------------------------------------------------------------- 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 V 8 GLN W 8 GLN X 8 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.105781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.098306 restraints weight = 43133.952| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.33 r_work: 0.2944 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- 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 5.165 46824 Z= 0.259 Chirality : 0.036 0.121 4872 Planarity : 0.003 0.025 6216 Dihedral : 3.898 16.152 4584 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.10 % Allowed : 12.58 % Favored : 85.32 % 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 aren 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 U 138 PHE 0.013 0.002 PHE C 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 0.49645 (46824) hydrogen bonds : bond 0.03788 ( 2640) hydrogen bonds : angle 3.13610 ( 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 : 1.443 Fit side-chains REVERT: A 64 ARG cc_start: 0.8482 (tpp80) cc_final: 0.7481 (ttp-170) REVERT: A 113 GLN cc_start: 0.9058 (tp40) cc_final: 0.8766 (tp40) REVERT: A 125 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8725 (mmtm) REVERT: A 148 GLU cc_start: 0.8872 (tt0) cc_final: 0.8657 (tt0) REVERT: B 93 ASP cc_start: 0.8249 (t0) cc_final: 0.7989 (t70) REVERT: B 113 GLN cc_start: 0.9063 (tp40) cc_final: 0.8766 (tp40) REVERT: B 141 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7854 (mp0) REVERT: B 148 GLU cc_start: 0.8878 (tt0) cc_final: 0.8562 (tt0) REVERT: C 64 ARG cc_start: 0.8446 (tpp80) cc_final: 0.7474 (ttp-170) REVERT: C 93 ASP cc_start: 0.8279 (t0) cc_final: 0.8014 (t70) REVERT: C 141 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7846 (mp0) REVERT: D 93 ASP cc_start: 0.8269 (t0) cc_final: 0.8001 (t70) REVERT: D 141 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7853 (mp0) REVERT: E 64 ARG cc_start: 0.8458 (tpp80) cc_final: 0.7477 (ttp-170) REVERT: E 93 ASP cc_start: 0.8249 (t0) cc_final: 0.8007 (t70) REVERT: E 113 GLN cc_start: 0.9060 (tp40) cc_final: 0.8760 (tp40) REVERT: E 125 LYS cc_start: 0.8919 (mmtt) cc_final: 0.8685 (mmtm) REVERT: E 148 GLU cc_start: 0.8868 (tt0) cc_final: 0.8652 (tt0) REVERT: F 18 GLU cc_start: 0.8677 (tt0) cc_final: 0.8361 (tt0) REVERT: F 64 ARG cc_start: 0.8486 (tpp80) cc_final: 0.7517 (ttp-170) REVERT: F 113 GLN cc_start: 0.9071 (tp40) cc_final: 0.8774 (tp40) REVERT: F 141 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7856 (mp0) REVERT: F 148 GLU cc_start: 0.8870 (tt0) cc_final: 0.8650 (tt0) REVERT: G 62 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7865 (mm-30) REVERT: G 64 ARG cc_start: 0.8489 (tpp80) cc_final: 0.7491 (ttp-170) REVERT: G 93 ASP cc_start: 0.8283 (t0) cc_final: 0.8022 (t70) REVERT: G 120 LYS cc_start: 0.8921 (tttm) cc_final: 0.8563 (ttmp) REVERT: G 125 LYS cc_start: 0.8936 (mmtt) cc_final: 0.8702 (mmtm) REVERT: G 141 GLU cc_start: 0.8420 (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: 0.8000 (tpp80) REVERT: H 93 ASP cc_start: 0.8275 (t0) cc_final: 0.8036 (t70) REVERT: H 125 LYS cc_start: 0.8880 (mmtt) cc_final: 0.8624 (mmtm) REVERT: H 148 GLU cc_start: 0.8890 (tt0) cc_final: 0.8573 (tt0) REVERT: I 62 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7854 (mm-30) REVERT: I 64 ARG cc_start: 0.8484 (tpp80) cc_final: 0.7511 (ttp-170) REVERT: I 93 ASP cc_start: 0.8280 (t0) cc_final: 0.8004 (t70) REVERT: I 113 GLN cc_start: 0.9066 (tp40) cc_final: 0.8771 (tp40) REVERT: I 125 LYS cc_start: 0.8893 (mmtt) cc_final: 0.8678 (mmtm) REVERT: J 93 ASP cc_start: 0.8280 (t0) cc_final: 0.8005 (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: 0.8682 (mmtm) REVERT: K 64 ARG cc_start: 0.8453 (tpp80) cc_final: 0.7487 (ttp-170) REVERT: K 93 ASP cc_start: 0.8251 (t0) cc_final: 0.8014 (t70) REVERT: K 113 GLN cc_start: 0.9061 (tp40) cc_final: 0.8757 (tp40) REVERT: K 125 LYS cc_start: 0.8938 (mmtt) cc_final: 0.8701 (mmtm) REVERT: K 141 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7857 (mp0) REVERT: K 148 GLU cc_start: 0.8871 (tt0) cc_final: 0.8558 (tt0) REVERT: L 62 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7887 (mm-30) REVERT: L 64 ARG cc_start: 0.8480 (tpp80) cc_final: 0.7480 (ttp-170) REVERT: L 93 ASP cc_start: 0.8290 (t0) cc_final: 0.8032 (t70) REVERT: L 120 LYS cc_start: 0.8922 (tttm) cc_final: 0.8561 (ttmp) REVERT: L 125 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8696 (mmtm) REVERT: L 141 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7862 (mp0) REVERT: M 62 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7874 (mm-30) REVERT: M 64 ARG cc_start: 0.8483 (tpp80) cc_final: 0.7513 (ttp-170) REVERT: M 93 ASP cc_start: 0.8265 (t0) cc_final: 0.8034 (t70) REVERT: M 120 LYS cc_start: 0.8869 (tttm) cc_final: 0.8512 (ttmp) REVERT: M 124 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8233 (tm-30) REVERT: M 125 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8713 (mmtm) REVERT: M 141 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7844 (mp0) REVERT: M 148 GLU cc_start: 0.8853 (tt0) cc_final: 0.8618 (tt0) REVERT: N 93 ASP cc_start: 0.8258 (t0) cc_final: 0.8017 (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: 0.8885 (tt0) cc_final: 0.8670 (tt0) REVERT: O 64 ARG cc_start: 0.8495 (tpp80) cc_final: 0.7498 (ttp-170) REVERT: O 93 ASP cc_start: 0.8238 (t0) cc_final: 0.8006 (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: 0.8700 (mmtm) REVERT: P 59 GLN cc_start: 0.8619 (mm110) cc_final: 0.8410 (mm110) REVERT: P 62 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7920 (mm-30) REVERT: P 93 ASP cc_start: 0.8224 (t0) cc_final: 0.7990 (t70) REVERT: P 124 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8231 (tm-30) REVERT: P 125 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8673 (mmtm) REVERT: P 141 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7880 (mp0) REVERT: Q 62 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7864 (mm-30) REVERT: Q 93 ASP cc_start: 0.8246 (t0) cc_final: 0.7986 (t70) REVERT: Q 113 GLN cc_start: 0.9048 (tp40) cc_final: 0.8753 (tp40) REVERT: Q 141 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7848 (mp0) REVERT: Q 148 GLU cc_start: 0.8876 (tt0) cc_final: 0.8559 (tt0) REVERT: R 62 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7923 (mm-30) REVERT: R 91 ARG cc_start: 0.8375 (mtp85) cc_final: 0.8174 (mtp85) REVERT: R 93 ASP cc_start: 0.8270 (t0) cc_final: 0.8039 (t70) REVERT: R 141 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7864 (mp0) REVERT: S 18 GLU cc_start: 0.8677 (tt0) cc_final: 0.8362 (tt0) REVERT: S 64 