Starting phenix.real_space_refine on Sun Aug 24 19:09:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opf_17051/08_2025/8opf_17051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opf_17051/08_2025/8opf_17051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8opf_17051/08_2025/8opf_17051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opf_17051/08_2025/8opf_17051.map" model { file = "/net/cci-nas-00/data/ceres_data/8opf_17051/08_2025/8opf_17051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opf_17051/08_2025/8opf_17051.cif" } resolution = 2.83 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= 0.016 sd= 0.289 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: 4 Type Number sf(0) Gaussians S 209 5.16 5 C 14193 2.51 5 N 3800 2.21 5 O 4199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22401 Number of models: 1 Model: "" Number of chains: 1 Chain: "Aa" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1179 Classifications: {'peptide': 147} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 136} Restraints were copied for chains: Ab, Ac, Ad, Ae, Af, Ag, Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, As Time building chain proxies: 1.91, per 1000 atoms: 0.09 Number of scatterers: 22401 At special positions: 0 Unit cell: (132.05, 132.05, 158.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 209 16.00 O 4199 8.00 N 3800 7.00 C 14193 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: 1.61 Conformation dependent library (CDL) restraints added in 900.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5320 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 38 sheets defined 44.9% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'Aa' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAa 71 " --> pdb=" O LEUAa 67 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 86 through 102 Processing helix chain 'Aa' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAa 111 " --> pdb=" O GLUAa 107 " (cutoff:3.500A) Processing helix chain 'Aa' and resid 145 through 150 Processing helix chain 'Aa' and resid 155 through 161 Processing helix chain 'Aa' and resid 163 through 176 Processing helix chain 'Ab' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAb 71 " --> pdb=" O LEUAb 67 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 86 through 102 Processing helix chain 'Ab' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAb 111 " --> pdb=" O GLUAb 107 " (cutoff:3.500A) Processing helix chain 'Ab' and resid 145 through 150 Processing helix chain 'Ab' and resid 155 through 161 Processing helix chain 'Ab' and resid 163 through 176 Processing helix chain 'Ac' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAc 71 " --> pdb=" O LEUAc 67 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 86 through 102 Processing helix chain 'Ac' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAc 111 " --> pdb=" O GLUAc 107 " (cutoff:3.500A) Processing helix chain 'Ac' and resid 145 through 150 Processing helix chain 'Ac' and resid 155 through 161 Processing helix chain 'Ac' and resid 163 through 176 Processing helix chain 'Ad' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAd 71 " --> pdb=" O LEUAd 67 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 86 through 102 Processing helix chain 'Ad' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAd 111 " --> pdb=" O GLUAd 107 " (cutoff:3.500A) Processing helix chain 'Ad' and resid 145 through 150 Processing helix chain 'Ad' and resid 155 through 161 Processing helix chain 'Ad' and resid 163 through 176 Processing helix chain 'Ae' and resid 66 through 71 removed outlier: 3.741A pdb=" N LEUAe 71 " --> pdb=" O LEUAe 67 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 86 through 102 Processing helix chain 'Ae' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAe 111 " --> pdb=" O GLUAe 107 " (cutoff:3.500A) Processing helix chain 'Ae' and resid 145 through 150 Processing helix chain 'Ae' and resid 155 through 161 Processing helix chain 'Ae' and resid 163 through 176 Processing helix chain 'Af' and resid 66 through 71 removed outlier: 3.741A pdb=" N LEUAf 71 " --> pdb=" O LEUAf 67 " (cutoff:3.500A) Processing helix chain 'Af' and resid 86 through 102 Processing helix chain 'Af' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAf 111 " --> pdb=" O GLUAf 107 " (cutoff:3.500A) Processing helix chain 'Af' and resid 145 through 150 Processing helix chain 'Af' and resid 155 through 161 Processing helix chain 'Af' and resid 163 through 176 Processing helix chain 'Ag' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAg 71 " --> pdb=" O LEUAg 67 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 86 through 102 Processing helix chain 'Ag' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAg 111 " --> pdb=" O GLUAg 107 " (cutoff:3.500A) Processing helix chain 'Ag' and resid 145 through 150 Processing helix chain 'Ag' and resid 155 through 161 Processing helix chain 'Ag' and resid 163 through 176 Processing helix chain 'Ah' and resid 66 through 71 removed outlier: 3.743A pdb=" N LEUAh 71 " --> pdb=" O LEUAh 67 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 86 through 102 Processing helix chain 'Ah' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAh 111 " --> pdb=" O GLUAh 107 " (cutoff:3.500A) Processing helix chain 'Ah' and resid 145 through 150 Processing helix chain 'Ah' and resid 155 through 161 Processing helix chain 'Ah' and resid 163 through 176 Processing helix chain 'Ai' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAi 71 " --> pdb=" O LEUAi 67 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 86 through 102 Processing helix chain 'Ai' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAi 111 " --> pdb=" O GLUAi 107 " (cutoff:3.500A) Processing helix chain 'Ai' and resid 145 through 150 Processing helix chain 'Ai' and resid 155 through 161 Processing helix chain 'Ai' and resid 163 through 176 Processing helix chain 'Aj' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAj 71 " --> pdb=" O LEUAj 67 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 86 through 102 Processing helix chain 'Aj' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAj 111 " --> pdb=" O GLUAj 107 " (cutoff:3.500A) Processing helix chain 'Aj' and resid 145 through 150 Processing helix chain 'Aj' and resid 155 through 161 Processing helix chain 'Aj' and resid 163 through 176 Processing helix chain 'Ak' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAk 71 " --> pdb=" O LEUAk 67 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 86 through 102 Processing helix chain 'Ak' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAk 111 " --> pdb=" O GLUAk 107 " (cutoff:3.500A) Processing helix chain 'Ak' and resid 145 through 150 Processing helix chain 'Ak' and resid 155 through 161 Processing helix chain 'Ak' and resid 163 through 176 Processing helix chain 'Al' and resid 66 through 71 removed outlier: 3.741A pdb=" N LEUAl 71 " --> pdb=" O LEUAl 67 " (cutoff:3.500A) Processing helix chain 'Al' and resid 86 through 102 Processing helix chain 'Al' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAl 111 " --> pdb=" O GLUAl 107 " (cutoff:3.500A) Processing helix chain 'Al' and resid 145 through 150 Processing helix chain 'Al' and resid 155 through 161 Processing helix chain 'Al' and resid 163 through 176 Processing helix chain 'Am' and resid 66 through 71 removed outlier: 3.741A pdb=" N LEUAm 71 " --> pdb=" O LEUAm 67 " (cutoff:3.500A) Processing helix chain 'Am' and resid 86 through 102 Processing helix chain 'Am' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAm 111 " --> pdb=" O GLUAm 107 " (cutoff:3.500A) Processing helix chain 'Am' and resid 145 through 150 Processing helix chain 'Am' and resid 155 through 161 Processing helix chain 'Am' and resid 163 through 176 Processing helix chain 'An' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAn 71 " --> pdb=" O LEUAn 67 " (cutoff:3.500A) Processing helix chain 'An' and resid 86 through 102 Processing helix chain 'An' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAn 111 " --> pdb=" O GLUAn 107 " (cutoff:3.500A) Processing helix chain 'An' and resid 145 through 150 Processing helix chain 'An' and resid 155 through 161 Processing helix chain 'An' and resid 163 through 176 Processing helix chain 'Ao' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAo 71 " --> pdb=" O LEUAo 67 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 86 through 102 Processing helix chain 'Ao' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAo 111 " --> pdb=" O GLUAo 107 " (cutoff:3.500A) Processing helix chain 'Ao' and resid 145 through 150 Processing helix chain 'Ao' and resid 155 through 161 Processing helix chain 'Ao' and resid 163 through 176 Processing helix chain 'Ap' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAp 71 " --> pdb=" O LEUAp 67 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 86 through 102 Processing helix chain 'Ap' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAp 111 " --> pdb=" O GLUAp 107 " (cutoff:3.500A) Processing helix chain 'Ap' and resid 145 through 150 Processing helix chain 'Ap' and resid 155 through 161 Processing helix chain 'Ap' and resid 163 through 176 Processing helix chain 'Aq' and resid 66 through 71 removed outlier: 3.742A pdb=" N LEUAq 71 " --> pdb=" O LEUAq 67 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 86 through 102 Processing helix chain 'Aq' and resid 107 through 122 removed outlier: 3.559A pdb=" N VALAq 111 " --> pdb=" O GLUAq 107 " (cutoff:3.500A) Processing helix chain 'Aq' and resid 145 through 150 Processing helix chain 'Aq' and resid 155 through 161 Processing helix chain 'Aq' and resid 163 through 176 Processing helix chain 'Ar' and resid 66 through 71 removed outlier: 3.741A pdb=" N LEUAr 71 " --> pdb=" O LEUAr 67 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 86 through 102 Processing helix chain 'Ar' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAr 111 " --> pdb=" O GLUAr 107 " (cutoff:3.500A) Processing helix chain 'Ar' and resid 145 through 150 Processing helix chain 'Ar' and resid 155 through 161 Processing helix chain 'Ar' and resid 163 through 176 Processing helix chain 'As' and resid 66 through 71 removed outlier: 3.741A pdb=" N LEUAs 71 " --> pdb=" O LEUAs 67 " (cutoff:3.500A) Processing helix chain 'As' and resid 86 through 102 Processing helix chain 'As' and resid 107 through 122 removed outlier: 3.560A pdb=" N VALAs 111 " --> pdb=" O GLUAs 107 " (cutoff:3.500A) Processing helix chain 'As' and resid 145 through 150 Processing helix chain 'As' and resid 155 through 161 Processing helix chain 'As' and resid 163 through 176 Processing sheet with id=AA1, first strand: chain 'Aa' and resid 58 through 59 Processing sheet with id=AA2, first strand: chain 'Aa' and resid 131 through 135 Processing sheet with id=AA3, first strand: chain 'Ab' and resid 58 through 59 Processing sheet with id=AA4, first strand: chain 'Ab' and resid 131 through 135 Processing sheet with id=AA5, first strand: chain 'Ac' and resid 58 through 59 Processing sheet with id=AA6, first strand: chain 'Ac' and resid 131 through 135 Processing sheet with id=AA7, first strand: chain 'Ad' and resid 58 through 59 Processing sheet with id=AA8, first strand: chain 'Ad' and resid 131 through 135 Processing sheet with id=AA9, first strand: chain 'Ae' and resid 58 through 59 Processing sheet with id=AB1, first strand: chain 'Ae' and resid 131 through 135 Processing sheet with id=AB2, first strand: chain 'Af' and resid 58 through 59 Processing sheet with id=AB3, first strand: chain 'Af' and resid 131 through 135 Processing sheet with id=AB4, first strand: chain 'Ag' and resid 58 through 59 Processing sheet with id=AB5, first strand: chain 'Ag' and resid 131 through 135 Processing sheet with id=AB6, first strand: chain 'Ah' and resid 58 through 59 Processing sheet with id=AB7, first strand: chain 'Ah' and resid 131 through 135 Processing sheet with id=AB8, first strand: chain 'Ai' and resid 58 through 59 Processing sheet with id=AB9, first strand: chain 'Ai' and resid 131 through 135 Processing sheet with id=AC1, first strand: chain 'Aj' and resid 58 through 59 Processing sheet with id=AC2, first strand: chain 'Aj' and resid 131 through 135 Processing sheet with id=AC3, first strand: chain 'Ak' and resid 58 through 59 Processing sheet with id=AC4, first strand: chain 'Ak' and resid 131 through 135 Processing sheet with id=AC5, first strand: chain 'Al' and resid 58 through 59 Processing sheet with id=AC6, first strand: chain 'Al' and resid 131 through 135 Processing sheet with id=AC7, first strand: chain 'Am' and resid 58 through 59 Processing sheet with id=AC8, first strand: chain 'Am' and resid 131 through 135 Processing sheet with id=AC9, first strand: chain 'An' and resid 58 through 59 Processing sheet with id=AD1, first strand: chain 'An' and resid 131 through 135 Processing sheet with id=AD2, first strand: chain 'Ao' and resid 58 through 59 Processing sheet with id=AD3, first strand: chain 'Ao' and resid 131 through 135 Processing sheet with id=AD4, first strand: chain 'Ap' and resid 58 through 59 Processing sheet with id=AD5, first strand: chain 'Ap' and resid 131 through 135 Processing sheet with id=AD6, first strand: chain 'Aq' and resid 58 through 59 Processing sheet with id=AD7, first strand: chain 'Aq' and resid 131 through 135 Processing sheet with id=AD8, first strand: chain 'Ar' and resid 58 through 59 Processing sheet with id=AD9, first strand: chain 'Ar' and resid 131 through 135 Processing sheet with id=AE1, first strand: chain 'As' and resid 58 through 59 Processing sheet with id=AE2, first strand: chain 'As' and resid 131 through 135 874 hydrogen bonds defined for protein. 