Starting phenix.real_space_refine on Fri Jan 24 19:25:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8opf_17051/01_2025/8opf_17051.cif Found real_map, /net/cci-nas-00/data/ceres_data/8opf_17051/01_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_17051/01_2025/8opf_17051.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8opf_17051/01_2025/8opf_17051.map" model { file = "/net/cci-nas-00/data/ceres_data/8opf_17051/01_2025/8opf_17051.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8opf_17051/01_2025/8opf_17051.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: Ac, Ab, Ae, Ad, Ag, Af, Ai, Ah, Ak, Aj, Am, Al, Ao, An, Aq, Ap, As, Ar Time building chain proxies: 5.24, per 1000 atoms: 0.23 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: 4.83 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.06 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: 6.01 Time building geometry restraints manager: 5.66 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: 0.19 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ac' selection = chain 'Ab' selection = chain 'Ae' selection = chain 'Ad' selection = chain 'Ag' selection = chain 'Af' selection = chain 'Ai' selection = chain 'Ah' selection = chain 'Ak' selection = chain 'Aj' selection = chain 'Am' selection = chain 'Al' selection = chain 'Ao' selection = chain 'An' selection = chain 'Aq' selection = chain 'Ap' selection = chain 'As' selection = chain 'Ar' } 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: 2.040 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: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 37.030 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:15.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.990 ------------------------------------------------------------------------------- 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= 0.244 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRPAo 132 HIS 0.002 0.001 HISAm 42 PHE 0.004 0.001 PHEAk 163 TYR 0.005 0.001 TYRAp 73 ARG 0.003 0.001 ARGAl 188 *********************** 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 : 2.449 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: 1.6584 time to fit residues: 1363.6127 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 : 2.447 ------------------------------------------------------------------------------- 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 224 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 111 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 chunk 155 optimal weight: 0.2980 chunk 241 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 113 ASN Aa 175 ASN Ac 113 ASN Ad 113 ASN Ad 175 ASN Ae 113 ASN Ae 158 GLN Af 113 ASN Ag 113 ASN Ah 113 ASN ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 113 ASN Ak 113 ASN ** Al 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Al 175 ASN Am 113 ASN Am 175 ASN An 175 ASN Ao 113 ASN Ap 113 ASN Ap 175 ASN Aq 113 ASN Ar 113 ASN Ar 175 ASN As 113 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.160174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135483 restraints weight = 24435.313| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.01 r_work: 0.3375 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22914 Z= 0.313 Angle : 0.596 6.029 31103 Z= 0.305 Chirality : 0.043 0.183 3420 Planarity : 0.005 0.036 4009 Dihedral : 4.208 20.627 3044 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 4.49 % Allowed : 20.77 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2755 helix: 1.27 (0.16), residues: 988 sheet: 1.87 (0.33), residues: 228 loop : -1.71 