ARG cc_start: 0.8467 (tpp80) cc_final: 0.7491 (ttp-170) REVERT: S 91 ARG cc_start: 0.8372 (mtp85) cc_final: 0.8171 (mtp85) REVERT: S 93 ASP cc_start: 0.8269 (t0) cc_final: 0.8042 (t70) REVERT: S 124 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8246 (tm-30) REVERT: S 141 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7865 (mp0) REVERT: S 148 GLU cc_start: 0.8847 (tt0) cc_final: 0.8644 (tt0) REVERT: T 62 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7931 (mm-30) REVERT: T 113 GLN cc_start: 0.9064 (tp40) cc_final: 0.8764 (tp40) REVERT: T 125 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8700 (mmtm) REVERT: T 141 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7866 (mp0) REVERT: T 148 GLU cc_start: 0.8881 (tt0) cc_final: 0.8570 (tt0) REVERT: U 64 ARG cc_start: 0.8488 (tpp80) cc_final: 0.7537 (ttp-170) REVERT: U 93 ASP cc_start: 0.8221 (t0) cc_final: 0.7985 (t70) REVERT: U 141 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7855 (mp0) REVERT: V 93 ASP cc_start: 0.8238 (t0) cc_final: 0.7999 (t70) REVERT: V 113 GLN cc_start: 0.9062 (tp40) cc_final: 0.8763 (tp40) REVERT: W 64 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.8013 (tpp80) REVERT: W 93 ASP cc_start: 0.8259 (t0) cc_final: 0.8016 (t70) REVERT: W 125 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8655 (mmtm) REVERT: W 148 GLU cc_start: 0.8903 (tt0) cc_final: 0.8592 (tt0) REVERT: X 93 ASP cc_start: 0.8252 (t0) cc_final: 0.8020 (t70) REVERT: X 120 LYS cc_start: 0.8864 (tttm) cc_final: 0.8505 (ttmp) REVERT: X 124 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8238 (tm-30) REVERT: X 125 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8718 (mmtm) REVERT: X 141 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7847 (mp0) REVERT: X 148 GLU cc_start: 0.8874 (tt0) cc_final: 0.8642 (tt0) outliers start: 77 outliers final: 70 residues processed: 1033 average time/residue: 0.8853 time to fit residues: 1055.7392 Evaluate side-chains 1037 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 965 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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: 4.9990 chunk 373 optimal weight: 0.6980 chunk 394 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 276 optimal weight: 4.9990 chunk 368 optimal weight: 2.9990 chunk 316 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 59 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 L 8 GLN M 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 V 59 GLN W 8 GLN X 8 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.095759 restraints weight = 42996.896| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.31 r_work: 0.2910 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 34776 Z= 0.239 Angle : 0.585 5.922 46824 Z= 0.301 Chirality : 0.040 0.132 4872 Planarity : 0.004 0.028 6216 Dihedral : 4.110 14.575 4584 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.10 % Allowed : 13.15 % Favored : 84.75 % 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 aren not related in a simple way. whole: 4.74 (0.13), residues: 4104 helix: 3.82 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.16 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG V 157 TYR 0.014 0.002 TYR A 40 PHE 0.014 0.003 PHE I 133 TRP 0.005 0.002 TRP N 94 HIS 0.003 0.001 HIS N 137 Details of bonding type rmsd covalent geometry : bond 0.00547 (34776) covalent geometry : angle 0.58532 (46824) hydrogen bonds : bond 0.04546 ( 2640) hydrogen bonds : angle 3.41743 ( 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 1058 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 981 time to evaluate : 1.376 Fit side-chains REVERT: A 64 ARG cc_start: 0.8472 (tpp80) cc_final: 0.7517 (ttp-170) REVERT: A 125 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8722 (mmtm) REVERT: A 148 GLU cc_start: 0.8866 (tt0) cc_final: 0.8662 (tt0) REVERT: B 113 GLN cc_start: 0.9072 (tp40) cc_final: 0.8838 (tp40) REVERT: B 141 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7873 (mp0) REVERT: B 148 GLU cc_start: 0.8907 (tt0) cc_final: 0.8610 (tt0) REVERT: C 64 ARG cc_start: 0.8453 (tpp80) cc_final: 0.7515 (ttp-170) REVERT: C 141 GLU cc_start: 0.8420 (mm-30) cc_final: 0.7859 (mp0) REVERT: D 141 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7851 (mp0) REVERT: E 64 ARG cc_start: 0.8477 (tpp80) cc_final: 0.7504 (ttp-170) REVERT: E 113 GLN cc_start: 0.9077 (tp40) cc_final: 0.8799 (tp40) REVERT: E 125 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8702 (mmtm) REVERT: F 64 ARG cc_start: 0.8467 (tpp80) cc_final: 0.7528 (ttp-170) REVERT: F 141 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7895 (mp0) REVERT: F 148 GLU cc_start: 0.8869 (tt0) cc_final: 0.8667 (tt0) REVERT: G 62 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7947 (mm-30) REVERT: G 64 ARG cc_start: 0.8472 (tpp80) cc_final: 0.7533 (ttp-170) REVERT: G 125 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8669 (mmtm) REVERT: G 141 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7906 (mp0) REVERT: H 93 ASP cc_start: 0.8402 (t0) cc_final: 0.8130 (t70) REVERT: H 125 LYS cc_start: 0.8889 (mmtt) cc_final: 0.8642 (mmtm) REVERT: H 148 GLU cc_start: 0.8920 (tt0) cc_final: 0.8617 (tt0) REVERT: I 50 LYS cc_start: 0.8671 (mttp) cc_final: 0.8147 (mmpt) REVERT: I 62 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7957 (mm-30) REVERT: I 64 ARG cc_start: 0.8469 (tpp80) cc_final: 0.7533 (ttp-170) REVERT: I 113 GLN cc_start: 0.9086 (tp40) cc_final: 0.8858 (tp40) REVERT: I 125 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8641 (mmtm) REVERT: J 50 LYS cc_start: 0.8680 (mttp) cc_final: 0.8150 (mmpt) REVERT: J 113 GLN cc_start: 0.9080 (tp40) cc_final: 0.8855 (tp40) REVERT: J 125 LYS cc_start: 0.8875 (mmtt) cc_final: 0.8650 (mmtm) REVERT: K 64 ARG cc_start: 0.8479 (tpp80) cc_final: 0.7526 (ttp-170) REVERT: K 113 GLN cc_start: 0.9077 (tp40) cc_final: 0.8841 (tp40) REVERT: K 125 LYS cc_start: 0.8939 (mmtt) cc_final: 0.8716 (mmtm) REVERT: K 141 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7877 (mp0) REVERT: K 148 GLU cc_start: 0.8878 (tt0) cc_final: 0.8578 (tt0) REVERT: L 62 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7954 (mm-30) REVERT: L 64 ARG cc_start: 0.8476 (tpp80) cc_final: 0.7524 (ttp-170) REVERT: L 125 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8663 (mmtm) REVERT: L 141 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7899 (mp0) REVERT: M 18 GLU cc_start: 0.8811 (tt0) cc_final: 0.8566 (tt0) REVERT: M 64 ARG cc_start: 0.8467 (tpp80) cc_final: 0.7537 (ttp-170) REVERT: M 93 ASP cc_start: 0.8420 (t0) cc_final: 0.8150 (t70) REVERT: M 120 LYS cc_start: 0.8921 (tttm) cc_final: 0.8523 (ttmp) REVERT: M 141 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7886 (mp0) REVERT: M 148 GLU cc_start: 0.8849 (tt0) cc_final: 0.8627 (tt0) REVERT: N 113 GLN cc_start: 0.9081 (tp40) cc_final: 0.8801 (tp40) REVERT: N 125 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8640 (mmtm) REVERT: O 64 ARG cc_start: 0.8483 (tpp80) cc_final: 0.7522 (ttp-170) REVERT: O 113 GLN cc_start: 0.9084 (tp40) cc_final: 0.8853 (tp40) REVERT: O 125 LYS cc_start: 0.8876 (mmtt) cc_final: 0.8653 (mmtm) REVERT: P 62 GLU cc_start: 0.8156 (mm-30) cc_final: 0.7939 (mm-30) REVERT: P 125 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8728 (mmtm) REVERT: P 141 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7902 (mp0) REVERT: Q 62 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7921 (mm-30) REVERT: Q 113 GLN cc_start: 0.9074 (tp40) cc_final: 0.8841 (tp40) REVERT: Q 141 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7865 (mp0) REVERT: Q 148 GLU cc_start: 0.8898 (tt0) cc_final: 0.8600 (tt0) REVERT: R 141 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7920 (mp0) REVERT: S 64 ARG cc_start: 0.8484 (tpp80) cc_final: 0.7511 (ttp-170) REVERT: S 141 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7921 (mp0) REVERT: T 62 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7988 (mm-30) REVERT: T 113 GLN cc_start: 0.9087 (tp40) cc_final: 0.8853 (tp40) REVERT: T 125 LYS cc_start: 0.8951 (mmtt) cc_final: 0.8722 (mmtm) REVERT: T 141 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7880 (mp0) REVERT: T 148 GLU cc_start: 0.8900 (tt0) cc_final: 0.8602 (tt0) REVERT: U 64 ARG cc_start: 0.8499 (tpp80) cc_final: 0.7592 (ttp-170) REVERT: U 141 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7899 (mp0) REVERT: V 113 GLN cc_start: 0.9080 (tp40) cc_final: 0.8800 (tp40) REVERT: W 93 ASP cc_start: 0.8380 (t0) cc_final: 0.8110 (t70) REVERT: W 148 GLU cc_start: 0.8920 (tt0) cc_final: 0.8617 (tt0) REVERT: X 18 GLU cc_start: 0.8813 (tt0) cc_final: 0.8568 (tt0) REVERT: X 93 ASP cc_start: 0.8419 (t0) cc_final: 0.8144 (t70) REVERT: X 120 LYS cc_start: 0.8919 (tttm) cc_final: 0.8524 (ttmp) REVERT: X 141 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7883 (mp0) REVERT: X 148 GLU cc_start: 0.8875 (tt0) cc_final: 0.8658 (tt0) outliers start: 77 outliers final: 75 residues processed: 1005 average time/residue: 0.9000 time to fit residues: 1041.2801 Evaluate side-chains 995 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 920 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 95 GLU 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 212 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 336 optimal weight: 2.9990 chunk 398 optimal weight: 4.9990 chunk 231 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 B 137 HIS C 8 GLN E 8 GLN E 137 HIS G 8 GLN H 8 GLN I 8 GLN I 137 HIS J 8 GLN J 137 HIS K 8 GLN M 137 HIS N 8 GLN N 137 HIS O 8 GLN O 137 HIS P 8 GLN P 137 HIS Q 8 GLN Q 137 HIS R 8 GLN 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 X 8 GLN X 137 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.104525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.096908 restraints weight = 43048.532| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.34 r_work: 0.2905 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 34776 Z= 0.159 Angle : 0.517 5.275 46824 Z= 0.270 Chirality : 0.037 0.123 4872 Planarity : 0.003 0.026 6216 Dihedral : 3.974 15.820 4584 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.04 % Allowed : 13.37 % Favored : 84.59 % 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 aren not related in a simple way. whole: 5.00 (0.13), residues: 4104 helix: 3.95 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.39 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 157 TYR 0.014 0.002 TYR F 40 PHE 0.014 0.002 PHE U 133 TRP 0.003 0.001 TRP G 94 HIS 0.002 0.001 HIS J 66 Details of bonding type rmsd covalent geometry : bond 0.00361 (34776) covalent geometry : angle 0.51699 (46824) hydrogen bonds : bond 0.03946 ( 2640) hydrogen bonds : angle 3.21501 ( 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 1055 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 980 time to evaluate : 1.455 Fit side-chains REVERT: A 64 ARG cc_start: 0.8460 (tpp80) cc_final: 0.7478 (ttp-170) REVERT: A 95 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8086 (mm-30) REVERT: A 125 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8672 (mmtm) REVERT: A 148 GLU cc_start: 0.8861 (tt0) cc_final: 0.8647 (tt0) REVERT: B 62 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7939 (mm-30) REVERT: B 113 GLN cc_start: 0.9068 (tp40) cc_final: 0.8780 (tp40) REVERT: B 141 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7853 (mp0) REVERT: B 148 GLU cc_start: 0.8889 (tt0) cc_final: 0.8591 (tt0) REVERT: C 64 ARG cc_start: 0.8461 (tpp80) cc_final: 0.7477 (ttp-170) REVERT: C 93 ASP cc_start: 0.8254 (t0) cc_final: 0.7968 (t70) REVERT: C 141 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7852 (mp0) REVERT: D 93 ASP cc_start: 0.8237 (t0) cc_final: 0.7953 (t70) REVERT: D 141 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7844 (mp0) REVERT: E 64 ARG cc_start: 0.8478 (tpp80) cc_final: 0.7470 (ttp-170) REVERT: E 113 GLN cc_start: 0.9050 (tp40) cc_final: 0.8770 (tp40) REVERT: E 125 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8627 (mmtm) REVERT: F 64 ARG cc_start: 0.8469 (tpp80) cc_final: 0.7478 (ttp-170) REVERT: F 95 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8086 (mm-30) REVERT: F 141 GLU cc_start: 0.8407 (mm-30) cc_final: 0.7860 (mp0) REVERT: F 148 GLU cc_start: 0.8862 (tt0) cc_final: 0.8647 (tt0) REVERT: G 62 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7970 (mm-30) REVERT: G 64 ARG cc_start: 0.8475 (tpp80) cc_final: 0.7489 (ttp-170) REVERT: G 125 LYS cc_start: 0.8874 (mmtt) cc_final: 0.8645 (mmtm) REVERT: G 141 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7866 (mp0) REVERT: H 64 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8057 (tpp80) REVERT: H 93 ASP cc_start: 0.8335 (t0) cc_final: 0.8053 (t70) REVERT: H 125 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8596 (mmtm) REVERT: H 148 GLU cc_start: 0.8896 (tt0) cc_final: 0.8580 (tt0) REVERT: I 62 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7944 (mm-30) REVERT: I 64 ARG cc_start: 0.8478 (tpp80) cc_final: 0.7493 (ttp-170) REVERT: I 113 GLN cc_start: 0.9079 (tp40) cc_final: 0.8799 (tp40) REVERT: I 125 LYS cc_start: 0.8847 (mmtt) cc_final: 0.8621 (mmtm) REVERT: J 95 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8080 (mm-30) REVERT: J 113 GLN cc_start: 0.9066 (tp40) cc_final: 0.8785 (tp40) REVERT: J 125 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8628 (mmtm) REVERT: K 64 ARG cc_start: 0.8466 (tpp80) cc_final: 0.7496 (ttp-170) REVERT: K 93 ASP cc_start: 0.8249 (t0) cc_final: 0.8028 (t70) REVERT: K 113 GLN cc_start: 0.9055 (tp40) cc_final: 0.8763 (tp40) REVERT: K 125 LYS cc_start: 0.8911 (mmtt) cc_final: 0.8687 (mmtm) REVERT: K 141 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7852 (mp0) REVERT: K 148 GLU cc_start: 0.8878 (tt0) cc_final: 0.8583 (tt0) REVERT: L 62 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7973 (mm-30) REVERT: L 64 ARG cc_start: 0.8475 (tpp80) cc_final: 0.7483 (ttp-170) REVERT: L 93 ASP cc_start: 0.8261 (t0) cc_final: 0.7985 (t70) REVERT: L 125 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8633 (mmtm) REVERT: L 141 GLU cc_start: 0.8418 (mm-30) cc_final: 0.7864 (mp0) REVERT: M 64 ARG cc_start: 0.8476 (tpp80) cc_final: 0.7454 (ttp-170) REVERT: M 93 ASP cc_start: 0.8350 (t0) cc_final: 0.8066 (t70) REVERT: M 120 LYS cc_start: 0.8916 (tttm) cc_final: 0.8550 (ttmp) REVERT: M 141 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7851 (mp0) REVERT: M 148 GLU cc_start: 0.8855 (tt0) cc_final: 0.8620 (tt0) REVERT: N 113 GLN cc_start: 0.9052 (tp40) cc_final: 0.8775 (tp40) REVERT: N 125 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8607 (mmtm) REVERT: O 64 ARG cc_start: 0.8475 (tpp80) cc_final: 0.7471 (ttp-170) REVERT: O 113 GLN cc_start: 0.9081 (tp40) cc_final: 0.8794 (tp40) REVERT: O 125 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8621 (mmtm) REVERT: P 62 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7917 (mm-30) REVERT: P 125 LYS cc_start: 0.8922 (mmtt) cc_final: 0.8670 (mmtm) REVERT: P 141 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7872 (mp0) REVERT: Q 113 GLN cc_start: 0.9065 (tp40) cc_final: 0.8777 (tp40) REVERT: Q 141 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7862 (mp0) REVERT: Q 148 GLU cc_start: 0.8878 (tt0) cc_final: 0.8580 (tt0) REVERT: R 62 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7979 (mm-30) REVERT: R 93 ASP cc_start: 0.8252 (t0) cc_final: 0.8043 (t70) REVERT: R 95 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8097 (mm-30) REVERT: R 141 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7881 (mp0) REVERT: S 64 ARG cc_start: 0.8472 (tpp80) cc_final: 0.7468 (ttp-170) REVERT: S 93 ASP cc_start: 0.8269 (t0) cc_final: 0.8063 (t70) REVERT: S 95 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8098 (mm-30) REVERT: S 141 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7885 (mp0) REVERT: T 62 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7983 (mm-30) REVERT: T 93 ASP cc_start: 0.8248 (t0) cc_final: 0.8033 (t70) REVERT: T 113 GLN cc_start: 0.9068 (tp40) cc_final: 0.8778 (tp40) REVERT: T 125 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8671 (mmtm) REVERT: T 141 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7862 (mp0) REVERT: T 148 GLU cc_start: 0.8897 (tt0) cc_final: 0.8603 (tt0) REVERT: U 64 ARG cc_start: 0.8485 (tpp80) cc_final: 0.7524 (ttp-170) REVERT: U 93 ASP cc_start: 0.8231 (t0) cc_final: 0.8016 (t70) REVERT: U 124 GLU cc_start: 0.8444 (tm-30) cc_final: 0.8155 (pp20) REVERT: U 125 LYS cc_start: 0.9005 (mmtm) cc_final: 0.8783 (mmtm) REVERT: U 141 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7856 (mp0) REVERT: V 62 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7903 (mm-30) REVERT: V 113 GLN cc_start: 0.9071 (tp40) cc_final: 0.8784 (tp40) REVERT: V 124 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8112 (pp20) REVERT: V 125 LYS cc_start: 0.9022 (mmtm) cc_final: 0.8792 (mmtm) REVERT: V 158 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8057 (mptm) REVERT: W 93 ASP cc_start: 0.8332 (t0) cc_final: 0.8047 (t70) REVERT: W 148 GLU cc_start: 0.8894 (tt0) cc_final: 0.8587 (tt0) REVERT: X 93 ASP cc_start: 0.8343 (t0) cc_final: 0.8060 (t70) REVERT: X 120 LYS cc_start: 0.8922 (tttm) cc_final: 0.8553 (ttmp) REVERT: X 141 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7852 (mp0) REVERT: X 148 GLU cc_start: 0.8880 (tt0) cc_final: 0.8648 (tt0) outliers start: 75 outliers final: 66 residues processed: 1004 average time/residue: 0.8866 time to fit residues: 1027.8799 Evaluate side-chains 1026 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 954 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 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 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 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 M residue 110 SER 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 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 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 V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain V residue 158 LYS 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 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: 5.9990 chunk 5 optimal weight: 4.9990 chunk 219 optimal weight: 7.9990 chunk 321 optimal weight: 7.9990 chunk 117 optimal weight: 0.7980 chunk 269 optimal weight: 0.7980 chunk 195 optimal weight: 6.9990 chunk 384 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 W 59 GLN X 8 GLN X 59 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.096268 restraints weight = 42870.511| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.33 r_work: 0.2918 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 34776 Z= 0.202 Angle : 0.564 5.663 46824 Z= 0.292 Chirality : 0.038 0.126 4872 Planarity : 0.004 0.028 6216 Dihedral : 4.059 14.818 4584 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.29 % Allowed : 13.81 % Favored : 83.91 % 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 aren not related in a simple way. whole: 4.77 (0.13), residues: 4104 helix: 3.85 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.16 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG U 157 TYR 0.013 0.002 TYR Q 40 PHE 0.015 0.002 PHE C 133 TRP 0.005 0.002 TRP S 94 HIS 0.002 0.001 HIS H 137 Details of bonding type rmsd covalent geometry : bond 0.00462 (34776) covalent geometry : angle 0.56376 (46824) hydrogen bonds : bond 0.04280 ( 2640) hydrogen bonds : angle 3.33966 ( 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 1053 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 969 time to evaluate : 1.400 Fit side-chains REVERT: A 64 ARG cc_start: 0.8457 (tpp80) cc_final: 0.7499 (ttp-170) REVERT: A 125 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8630 (mmtm) REVERT: A 148 GLU cc_start: 0.8852 (tt0) cc_final: 0.8646 (tt0) REVERT: B 62 