2565 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: 2.64 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7103 1.34 - 1.45: 2897 1.45 - 1.57: 12515 1.57 - 1.69: 0 1.69 - 1.81: 399 Bond restraints: 22914 Sorted by residual: bond pdb=" C LYSAg 48 " pdb=" N ALAAg 49 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.36e-02 5.41e+03 9.31e+00 bond pdb=" C LYSAc 48 " pdb=" N ALAAc 49 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.36e-02 5.41e+03 9.16e+00 bond pdb=" C LYSAk 48 " pdb=" N ALAAk 49 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.36e-02 5.41e+03 9.07e+00 bond pdb=" C LYSAm 48 " pdb=" N ALAAm 49 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.36e-02 5.41e+03 9.06e+00 bond pdb=" C LYSAi 48 " pdb=" N ALAAi 49 " ideal model delta sigma weight residual 1.335 1.376 -0.041 1.36e-02 5.41e+03 9.05e+00 ... (remaining 22909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 28892 0.93 - 1.85: 1483 1.85 - 2.78: 461 2.78 - 3.71: 184 3.71 - 4.64: 83 Bond angle restraints: 31103 Sorted by residual: angle pdb=" N ILEAq 47 " pdb=" CA ILEAq 47 " pdb=" C ILEAq 47 " ideal model delta sigma weight residual 109.21 112.46 -3.25 1.36e+00 5.41e-01 5.70e+00 angle pdb=" N ILEAe 47 " pdb=" CA ILEAe 47 " pdb=" C ILEAe 47 " ideal model delta sigma weight residual 109.21 112.44 -3.23 1.36e+00 5.41e-01 5.65e+00 angle pdb=" N ILEAi 47 " pdb=" CA ILEAi 47 " pdb=" C ILEAi 47 " ideal model delta sigma weight residual 109.21 112.44 -3.23 1.36e+00 5.41e-01 5.64e+00 angle pdb=" N ILEAc 47 " pdb=" CA ILEAc 47 " pdb=" C ILEAc 47 " ideal model delta sigma weight residual 109.21 112.44 -3.23 1.36e+00 5.41e-01 5.64e+00 angle pdb=" N ILEAa 47 " pdb=" CA ILEAa 47 " pdb=" C ILEAa 47 " ideal model delta sigma weight residual 109.21 112.43 -3.22 1.36e+00 5.41e-01 5.60e+00 ... (remaining 31098 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 12350 16.61 - 33.21: 994 33.21 - 49.82: 488 49.82 - 66.43: 209 66.43 - 83.03: 38 Dihedral angle restraints: 14079 sinusoidal: 5852 harmonic: 8227 Sorted by residual: dihedral pdb=" CA ARGAn 174 " pdb=" CB ARGAn 174 " pdb=" CG ARGAn 174 " pdb=" CD ARGAn 174 " ideal model delta sinusoidal sigma weight residual -60.00 -117.25 57.25 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA ARGAp 174 " pdb=" CB ARGAp 174 " pdb=" CG ARGAp 174 " pdb=" CD ARGAp 174 " ideal model delta sinusoidal sigma weight residual -60.00 -117.21 57.21 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CA ARGAb 174 " pdb=" CB ARGAb 174 " pdb=" CG ARGAb 174 " pdb=" CD ARGAb 174 " ideal model delta sinusoidal sigma weight residual -60.00 -117.20 57.20 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 14076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1818 0.026 - 0.052: 1019 0.052 - 0.077: 362 0.077 - 0.103: 174 0.103 - 0.129: 47 Chirality restraints: 3420 Sorted by residual: chirality pdb=" CG LEUAf 71 " pdb=" CB LEUAf 71 " pdb=" CD1 LEUAf 71 " pdb=" CD2 LEUAf 71 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CG LEUAe 71 " pdb=" CB LEUAe 71 " pdb=" CD1 LEUAe 71 " pdb=" CD2 LEUAe 71 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CG LEUAg 71 " pdb=" CB LEUAg 71 " pdb=" CD1 LEUAg 71 " pdb=" CD2 LEUAg 71 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.15e-01 ... (remaining 3417 not shown) Planarity restraints: 4009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYSAa 48 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C LYSAa 48 " 0.031 2.00e-02 2.50e+03 pdb=" O LYSAa 48 " -0.012 2.00e-02 2.50e+03 pdb=" N ALAAa 49 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYSAf 48 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C LYSAf 48 " 0.030 2.00e-02 2.50e+03 pdb=" O LYSAf 48 " -0.012 2.00e-02 2.50e+03 pdb=" N ALAAf 49 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYSAm 48 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C LYSAm 48 " 0.030 2.00e-02 2.50e+03 pdb=" O LYSAm 48 " -0.012 2.00e-02 2.50e+03 pdb=" N ALAAm 49 " -0.010 2.00e-02 2.50e+03 ... (remaining 4006 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 9198 2.93 - 3.43: 21177 3.43 - 3.92: 37396 3.92 - 4.41: 42820 4.41 - 4.90: 70201 Nonbonded interactions: 180792 Sorted by model distance: nonbonded pdb=" O PROAo 75 " pdb=" NH1 ARGAp 174 " model vdw 2.443 3.120 nonbonded pdb=" NH1 ARGAa 174 " pdb=" O PROAq 75 " model vdw 2.458 3.120 nonbonded pdb=" NH1 ARGAd 174 " pdb=" O PROAs 75 " model vdw 2.459 3.120 nonbonded pdb=" O PROAm 75 " pdb=" NH1 ARGAn 174 " model vdw 2.466 3.120 nonbonded pdb=" O PROAg 75 " pdb=" NH1 ARGAh 174 " model vdw 2.467 3.120 ... (remaining 180787 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: 0.06 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' } 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=0.00 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.190 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 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 : 0.004 0.044 22914 Z= 0.201 Angle : 0.586 4.635 31103 Z= 0.327 Chirality : 0.039 0.129 3420 Planarity : 0.006 0.039 4009 Dihedral : 17.430 83.032 8759 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.53 % Allowed : 22.55 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.34 (0.15), residues: 2755 helix: -0.40 (0.14), residues: 1102 sheet: 2.86 (0.35), residues: 190 loop : -1.86 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARGAl 188 TYR 0.005 0.001 TYRAp 73 PHE 0.004 0.001 PHEAk 163 TRP 0.007 0.001 TRPAo 132 HIS 0.002 0.001 HISAm 42 Details of bonding type rmsd covalent geometry : bond 0.00372 (22914) covalent geometry : angle 0.58593 (31103) hydrogen bonds : bond 0.22336 ( 874) hydrogen bonds : angle 7.54788 ( 2565) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 736 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 134 MET cc_start: 0.8918 (ttt) cc_final: 0.8338 (ttt) REVERT: Aa 160 MET cc_start: 0.9072 (mmp) cc_final: 0.8834 (mmt) REVERT: Aa 168 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7524 (mt-10) REVERT: Aa 173 MET cc_start: 0.7501 (ttp) cc_final: 0.6945 (ttt) REVERT: Aa 177 LYS cc_start: 0.8077 (mtpp) cc_final: 0.7637 (mptt) REVERT: Ab 76 GLN cc_start: 0.8425 (mt0) cc_final: 0.7954 (mt0) REVERT: Ab 127 ASN cc_start: 0.8432 (t0) cc_final: 0.8198 (t0) REVERT: Ab 173 MET cc_start: 0.7560 (ttp) cc_final: 0.7206 (ttt) REVERT: Ac 71 LEU cc_start: 0.8816 (mm) cc_final: 0.8611 (mt) REVERT: Ac 157 ARG cc_start: 0.8468 (ttm110) cc_final: 0.8236 (ttp-110) REVERT: Ac 173 MET cc_start: 0.7468 (ttp) cc_final: 0.7131 (ttt) REVERT: Ac 181 MET cc_start: 0.7066 (mmt) cc_final: 0.6844 (mtm) REVERT: Ad 56 MET cc_start: 0.8646 (mmp) cc_final: 0.8392 (mmm) REVERT: Ad 139 GLU cc_start: 0.7507 (pt0) cc_final: 0.6764 (pm20) REVERT: Ad 157 ARG cc_start: 0.8405 (OUTLIER) cc_final: 0.8172 (ttp-110) REVERT: Ad 160 MET cc_start: 0.9142 (mmp) cc_final: 0.8626 (mmp) REVERT: Ad 173 MET cc_start: 0.7446 (ttp) cc_final: 0.7086 (ttt) REVERT: Ae 56 MET cc_start: 0.8736 (mmp) cc_final: 0.8527 (mmt) REVERT: Ae 139 GLU cc_start: 0.7384 (pt0) cc_final: 0.6695 (pm20) REVERT: Af 46 ARG cc_start: 0.9147 (mpt180) cc_final: 0.8938 (mpt180) REVERT: Af 153 LYS cc_start: 0.8599 (mmtp) cc_final: 0.8395 (mmtt) REVERT: Af 168 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7424 (mt-10) REVERT: Af 173 MET cc_start: 0.7540 (ttp) cc_final: 0.7126 (ttp) REVERT: Af 177 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7594 (mptt) REVERT: Ag 50 ILE cc_start: 0.8201 (mm) cc_final: 0.7913 (mm) REVERT: Ag 91 ASP cc_start: 0.8786 (m-30) cc_final: 0.8494 (m-30) REVERT: Ag 116 MET cc_start: 0.9048 (ttm) cc_final: 0.8482 (ttm) REVERT: Ag 139 GLU cc_start: 0.7504 (pt0) cc_final: 0.6831 (pm20) REVERT: Ag 173 MET cc_start: 0.7526 (ttp) cc_final: 0.7298 (ttp) REVERT: Ag 177 LYS cc_start: 0.7945 (mtpp) cc_final: 0.7462 (mptt) REVERT: Ah 91 ASP cc_start: 0.8862 (m-30) cc_final: 0.8657 (m-30) REVERT: Ah 108 MET cc_start: 0.9236 (tpt) cc_final: 0.8455 (tpt) REVERT: Ah 173 MET cc_start: 0.7442 (ttp) cc_final: 0.6931 (ttt) REVERT: Ah 177 LYS cc_start: 0.7868 (mtpp) cc_final: 0.7478 (mptt) REVERT: Ah 181 MET cc_start: 0.6969 (mmt) cc_final: 0.6679 (mtm) REVERT: Ai 56 MET cc_start: 0.8693 (mmp) cc_final: 0.8483 (mmm) REVERT: Ai 108 MET cc_start: 0.9251 (tpt) cc_final: 0.8706 (tpt) REVERT: Ai 173 MET cc_start: 0.7497 (ttp) cc_final: 0.7067 (ttt) REVERT: Ai 177 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7577 (mptt) REVERT: Aj 139 GLU cc_start: 0.7382 (pt0) cc_final: 0.6718 (pm20) REVERT: Aj 158 GLN cc_start: 0.8900 (mt0) cc_final: 0.8647 (mt0) REVERT: Aj 168 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7547 (mt-10) REVERT: Aj 173 MET cc_start: 0.7611 (ttp) cc_final: 0.7219 (ttt) REVERT: Ak 157 ARG cc_start: 0.8473 (ttm110) cc_final: 0.8268 (ttp-110) REVERT: Ak 173 MET cc_start: 0.7541 (ttp) cc_final: 0.7029 (ttt) REVERT: Ak 177 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7522 (mptt) REVERT: Ak 181 MET cc_start: 0.6970 (mmt) cc_final: 0.6704 (mtm) REVERT: Al 153 LYS cc_start: 0.8697 (mmtp) cc_final: 0.8463 (mmtt) REVERT: Al 177 LYS cc_start: 0.7891 (mtpp) cc_final: 0.7512 (mptt) REVERT: Am 139 GLU cc_start: 0.7509 (pt0) cc_final: 0.7190 (pt0) REVERT: Am 173 MET cc_start: 0.7510 (ttp) cc_final: 0.7094 (ttt) REVERT: Am 177 LYS cc_start: 0.7960 (mtpp) cc_final: 0.7535 (mptt) REVERT: An 108 MET cc_start: 0.9212 (tpt) cc_final: 0.8875 (tpt) REVERT: An 135 MET cc_start: 0.8990 (mmm) cc_final: 0.8692 (mmm) REVERT: An 173 MET cc_start: 0.7419 (ttp) cc_final: 0.6997 (ttt) REVERT: An 177 LYS cc_start: 0.7947 (mtpp) cc_final: 0.7725 (mtmm) REVERT: Ao 56 MET cc_start: 0.8735 (mmp) cc_final: 0.8431 (mmt) REVERT: Ao 91 ASP cc_start: 0.8763 (m-30) cc_final: 0.8474 (m-30) REVERT: Ao 135 MET cc_start: 0.9062 (mmm) cc_final: 0.8770 (mmm) REVERT: Ao 173 MET cc_start: 0.7410 (ttp) cc_final: 0.6891 (ttt) REVERT: Ao 177 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7689 (mptt) REVERT: Ap 116 MET cc_start: 0.9030 (ttm) cc_final: 0.8825 (ttp) REVERT: Ap 160 MET cc_start: 0.9091 (mmp) cc_final: 0.8498 (mmp) REVERT: Ap 168 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7485 (mt-10) REVERT: Ap 173 MET cc_start: 0.7407 (ttp) cc_final: 0.7085 (ttt) REVERT: Aq 60 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8276 (mmtm) REVERT: Aq 139 GLU cc_start: 0.7514 (pt0) cc_final: 0.6813 (pm20) REVERT: Ar 91 ASP cc_start: 0.8821 (m-30) cc_final: 0.8604 (m-30) REVERT: Ar 139 GLU cc_start: 0.7507 (pt0) cc_final: 0.6738 (pm20) REVERT: Ar 173 MET cc_start: 0.7519 (ttp) cc_final: 0.7029 (ttt) REVERT: Ar 177 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7538 (mptt) REVERT: As 173 MET cc_start: 0.7460 (ttp) cc_final: 0.7096 (ttt) REVERT: As 177 LYS cc_start: 0.8076 (mtpp) cc_final: 0.7719 (mptt) outliers start: 13 outliers final: 0 residues processed: 740 average time/residue: 0.7045 time to fit residues: 579.2729 Evaluate side-chains 694 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 693 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ad residue 157 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.2980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 113 ASN ** Ac 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 113 ASN Ae 113 ASN Ae 158 GLN Af 113 ASN Ag 113 ASN ** Ah 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 113 ASN Ak 113 ASN ** Al 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 113 ASN Am 175 ASN An 175 ASN Ao 113 ASN Ap 113 ASN Aq 113 ASN Ar 113 ASN As 113 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.163133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138416 restraints weight = 24604.890| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.06 r_work: 0.3406 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3439 r_free = 0.3439 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22914 Z= 0.144 Angle : 0.555 5.713 31103 Z= 0.283 Chirality : 0.041 0.167 3420 Planarity : 0.005 0.034 4009 Dihedral : 3.986 18.570 3044 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.13 % Allowed : 20.81 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.40 (0.16), residues: 2755 helix: 0.81 (0.15), residues: 1121 sheet: 2.81 (0.33), residues: 190 loop : -1.66 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGAp 55 TYR 0.018 0.001 TYRAq 180 PHE 0.010 0.002 PHEAi 163 TRP 0.011 0.001 TRPAf 132 HIS 0.001 0.000 HISAc 69 Details of bonding type rmsd covalent geometry : bond 0.00358 (22914) covalent geometry : angle 0.55484 (31103) hydrogen bonds : bond 0.04565 ( 874) hydrogen bonds : angle 4.67764 ( 2565) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 728 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 91 ASP cc_start: 0.8461 (m-30) cc_final: 0.8234 (m-30) REVERT: Aa 160 MET cc_start: 0.8997 (mmp) cc_final: 