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAf 132 HIS 0.002 0.000 HISAg 162 PHE 0.012 0.002 PHEAi 163 TYR 0.019 0.002 TYRAq 180 ARG 0.006 0.001 ARGAk 55 *********************** 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 859 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 748 time to evaluate : 2.695 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: 0.8716 (m-30) cc_final: 0.8503 (m-30) REVERT: Aa 112 MET cc_start: 0.9339 (mmp) cc_final: 0.9113 (mmp) REVERT: Aa 134 MET cc_start: 0.9116 (ttt) cc_final: 0.8551 (ttt) REVERT: Aa 160 MET cc_start: 0.9131 (mmp) cc_final: 0.8737 (mmt) REVERT: Aa 168 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7586 (mt-10) REVERT: Aa 181 MET cc_start: 0.7552 (mmt) cc_final: 0.6957 (mtm) REVERT: Ab 76 GLN cc_start: 0.8600 (mt0) cc_final: 0.8150 (mt0) REVERT: Ab 99 LEU cc_start: 0.8593 (tt) cc_final: 0.8277 (tp) REVERT: Ab 113 ASN cc_start: 0.8873 (m110) cc_final: 0.8606 (m110) REVERT: Ab 121 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7541 (tm-30) REVERT: Ab 127 ASN cc_start: 0.8582 (t0) cc_final: 0.8334 (t0) REVERT: Ab 173 MET cc_start: 0.8074 (ttp) cc_final: 0.7724 (ttp) REVERT: Ab 177 LYS cc_start: 0.8243 (mtpp) cc_final: 0.7818 (mptt) REVERT: Ac 121 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7644 (tm-30) REVERT: Ac 173 MET cc_start: 0.7976 (ttp) cc_final: 0.7627 (ttp) REVERT: Ac 177 LYS cc_start: 0.8219 (mtpp) cc_final: 0.7702 (mptt) REVERT: Ac 181 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7014 (mtm) REVERT: Ad 56 MET cc_start: 0.8712 (mmp) cc_final: 0.8446 (mmm) REVERT: Ad 168 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7798 (mt-10) REVERT: Ad 173 MET cc_start: 0.8001 (ttp) cc_final: 0.7743 (ttp) REVERT: Ad 181 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7048 (mtm) REVERT: Ae 56 MET cc_start: 0.8749 (mmp) cc_final: 0.8534 (mmt) REVERT: Ae 121 GLU cc_start: 0.7825 (tp30) cc_final: 0.7593 (tm-30) REVERT: Ae 139 GLU cc_start: 0.7875 (pt0) cc_final: 0.7107 (pm20) REVERT: Ae 173 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7952 (ttp) REVERT: Ae 181 MET cc_start: 0.7489 (OUTLIER) cc_final: 0.6985 (mtm) REVERT: Af 46 ARG cc_start: 0.9298 (mpt180) cc_final: 0.8974 (mpt180) REVERT: Af 60 LYS cc_start: 0.8604 (mptm) cc_final: 0.8353 (mptt) REVERT: Af 69 HIS cc_start: 0.8109 (m-70) cc_final: 0.6423 (t-90) REVERT: Af 95 GLU cc_start: 0.8666 (mp0) cc_final: 0.8317 (mp0) REVERT: Af 153 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8520 (mmtt) REVERT: Af 168 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7821 (mt-10) REVERT: Af 173 MET cc_start: 0.8041 (ttp) cc_final: 0.7768 (ttp) REVERT: Af 177 LYS cc_start: 0.8221 (mtpp) cc_final: 0.7510 (mptt) REVERT: Af 178 GLU cc_start: 0.7471 (pt0) cc_final: 0.7198 (pt0) REVERT: Ag 50 ILE cc_start: 0.8157 (mm) cc_final: 0.7801 (mm) REVERT: Ag 108 MET cc_start: 0.8960 (tpt) cc_final: 0.8736 (tpt) REVERT: Ag 116 MET cc_start: 0.9126 (OUTLIER) cc_final: 0.8840 (tmm) REVERT: Ag 139 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7109 (pm20) REVERT: Ag 177 LYS cc_start: 0.8190 (mtpp) cc_final: 0.7620 (mptt) REVERT: Ag 181 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.6959 (mtm) REVERT: Ah 71 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8342 (mt) REVERT: Ah 76 GLN cc_start: 0.8621 (mt0) cc_final: 0.8266 (mt0) REVERT: Ah 91 ASP cc_start: 0.8769 (m-30) cc_final: 0.8561 (m-30) REVERT: Ah 173 MET cc_start: 0.8099 (ttp) cc_final: 0.7472 (ttt) REVERT: Ah 177 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7527 (mptt) REVERT: Ah 181 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.6916 (mtm) REVERT: Ai 