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7934 (mm-30) REVERT: B 113 GLN cc_start: 0.9065 (tp40) cc_final: 0.8776 (tp40) REVERT: B 124 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8120 (pp20) REVERT: B 141 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7864 (mp0) REVERT: B 148 GLU cc_start: 0.8886 (tt0) cc_final: 0.8592 (tt0) REVERT: C 64 ARG cc_start: 0.8456 (tpp80) cc_final: 0.7508 (ttp-170) REVERT: C 141 GLU cc_start: 0.8417 (mm-30) cc_final: 0.7864 (mp0) REVERT: D 124 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8165 (pp20) REVERT: D 141 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7872 (mp0) REVERT: E 64 ARG cc_start: 0.8495 (tpp80) cc_final: 0.7487 (ttp-170) REVERT: E 113 GLN cc_start: 0.9073 (tp40) cc_final: 0.8795 (tp40) REVERT: E 125 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8648 (mmtm) REVERT: F 64 ARG cc_start: 0.8463 (tpp80) cc_final: 0.7510 (ttp-170) REVERT: F 141 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7911 (mp0) REVERT: F 148 GLU cc_start: 0.8859 (tt0) cc_final: 0.8651 (tt0) REVERT: G 62 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7916 (mm-30) REVERT: G 64 ARG cc_start: 0.8482 (tpp80) cc_final: 0.7516 (ttp-170) REVERT: G 125 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8637 (mmtm) REVERT: G 141 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7898 (mp0) REVERT: H 93 ASP cc_start: 0.8369 (t0) cc_final: 0.8100 (t70) REVERT: H 125 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8628 (mmtm) REVERT: H 148 GLU cc_start: 0.8907 (tt0) cc_final: 0.8601 (tt0) REVERT: I 62 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7949 (mm-30) REVERT: I 64 ARG cc_start: 0.8468 (tpp80) cc_final: 0.7518 (ttp-170) REVERT: I 113 GLN cc_start: 0.9086 (tp40) cc_final: 0.8807 (tp40) REVERT: I 125 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8635 (mmtm) REVERT: J 64 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8137 (tpp80) REVERT: J 113 GLN cc_start: 0.9083 (tp40) cc_final: 0.8804 (tp40) REVERT: J 125 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8642 (mmtm) REVERT: K 62 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7944 (mm-30) REVERT: K 64 ARG cc_start: 0.8463 (tpp80) cc_final: 0.7514 (ttp-170) REVERT: K 113 GLN cc_start: 0.9055 (tp40) cc_final: 0.8763 (tp40) REVERT: K 125 LYS cc_start: 0.8907 (mmtt) cc_final: 0.8657 (mmtm) REVERT: K 141 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7875 (mp0) REVERT: K 148 GLU cc_start: 0.8877 (tt0) cc_final: 0.8582 (tt0) REVERT: L 62 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7961 (mm-30) REVERT: L 64 ARG cc_start: 0.8480 (tpp80) cc_final: 0.7514 (ttp-170) REVERT: L 125 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8626 (mmtm) REVERT: L 141 GLU cc_start: 0.8455 (mm-30) cc_final: 0.7895 (mp0) REVERT: M 64 ARG cc_start: 0.8445 (tpp80) cc_final: 0.7470 (ttp-170) REVERT: M 93 ASP cc_start: 0.8396 (t0) cc_final: 0.8129 (t70) REVERT: M 120 LYS cc_start: 0.8887 (tttm) cc_final: 0.8517 (ttmp) REVERT: M 141 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7887 (mp0) REVERT: M 148 GLU cc_start: 0.8849 (tt0) cc_final: 0.8619 (tt0) REVERT: N 113 GLN cc_start: 0.9078 (tp40) cc_final: 0.8800 (tp40) REVERT: N 125 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8620 (mmtm) REVERT: O 64 ARG cc_start: 0.8467 (tpp80) cc_final: 0.7503 (ttp-170) REVERT: O 113 GLN cc_start: 0.9082 (tp40) cc_final: 0.8796 (tp40) REVERT: O 125 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8626 (mmtm) REVERT: P 62 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7944 (mm-30) REVERT: P 125 LYS cc_start: 0.8909 (mmtt) cc_final: 0.8634 (mmtm) REVERT: P 141 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7901 (mp0) REVERT: P 148 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: Q 113 GLN cc_start: 0.9068 (tp40) cc_final: 0.8780 (tp40) REVERT: Q 141 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7868 (mp0) REVERT: Q 148 GLU cc_start: 0.8882 (tt0) cc_final: 0.8590 (tt0) REVERT: R 95 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8102 (mm-30) REVERT: R 124 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8102 (pp20) REVERT: R 141 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7912 (mp0) REVERT: S 64 ARG cc_start: 0.8483 (tpp80) cc_final: 0.7497 (ttp-170) REVERT: S 141 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7918 (mp0) REVERT: T 62 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7982 (mm-30) REVERT: T 113 GLN cc_start: 0.9068 (tp40) cc_final: 0.8779 (tp40) REVERT: T 125 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8643 (mmtm) REVERT: T 141 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7883 (mp0) REVERT: T 148 GLU cc_start: 0.8885 (tt0) cc_final: 0.8593 (tt0) REVERT: U 64 ARG cc_start: 0.8501 (tpp80) cc_final: 0.7583 (ttp-170) REVERT: U 124 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8149 (pp20) REVERT: U 125 LYS cc_start: 0.9017 (mmtm) cc_final: 0.8789 (mmtm) REVERT: U 141 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7891 (mp0) REVERT: V 62 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7905 (mm-30) REVERT: V 113 GLN cc_start: 0.9076 (tp40) cc_final: 0.8790 (tp40) REVERT: V 124 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8120 (pp20) REVERT: V 125 LYS cc_start: 0.9041 (mmtm) cc_final: 0.8826 (mmtm) REVERT: V 158 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8196 (mptm) REVERT: W 93 ASP cc_start: 0.8347 (t0) cc_final: 0.8076 (t70) REVERT: W 148 GLU cc_start: 0.8913 (tt0) cc_final: 0.8605 (tt0) REVERT: X 93 ASP cc_start: 0.8385 (t0) cc_final: 0.8118 (t70) REVERT: X 120 LYS cc_start: 0.8888 (tttm) cc_final: 0.8519 (ttmp) REVERT: X 141 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7884 (mp0) REVERT: X 148 GLU cc_start: 0.8875 (tt0) cc_final: 0.8650 (tt0) outliers start: 84 outliers final: 79 residues processed: 994 average time/residue: 0.8741 time to fit residues: 1004.1563 Evaluate side-chains 1045 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 962 time to evaluate : 1.468 ------------------------------------------------------------------------------- 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 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 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 95 GLU 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 M residue 110 SER 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 P residue 148 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 V residue 158 LYS 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 Chi-restraints excluded: chain X residue 110 SER 