0.8438 (mmt) REVERT: Aa 168 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7312 (mt-10) REVERT: Aa 181 MET cc_start: 0.7277 (mmt) cc_final: 0.6913 (mtm) REVERT: Ab 121 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7328 (tm-30) REVERT: Ab 127 ASN cc_start: 0.8448 (t0) cc_final: 0.8201 (t0) REVERT: Ab 173 MET cc_start: 0.7733 (ttp) cc_final: 0.7339 (ttp) REVERT: Ab 177 LYS cc_start: 0.8253 (mtpp) cc_final: 0.7812 (mptt) REVERT: Ac 121 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7419 (tm-30) REVERT: Ac 173 MET cc_start: 0.7609 (ttp) cc_final: 0.7094 (ttp) REVERT: Ac 177 LYS cc_start: 0.8186 (mtpp) cc_final: 0.7630 (mptt) REVERT: Ac 181 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6938 (mtm) REVERT: Ad 56 MET cc_start: 0.8692 (mmp) cc_final: 0.8412 (mmm) REVERT: Ad 173 MET cc_start: 0.7729 (ttp) cc_final: 0.7492 (ttp) REVERT: Ad 181 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6976 (mtm) REVERT: Ae 56 MET cc_start: 0.8697 (mmp) cc_final: 0.8485 (mmt) REVERT: Ae 139 GLU cc_start: 0.7576 (pt0) cc_final: 0.6836 (pm20) REVERT: Ae 173 MET cc_start: 0.7966 (OUTLIER) cc_final: 0.7645 (ttp) REVERT: Ae 181 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6854 (mtm) REVERT: Af 46 ARG cc_start: 0.9237 (mpt180) cc_final: 0.8918 (mpt180) REVERT: Af 69 HIS cc_start: 0.8113 (m-70) cc_final: 0.6530 (t-90) REVERT: Af 95 GLU cc_start: 0.8400 (mp0) cc_final: 0.8009 (mp0) REVERT: Af 153 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8490 (mmtt) REVERT: Af 168 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7501 (mt-10) REVERT: Af 173 MET cc_start: 0.7647 (ttp) cc_final: 0.7262 (ttp) REVERT: Af 177 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7642 (mptt) REVERT: Ag 50 ILE cc_start: 0.8069 (mm) cc_final: 0.7696 (mm) REVERT: Ag 116 MET cc_start: 0.9021 (OUTLIER) cc_final: 0.8733 (tmm) REVERT: Ag 139 GLU cc_start: 0.7539 (pt0) cc_final: 0.6856 (pm20) REVERT: Ag 177 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7593 (mptt) REVERT: Ag 181 MET cc_start: 0.7374 (mmt) cc_final: 0.6861 (mtm) REVERT: Ah 71 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8374 (mt) REVERT: Ah 91 ASP cc_start: 0.8551 (m-30) cc_final: 0.8314 (m-30) REVERT: Ah 173 MET cc_start: 0.7731 (ttp) cc_final: 0.7172 (ttt) REVERT: Ah 177 LYS cc_start: 0.8145 (mtpp) cc_final: 0.7593 (mptt) REVERT: Ah 181 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6865 (mtm) REVERT: Ai 99 LEU cc_start: 0.8622 (tt) cc_final: 0.8188 (tp) REVERT: Ai 108 MET cc_start: 0.8940 (tpt) cc_final: 0.8642 (tpt) REVERT: Ai 153 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.7183 (mptp) REVERT: Ai 173 MET cc_start: 0.7847 (ttp) cc_final: 0.7336 (ttt) REVERT: Ai 177 LYS cc_start: 0.8249 (mtpp) cc_final: 0.7681 (mptt) REVERT: Ai 181 MET cc_start: 0.7334 (tpt) cc_final: 0.7032 (tpp) REVERT: Aj 67 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8254 (mp) REVERT: Aj 102 ASP cc_start: 0.8746 (t0) cc_final: 0.8540 (t0) REVERT: Aj 139 GLU cc_start: 0.7542 (pt0) cc_final: 0.6853 (pm20) REVERT: Aj 158 GLN cc_start: 0.8912 (mt0) cc_final: 0.8683 (mt0) REVERT: Aj 168 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7536 (mt-10) REVERT: Aj 173 MET cc_start: 0.7812 (ttp) cc_final: 0.7518 (ttp) REVERT: Aj 177 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7677 (mptt) REVERT: Aj 181 MET cc_start: 0.7084 (mmt) cc_final: 0.6807 (mtm) REVERT: Ak 173 MET cc_start: 0.7594 (ttp) cc_final: 0.7055 (ttt) REVERT: Ak 177 LYS cc_start: 0.8053 (mtpp) cc_final: 0.7491 (mptt) REVERT: Ak 181 MET cc_start: 0.7286 (mmt) cc_final: 0.6792 (mtm) REVERT: Al 108 MET cc_start: 0.8956 (tpt) cc_final: 0.8753 (tpt) REVERT: Al 177 LYS cc_start: 0.8093 (mtpp) cc_final: 0.7642 (mptt) REVERT: Am 108 MET cc_start: 0.9085 (tpt) cc_final: 0.8837 (tpt) REVERT: Am 173 MET cc_start: 0.7773 (ttp) cc_final: 0.7571 (ttp) REVERT: An 99 LEU cc_start: 0.8424 (tt) cc_final: 0.7996 (tp) REVERT: An 108 MET cc_start: 0.8989 (tpt) cc_final: 0.8322 (tpt) REVERT: An 135 MET cc_start: 0.9018 (mmm) cc_final: 0.8710 (mmm) REVERT: An 173 MET cc_start: 0.7657 (ttp) cc_final: 0.7159 (ttt) REVERT: An 177 LYS cc_start: 0.8136 (mtpp) cc_final: 0.7883 (mtmm) REVERT: Ao 56 MET cc_start: 0.8638 (mmp) cc_final: 0.8385 (mmt) REVERT: Ao 91 ASP cc_start: 0.8585 (m-30) cc_final: 0.8306 (m-30) REVERT: Ao 135 MET cc_start: 0.9108 (mmm) cc_final: 0.8686 (mmm) REVERT: Ao 173 MET cc_start: 0.7788 (ttp) cc_final: 0.7360 (ttt) REVERT: Ap 116 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8678 (ttp) REVERT: Ap 173 MET cc_start: 0.7803 (ttp) cc_final: 0.7367 (ttt) REVERT: Ap 181 MET cc_start: 0.7280 (OUTLIER) cc_final: 0.6956 (mtm) REVERT: Aq 60 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8155 (mmtm) REVERT: Aq 160 MET cc_start: 0.9151 (mmt) cc_final: 0.8690 (mmt) REVERT: Aq 181 MET cc_start: 0.7309 (mmt) cc_final: 0.6904 (mtm) REVERT: Ar 67 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8409 (mp) REVERT: Ar 139 GLU cc_start: 0.7670 (pt0) cc_final: 0.6859 (pm20) REVERT: Ar 168 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7526 (mt-10) REVERT: Ar 173 MET cc_start: 0.7754 (ttp) cc_final: 0.7355 (ttt) REVERT: As 56 MET cc_start: 0.8608 (mmt) cc_final: 0.8406 (mmt) REVERT: As 146 LYS cc_start: 0.8684 (ttpt) cc_final: 0.8468 (ttpp) REVERT: As 181 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7036 (mtm) outliers start: 102 outliers final: 16 residues processed: 752 average time/residue: 0.8185 time to fit residues: 682.9082 Evaluate side-chains 753 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 723 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 181 MET Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ad residue 181 MET Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 173 MET Chi-restraints excluded: chain Ae residue 181 MET Chi-restraints excluded: chain Af residue 116 MET Chi-restraints excluded: chain Af residue 153 LYS Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ah residue 71 LEU Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 153 LYS Chi-restraints excluded: chain Aj residue 67 LEU Chi-restraints excluded: chain Aj residue 116 MET Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 48 LYS Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Ap residue 181 MET Chi-restraints excluded: chain Aq residue 175 ASN Chi-restraints excluded: chain Ar residue 67 LEU Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 181 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 119 optimal weight: 0.8980 chunk 257 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 234 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 245 optimal weight: 0.9980 chunk 42 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ae 77 GLN Ae 113 ASN Ae 158 GLN Af 113 ASN Ag 113 ASN ** Ah 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 113 ASN Am 113 ASN As 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.164212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.139261 restraints weight = 24654.044| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.08 r_work: 0.3408 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22914 Z= 0.125 Angle : 0.519 4.957 31103 Z= 0.263 Chirality : 0.040 0.162 3420 Planarity : 0.005 0.035 4009 Dihedral : 3.830 15.580 3040 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.44 % Allowed : 23.40 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.23 (0.16), residues: 2755 helix: 1.43 (0.15), residues: 1102 sheet: 2.66 (0.34), residues: 190 loop : -1.27 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARGAp 55 TYR 0.017 0.001 TYRAs 180 PHE 0.010 0.002 PHEAi 163 TRP 0.011 0.001 TRPAf 132 HIS 0.001 0.000 HISAc 69 Details of bonding type rmsd covalent geometry : bond 0.00315 (22914) covalent geometry : angle 0.51856 (31103) hydrogen bonds : bond 0.03923 ( 874) hydrogen bonds : angle 4.29790 ( 2565) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 732 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 91 ASP cc_start: 0.8497 (m-30) cc_final: 0.8252 (m-30) REVERT: Aa 160 MET cc_start: 0.9017 (mmp) cc_final: 0.8581 (mmt) REVERT: Aa 168 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7262 (mt-10) REVERT: Aa 173 MET cc_start: 0.7663 (ttp) cc_final: 0.7211 (ttt) REVERT: Aa 177 LYS cc_start: 0.8220 (mtpm) cc_final: 0.7688 (mptt) REVERT: Aa 181 MET cc_start: 0.7347 (mmt) cc_final: 0.6902 (mtm) REVERT: Ab 55 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.8003 (mmm-85) REVERT: Ab 121 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: Ab 127 ASN cc_start: 0.8449 (t0) cc_final: 0.8180 (t0) REVERT: Ab 173 MET cc_start: 0.7740 (ttp) cc_final: 0.7340 (ttt) REVERT: Ac 108 MET cc_start: 0.8981 (tpt) cc_final: 0.8761 (mmp) REVERT: Ac 121 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7476 (tm-30) REVERT: Ac 173 MET cc_start: 0.7528 (ttp) cc_final: 0.6999 (ttp) REVERT: Ac 177 LYS cc_start: 0.8163 (mtpp) cc_final: 0.7594 (mptt) REVERT: Ac 181 MET cc_start: 0.7426 (mmt) cc_final: 0.6952 (mtm) REVERT: Ad 56 MET cc_start: 0.8687 (mmp) cc_final: 0.8373 (mmm) REVERT: Ad 160 MET cc_start: 0.9232 (mmp) cc_final: 0.8811 (mmp) REVERT: Ad 173 MET cc_start: 0.7630 (ttp) cc_final: 0.7409 (ttp) REVERT: Ad 181 MET cc_start: 0.7347 (OUTLIER) cc_final: 0.7008 (mtm) REVERT: Ae 139 GLU cc_start: 0.7650 (pt0) cc_final: 0.6915 (pm20) REVERT: Af 46 ARG cc_start: 0.9232 (mpt180) cc_final: 0.8893 (mpt180) REVERT: Af 69 HIS cc_start: 0.8048 (m-70) cc_final: 0.6370 (t-90) REVERT: Af 95 GLU cc_start: 0.8331 (mp0) cc_final: 0.8074 (mp0) REVERT: Af 168 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7569 (mt-10) REVERT: Af 173 MET cc_start: 0.7509 (ttp) cc_final: 0.7220 (ttp) REVERT: Af 177 LYS cc_start: 0.8122 (mtpp) cc_final: 0.7662 (mptt) REVERT: Af 181 MET cc_start: 0.7003 (mmt) cc_final: 0.6730 (mtm) REVERT: Ag 116 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8720 (tmm) REVERT: Ag 177 LYS cc_start: 0.8106 (mtpp) cc_final: 0.7508 (mptt) REVERT: Ag 181 MET cc_start: 0.7412 (mmt) cc_final: 0.6946 (mtm) REVERT: Ah 91 ASP cc_start: 0.8526 (m-30) cc_final: 0.8262 (m-30) REVERT: Ah 173 MET cc_start: 0.7680 (ttp) cc_final: 0.7157 (ttt) REVERT: Ah 177 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7610 (mptt) REVERT: Ah 181 MET cc_start: 0.7451 (mmt) cc_final: 0.6867 (mtm) REVERT: Ai 56 MET cc_start: 0.8561 (mmt) cc_final: 0.8321 (mmp) REVERT: Ai 108 MET cc_start: 0.8950 (tpt) cc_final: 0.8615 (mmm) REVERT: Ai 121 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7447 (tp30) REVERT: Ai 139 GLU cc_start: 0.7678 (pt0) cc_final: 0.6951 (pm20) REVERT: Ai 173 MET cc_start: 0.7773 (ttp) cc_final: 0.7270 (ttt) REVERT: Ai 177 LYS cc_start: 0.8233 (mtpp) cc_final: 0.7644 (mptt) REVERT: Aj 139 GLU cc_start: 0.7669 (pt0) cc_final: 0.6961 (pm20) REVERT: Aj 158 GLN cc_start: 0.8916 (mt0) cc_final: 0.8644 (mt0) REVERT: Aj 168 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7558 (mt-10) REVERT: Aj 173 MET cc_start: 0.7777 (ttp) cc_final: 0.7476 (ttp) REVERT: Aj 177 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7597 (mptt) REVERT: Aj 181 MET cc_start: 0.7082 (mmt) cc_final: 0.6848 (mtm) REVERT: Ak 173 MET cc_start: 0.7582 (ttp) cc_final: 0.6801 (ttt) REVERT: Ak 177 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7384 (mptt) REVERT: Ak 181 MET cc_start: 0.7248 (mmt) cc_final: 0.6845 (mtt) REVERT: Al 108 MET cc_start: 0.8980 (tpt) cc_final: 0.8619 (tpt) REVERT: Al 168 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7598 (mt-10) REVERT: Al 177 LYS cc_start: 0.8094 (mtpp) cc_final: 0.7475 (mptt) REVERT: Am 139 GLU cc_start: 0.7751 (pt0) cc_final: 0.7440 (pt0) REVERT: Am 168 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7610 (mt-10) REVERT: Am 173 MET cc_start: 0.7753 (ttp) cc_final: 0.7205 (ttt) REVERT: Am 177 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7506 (mptt) REVERT: An 99 LEU cc_start: 0.8374 (tt) cc_final: 0.8002 (tp) REVERT: An 121 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7209 (tp30) REVERT: An 135 MET cc_start: 0.9016 (mmm) cc_final: 0.8750 (mmm) REVERT: An 173 MET cc_start: 0.7609 (ttp) cc_final: 0.7094 (ttt) REVERT: An 175 ASN cc_start: 0.8269 (m-40) cc_final: 0.7986 (m-40) REVERT: An 177 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7818 (mtmm) REVERT: Ao 56 MET cc_start: 0.8665 (mmp) cc_final: 0.8360 (mmt) REVERT: Ao 91 ASP cc_start: 0.8609 (m-30) cc_final: 0.8374 (m-30) REVERT: Ao 135 MET cc_start: 0.9091 (mmm) cc_final: 0.8755 (mmm) REVERT: Ao 153 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7495 (mptp) REVERT: Ao 173 MET cc_start: 0.7719 (ttp) cc_final: 0.7222 (ttt) REVERT: Ao 177 LYS cc_start: 0.8266 (mtpp) cc_final: 0.7960 (mtmm) REVERT: Ap 60 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.7437 (mptt) REVERT: Ap 99 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7930 (mt) REVERT: Ap 116 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8628 (ttp) REVERT: Ap 173 MET cc_start: 0.7721 (ttp) cc_final: 0.7307 (ttt) REVERT: Ap 181 MET cc_start: 0.7389 (mmt) cc_final: 0.6929 (mtm) REVERT: Aq 60 LYS cc_start: 0.8461 (mmtt) cc_final: 0.8185 (mmtm) REVERT: Aq 91 ASP cc_start: 0.8564 (m-30) cc_final: 0.8240 (m-30) REVERT: Aq 112 MET cc_start: 0.9240 (mmp) cc_final: 0.8830 (mmp) REVERT: Aq 153 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7474 (mptp) REVERT: Aq 160 MET cc_start: 0.9155 (mmt) cc_final: 0.8657 (mmt) REVERT: Aq 181 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.7054 (mtm) REVERT: Ar 168 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7476 (mt-10) REVERT: Ar 173 MET cc_start: 0.7731 (ttp) cc_final: 0.7343 (ttt) REVERT: As 146 LYS cc_start: 0.8671 (ttpt) cc_final: 0.8415 (ttpp) REVERT: As 181 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7008 (mtm) outliers start: 85 outliers final: 22 residues processed: 755 average time/residue: 0.8638 time to fit residues: 720.2883 Evaluate side-chains 766 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 734 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 121 GLU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ad residue 181 MET Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Ag residue 48 LYS Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Aj residue 116 MET Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 116 MET Chi-restraints excluded: chain Ao residue 110 THR Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 181 MET Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 181 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 69 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 234 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ae 77 GLN Ae 158 GLN Af 113 ASN Ag 113 ASN Ah 113 ASN Ai 113 ASN Aj 113 ASN Al 113 ASN Am 113 ASN As 113 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.157894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132532 restraints weight = 24495.450| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.03 r_work: 0.3332 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 22914 Z= 0.246 Angle : 0.618 7.157 31103 Z= 0.313 Chirality : 0.045 0.171 3420 Planarity : 0.005 0.038 4009 Dihedral : 4.406 15.925 3040 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.41 % Allowed : 23.81 % Favored : 71.