67 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8699 (mp) REVERT: Ai 99 LEU cc_start: 0.8722 (tt) cc_final: 0.8308 (tp) REVERT: Ai 108 MET cc_start: 0.8961 (tpt) cc_final: 0.8749 (tpt) REVERT: Ai 153 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.7205 (mptp) REVERT: Ai 173 MET cc_start: 0.8257 (ttp) cc_final: 0.7810 (ttt) REVERT: Ai 181 MET cc_start: 0.7526 (tpt) cc_final: 0.7124 (tpp) REVERT: Aj 67 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8307 (mp) REVERT: Aj 139 GLU cc_start: 0.7914 (pt0) cc_final: 0.7670 (pt0) REVERT: Aj 168 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7894 (mt-10) REVERT: Aj 177 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7649 (mptt) REVERT: Aj 181 MET cc_start: 0.7374 (mmt) cc_final: 0.6905 (mtm) REVERT: Ak 173 MET cc_start: 0.7978 (ttp) cc_final: 0.7393 (ttt) REVERT: Ak 177 LYS cc_start: 0.8169 (mtpp) cc_final: 0.7545 (mptt) REVERT: Ak 181 MET cc_start: 0.7517 (OUTLIER) cc_final: 0.6863 (mtm) REVERT: Al 54 MET cc_start: 0.7764 (ttp) cc_final: 0.7503 (ttt) REVERT: Al 168 GLU cc_start: 0.8277 (mt-10) cc_final: 0.7958 (mt-10) REVERT: Al 177 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7666 (mptt) REVERT: Al 181 MET cc_start: 0.7578 (tpt) cc_final: 0.7271 (mtm) REVERT: Am 99 LEU cc_start: 0.8703 (tt) cc_final: 0.8271 (tp) REVERT: Am 108 MET cc_start: 0.9123 (tpt) cc_final: 0.8846 (tpt) REVERT: Am 121 GLU cc_start: 0.8012 (tp30) cc_final: 0.7615 (mt-10) REVERT: Am 139 GLU cc_start: 0.7980 (pt0) cc_final: 0.7645 (pt0) REVERT: Am 168 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7938 (mt-10) REVERT: An 67 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8571 (mp) REVERT: An 99 LEU cc_start: 0.8519 (tt) cc_final: 0.8110 (tp) REVERT: An 108 MET cc_start: 0.9030 (tpt) cc_final: 0.8510 (tpt) REVERT: An 173 MET cc_start: 0.8072 (ttp) cc_final: 0.7523 (ttt) REVERT: An 177 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8077 (mtmm) REVERT: An 181 MET cc_start: 0.7627 (tpt) cc_final: 0.7365 (tpp) REVERT: Ao 56 MET cc_start: 0.8681 (mmp) cc_final: 0.8433 (mmt) REVERT: Ao 67 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8589 (mp) REVERT: Ao 91 ASP cc_start: 0.8812 (m-30) cc_final: 0.8559 (m-30) REVERT: Ao 135 MET cc_start: 0.9222 (mmm) cc_final: 0.8956 (mmm) REVERT: Ao 153 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.7650 (mptp) REVERT: Ao 173 MET cc_start: 0.8125 (ttp) cc_final: 0.7652 (ttt) REVERT: Ap 60 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7357 (mptt) REVERT: Ap 116 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8787 (ttp) REVERT: Ap 168 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7646 (mt-10) REVERT: Ap 173 MET cc_start: 0.8188 (ttp) cc_final: 0.7737 (ttt) REVERT: Ap 181 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7070 (mtm) REVERT: Aq 60 LYS cc_start: 0.8371 (mmtt) cc_final: 0.8074 (mmtm) REVERT: Aq 91 ASP cc_start: 0.8762 (m-30) cc_final: 0.8479 (m-30) REVERT: Aq 112 MET cc_start: 0.9382 (mmp) cc_final: 0.9128 (mmp) REVERT: Aq 121 GLU cc_start: 0.7790 (tp30) cc_final: 0.7559 (tm-30) REVERT: Aq 153 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.7498 (mptp) REVERT: Aq 160 MET cc_start: 0.9231 (mmt) cc_final: 0.8798 (mmt) REVERT: Aq 181 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.6979 (mtm) REVERT: Ar 67 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8496 (mp) REVERT: Ar 168 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7711 (mt-10) REVERT: Ar 173 MET cc_start: 0.8081 (ttp) cc_final: 0.7531 (ttt) REVERT: Ar 177 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7963 (mtmm) REVERT: As 56 MET cc_start: 