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: 0.9980 chunk 345 optimal weight: 3.9990 chunk 268 optimal weight: 7.9990 chunk 182 optimal weight: 0.5980 chunk 56 optimal weight: 0.7980 chunk 45 optimal weight: 5.9990 chunk 356 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 385 optimal weight: 0.9990 chunk 377 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN E 8 GLN I 8 GLN I 15 GLN J 15 GLN P 8 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.106435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.098798 restraints weight = 42966.546| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.36 r_work: 0.2972 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 34776 Z= 0.104 Angle : 0.475 5.439 46824 Z= 0.250 Chirality : 0.033 0.115 4872 Planarity : 0.003 0.024 6216 Dihedral : 3.805 16.603 4584 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.23 % Allowed : 14.98 % Favored : 83.80 % 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 aren not related in a simple way. whole: 5.47 (0.13), residues: 4104 helix: 4.27 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.59 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 157 TYR 0.010 0.001 TYR N 40 PHE 0.013 0.002 PHE D 133 TRP 0.003 0.001 TRP C 94 HIS 0.002 0.001 HIS M 119 Details of bonding type rmsd covalent geometry : bond 0.00227 (34776) covalent geometry : angle 0.47459 (46824) hydrogen bonds : bond 0.03306 ( 2640) hydrogen bonds : angle 2.98093 ( 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 1068 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 1023 time to evaluate : 1.458 Fit side-chains REVERT: A 64 ARG cc_start: 0.8424 (tpp80) cc_final: 0.7431 (ttp-170) REVERT: A 125 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8593 (mmtm) REVERT: A 148 GLU cc_start: 0.8854 (tt0) cc_final: 0.8631 (tt0) REVERT: B 62 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7895 (mm-30) REVERT: B 113 GLN cc_start: 0.9026 (tp40) cc_final: 0.8738 (tp40) REVERT: B 124 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8119 (pp20) REVERT: B 141 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7810 (mp0) REVERT: B 148 GLU cc_start: 0.8875 (tt0) cc_final: 0.8563 (tt0) REVERT: C 62 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7867 (mm-30) REVERT: C 64 ARG cc_start: 0.8447 (tpp80) cc_final: 0.7469 (ttp-170) REVERT: C 93 ASP cc_start: 0.8157 (t0) cc_final: 0.7916 (t70) REVERT: C 125 LYS cc_start: 0.8969 (mmtm) cc_final: 0.8766 (mmtm) REVERT: C 141 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7809 (mp0) REVERT: D 16 ASP cc_start: 0.9085 (m-30) cc_final: 0.8881 (m-30) REVERT: D 93 ASP cc_start: 0.8098 (t0) cc_final: 0.7857 (t70) REVERT: D 124 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8197 (pp20) REVERT: D 125 LYS cc_start: 0.8995 (mmtm) cc_final: 0.8742 (mmtm) REVERT: D 141 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7806 (mp0) REVERT: E 16 ASP cc_start: 0.9110 (m-30) cc_final: 0.8788 (m-30) REVERT: E 64 ARG cc_start: 0.8444 (tpp80) cc_final: 0.7531 (ttm110) REVERT: E 113 GLN cc_start: 0.9027 (tp40) cc_final: 0.8734 (tp40) REVERT: E 125 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8591 (mmtm) REVERT: F 62 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7947 (mm-30) REVERT: F 64 ARG cc_start: 0.8422 (tpp80) cc_final: 0.7461 (ttp-170) REVERT: F 124 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8166 (pp20) REVERT: F 141 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7844 (mp0) REVERT: F 148 GLU cc_start: 0.8852 (tt0) cc_final: 0.8629 (tt0) REVERT: G 62 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7890 (mm-30) REVERT: G 64 ARG cc_start: 0.8455 (tpp80) cc_final: 0.7447 (ttp-170) REVERT: G 93 ASP cc_start: 0.8150 (t0) cc_final: 0.7916 (t70) REVERT: G 120 LYS cc_start: 0.8857 (tttm) cc_final: 0.8454 (ttmp) REVERT: G 125 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8571 (mmtm) REVERT: G 141 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7830 (mp0) REVERT: H 93 ASP cc_start: 0.8185 (t0) cc_final: 0.7982 (t70) REVERT: H 125 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8608 (mmtm) REVERT: H 148 GLU cc_start: 0.8879 (tt0) cc_final: 0.8664 (tt0) REVERT: I 62 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7907 (mm-30) REVERT: I 64 ARG cc_start: 0.8463 (tpp80) cc_final: 0.7482 (ttp-170) REVERT: I 113 GLN cc_start: 0.9059 (tp40) cc_final: 0.8778 (tp40) REVERT: I 125 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8602 (mmtm) REVERT: J 64 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7970 (tpp80) REVERT: J 95 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8101 (mm-30) REVERT: J 113 GLN cc_start: 0.9054 (tp40) cc_final: 0.8774 (tp40) REVERT: K 59 GLN cc_start: 0.8585 (mm110) cc_final: 0.8371 (mm110) REVERT: K 64 ARG cc_start: 0.8455 (tpp80) cc_final: 0.7431 (ttp-170) REVERT: K 113 GLN cc_start: 0.9034 (tp40) cc_final: 0.8743 (tp40) REVERT: K 125 LYS cc_start: 0.8864 (mmtt) cc_final: 0.8633 (mmtm) REVERT: K 141 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7804 (mp0) REVERT: K 148 GLU cc_start: 0.8860 (tt0) cc_final: 0.8548 (tt0) REVERT: L 62 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7910 (mm-30) REVERT: L 64 ARG cc_start: 0.8437 (tpp80) cc_final: 0.7457 (ttp-170) REVERT: L 93 ASP cc_start: 0.8151 (t0) cc_final: 0.7916 (t70) REVERT: L 120 LYS cc_start: 0.8858 (tttm) cc_final: 0.8451 (ttmp) REVERT: L 125 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8573 (mmtm) REVERT: L 141 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7827 (mp0) REVERT: M 64 ARG cc_start: 0.8458 (tpp80) cc_final: 0.7453 (ttp-170) REVERT: M 93 ASP cc_start: 0.8222 (t0) cc_final: 0.8012 (t70) REVERT: M 120 LYS cc_start: 0.8819 (tttm) cc_final: 0.8441 (ttmp) REVERT: M 141 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7786 (mp0) REVERT: M 148 GLU cc_start: 0.8851 (tt0) cc_final: 0.8626 (tt0) REVERT: N 16 ASP cc_start: 0.9041 (m-30) cc_final: 0.8794 (m-30) REVERT: N 113 GLN cc_start: 0.9032 (tp40) cc_final: 0.8746 (tp40) REVERT: N 125 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8570 (mmtm) REVERT: O 64 ARG cc_start: 0.8442 (tpp80) cc_final: 0.7476 (ttp-170) REVERT: O 113 GLN cc_start: 0.9049 (tp40) cc_final: 0.8764 (tp40) REVERT: O 125 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8597 (mmtm) REVERT: P 59 GLN cc_start: 0.8615 (mm110) cc_final: 0.8395 (mm110) REVERT: P 125 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8620 (mmtm) REVERT: P 141 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7833 (mp0) REVERT: Q 113 GLN cc_start: 0.9031 (tp40) cc_final: 0.8746 (tp40) REVERT: Q 141 