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -0.10 (0.16), residues: 2755 helix: 1.46 (0.15), residues: 988 sheet: 1.34 (0.33), residues: 228 loop : -1.40 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAc 55 TYR 0.020 0.002 TYRAs 180 PHE 0.016 0.003 PHEAi 163 TRP 0.012 0.002 TRPAf 132 HIS 0.002 0.001 HISAr 69 Details of bonding type rmsd covalent geometry : bond 0.00617 (22914) covalent geometry : angle 0.61846 (31103) hydrogen bonds : bond 0.04637 ( 874) hydrogen bonds : angle 4.37286 ( 2565) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 785 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 160 MET cc_start: 0.9134 (mmp) cc_final: 0.8887 (mmt) REVERT: Aa 177 LYS cc_start: 0.8195 (mtpm) cc_final: 0.7504 (mptt) REVERT: Aa 181 MET cc_start: 0.7572 (OUTLIER) cc_final: 0.6906 (mtm) REVERT: Ab 99 LEU cc_start: 0.8615 (tt) cc_final: 0.8280 (tp) REVERT: Ab 108 MET cc_start: 0.9015 (tpt) cc_final: 0.8718 (mmp) REVERT: Ab 113 ASN cc_start: 0.9040 (m110) cc_final: 0.8809 (m-40) REVERT: Ab 121 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: Ab 168 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7618 (mt-10) REVERT: Ab 173 MET cc_start: 0.8142 (ttp) cc_final: 0.7830 (ttp) REVERT: Ac 88 SER cc_start: 0.8792 (p) cc_final: 0.8493 (p) REVERT: Ac 173 MET cc_start: 0.7984 (ttp) cc_final: 0.7429 (ttp) REVERT: Ac 177 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7602 (mptt) REVERT: Ac 181 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6995 (mtm) REVERT: Ad 60 LYS cc_start: 0.8782 (mptt) cc_final: 0.8437 (mmtm) REVERT: Ad 91 ASP cc_start: 0.8687 (m-30) cc_final: 0.8315 (m-30) REVERT: Ad 95 GLU cc_start: 0.8460 (mp0) cc_final: 0.7918 (mp0) REVERT: Ad 139 GLU cc_start: 0.8164 (pt0) cc_final: 0.7837 (tt0) REVERT: Ad 173 MET cc_start: 0.7998 (ttp) cc_final: 0.7749 (ttp) REVERT: Ad 181 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7054 (mtm) REVERT: Ae 95 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: Ae 173 MET cc_start: 0.8283 (ttp) cc_final: 0.8040 (ttp) REVERT: Ae 181 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.7024 (mtt) REVERT: Af 46 ARG cc_start: 0.9285 (mpt180) cc_final: 0.8947 (mpt180) REVERT: Af 69 HIS cc_start: 0.8092 (m-70) cc_final: 0.6429 (t70) REVERT: Af 95 GLU cc_start: 0.8590 (mp0) cc_final: 0.8270 (mp0) REVERT: Af 168 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7720 (mt-10) REVERT: Af 172 GLU cc_start: 0.7329 (mt-10) cc_final: 0.7065 (mm-30) REVERT: Af 173 MET cc_start: 0.8025 (ttp) cc_final: 0.7753 (ttp) REVERT: Af 181 MET cc_start: 0.7440 (OUTLIER) cc_final: 0.6869 (mtm) REVERT: Ag 168 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7861 (mt-10) REVERT: Ag 175 ASN cc_start: 0.8486 (m-40) cc_final: 0.8228 (m-40) REVERT: Ag 177 LYS cc_start: 0.8138 (mtpp) cc_final: 0.7517 (mptt) REVERT: Ag 181 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7073 (mtm) REVERT: Ah 76 GLN cc_start: 0.8701 (mt0) cc_final: 0.8304 (mt0) REVERT: Ah 91 ASP cc_start: 0.8850 (m-30) cc_final: 0.8585 (m-30) REVERT: Ah 173 MET cc_start: 0.8097 (ttp) cc_final: 0.7582 (ttt) REVERT: Ah 177 LYS cc_start: 0.8242 (mtpp) cc_final: 0.7687 (mptt) REVERT: Ah 181 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7028 (mtm) REVERT: Ai 67 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8656 (mp) REVERT: Ai 99 LEU cc_start: 0.8655 (tt) cc_final: 0.8262 (tp) REVERT: Ai 121 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7914 (tp30) REVERT: Ai 168 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7737 (mt-10) REVERT: Ai 173 MET cc_start: 0.8312 (ttp) cc_final: 0.7897 (ttt) REVERT: Aj 177 LYS cc_start: 0.8249 (mtpp) cc_final: 0.7720 (mptt) REVERT: Aj 181 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6890 (mtm) REVERT: Ak 173 MET cc_start: 0.8014 (ttp) cc_final: 0.7412 (ttt) REVERT: Ak 177 LYS cc_start: 0.8173 (mtpp) cc_final: 0.7527 (mptt) REVERT: Ak 181 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.6902 (mtt) REVERT: Al 139 GLU cc_start: 0.8098 (pt0) cc_final: 0.7877 (tt0) REVERT: Al 172 GLU cc_start: 0.7259 (mt-10) cc_final: 0.7006 (mm-30) REVERT: Am 168 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7895 (mt-10) REVERT: Am 173 MET cc_start: 0.8246 (ttp) cc_final: 0.7968 (ttp) REVERT: Am 177 LYS cc_start: 0.8263 (mtpp) cc_final: 0.7961 (mtmm) REVERT: An 67 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8552 (mp) REVERT: An 99 LEU cc_start: 0.8428 (tt) cc_final: 0.8071 (tp) REVERT: An 102 ASP cc_start: 0.8740 (t0) cc_final: 0.8321 (t0) REVERT: An 121 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7871 (tp30) REVERT: An 139 GLU cc_start: 0.8050 (pt0) cc_final: 0.7841 (tt0) REVERT: An 173 MET cc_start: 0.8087 (ttp) cc_final: 0.7544 (ttt) REVERT: An 175 ASN cc_start: 0.8389 (m-40) cc_final: 0.8127 (m-40) REVERT: An 177 LYS cc_start: 0.8360 (mtpp) cc_final: 0.8073 (mtmm) REVERT: Ao 67 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8572 (mp) REVERT: Ao 91 ASP cc_start: 0.8846 (m-30) cc_final: 0.8604 (m-30) REVERT: Ao 121 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7406 (tm-30) REVERT: Ao 153 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7595 (mptp) REVERT: Ao 173 MET cc_start: 0.8063 (ttp) cc_final: 0.7617 (ttt) REVERT: Ap 60 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7280 (mptt) REVERT: Ap 116 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8882 (ttp) REVERT: Ap 173 MET cc_start: 0.8177 (ttp) cc_final: 0.7769 (ttt) REVERT: Ap 181 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7107 (mtm) REVERT: Aq 54 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7405 (ttt) REVERT: Aq 60 LYS cc_start: 0.8442 (mmtt) cc_final: 0.8070 (mmtm) REVERT: Aq 112 MET cc_start: 0.9339 (mmp) cc_final: 0.9017 (mmp) REVERT: Aq 153 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.7505 (mptp) REVERT: Aq 181 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7097 (mtm) REVERT: Ar 99 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8325 (tp) REVERT: Ar 135 MET cc_start: 0.9194 (mmm) cc_final: 0.8860 (mmm) REVERT: Ar 168 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7883 (mt-10) REVERT: Ar 173 MET cc_start: 0.8189 (ttp) cc_final: 0.7771 (ttt) REVERT: As 139 GLU cc_start: 0.7976 (pt0) cc_final: 0.7771 (tt0) REVERT: As 153 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.7440 (mptp) REVERT: As 181 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6885 (mtm) outliers start: 109 outliers final: 34 residues processed: 808 average time/residue: 0.8525 time to fit residues: 760.9244 Evaluate side-chains 841 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 782 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 181 MET Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 121 GLU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 181 MET Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 181 MET Chi-restraints excluded: chain Ae residue 67 LEU Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 95 GLU Chi-restraints excluded: chain Ae residue 181 MET Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 181 MET Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 95 GLU Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 181 MET Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 67 LEU Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 116 MET Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Aj residue 181 MET Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Al residue 178 GLU Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 67 LEU Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain Ao residue 67 LEU Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 110 THR Chi-restraints excluded: chain Ao residue 121 GLU Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Ap residue 181 MET Chi-restraints excluded: chain Aq residue 54 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 181 MET Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 153 LYS Chi-restraints excluded: chain As residue 181 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 236 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 143 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 42 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 113 ASN Ae 77 GLN Ae 113 ASN Ae 151 ASN Af 113 ASN Ag 113 ASN Ah 113 ASN Aj 113 ASN ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 113 ASN Ap 113 ASN Aq 113 ASN As 113 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.159853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.134661 restraints weight = 24422.321| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.03 r_work: 0.3355 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22914 Z= 0.170 Angle : 0.556 6.553 31103 Z= 0.281 Chirality : 0.042 0.175 3420 Planarity : 0.005 0.037 4009 Dihedral : 4.172 16.096 3040 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.49 % Allowed : 24.01 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.07 (0.16), residues: 2755 helix: 1.64 (0.15), residues: 988 sheet: 1.13 (0.33), residues: 228 loop : -1.27 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAe 55 TYR 0.017 0.002 TYRAl 180 PHE 0.014 0.002 PHEAi 163 TRP 0.013 0.002 TRPAf 132 HIS 0.002 0.000 HISAa 69 Details of bonding type rmsd covalent geometry : bond 0.00428 (22914) covalent geometry : angle 0.55632 (31103) hydrogen bonds : bond 0.04055 ( 874) hydrogen bonds : angle 4.29701 ( 2565) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 763 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 160 MET cc_start: 0.9116 (mmp) cc_final: 0.8767 (mmt) REVERT: Aa 173 MET cc_start: 0.8032 (ttp) cc_final: 0.7582 (ttt) REVERT: Aa 177 LYS cc_start: 0.8208 (mtpm) cc_final: 0.7643 (mptt) REVERT: Aa 181 MET cc_start: 0.7571 (mmt) cc_final: 0.6970 (mtt) REVERT: Ab 99 LEU cc_start: 0.8625 (tt) cc_final: 0.8282 (tp) REVERT: Ab 108 MET cc_start: 0.9030 (tpt) cc_final: 0.8702 (mmp) REVERT: Ab 113 ASN cc_start: 0.8906 (m110) cc_final: 0.8600 (m110) REVERT: Ab 121 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: Ab 173 MET cc_start: 0.8056 (ttp) cc_final: 0.7741 (ttp) REVERT: Ac 173 MET cc_start: 0.7953 (ttp) cc_final: 0.7579 (ttp) REVERT: Ac 177 LYS cc_start: 0.8158 (mtpp) cc_final: 0.7580 (mptt) REVERT: Ac 181 MET cc_start: 0.7612 (mmt) cc_final: 0.6984 (mtm) REVERT: Ad 60 LYS cc_start: 0.8803 (mptt) cc_final: 0.8455 (mmtm) REVERT: Ad 95 GLU cc_start: 0.8475 (mp0) cc_final: 0.7967 (mp0) REVERT: Ad 139 GLU cc_start: 0.8213 (pt0) cc_final: 0.7840 (tt0) REVERT: Ad 173 MET cc_start: 0.7957 (ttp) cc_final: 0.7689 (ttp) REVERT: Ad 181 MET cc_start: 0.7508 (OUTLIER) cc_final: 0.7019 (mtt) REVERT: Ae 95 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: Ae 173 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7983 (ttp) REVERT: Af 69 HIS cc_start: 0.8087 (m-70) cc_final: 0.6405 (t70) REVERT: Af 95 GLU cc_start: 0.8576 (mp0) cc_final: 0.8303 (mp0) REVERT: Af 168 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7897 (mt-10) REVERT: Af 172 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7038 (mm-30) REVERT: Af 181 MET cc_start: 0.7418 (OUTLIER) cc_final: 0.6807 (mtm) REVERT: Ag 116 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8884 (tmm) REVERT: Ag 168 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7813 (mt-10) REVERT: Ag 175 ASN cc_start: 0.8486 (m-40) cc_final: 0.8283 (m-40) REVERT: Ag 177 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7514 (mptt) REVERT: Ag 181 MET cc_start: 0.7728 (OUTLIER) cc_final: 0.7075 (mtt) REVERT: Ah 76 GLN cc_start: 0.8667 (mt0) cc_final: 0.8334 (mt0) REVERT: Ah 173 MET cc_start: 0.8091 (ttp) cc_final: 0.7534 (ttt) REVERT: Ah 177 LYS cc_start: 0.8181 (mtpp) cc_final: 0.7683 (mptt) REVERT: Ah 181 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.6970 (mtt) REVERT: Ai 99 LEU cc_start: 0.8678 (tt) cc_final: 0.8283 (tp) REVERT: Ai 121 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7860 (tp30) REVERT: Ai 168 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7714 (mt-10) REVERT: Ai 173 MET cc_start: 0.8265 (ttp) cc_final: 0.7789 (ttt) REVERT: Ai 175 ASN cc_start: 0.8499 (m-40) cc_final: 0.8292 (m-40) REVERT: Ai 177 LYS cc_start: 0.8267 (mtpm) cc_final: 0.7794 (mptt) REVERT: Aj 172 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7296 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8195 (mtpp) cc_final: 0.7708 (mptt) REVERT: Aj 181 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6888 (mtm) REVERT: Ak 67 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8618 (mp) REVERT: Ak 142 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8126 (mt-10) REVERT: Ak 173 MET cc_start: 0.7951 (ttp) cc_final: 0.7350 (ttt) REVERT: Ak 177 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7531 (mptt) REVERT: Ak 181 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6920 (mtt) REVERT: Al 139 GLU cc_start: 0.8183 (pt0) cc_final: 0.7897 (tt0) REVERT: Al 172 GLU cc_start: 0.7237 (mt-10) cc_final: 0.6978 (mm-30) REVERT: Al 177 LYS cc_start: 0.8058 (mtpm) cc_final: 0.7552 (mptt) REVERT: Am 139 GLU cc_start: 0.8091 (tt0) cc_final: 0.7803 (tt0) REVERT: Am 168 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7905 (mt-10) REVERT: An 67 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8543 (mp) REVERT: An 91 ASP cc_start: 0.8643 (m-30) cc_final: 0.8330 (m-30) REVERT: An 95 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: An 99 LEU cc_start: 0.8445 (tt) cc_final: 0.8101 (tp) REVERT: An 102 ASP cc_start: 0.8766 (t0) cc_final: 0.8324 (t0) REVERT: An 121 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7896 (tp30) REVERT: An 139 GLU cc_start: 0.8122 (pt0) cc_final: 0.7821 (tt0) REVERT: An 153 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8555 (mmtm) REVERT: An 173 MET cc_start: 0.7917 (ttp) cc_final: 0.7499 (ttt) REVERT: An 175 ASN cc_start: 0.8335 (m-40) cc_final: 0.8077 (m-40) REVERT: Ao 91 ASP cc_start: 0.8840 (m-30) cc_final: 0.8611 (m-30) REVERT: Ao 139 GLU cc_start: 0.8117 (pt0) cc_final: 0.7814 (tt0) REVERT: Ao 153 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.7518 (mptp) REVERT: Ao 173 MET cc_start: 0.7955 (ttp) cc_final: 0.7415 (ttt) REVERT: Ao 177 LYS cc_start: 0.8269 (mtpm) cc_final: 0.7946 (mtmm) REVERT: Ap 60 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7247 (mptt) REVERT: Ap 99 LEU cc_start: 0.8465 (tt) cc_final: 0.7968 (mt) REVERT: Ap 116 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8777 (ttp) REVERT: Ap 173 MET cc_start: 0.8063 (ttp) cc_final: 0.7640 (ttt) REVERT: Ap 181 MET cc_start: 0.7647 (OUTLIER) cc_final: 0.7048 (mtm) REVERT: Aq 60 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8076 (mmtm) REVERT: Aq 67 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8077 (mp) REVERT: Aq 112 MET cc_start: 0.9304 (mmp) cc_final: 0.9076 (mmp) REVERT: Aq 153 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.7500 (mptp) REVERT: Aq 177 LYS cc_start: 0.8177 (mtpm) cc_final: 0.7621 (mptt) REVERT: Aq 181 MET cc_start: 0.7554 (OUTLIER) cc_final: 0.7121 (mtm) REVERT: Ar 77 GLN cc_start: 0.8549 (mt0) cc_final: 0.7594 (mp-120) REVERT: Ar 99 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8343 (tp) REVERT: Ar 135 MET cc_start: 0.9212 (mmm) cc_final: 0.8770 (mmm) REVERT: Ar 168 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7862 (mt-10) REVERT: Ar 173 MET cc_start: 0.8162 (ttp) cc_final: 0.7735 (ttt) REVERT: As 139 GLU cc_start: 0.8014 (pt0) cc_final: 0.7760 (tm-30) REVERT: As 181 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6972 (mtm) outliers start: 111 outliers final: 39 residues processed: 801 average time/residue: 0.7311 time to fit residues: 649.8149 Evaluate side-chains 823 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 761 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 121 GLU Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ad residue 181 MET Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 95 GLU Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 173 MET Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 181 MET Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 95 GLU Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 181 MET Chi-restraints excluded: chain Ah residue 48 LYS Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 67 LEU Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 116 MET Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Aj residue 181 MET Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 67 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 67 LEU Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 110 THR Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Ap residue 181 MET Chi-restraints excluded: chain Aq residue 67 LEU Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 181 MET Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 181 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 94 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 113 ASN Ad 113 ASN Ae 77 GLN Ae 113 ASN Af 113 ASN Ag 113 ASN Ah 113 ASN Aj 113 ASN ** Al 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 113 ASN Aq 113 ASN As 113 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.158412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133134 restraints weight = 24442.248| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.04 r_work: 0.3335 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22914 Z= 0.198 Angle : 0.579 6.438 31103 Z= 0.292 Chirality : 0.043 0.167 3420 Planarity : 0.005 0.040 4009 Dihedral : 4.280 16.292 3040 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.78 % Allowed : 24.05 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.03 (0.16), residues: 2755 helix: 1.57 (0.15), residues: 988 sheet: 1.03 (0.32), residues: 228 loop : -1.25 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAe 55 TYR 0.018 0.002 TYRAr 180 PHE 0.013 0.002 PHEAi 163 TRP 0.012 0.002 TRPAf 132 HIS 0.003 0.001 HISAc 69 Details of bonding type rmsd covalent geometry : bond 0.00496 (22914) covalent geometry : angle 0.57908 (31103) hydrogen bonds : bond 0.04250 ( 874) hydrogen bonds : angle 4.29307 ( 2565) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 757 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 67 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8479 (mp) REVERT: Aa 160 MET cc_start: 0.9114 (mmp) cc_final: 0.8817 (mmt) REVERT: Aa 173 MET cc_start: 0.8035 (ttp) cc_final: 0.7555 (ttt) REVERT: Aa 177 LYS cc_start: 0.8201 (mtpm) cc_final: 0.7602 (mptt) REVERT: Aa 181 MET cc_start: 0.7580 (OUTLIER) cc_final: 0.6952 (mtt) REVERT: Ab 99 LEU cc_start: 0.8620 (tt) cc_final: 0.8282 (tp) REVERT: Ab 108 MET cc_start: 0.9034 (tpt) cc_final: 0.8699 (mmp) REVERT: Ab 113 ASN cc_start: 0.8975 (m110) cc_final: 0.8644 (m110) REVERT: Ab 121 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7666 (tm-30) REVERT: Ab 173 MET cc_start: 0.8094 (ttp) cc_final: 0.7802 (ttp) REVERT: Ac 173 MET cc_start: 0.7986 (ttp) cc_final: 0.7615 (ttp) REVERT: Ac 177 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7562 (mptt) REVERT: Ac 181 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.6946 (mtm) REVERT: Ad 95 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: Ad 139 GLU cc_start: 0.8233 (pt0) cc_final: 0.7844 (tt0) REVERT: Ad 173 MET cc_start: 0.7976 (ttp) cc_final: 0.7704 (ttp) REVERT: Ad 181 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7025 (mtt) REVERT: Ae 173 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.8015 (ttp) REVERT: Af 69 HIS cc_start: 0.8130 (m-70) cc_final: 0.6424 (t70) REVERT: Af 95 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: Af 168 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7697 (mt-10) REVERT: Af 172 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6989 (mm-30) REVERT: Af 181 MET cc_start: 0.7472 (OUTLIER) cc_final: 0.6852 (mtm) REVERT: Ag 116 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8846 (tmm) REVERT: Ag 168 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7835 (mt-10) REVERT: Ag 175 ASN cc_start: 0.8518 (m-40) cc_final: 0.8289 (m-40) REVERT: Ag 177 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7533 (mptt) REVERT: Ag 181 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7115 (mtt) REVERT: Ah 76 GLN cc_start: 0.8670 (mt0) cc_final: 0.8322 (mt0) REVERT: Ah 139 GLU cc_start: 0.7980 (pt0) cc_final: 0.7709 (tt0) REVERT: Ah 173 MET cc_start: 0.8148 (ttp) cc_final: 0.7623 (ttt) REVERT: Ah 177 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7665 (mptt) REVERT: Ah 181 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7007 (mtt) REVERT: Ai 99 LEU cc_start: 0.8660 (tt) cc_final: 0.8275 (tp) REVERT: Ai 168 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7719 (mt-10) REVERT: Ai 173 MET cc_start: 0.8309 (ttp) cc_final: 0.7842 (ttt) REVERT: Ai 177 LYS cc_start: 0.8297 (mtpm) cc_final: 0.7807 (mptt) REVERT: Aj 172 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7274 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7715 (mptt) REVERT: Aj 181 MET cc_start: 0.7370 (OUTLIER) cc_final: 0.6908 (mtm) REVERT: Ak 67 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8634 (mp) REVERT: Ak 173 MET cc_start: 0.8006 (ttp) cc_final: 0.7282 (ttt) REVERT: Ak 177 LYS cc_start: 0.8129 (mtpp) cc_final: 0.7400 (mptt) REVERT: Ak 181 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6906 (mtm) REVERT: Al 139 GLU cc_start: 0.8177 (pt0) cc_final: 0.7805 (tt0) REVERT: Al 172 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6993 (mm-30) REVERT: Al 177 LYS cc_start: 0.8115 (mtpm) cc_final: 0.7606 (mptt) REVERT: Am 139 GLU cc_start: 0.8103 (tt0) cc_final: 0.7834 (tt0) REVERT: Am 168 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7923 (mt-10) REVERT: Am 177 LYS cc_start: 0.8170 (mtpm) cc_final: 0.7525 (mptt) REVERT: An 91 ASP cc_start: 0.8718 (m-30) cc_final: 0.8403 (m-30) REVERT: An 95 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: An 99 LEU cc_start: 0.8503 (tt) cc_final: 0.8136 (tp) REVERT: An 102 ASP cc_start: 0.8761 (t0) cc_final: 0.8311 (t0) REVERT: An 121 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7894 (tp30) REVERT: An 135 MET cc_start: 0.9154 (mmm) cc_final: 0.8854 (mmm) REVERT: An 139 GLU cc_start: 0.8193 (pt0) cc_final: 0.7777 (tm-30) REVERT: An 153 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8571 (mmtm) REVERT: An 173 MET cc_start: 0.8009 (ttp) cc_final: 0.7466 (ttt) REVERT: An 175 ASN cc_start: 0.8349 (m-40) cc_final: 0.8098 (m-40) REVERT: An 177 LYS cc_start: 0.8280 (mtpm) cc_final: 0.7683 (mptt) REVERT: Ao 91 ASP cc_start: 0.8854 (m-30) cc_final: 0.8629 (m-30) REVERT: Ao 139 GLU cc_start: 0.8156 (pt0) cc_final: 0.7787 (tt0) REVERT: Ao 153 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.7530 (mptp) REVERT: Ao 173 MET cc_start: 0.7984 (ttp) cc_final: 0.7387 (ttt) REVERT: Ao 177 LYS cc_start: 0.8317 (mtpm) cc_final: 0.7914 (mtmm) REVERT: Ap 60 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.7333 (mptt) REVERT: Ap 116 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8837 (ttp) REVERT: Ap 139 GLU cc_start: 0.8210 (pt0) cc_final: 0.7901 (tt0) REVERT: Ap 173 MET cc_start: 0.8139 (ttp) cc_final: 0.7732 (ttt) REVERT: Ap 181 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7072 (mtm) REVERT: Aq 60 LYS cc_start: 0.8443 (mmtt) cc_final: 0.8063 (mmtm) REVERT: Aq 67 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8164 (mp) REVERT: Aq 153 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.7510 (mptp) REVERT: Aq 177 LYS cc_start: 0.8156 (mtpm) cc_final: 0.7525 (mptt) REVERT: Aq 181 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.6989 (mtm) REVERT: Ar 77 GLN cc_start: 0.8521 (mt0) cc_final: 0.7439 (mp-120) REVERT: Ar 99 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8327 (tp) REVERT: Ar 135 MET cc_start: 0.9218 (mmm) cc_final: 0.8774 (mmm) REVERT: Ar 168 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7854 (mt-10) REVERT: Ar 173 MET cc_start: 0.8134 (ttp) cc_final: 0.7555 (ttt) REVERT: Ar 177 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7583 (mptt) REVERT: As 139 GLU cc_start: 0.8028 (pt0) cc_final: 0.7724 (tt0) REVERT: As 153 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.7424 (mptp) REVERT: As 181 MET cc_start: 0.7407 (OUTLIER) cc_final: 0.7018 (mtm) outliers start: 118 outliers final: 54 residues processed: 798 average time/residue: 0.7614 time to fit residues: 672.9498 Evaluate side-chains 839 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 758 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 67 LEU Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 181 MET Chi-restraints excluded: chain Ab residue 67 LEU Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 121 GLU Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 181 MET Chi-restraints excluded: chain Ac residue 187 VAL Chi-restraints excluded: chain Ad residue 95 GLU Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 181 MET Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 173 MET Chi-restraints excluded: chain Ae residue 181 MET Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 95 GLU Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 160 MET Chi-restraints excluded: chain Af residue 181 MET Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 95 GLU Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 181 MET Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 67 LEU Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 95 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 116 MET Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Aj residue 181 MET Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 67 LEU Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 58 LYS Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 67 LEU Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 110 THR Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 71 LEU Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Ap residue 181 MET Chi-restraints excluded: chain Aq residue 67 LEU Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 181 MET Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 153 LYS Chi-restraints excluded: chain As residue 181 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 23 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 187 optimal weight: 6.9990 chunk 170 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 136 optimal weight: 0.2980 chunk 246 optimal weight: 10.