0.8671 (mmt) cc_final: 0.8441 (mmt) REVERT: As 181 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.6933 (mtm) outliers start: 111 outliers final: 15 residues processed: 769 average time/residue: 1.7714 time to fit residues: 1509.9666 Evaluate side-chains 785 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 746 time to evaluate : 2.452 ------------------------------------------------------------------------------- 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 173 MET Chi-restraints excluded: chain Ae residue 181 MET Chi-restraints excluded: chain Af residue 153 LYS Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 139 GLU Chi-restraints excluded: chain Ag residue 181 MET Chi-restraints excluded: chain Ah residue 48 LYS Chi-restraints excluded: chain Ah residue 71 LEU Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 67 LEU 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 Aj residue 120 ILE 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 48 LYS Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 67 LEU Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 175 ASN Chi-restraints excluded: chain Ao residue 67 LEU Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Ap residue 181 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 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 213 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 187 optimal weight: 7.9990 chunk 143 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 197 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 93 optimal weight: 0.4980 chunk 14 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- 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 Ai 113 ASN Aj 113 ASN Al 113 ASN Al 175 ASN An 175 ASN Aq 113 ASN Ar 113 ASN As 113 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.157242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131987 restraints weight = 24289.357| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.03 r_work: 0.3324 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 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 = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 22914 Z= 0.429 Angle : 0.638 5.972 31103 Z= 0.326 Chirality : 0.046 0.196 3420 Planarity : 0.005 0.040 4009 Dihedral : 4.535 16.569 3040 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.98 % Allowed : 22.35 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 2755 helix: 1.12 (0.15), residues: 988 sheet: 1.53 (0.33), residues: 228 loop : -1.69 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAf 132 HIS 0.002 0.001 HISAc 162 PHE 0.015 0.002 PHEAi 163 TYR 0.020 0.002 TYRAa 180 ARG 0.006 0.001 ARGAp 55 *********************** 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 903 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 780 time to evaluate : 2.283 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 134 MET cc_start: 0.9185 (ttt) cc_final: 0.8591 (ttt) REVERT: Aa 139 GLU cc_start: 0.8062 (pt0) cc_final: 0.7845 (tt0) REVERT: Aa 160 MET cc_start: 0.9095 (mmp) cc_final: 0.8775 (mmt) REVERT: Aa 177 LYS cc_start: 0.8160 (mtpm) cc_final: 0.7390 (mptt) REVERT: Aa 181 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.6906 (mtm) REVERT: Ab 76 GLN cc_start: 0.8636 (mt0) cc_final: 0.8183 (mt0) REVERT: Ab 99 LEU cc_start: 0.8610 (tt) cc_final: 0.8254 (tp) REVERT: Ab 113 ASN cc_start: 0.9020 (m110) cc_final: 0.8785 (m-40) REVERT: Ab 121 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7651 (tm-30) REVERT: Ab 168 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7627 (mt-10) REVERT: Ab 173 MET cc_start: 0.8070 (ttp) cc_final: 0.7750 (ttp) REVERT: Ac 88 SER cc_start: 0.8781 (p) cc_final: 0.8481 (p) REVERT: Ac 153 LYS cc_start: 0.8575 (mmtm) cc_final: 0.8359 (mmtp) REVERT: Ac 173 MET cc_start: 0.7978 (ttp) cc_final: 0.7406 (ttp) REVERT: Ac 177 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7703 (mptt) REVERT: Ac 181 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7018 (mtm) REVERT: Ad 139 GLU cc_start: 0.8117 (pt0) cc_final: 0.7897 (tt0) REVERT: Ad 173 MET cc_start: 0.8009 (ttp) cc_final: 0.7730 (ttp) REVERT: Ad 181 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.6997 (mtm) REVERT: Ae 56 MET cc_start: 0.8787 (mmp) cc_final: 0.8526 (mmt) REVERT: Ae 121 GLU cc_start: 0.7860 (tp30) cc_final: 0.7591 (tm-30) REVERT: Ae 139 GLU cc_start: 0.8041 (pt0) cc_final: 0.7801 (tt0) REVERT: Ae 173 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7941 (ttp) REVERT: Ae 181 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7067 (mtm) REVERT: Af 46 ARG cc_start: 0.9279 (mpt180) cc_final: 0.8987 (mpt180) REVERT: Af 69 HIS cc_start: 0.8049 (m-70) cc_final: 0.6379 (t70) REVERT: Af 95 GLU cc_start: 0.8548 (mp0) cc_final: 0.8224 (mp0) REVERT: Af 139 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: Af 168 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7913 (mt-10) REVERT: Af 172 GLU cc_start: 0.7250 (mt-10) cc_final: 0.7009 (mm-30) REVERT: Af 173 MET cc_start: 0.7991 (ttp) cc_final: 0.7734 (ttp) REVERT: Af 181 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6807 (mtm) REVERT: Ag 108 MET cc_start: 0.8994 (tpt) cc_final: 0.8658 (tpt) REVERT: Ag 116 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8881 (tmm) REVERT: Ag 153 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8466 (mmtm) REVERT: Ag 168 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7831 (mt-10) REVERT: Ag 175 ASN cc_start: 0.8431 (m-40) cc_final: 0.8180 (m-40) REVERT: Ag 177 LYS cc_start: 0.8224 (mtpp) cc_final: 0.7527 (mptt) REVERT: Ag 181 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.6976 (mtm) REVERT: Ah 46 ARG cc_start: 0.9314 (mpt180) cc_final: 0.9031 (mpt180) REVERT: Ah 48 LYS cc_start: 0.8503 (mtmm) cc_final: 0.8238 (mtmt) REVERT: Ah 76 GLN cc_start: 0.8692 (mt0) cc_final: 0.8328 (mt0) REVERT: Ah 91 ASP cc_start: 0.8855 (m-30) cc_final: 0.8600 (m-30) REVERT: Ah 116 MET cc_start: 0.9073 (ttp) cc_final: 0.8817 (ttp) REVERT: Ah 173 MET cc_start: 0.8080 (ttp) cc_final: 0.7668 (ttp) REVERT: Ah 177 LYS cc_start: 0.8152 (mtpp) cc_final: 0.7562 (mptt) REVERT: Ah 178 GLU cc_start: 0.7561 (pt0) cc_final: 0.7333 (pt0) REVERT: Ah 181 MET cc_start: 0.7769 (OUTLIER) cc_final: 0.6975 (mtm) REVERT: Ai 67 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8746 (mp) REVERT: Ai 99 LEU cc_start: 0.8656 (tt) cc_final: 0.8290 (tp) REVERT: Ai 108 MET cc_start: 0.8957 (tpt) cc_final: 0.8718 (tpt) REVERT: Ai 139 GLU cc_start: 0.7965 (pt0) cc_final: 0.7709 (tt0) REVERT: Ai 153 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7011 (mptp) REVERT: Ai 168 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7682 (mt-10) REVERT: Ai 173 MET cc_start: 0.8248 (ttp) cc_final: 0.7773 (ttt) REVERT: Ai 177 LYS cc_start: 0.8275 (mtpm) cc_final: 0.7805 (mptt) REVERT: Aj 102 ASP cc_start: 0.8963 (t0) cc_final: 0.8748 (t0) REVERT: Aj 172 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6927 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8276 (mtpp) cc_final: 0.7742 (mptt) REVERT: Aj 181 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6903 (mtm) REVERT: Ak 60 LYS cc_start: 0.8520 (mmtm) cc_final: 0.8235 (mmtm) REVERT: Ak 99 LEU cc_start: 0.8613 (tt) cc_final: 0.8203 (tp) REVERT: Ak 173 MET cc_start: 0.7994 (ttp) cc_final: 