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7804 (mp0) REVERT: Q 148 GLU cc_start: 0.8859 (tt0) cc_final: 0.8548 (tt0) REVERT: R 62 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7909 (mm-30) REVERT: R 95 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8081 (mm-30) REVERT: R 124 GLU cc_start: 0.8399 (tm-30) cc_final: 0.8073 (pp20) REVERT: R 125 LYS cc_start: 0.8987 (mmtm) cc_final: 0.8762 (mmtm) REVERT: R 141 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7812 (mp0) REVERT: S 62 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7967 (mm-30) REVERT: S 64 ARG cc_start: 0.8446 (tpp80) cc_final: 0.7416 (ttp-170) REVERT: S 95 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8093 (mm-30) REVERT: S 124 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8182 (pp20) REVERT: S 141 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7834 (mp0) REVERT: T 62 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7937 (mm-30) REVERT: T 113 GLN cc_start: 0.9043 (tp40) cc_final: 0.8756 (tp40) REVERT: T 125 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8627 (mmtm) REVERT: T 141 GLU cc_start: 0.8330 (mm-30) cc_final: 0.7802 (mp0) REVERT: T 148 GLU cc_start: 0.8875 (tt0) cc_final: 0.8564 (tt0) REVERT: U 64 ARG cc_start: 0.8506 (tpp80) cc_final: 0.7532 (ttp-170) REVERT: U 124 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8105 (pp20) REVERT: U 125 LYS cc_start: 0.9004 (mmtm) cc_final: 0.8712 (mmtm) REVERT: U 141 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7809 (mp0) REVERT: V 62 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7900 (mm-30) REVERT: V 113 GLN cc_start: 0.9048 (tp40) cc_final: 0.8767 (tp40) REVERT: V 124 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8035 (pp20) REVERT: V 158 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8356 (tppp) REVERT: W 64 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8009 (tpp80) REVERT: W 93 ASP cc_start: 0.8179 (t0) cc_final: 0.7956 (t70) REVERT: W 124 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8171 (pp20) REVERT: W 148 GLU cc_start: 0.8870 (tt0) cc_final: 0.8656 (tt0) REVERT: X 63 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7660 (mm-30) REVERT: X 93 ASP cc_start: 0.8210 (t0) cc_final: 0.8007 (t70) REVERT: X 120 LYS cc_start: 0.8813 (tttm) cc_final: 0.8437 (ttmp) REVERT: X 141 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7803 (mp0) REVERT: X 148 GLU cc_start: 0.8861 (tt0) cc_final: 0.8635 (tt0) outliers start: 45 outliers final: 37 residues processed: 1047 average time/residue: 0.8625 time to fit residues: 1044.8827 Evaluate side-chains 1027 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 987 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER 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 C residue 7 SER Chi-restraints excluded: chain D residue 7 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 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 J residue 64 ARG Chi-restraints excluded: chain K residue 7 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 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 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 U residue 7 SER Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 158 LYS 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 Chi-restraints excluded: chain X residue 110 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: 0.0170 chunk 361 optimal weight: 0.9990 chunk 402 optimal weight: 6.9990 chunk 352 optimal weight: 0.6980 chunk 365 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 166 optimal weight: 0.0570 chunk 219 optimal weight: 7.9990 chunk 275 optimal weight: 0.9990 chunk 337 optimal weight: 7.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN B 8 GLN B 59 GLN B 137 HIS C 8 GLN C 59 GLN D 59 GLN E 8 GLN E 59 GLN E 137 HIS F 59 GLN G 8 GLN G 59 GLN H 8 GLN H 59 GLN I 59 GLN I 137 HIS J 59 GLN J 137 HIS K 8 GLN L 8 GLN L 59 GLN M 59 GLN M 137 HIS N 8 GLN N 59 GLN N 137 HIS O 8 GLN O 59 GLN O 137 HIS P 8 GLN P 137 HIS Q 8 GLN Q 59 GLN Q 137 HIS R 8 GLN R 59 GLN R 137 HIS S 59 GLN S 137 HIS T 8 GLN T 59 GLN U 8 GLN U 137 HIS V 59 GLN V 137 HIS W 8 GLN W 59 GLN X 59 GLN X 137 HIS Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.109843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.102214 restraints weight = 42919.498| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.36 r_work: 0.3006 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1890 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= 0.094 Angle : 0.467 6.364 46824 Z= 0.247 Chirality : 0.032 0.113 4872 Planarity : 0.003 0.023 6216 Dihedral : 3.639 16.893 4584 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.16 % Allowed : 16.18 % Favored : 83.66 % 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 aren not related in a simple way. whole: 5.80 (0.13), residues: 4104 helix: 4.48 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.79 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 157 TYR 0.010 0.001 TYR X 138 PHE 0.012 0.002 PHE D 133 TRP 0.004 0.001 TRP X 94 HIS 0.002 0.000 HIS P 66 Details of bonding type rmsd covalent geometry : bond 0.00207 (34776) covalent geometry : angle 0.46651 (46824) hydrogen bonds : bond 0.02913 ( 2640) hydrogen bonds : angle 2.83913 ( 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 1078 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 1072 time to evaluate : 1.357 Fit side-chains REVERT: A 64 ARG cc_start: 0.8462 (tpp80) cc_final: 0.7546 (ttp-170) REVERT: A 148 GLU cc_start: 0.8826 (tt0) cc_final: 0.8610 (tt0) REVERT: B 113 GLN cc_start: 0.9006 (tp40) cc_final: 0.8714 (tp40) REVERT: B 141 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7767 (mp0) REVERT: B 148 GLU cc_start: 0.8877 (tt0) cc_final: 0.8564 (tt0) REVERT: C 64 ARG cc_start: 0.8438 (tpp80) cc_final: 0.7550 (ttp-170) REVERT: C 141 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7720 (mp0) REVERT: D 16 ASP cc_start: 0.9009 (m-30) cc_final: 0.8774 (m-30) REVERT: D 93 ASP cc_start: 0.8013 (t0) cc_final: 0.7774 (t70) REVERT: D 124 GLU cc_start: 0.8356 (tm-30) cc_final: 0.8142 (pp20) REVERT: D 125 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8719 (mmtm) REVERT: D 141 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7722 (mp0) REVERT: E 64 ARG cc_start: 0.8485 (tpp80) cc_final: 0.7508 (ttp-170) REVERT: E 113 GLN cc_start: 0.9010 (tp40) cc_final: 0.8707 (tp40) REVERT: F 62 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7950 (mm-30) REVERT: F 64 ARG cc_start: 0.8456 (tpp80) cc_final: 0.7546 (ttp-170) REVERT: F 141 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7807 (mp0) REVERT: F 148 GLU cc_start: 0.8834 (tt0) cc_final: 0.8614 (tt0) REVERT: G 64 ARG cc_start: 0.8494 (tpp80) cc_final: 0.7553 (ttp-170) REVERT: G 93 ASP cc_start: 0.7995 (t0) cc_final: 0.7777 (t70) REVERT: G 120 LYS cc_start: 0.8830 (tttm) cc_final: 0.8432 (ttmp) REVERT: G 125 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8604 (mmtm) REVERT: G 141 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7775 (mp0) REVERT: H 148 GLU cc_start: 0.8890 (tt0) cc_final: 0.8576 (tt0) REVERT: I 62 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7819 (mm-30) REVERT: I 64 ARG cc_start: 0.8440 (tpp80) cc_final: 0.7503 (ttp-170) REVERT: I 113 GLN cc_start: 0.9047 (tp40) cc_final: 0.8755 (tp40) REVERT: I 125 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8579 (mmtm) REVERT: J 95 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8158 (mm-30) REVERT: J 113 GLN cc_start: 0.9029 (tp40) cc_final: 0.8736 (tp40) REVERT: K 63 GLU cc_start: 0.8332 (mm-30) cc_final: 0.7616 (mm-30) REVERT: K 64 ARG cc_start: 0.8451 (tpp80) cc_final: 0.7516 (ttp-170) REVERT: K 113 GLN cc_start: 0.9035 (tp40) cc_final: 0.8733 (tp40) REVERT: K 141 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7736 (mp0) REVERT: K 148 GLU cc_start: 0.8874 (tt0) cc_final: 0.8556 (tt0) REVERT: L 64 ARG cc_start: 0.8479 (tpp80) cc_final: 0.7557 (ttp-170) REVERT: L 93 ASP cc_start: 0.8000 (t0) cc_final: 0.7773 (t70) REVERT: L 120 LYS cc_start: 0.8841 (tttm) cc_final: 0.8439 (ttmp) REVERT: L 125 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8609 (mmtm) REVERT: L 141 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7792 (mp0) REVERT: M 64 ARG cc_start: 0.8448 (tpp80) cc_final: 0.7517 (ttp-170) REVERT: M 93 ASP cc_start: 0.8129 (t0) cc_final: 0.7906 (t70) REVERT: M 120 LYS cc_start: 0.8781 (tttm) cc_final: 0.8418 (ttmp) REVERT: M 141 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7747 (mp0) REVERT: M 148 GLU cc_start: 0.8824 (tt0) cc_final: 0.8594 (tt0) REVERT: N 113 GLN cc_start: 0.9028 (tp40) cc_final: 0.8729 (tp40) REVERT: N 125 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8587 (mmtm) REVERT: O 64 ARG cc_start: 0.8453 (tpp80) cc_final: 0.7508 (ttp-170) REVERT: O 95 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8103 (mm-30) REVERT: O 113 GLN cc_start: 0.9037 (tp40) cc_final: 0.8753 (tp40) REVERT: O 120 LYS cc_start: 0.8812 (tttm) cc_final: 0.8548 (ttpt) REVERT: O 125 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8569 (mmtm) REVERT: P 59 GLN cc_start: 0.8578 (mm110) cc_final: 0.8373 (mm110) REVERT: P 125 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8605 (mmtm) REVERT: P 141 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7779 (mp0) REVERT: Q 113 GLN cc_start: 0.8996 (tp40) cc_final: 0.8705 (tp40) REVERT: Q 141 GLU cc_start: 0.8371 (mm-30) cc_final: 0.7769 (mp0) REVERT: Q 148 GLU cc_start: 0.8865 (tt0) cc_final: 0.8534 (tt0) REVERT: R 95 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8115 (mm-30) REVERT: R 124 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8071 (pp20) REVERT: R 125 LYS cc_start: 0.8962 (mmtm) cc_final: 0.8749 (mmtm) REVERT: R 141 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7771 (mp0) REVERT: S 62 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7904 (mm-30) REVERT: S 64 ARG cc_start: 0.8495 (tpp80) cc_final: 0.7529 (ttp-170) REVERT: S 124 GLU cc_start: 0.8362 (tm-30) cc_final: 0.8154 (pp20) REVERT: S 141 GLU cc_start: 0.8359 (mm-30) cc_final: 0.7779 (mp0) REVERT: S 158 LYS cc_start: 0.8331 (mttt) cc_final: 0.8084 (mtmt) REVERT: T 62 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7878 (mm-30) REVERT: T 113 GLN cc_start: 0.9042 (tp40) cc_final: 0.8742 (tp40) REVERT: T 125 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8625 (mmtm) REVERT: T 141 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7732 (mp0) REVERT: T 148 GLU cc_start: 0.8894 (tt0) cc_final: 0.8594 (tt0) REVERT: U 63 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7681 (mm-30) REVERT: U 64 ARG cc_start: 0.8465 (tpp80) cc_final: 0.7518 (ttp-170) REVERT: U 141 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7767 (mp0) REVERT: V 62 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7916 (mm-30) REVERT: V 95 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8133 (mm-30) REVERT: V 113 GLN cc_start: 0.9030 (tp40) cc_final: 0.8751 (tp40) REVERT: V 120 LYS cc_start: 0.8804 (tttm) cc_final: 0.8499 (ttpt) REVERT: W 93 ASP cc_start: 0.8061 (t0) cc_final: 0.7849 (t70) REVERT: W 148 GLU cc_start: 0.8894 (tt0) cc_final: 0.8659 (tt0) REVERT: X 93 ASP cc_start: 0.8128 (t0) cc_final: 0.7903 (t70) REVERT: X 120 LYS cc_start: 0.8786 (tttm) cc_final: 0.8418 (ttmp) REVERT: X 141 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7752 (mp0) REVERT: X 148 GLU cc_start: 0.8825 (tt0) cc_final: 0.8592 (tt0) outliers start: 6 outliers final: 2 residues processed: 1072 average time/residue: 0.8631 time to fit residues: 1069.8190 Evaluate side-chains 958 residues out of total 3672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 956 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain X residue 110 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 287 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 252 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 382 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN C 8 GLN C 59 GLN E 8 GLN G 8 GLN G 61 HIS I 8 GLN J 8 GLN K 8 GLN K 59 GLN L 8 GLN O 8 GLN P 8 GLN Q 8 GLN R 8 GLN S 8 GLN T 8 GLN U 59 GLN V 8 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.105905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.098354 restraints weight = 42950.626| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.33 r_work: 0.2950 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34776 Z= 0.149 Angle : 0.533 6.046 46824 Z= 0.278 Chirality : 0.036 0.118 4872 Planarity : 0.003 0.026 6216 Dihedral : 3.807 15.136 4584 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.52 % Allowed : 16.50 % Favored : 82.98 % 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 aren not related in a simple way. whole: 5.37 (0.13), residues: 4104 helix: 4.20 (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 J 157 TYR 0.012 0.001 TYR C 138 PHE 0.014 0.002 PHE I 133 TRP 0.005 0.002 TRP T 94 HIS 0.002 0.001 HIS P 58 Details of bonding type rmsd covalent geometry : bond 0.00343 (34776) covalent geometry : angle 0.53272 (46824) hydrogen bonds : bond 0.03695 ( 2640) hydrogen bonds : angle 3.11066 ( 7920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16549.24 seconds wall clock time: 281 minutes 40.68 seconds (16900.68 seconds total)