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 113 ASN Ae 77 GLN Af 113 ASN Ag 113 ASN ** Ah 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 113 ASN ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ap 113 ASN Aq 113 ASN As 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.159005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.133822 restraints weight = 24425.014| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.03 r_work: 0.3342 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 22914 Z= 0.180 Angle : 0.565 6.045 31103 Z= 0.285 Chirality : 0.042 0.188 3420 Planarity : 0.005 0.042 4009 Dihedral : 4.220 16.425 3040 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.57 % Allowed : 23.89 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.11 (0.16), residues: 2755 helix: 1.62 (0.15), residues: 988 sheet: 0.96 (0.32), residues: 228 loop : -1.17 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAm 55 TYR 0.017 0.002 TYRAl 180 PHE 0.013 0.002 PHEAi 163 TRP 0.012 0.002 TRPAf 132 HIS 0.004 0.001 HISAg 69 Details of bonding type rmsd covalent geometry : bond 0.00451 (22914) covalent geometry : angle 0.56478 (31103) hydrogen bonds : bond 0.04106 ( 874) hydrogen bonds : angle 4.26385 ( 2565) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 752 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 160 MET cc_start: 0.9119 (mmp) cc_final: 0.8813 (mmt) REVERT: Aa 173 MET cc_start: 0.7991 (ttp) cc_final: 0.7493 (ttt) REVERT: Aa 177 LYS cc_start: 0.8277 (mtpm) cc_final: 0.7623 (mptt) REVERT: Aa 181 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.6980 (mtt) REVERT: Ab 99 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8278 (tp) REVERT: Ab 108 MET cc_start: 0.9030 (tpt) cc_final: 0.8702 (mmp) REVERT: Ab 113 ASN cc_start: 0.8951 (m110) cc_final: 0.8635 (m110) REVERT: Ab 121 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7660 (tm-30) REVERT: Ab 173 MET cc_start: 0.8103 (ttp) cc_final: 0.7822 (ttp) REVERT: Ac 60 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8324 (mptt) REVERT: Ac 69 HIS cc_start: 0.7882 (m-70) cc_final: 0.7680 (m-70) REVERT: Ac 108 MET cc_start: 0.9041 (tpt) cc_final: 0.8748 (mmt) REVERT: Ac 139 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: Ac 142 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8277 (mp0) REVERT: Ac 173 MET cc_start: 0.7968 (ttp) cc_final: 0.7592 (ttp) REVERT: Ac 177 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7558 (mptt) REVERT: Ac 181 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.6958 (mtm) REVERT: Ad 91 ASP cc_start: 0.8711 (m-30) cc_final: 0.8468 (m-30) REVERT: Ad 95 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: Ad 181 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7011 (mtt) REVERT: Ae 173 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.8024 (ttp) REVERT: Ae 181 MET cc_start: 0.7617 (OUTLIER) cc_final: 0.6933 (mtt) REVERT: Af 69 HIS cc_start: 0.8150 (m-70) cc_final: 0.6454 (t70) REVERT: Af 95 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: Af 172 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6967 (mm-30) REVERT: Af 181 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6842 (mtm) REVERT: Ag 116 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8835 (tmm) REVERT: Ag 168 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7828 (mt-10) REVERT: Ag 175 ASN cc_start: 0.8500 (m-40) cc_final: 0.8279 (m-40) REVERT: Ag 177 LYS cc_start: 0.8117 (mtpp) cc_final: 0.7540 (mptt) REVERT: Ag 181 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7106 (mtt) REVERT: Ah 76 GLN cc_start: 0.8686 (mt0) cc_final: 0.8314 (mt0) REVERT: Ah 139 GLU cc_start: 0.8022 (pt0) cc_final: 0.7723 (tt0) REVERT: Ah 173 MET cc_start: 0.8095 (ttp) cc_final: 0.7544 (ttt) REVERT: Ah 177 LYS cc_start: 0.8128 (mtpp) cc_final: 0.7623 (mptt) REVERT: Ah 181 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.6967 (mtt) REVERT: Ai 99 LEU cc_start: 0.8661 (tt) cc_final: 0.8267 (tp) REVERT: Ai 121 GLU cc_start: 0.8239 (tp30) cc_final: 0.7747 (tp30) REVERT: Ai 168 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7710 (mt-10) REVERT: Ai 173 MET cc_start: 0.8276 (ttp) cc_final: 0.7814 (ttt) REVERT: Ai 177 LYS cc_start: 0.8286 (mtpm) cc_final: 0.7775 (mptt) REVERT: Ai 181 MET cc_start: 0.7397 (tpt) cc_final: 0.6903 (mtt) REVERT: Aj 172 GLU cc_start: 0.7607 (mm-30) cc_final: 0.7232 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8207 (mtpp) cc_final: 0.7710 (mptt) REVERT: Aj 181 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6900 (mtm) REVERT: Ak 67 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8607 (mp) REVERT: Ak 99 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8246 (tp) REVERT: Ak 177 LYS cc_start: 0.8097 (mtpp) cc_final: 0.7394 (mptt) REVERT: Ak 181 MET cc_start: 0.7585 (OUTLIER) cc_final: 0.6918 (mtm) REVERT: Al 139 GLU cc_start: 0.8181 (pt0) cc_final: 0.7779 (tt0) REVERT: Al 172 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6990 (mm-30) REVERT: Al 177 LYS cc_start: 0.8074 (mtpm) cc_final: 0.7553 (mptt) REVERT: Am 139 GLU cc_start: 0.8093 (tt0) cc_final: 0.7820 (tt0) REVERT: Am 168 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7906 (mt-10) REVERT: Am 177 LYS cc_start: 0.8151 (mtpm) cc_final: 0.7629 (mppt) REVERT: An 95 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8010 (mp0) REVERT: An 99 LEU cc_start: 0.8518 (tt) cc_final: 0.8163 (tp) REVERT: An 121 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7810 (tp30) REVERT: An 139 GLU cc_start: 0.8220 (pt0) cc_final: 0.7776 (tm-30) REVERT: An 153 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8593 (mmtm) REVERT: An 173 MET cc_start: 0.7899 (ttp) cc_final: 0.7399 (ttt) REVERT: An 175 ASN cc_start: 0.8325 (m-40) cc_final: 0.8086 (m-40) REVERT: An 177 LYS cc_start: 0.8295 (mtpm) cc_final: 0.7758 (mppt) REVERT: Ao 91 ASP cc_start: 0.8856 (m-30) cc_final: 0.8628 (m-30) REVERT: Ao 139 GLU cc_start: 0.8116 (pt0) cc_final: 0.7745 (tt0) REVERT: Ao 153 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.7508 (mptp) REVERT: Ao 173 MET cc_start: 0.7941 (ttp) cc_final: 0.7352 (ttt) REVERT: Ao 177 LYS cc_start: 0.8314 (mtpm) cc_final: 0.7913 (mtmm) REVERT: Ao 181 MET cc_start: 0.7540 (tpt) cc_final: 0.7307 (tpp) REVERT: Ap 60 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7231 (mptt) REVERT: Ap 116 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8816 (ttp) REVERT: Ap 139 GLU cc_start: 0.8207 (pt0) cc_final: 0.7884 (tt0) REVERT: Ap 173 MET cc_start: 0.8125 (ttp) cc_final: 0.7715 (ttt) REVERT: Ap 181 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7123 (mtm) REVERT: Aq 60 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8191 (mmtm) REVERT: Aq 67 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8220 (mp) REVERT: Aq 153 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.7484 (mptp) REVERT: Aq 177 LYS cc_start: 0.8222 (mtpm) cc_final: 0.7601 (mptt) REVERT: Aq 181 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.7029 (mtm) REVERT: Ar 77 GLN cc_start: 0.8570 (mt0) cc_final: 0.7569 (mp-120) REVERT: Ar 99 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8318 (tp) REVERT: Ar 135 MET cc_start: 0.9230 (mmm) cc_final: 0.8720 (mmm) REVERT: Ar 168 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7845 (mt-10) REVERT: Ar 173 MET cc_start: 0.8135 (ttp) cc_final: 0.7598 (ttt) REVERT: Ar 177 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7691 (mptt) REVERT: As 139 GLU cc_start: 0.8047 (pt0) cc_final: 0.7716 (tt0) REVERT: As 153 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.7423 (mptp) REVERT: As 181 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.7128 (mtt) outliers start: 113 outliers final: 54 residues processed: 790 average time/residue: 0.6835 time to fit residues: 599.1999 Evaluate side-chains 836 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 751 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 181 MET Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 121 GLU Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 60 LYS Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 139 GLU Chi-restraints excluded: chain Ac residue 181 MET Chi-restraints excluded: chain Ac residue 187 VAL Chi-restraints excluded: chain Ad residue 95 GLU Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ad residue 181 MET Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 173 MET Chi-restraints excluded: chain Ae residue 181 MET Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 95 GLU Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 160 MET Chi-restraints excluded: chain Af residue 181 MET Chi-restraints excluded: chain Af residue 187 VAL Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 95 GLU Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 181 MET Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 95 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 116 MET Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Aj residue 181 MET Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 67 LEU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 99 LEU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 48 LYS Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 110 THR Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Ap residue 181 MET Chi-restraints excluded: chain Aq residue 67 LEU Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 181 MET Chi-restraints excluded: chain Ar residue 67 LEU Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 153 LYS Chi-restraints excluded: chain As residue 181 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 42 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 195 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 127 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 113 ASN Af 113 ASN Ag 113 ASN Ah 113 ASN Aj 113 ASN Am 113 ASN Ap 113 ASN As 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.134239 restraints weight = 24325.576| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.03 r_work: 0.3348 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22914 Z= 0.167 Angle : 0.556 5.773 31103 Z= 0.281 Chirality : 0.042 0.175 3420 Planarity : 0.005 0.041 4009 Dihedral : 4.173 16.542 3040 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.17 % Allowed : 24.25 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.18 (0.16), residues: 2755 helix: 1.68 (0.15), residues: 988 sheet: 0.98 (0.31), residues: 228 loop : -1.12 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARGAb 55 TYR 0.016 0.001 TYRAl 180 PHE 0.013 0.002 PHEAi 163 TRP 0.012 0.002 TRPAf 132 HIS 0.002 0.000 HISAn 69 Details of bonding type rmsd covalent geometry : bond 0.00416 (22914) covalent geometry : angle 0.55552 (31103) hydrogen bonds : bond 0.03997 ( 874) hydrogen bonds : angle 4.26329 ( 2565) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 742 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 160 MET cc_start: 0.9121 (mmp) cc_final: 0.8730 (mmt) REVERT: Aa 173 MET cc_start: 0.7986 (ttp) cc_final: 0.7484 (ttt) REVERT: Aa 177 LYS cc_start: 0.8275 (mtpm) cc_final: 0.7605 (mptt) REVERT: Aa 181 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.7023 (mtt) REVERT: Ab 99 LEU cc_start: 0.8605 (tt) cc_final: 0.8282 (tp) REVERT: Ab 108 MET cc_start: 0.9059 (tpt) cc_final: 0.8750 (mmp) REVERT: Ab 113 ASN cc_start: 0.8905 (m110) cc_final: 0.8590 (m110) REVERT: Ab 173 MET cc_start: 0.8086 (ttp) cc_final: 