0.7403 (ttt) REVERT: Ak 177 LYS cc_start: 0.8196 (mtpp) cc_final: 0.7513 (mptt) REVERT: Ak 181 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.6826 (mtm) REVERT: Al 54 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7383 (ttt) REVERT: Al 108 MET cc_start: 0.9099 (tpt) cc_final: 0.8161 (tpt) REVERT: Al 139 GLU cc_start: 0.8165 (pt0) cc_final: 0.7896 (tt0) REVERT: Al 172 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6962 (mm-30) REVERT: Al 178 GLU cc_start: 0.7463 (pt0) cc_final: 0.7259 (pt0) REVERT: Al 181 MET cc_start: 0.7571 (tpt) cc_final: 0.7183 (mtm) REVERT: Am 121 GLU cc_start: 0.8092 (tp30) cc_final: 0.7497 (mt-10) REVERT: Am 168 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7852 (mt-10) REVERT: Am 177 LYS cc_start: 0.8332 (mtpp) cc_final: 0.8007 (mtmm) REVERT: An 67 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8560 (mp) REVERT: An 99 LEU cc_start: 0.8466 (tt) cc_final: 0.8086 (tp) REVERT: An 102 ASP cc_start: 0.8728 (t0) cc_final: 0.8299 (t0) REVERT: An 108 MET cc_start: 0.9048 (tpt) cc_final: 0.8396 (tpt) REVERT: An 139 GLU cc_start: 0.8098 (pt0) cc_final: 0.7778 (tt0) REVERT: An 173 MET cc_start: 0.7982 (ttp) cc_final: 0.7406 (ttt) REVERT: An 177 LYS cc_start: 0.8335 (mtpp) cc_final: 0.8023 (mtmm) REVERT: Ao 67 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8541 (mp) REVERT: Ao 91 ASP cc_start: 0.8800 (m-30) cc_final: 0.8540 (m-30) REVERT: Ao 139 GLU cc_start: 0.7999 (pt0) cc_final: 0.7725 (tt0) REVERT: Ao 153 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.7697 (mptp) REVERT: Ao 173 MET cc_start: 0.8042 (ttp) cc_final: 0.7579 (ttt) REVERT: Ap 60 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7442 (mptt) REVERT: Ap 116 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8875 (ttp) REVERT: Ap 173 MET cc_start: 0.8243 (ttp) cc_final: 0.7799 (ttt) REVERT: Ap 181 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7000 (mtm) REVERT: Aq 54 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7406 (ttt) REVERT: Aq 60 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8038 (mmtm) REVERT: Aq 121 GLU cc_start: 0.7769 (tp30) cc_final: 0.7522 (tm-30) REVERT: Aq 153 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.7532 (mptp) REVERT: Aq 181 MET cc_start: 0.7529 (OUTLIER) cc_final: 0.7068 (mtm) REVERT: Ar 77 GLN cc_start: 0.8610 (mt0) cc_final: 0.7693 (mp10) REVERT: Ar 99 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8313 (tp) REVERT: Ar 135 MET cc_start: 0.9200 (mmm) cc_final: 0.8750 (mmm) REVERT: Ar 168 GLU cc_start: 0.8108 (mt-10) cc_final: 0.7888 (mt-10) REVERT: Ar 173 MET cc_start: 0.8235 (ttp) cc_final: 0.7690 (ttt) REVERT: Ar 177 LYS cc_start: 0.8340 (mtpp) cc_final: 0.8035 (mtmm) REVERT: As 153 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.7435 (mptp) REVERT: As 181 MET cc_start: 0.7455 (OUTLIER) cc_final: 0.7012 (mtm) outliers start: 123 outliers final: 35 residues processed: 803 average time/residue: 1.7480 time to fit residues: 1551.1216 Evaluate side-chains 841 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 777 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET 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 121 GLU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 181 MET Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 67 LEU Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 181 MET Chi-restraints excluded: chain Ae residue 54 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 54 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 139 GLU Chi-restraints excluded: chain Af residue 181 MET Chi-restraints excluded: chain Ag residue 48 