0.7791 (ttp) REVERT: Ac 99 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8200 (tp) REVERT: Ac 108 MET cc_start: 0.9029 (tpt) cc_final: 0.8731 (mmt) REVERT: Ac 139 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7501 (tt0) REVERT: Ac 173 MET cc_start: 0.7874 (ttp) cc_final: 0.7461 (ttp) REVERT: Ac 177 LYS cc_start: 0.8162 (mtpp) cc_final: 0.7554 (mptt) REVERT: Ac 181 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.6949 (mtm) REVERT: Ad 91 ASP cc_start: 0.8697 (m-30) cc_final: 0.8471 (m-30) REVERT: Ad 95 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8012 (mp0) REVERT: Ad 121 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7844 (tm-30) REVERT: Ad 160 MET cc_start: 0.9280 (mmp) cc_final: 0.8765 (mmp) REVERT: Ad 181 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.6990 (mtt) REVERT: Ae 181 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.6897 (mtt) REVERT: Af 69 HIS cc_start: 0.8174 (m-70) cc_final: 0.6483 (t70) REVERT: Af 95 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8343 (mp0) REVERT: Af 172 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6904 (mm-30) REVERT: Af 181 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6838 (mtm) REVERT: Ag 116 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8896 (tmm) REVERT: Ag 168 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7817 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7553 (mptt) REVERT: Ag 181 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.7114 (mtt) REVERT: Ah 76 GLN cc_start: 0.8668 (mt0) cc_final: 0.8284 (mt0) REVERT: Ah 139 GLU cc_start: 0.8020 (pt0) cc_final: 0.7691 (tt0) REVERT: Ah 173 MET cc_start: 0.8059 (ttp) cc_final: 0.7508 (ttt) REVERT: Ah 177 LYS cc_start: 0.8108 (mtpp) cc_final: 0.7598 (mptt) REVERT: Ah 181 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.6970 (mtt) REVERT: Ai 69 HIS cc_start: 0.7888 (m-70) cc_final: 0.6161 (t-90) REVERT: Ai 99 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8269 (tp) REVERT: Ai 121 GLU cc_start: 0.8199 (tp30) cc_final: 0.7747 (tp30) REVERT: Ai 168 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7711 (mt-10) REVERT: Ai 173 MET cc_start: 0.8256 (ttp) cc_final: 0.7811 (ttt) REVERT: Ai 177 LYS cc_start: 0.8301 (mtpm) cc_final: 0.7837 (mptt) REVERT: Ai 181 MET cc_start: 0.7390 (tpt) cc_final: 0.6909 (mtt) REVERT: Aj 172 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7320 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8155 (mtpp) cc_final: 0.7657 (mptt) REVERT: Aj 181 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6930 (mtm) REVERT: Ak 67 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8592 (mp) REVERT: Ak 99 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8240 (tp) REVERT: Ak 181 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6911 (mtm) REVERT: Al 95 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8175 (mp0) REVERT: Al 172 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6964 (mm-30) REVERT: Al 177 LYS cc_start: 0.8068 (mtpm) cc_final: 0.7541 (mptt) REVERT: Am 139 GLU cc_start: 0.8107 (tt0) cc_final: 0.7840 (tt0) REVERT: Am 168 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7960 (mt-10) REVERT: Am 177 LYS cc_start: 0.8156 (mtpm) cc_final: 0.7630 (mppt) REVERT: An 95 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8044 (mp0) REVERT: An 99 LEU cc_start: 0.8488 (tt) cc_final: 0.8147 (tp) REVERT: An 102 ASP cc_start: 0.8778 (t0) cc_final: 0.8382 (t0) REVERT: An 121 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7817 (tp30) REVERT: An 139 GLU cc_start: 0.8246 (pt0) cc_final: 0.7771 (tm-30) REVERT: An 153 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8587 (mmtm) REVERT: An 173 MET cc_start: 0.7888 (ttp) cc_final: 0.7397 (ttt) REVERT: An 175 ASN cc_start: 0.8324 (m-40) cc_final: 0.8064 (m-40) REVERT: An 177 LYS cc_start: 0.8287 (mtpm) cc_final: 0.7748 (mppt) REVERT: Ao 91 ASP cc_start: 0.8873 (m-30) cc_final: 0.8646 (m-30) REVERT: Ao 121 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: Ao 139 GLU cc_start: 0.8104 (pt0) cc_final: 0.7717 (tt0) REVERT: Ao 153 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.7504 (mptp) REVERT: Ao 173 MET cc_start: 0.7926 (ttp) cc_final: 0.7333 (ttt) REVERT: Ao 177 LYS cc_start: 0.8321 (mtpm) cc_final: 0.7909 (mtmm) REVERT: Ap 60 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7172 (mptt) REVERT: Ap 116 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8774 (ttp) REVERT: Ap 139 GLU cc_start: 0.8196 (pt0) cc_final: 0.7874 (tt0) REVERT: Ap 173 MET cc_start: 0.8104 (ttp) cc_final: 0.7674 (ttt) REVERT: Ap 181 MET cc_start: 0.7656 (mmt) cc_final: 0.7114 (mtt) REVERT: Aq 60 LYS cc_start: 0.8418 (mmtt) cc_final: 0.8014 (mmtm) REVERT: Aq 153 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.7499 (mptp) REVERT: Aq 177 LYS cc_start: 0.8226 (mtpm) cc_final: 0.7613 (mptt) REVERT: Aq 181 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.6959 (mtm) REVERT: Ar 77 GLN cc_start: 0.8541 (mt0) cc_final: 0.7458 (mp-120) REVERT: Ar 99 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8319 (tp) REVERT: Ar 168 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7836 (mt-10) REVERT: Ar 173 MET cc_start: 0.8116 (ttp) cc_final: 0.7571 (ttt) REVERT: Ar 177 LYS cc_start: 0.8216 (mtmt) cc_final: 0.7659 (mptt) REVERT: As 121 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7716 (tm-30) REVERT: As 153 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.7421 (mptp) outliers start: 103 outliers final: 56 residues processed: 775 average time/residue: 0.7847 time to fit residues: 672.7985 Evaluate side-chains 823 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 739 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 181 MET Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 160 MET Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 139 GLU Chi-restraints excluded: chain Ac residue 181 MET Chi-restraints excluded: chain Ac residue 187 VAL Chi-restraints excluded: chain Ad residue 95 GLU Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ad residue 181 MET Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 181 MET Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 95 GLU Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 160 MET Chi-restraints excluded: chain Af residue 181 MET Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 95 GLU Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 181 MET Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 95 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 116 MET Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 175 ASN Chi-restraints excluded: chain Aj residue 181 MET Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 67 LEU Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 168 GLU Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 99 LEU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 48 LYS Chi-restraints excluded: chain Am residue 67 LEU Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 110 THR Chi-restraints excluded: chain Ao residue 121 GLU Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ao residue 187 VAL Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 181 MET Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 153 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 57 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 233 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 85 optimal weight: 9.9990 chunk 261 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 113 ASN Af 113 ASN Ag 113 ASN ** Ah 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 113 ASN ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 113 ASN As 113 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.160962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135696 restraints weight = 24399.729| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.06 r_work: 0.3366 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22914 Z= 0.139 Angle : 0.538 5.672 31103 Z= 0.272 Chirality : 0.041 0.166 3420 Planarity : 0.005 0.040 4009 Dihedral : 4.041 16.463 3040 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.81 % Allowed : 24.78 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.31 (0.16), residues: 2755 helix: 1.80 (0.15), residues: 988 sheet: 1.02 (0.32), residues: 228 loop : -1.04 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAe 55 TYR 0.017 0.001 TYRAg 180 PHE 0.011 0.002 PHEAi 163 TRP 0.013 0.002 TRPAf 132 HIS 0.004 0.000 HISAg 69 Details of bonding type rmsd covalent geometry : bond 0.00345 (22914) covalent geometry : angle 0.53793 (31103) hydrogen bonds : bond 0.03756 ( 874) hydrogen bonds : angle 4.22043 ( 2565) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 730 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 160 MET cc_start: 0.9030 (mmp) cc_final: 0.8654 (mmt) REVERT: Aa 173 MET cc_start: 0.7662 (ttp) cc_final: 0.7183 (ttt) REVERT: Aa 177 LYS cc_start: 0.8284 (mtpm) cc_final: 0.7560 (mptt) REVERT: Aa 181 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6967 (mtt) REVERT: Ab 99 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8213 (tp) REVERT: Ab 108 MET cc_start: 0.9014 (tpt) cc_final: 0.8727 (mmp) REVERT: Ab 160 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8752 (mmm) REVERT: Ab 173 MET cc_start: 0.7690 (ttp) cc_final: 0.7398 (ttp) REVERT: Ac 99 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8127 (tp) REVERT: Ac 108 MET cc_start: 0.8995 (tpt) cc_final: 0.8659 (mmp) REVERT: Ac 142 GLU cc_start: 0.8393 (mt-10) cc_final: 0.8055 (mp0) REVERT: Ac 173 MET cc_start: 0.7556 (ttp) cc_final: 0.7338 (ttp) REVERT: Ac 181 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6850 (mtm) REVERT: Ad 91 ASP cc_start: 0.8512 (m-30) cc_final: 0.8199 (m-30) REVERT: Ad 95 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7703 (mp0) REVERT: Ad 121 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7637 (tm-30) REVERT: Ad 160 MET cc_start: 0.9215 (mmp) cc_final: 0.8672 (mmt) REVERT: Ad 173 MET cc_start: 0.7593 (ttp) cc_final: 0.7225 (ttp) REVERT: Ad 177 LYS cc_start: 0.8276 (mtmt) cc_final: 0.7489 (mptt) REVERT: Ae 181 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6820 (mtt) REVERT: Af 69 HIS cc_start: 0.8165 (m-70) cc_final: 0.6563 (t70) REVERT: Af 95 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7903 (mp0) REVERT: Af 168 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7350 (mt-10) REVERT: Af 181 MET cc_start: 0.7222 (mmt) cc_final: 0.6821 (mtm) REVERT: Ag 116 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8828 (tmm) REVERT: Ag 168 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7479 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7486 (mptt) REVERT: Ah 69 HIS cc_start: 0.8132 (m-70) cc_final: 0.6742 (t-90) REVERT: Ah 139 GLU cc_start: 0.7821 (pt0) cc_final: 0.7569 (tt0) REVERT: Ah 173 MET cc_start: 0.7765 (ttp) cc_final: 0.7272 (ttt) REVERT: Ah 177 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7584 (mptt) REVERT: Ah 181 MET cc_start: 0.7537 (OUTLIER) cc_final: 0.6934 (mtt) REVERT: Ai 69 HIS cc_start: 0.7839 (m-70) cc_final: 0.6179 (t-90) REVERT: Ai 99 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8197 (tp) REVERT: Ai 121 GLU cc_start: 0.7988 (tp30) cc_final: 0.7608 (tp30) REVERT: Ai 168 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7437 (mt-10) REVERT: Ai 173 MET cc_start: 0.7927 (ttp) cc_final: 0.7477 (ttt) REVERT: Ai 177 LYS cc_start: 0.8185 (mtpm) cc_final: 0.7714 (mptt) REVERT: Ai 181 MET cc_start: 0.7168 (tpt) cc_final: 0.6942 (mtt) REVERT: Aj 69 HIS cc_start: 0.7941 (m90) cc_final: 0.7726 (m-70) REVERT: Aj 172 GLU cc_start: 0.7412 (mm-30) cc_final: 0.7102 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7674 (mptt) REVERT: Aj 181 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6888 (mtt) REVERT: Ak 60 LYS cc_start: 0.8592 (mmtt) cc_final: 0.8377 (mmtm) REVERT: Ak 99 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8141 (tp) REVERT: Ak 181 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.6867 (mtm) REVERT: Al 139 GLU cc_start: 0.7953 (pt0) cc_final: 0.7654 (tt0) REVERT: Al 177 LYS cc_start: 0.8016 (mtpm) cc_final: 0.7452 (mptt) REVERT: Am 139 GLU cc_start: 0.7833 (tt0) cc_final: 0.7564 (tt0) REVERT: Am 168 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7665 (mt-10) REVERT: Am 177 LYS cc_start: 0.8091 (mtpm) cc_final: 0.7544 (mptt) REVERT: An 95 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7916 (mm-30) REVERT: An 99 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8066 (tp) REVERT: An 121 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7074 (tp30) REVERT: An 139 GLU cc_start: 0.8057 (pt0) cc_final: 0.7733 (tm-30) REVERT: An 153 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8584 (mmtm) REVERT: An 173 MET cc_start: 0.7585 (ttp) cc_final: 0.7130 (ttt) REVERT: An 175 ASN cc_start: 0.8269 (m-40) cc_final: 0.8023 (m-40) REVERT: An 177 LYS cc_start: 0.8144 (mtpm) cc_final: 0.7635 (mptt) REVERT: Ao 91 ASP cc_start: 0.8652 (m-30) cc_final: 0.8409 (m-30) REVERT: Ao 121 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: Ao 139 GLU cc_start: 0.7889 (pt0) cc_final: 0.7519 (tt0) REVERT: Ao 153 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.7404 (mptp) REVERT: Ao 173 MET cc_start: 0.7579 (ttp) cc_final: 0.7112 (ttt) REVERT: Ao 177 LYS cc_start: 0.8252 (mtpm) cc_final: 0.7760 (mptt) REVERT: Ap 60 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7263 (mptt) REVERT: Ap 99 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7925 (mt) REVERT: Ap 116 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8679 (ttp) REVERT: Ap 139 GLU cc_start: 0.7960 (pt0) cc_final: 0.7718 (tt0) REVERT: Ap 173 MET cc_start: 0.7766 (ttp) cc_final: 0.7384 (ttt) REVERT: Ap 181 MET cc_start: 0.7345 (mmt) cc_final: 0.7018 (mtt) REVERT: Aq 60 LYS cc_start: 0.8477 (mmtt) cc_final: 0.8144 (mmtm) REVERT: Aq 91 ASP cc_start: 0.8423 (m-30) cc_final: 0.8203 (m-30) REVERT: Aq 153 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.7466 (mptp) REVERT: Aq 177 LYS cc_start: 0.8206 (mtpm) cc_final: 0.7644 (mptt) REVERT: Aq 181 MET cc_start: 0.7245 (OUTLIER) cc_final: 0.6993 (mtt) REVERT: Ar 77 GLN cc_start: 0.8360 (mt0) cc_final: 0.7387 (mp-120) REVERT: Ar 99 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8227 (tp) REVERT: Ar 135 MET cc_start: 0.9096 (mmm) cc_final: 0.8647 (mmm) REVERT: Ar 168 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7532 (mt-10) REVERT: Ar 173 MET cc_start: 0.7814 (ttp) cc_final: 0.7307 (ttt) REVERT: Ar 177 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7687 (mptt) REVERT: As 121 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7528 (tm-30) outliers start: 94 outliers final: 46 residues processed: 763 average time/residue: 0.7152 time to fit residues: 605.5159 Evaluate side-chains 800 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 729 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 181 MET Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 160 MET Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 181 MET Chi-restraints excluded: chain Ac residue 187 VAL Chi-restraints excluded: chain Ad residue 95 GLU Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 181 MET Chi-restraints excluded: chain Af residue 95 GLU Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 160 MET Chi-restraints excluded: chain Ag residue 95 GLU Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 95 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 181 MET Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 168 GLU Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 48 LYS Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 110 THR Chi-restraints excluded: chain Ao residue 121 GLU Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 181 MET Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain Ar residue 142 GLU Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 116 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 245 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 3 optimal weight: 0.0270 chunk 130 optimal weight: 0.6980 overall best weight: 1.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 113 ASN Af 113 ASN Ag 113 ASN Ah 113 ASN Aj 113 ASN Am 113 ASN An 69 HIS As 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.160342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135134 restraints weight = 24358.420| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.04 r_work: 0.3363 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22914 Z= 0.154 Angle : 0.560 6.277 31103 Z= 0.283 Chirality : 0.042 0.183 3420 Planarity : 0.005 0.041 4009 Dihedral : 4.093 16.770 3040 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 3.24 % Allowed : 25.67 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.31 (0.16), residues: 2755 helix: 1.78 (0.15), residues: 988 sheet: 0.95 (0.31), residues: 228 loop : -1.02 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAe 55 TYR 0.017 0.001 TYRAh 180 PHE 0.012 0.002 PHEAi 163 TRP 0.012 0.002 TRPAf 132 HIS 0.004 0.001 HISAg 69 Details of bonding type rmsd covalent geometry : bond 0.00382 (22914) covalent geometry : angle 0.55953 (31103) hydrogen bonds : bond 0.03868 ( 874) hydrogen bonds : angle 4.25611 ( 2565) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5510 Ramachandran restraints generated. 2755 Oldfield, 0 Emsley, 2755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 729 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Aa 160 MET cc_start: 0.9119 (mmp) cc_final: 0.8748 (mmt) REVERT: Aa 173 MET cc_start: 0.7921 (ttp) cc_final: 0.7436 (ttt) REVERT: Aa 177 LYS cc_start: 0.8290 (mtpm) cc_final: 0.7527 (mptt) REVERT: Aa 181 MET cc_start: 0.7604 (OUTLIER) cc_final: 0.7037 (mtt) REVERT: Ab 99 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8283 (tp) REVERT: Ab 108 MET cc_start: 0.9057 (tpt) cc_final: 0.8752 (mmp) REVERT: Ab 173 MET cc_start: 0.8037 (ttp) cc_final: 0.7746 (ttp) REVERT: Ac 99 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8200 (tp) REVERT: Ac 108 MET cc_start: 0.9038 (tpt) cc_final: 0.8718 (mmp) REVERT: Ac 142 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8283 (mp0) REVERT: Ac 173 MET cc_start: 0.7866 (ttp) cc_final: 0.7492 (ttp) REVERT: Ac 177 LYS cc_start: 0.8044 (mtpm) cc_final: 0.7366 (mptt) REVERT: Ac 181 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.6955 (mtm) REVERT: Ad 91 ASP cc_start: 0.8689 (m-30) cc_final: 0.8460 (m-30) REVERT: Ad 95 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8042 (mp0) REVERT: Ad 160 MET cc_start: 0.9292 (mmp) cc_final: 0.8769 (mmt) REVERT: Ad 181 MET cc_start: 0.7387 (mmt) cc_final: 0.6946 (mtm) REVERT: Ae 181 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.6882 (OUTLIER) REVERT: Af 69 HIS cc_start: 0.8182 (m-70) cc_final: 0.6492 (t70) REVERT: Af 95 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: Af 168 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7702 (mt-10) REVERT: Af 181 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.6871 (mtm) REVERT: Ag 116 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8911 (tmm) REVERT: Ag 168 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7834 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8049 (mtpp) cc_final: 0.7483 (mptt) REVERT: Ag 181 MET cc_start: 0.7802 (mmt) cc_final: 0.7492 (tpp) REVERT: Ah 139 GLU cc_start: 0.8020 (pt0) cc_final: 0.7683 (tt0) REVERT: Ah 173 MET cc_start: 0.8076 (ttp) cc_final: 0.7536 (ttt) REVERT: Ah 177 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7544 (mptt) REVERT: Ah 181 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.6989 (mtt) REVERT: Ai 69 HIS cc_start: 0.7911 (m-70) cc_final: 0.6161 (t-90) REVERT: Ai 99 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8295 (tp) REVERT: Ai 121 GLU cc_start: 0.8229 (tp30) cc_final: 0.7856 (tp30) REVERT: Ai 139 GLU cc_start: 0.7999 (tt0) cc_final: 0.7695 (pt0) REVERT: Ai 168 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7695 (mt-10) REVERT: Ai 173 MET cc_start: 0.8229 (ttp) cc_final: 0.7734 (ttt) REVERT: Ai 177 LYS cc_start: 0.8214 (mtpm) cc_final: 0.7682 (mptt) REVERT: Ai 181 MET cc_start: 0.7384 (tpt) cc_final: 0.6967 (mtt) REVERT: Aj 172 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7292 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8137 (mtpp) cc_final: 0.7634 (mptt) REVERT: Aj 181 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6965 (mtt) REVERT: Ak 60 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8333 (mmtm) REVERT: Ak 99 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8233 (tp) REVERT: Ak 181 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.6962 (mtm) REVERT: Al 177 LYS cc_start: 0.8017 (mtpm) cc_final: 0.7438 (mptt) REVERT: Am 139 GLU cc_start: 0.8094 (tt0) cc_final: 0.7830 (tt0) REVERT: Am 168 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7931 (mt-10) REVERT: Am 177 LYS cc_start: 0.8095 (mtpm) cc_final: 0.7517 (mptt) REVERT: An 95 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: An 99 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8168 (tp) REVERT: An 121 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7277 (tp30) REVERT: An 139 GLU cc_start: 0.8283 (pt0) cc_final: 0.7839 (tm-30) REVERT: An 153 LYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8624 (mmtm) REVERT: An 173 MET cc_start: 0.7883 (ttp) cc_final: 0.7379 (ttt) REVERT: An 175 ASN cc_start: 0.8336 (m-40) cc_final: 0.8088 (m-40) REVERT: An 177 LYS cc_start: 0.8223 (mtpm) cc_final: 0.7672 (mppt) REVERT: Ao 91 ASP cc_start: 0.8859 (m-30) cc_final: 0.8633 (m-30) REVERT: Ao 121 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7582 (tm-30) REVERT: Ao 139 GLU cc_start: 0.8152 (pt0) cc_final: 0.7723 (tt0) REVERT: Ao 153 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.7467 (mptp) REVERT: Ao 173 MET cc_start: 0.7919 (ttp) cc_final: 0.7406 (ttt) REVERT: Ao 177 LYS cc_start: 0.8241 (mtpm) cc_final: 0.7744 (mptt) REVERT: Ap 60 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.7185 (mptt) REVERT: Ap 99 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7969 (mt) REVERT: Ap 116 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8764 (ttp) REVERT: Ap 139 GLU cc_start: 0.8179 (pt0) cc_final: 0.7832 (tt0) REVERT: Ap 173 MET cc_start: 0.8057 (ttp) cc_final: 0.7619 (ttt) REVERT: Ap 181 MET cc_start: 0.7652 (mmt) cc_final: 0.7131 (mtt) REVERT: Aq 60 LYS cc_start: 0.8440 (mmtt) cc_final: 0.8071 (mmtm) REVERT: Aq 153 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.7512 (mptp) REVERT: Aq 177 LYS cc_start: 0.8254 (mtpm) cc_final: 0.7612 (mptt) REVERT: Aq 181 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6864 (mtm) REVERT: Ar 77 GLN cc_start: 0.8521 (mt0) cc_final: 0.7392 (mp10) REVERT: Ar 99 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8325 (tp) REVERT: Ar 135 MET cc_start: 0.9208 (mmm) cc_final: 0.8748 (mmm) REVERT: Ar 168 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7794 (mt-10) REVERT: Ar 173 MET cc_start: 0.8054 (ttp) cc_final: 0.7505 (ttt) REVERT: Ar 177 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7675 (mptt) REVERT: As 121 GLU cc_start: 0.8244 (tm-30) cc_final: 0.7734 (tm-30) REVERT: As 139 GLU cc_start: 0.8014 (tt0) cc_final: 0.7755 (tt0) REVERT: As 153 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.7408 (mptp) outliers start: 80 outliers final: 50 residues processed: 757 average time/residue: 0.8215 time to fit residues: 688.1623 Evaluate side-chains 802 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 728 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Aa residue 181 MET Chi-restraints excluded: chain Ab residue 99 LEU Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 160 MET Chi-restraints excluded: chain Ab residue 187 VAL Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 181 MET Chi-restraints excluded: chain Ac residue 187 VAL Chi-restraints excluded: chain Ad residue 95 GLU Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 181 MET Chi-restraints excluded: chain Af residue 95 GLU Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 160 MET Chi-restraints excluded: chain Af residue 181 MET Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 95 GLU Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 95 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 120 ILE Chi-restraints excluded: chain Aj residue 181 MET Chi-restraints excluded: chain Ak residue 54 MET Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 168 GLU Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 58 LYS Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 48 LYS Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 99 LEU Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 110 THR Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 181 MET Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain Ar residue 142 GLU Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 153 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 178 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 159 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 69 optimal weight: 0.0170 chunk 174 optimal weight: 0.9990 chunk 250 optimal weight: 7.9990 chunk 11 optimal weight: 0.0970 chunk 134 optimal weight: 10.0000 overall best weight: 1.2220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 113 ASN Af 113 ASN Ag 113 ASN Ah 113 ASN Aj 69 HIS Aj 113 ASN Al 151 ASN Ao 69 HIS As 113 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.162209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137331 restraints weight = 24405.636| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.02 r_work: 0.3386 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22914 Z= 0.125 Angle : 0.535 6.350 31103 Z= 0.270 Chirality : 0.041 0.164 3420 Planarity : 0.005 0.040 4009 Dihedral : 3.936 16.695 3040 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.36 % Allowed : 25.71 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.47 (0.16), residues: 2755 helix: 1.48 (0.15), residues: 1102 sheet: 2.05 (0.32), residues: 190 loop : -0.88 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAe 55 TYR 0.015 0.001 TYRAm 180 PHE 0.010 0.002 PHEAi 163 TRP 0.012 0.001 TRPAf 132 HIS 0.003 0.000 HISAh 69 Details of bonding type rmsd covalent geometry : bond 0.00308 (22914) covalent geometry : angle 0.53487 (31103) hydrogen bonds : bond 0.03586 ( 874) hydrogen bonds : angle 4.19183 ( 2565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11412.74 seconds wall clock time: 194 minutes 7.67 seconds (11647.67 seconds total)