LYS Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 153 LYS 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 Ai residue 153 LYS 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 71 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 181 MET Chi-restraints excluded: chain Al residue 54 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 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 95 GLU Chi-restraints excluded: chain Ao residue 67 LEU Chi-restraints excluded: chain Ao residue 71 LEU 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 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 103 ILE Chi-restraints excluded: chain As residue 153 LYS 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 42 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 170 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 154 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 252 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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 Af 113 ASN Ag 113 ASN Ah 113 ASN Ak 113 ASN Ap 113 ASN Aq 113 ASN As 113 ASN As 175 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.161605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136645 restraints weight = 24763.775| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.05 r_work: 0.3374 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2369 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= 0.218 Angle : 0.527 5.005 31103 Z= 0.268 Chirality : 0.040 0.153 3420 Planarity : 0.005 0.038 4009 Dihedral : 4.072 15.871 3040 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.40 % Allowed : 24.33 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2755 helix: 1.65 (0.15), residues: 988 sheet: 1.27 (0.33), residues: 228 loop : -1.37 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAf 132 HIS 0.002 0.000 HISAa 69 PHE 0.012 0.002 PHEAb 163 TYR 0.019 0.001 TYRAl 180 ARG 0.006 0.000 ARGAb 55 *********************** 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 833 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 749 time to evaluate : 2.551 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: 0.8659 (OUTLIER) cc_final: 0.8453 (mp) REVERT: Aa 160 MET cc_start: 0.9032 (mmp) cc_final: 0.8632 (mmt) REVERT: Aa 173 MET cc_start: 0.7803 (ttp) cc_final: 0.7340 (ttt) REVERT: Aa 177 LYS cc_start: 0.8205 (mtpm) cc_final: 0.7664 (mptt) REVERT: Aa 181 MET cc_start: 0.7340 (mmt) cc_final: 0.6831 (mtm) REVERT: Ab 76 GLN cc_start: 0.8509 (mt0) cc_final: 0.8040 (mt0) REVERT: Ab 99 LEU cc_start: 0.8546 (tt) cc_final: 0.8208 (tp) REVERT: Ab 108 MET cc_start: 0.8990 (tpt) cc_final: 0.8718 (mmp) REVERT: Ab 121 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: Ab 173 MET cc_start: 0.7734 (ttp) cc_final: 0.7467 (ttp) REVERT: Ac 108 MET cc_start: 0.9010 (tpt) cc_final: 0.8730 (mmp) REVERT: Ac 139 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: Ac 142 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7989 (mp0) REVERT: Ac 173 MET cc_start: 0.7624 (ttp) cc_final: 0.7228 (ttp) REVERT: Ac 177 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7647 (mptt) REVERT: Ac 181 MET cc_start: 0.7369 (mmt) cc_final: 0.6924 (mtm) REVERT: Ad 91 ASP cc_start: 0.8468 (m-30) cc_final: 0.7993 (m-30) REVERT: Ad 95 GLU cc_start: 0.8170 (mp0) cc_final: 0.7615 (mp0) REVERT: Ad 160 MET cc_start: 0.9225 (mmp) cc_final: 0.8710 (mmp) REVERT: Ad 173 MET cc_start: 0.7711 (ttp) cc_final: 0.7457 (ttp) REVERT: Ad 181 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.7001 (mtt) REVERT: Ae 56 MET cc_start: 0.8757 (mmp) cc_final: 0.8477 (mmt) REVERT: Ae 121 GLU cc_start: 0.7620 (tp30) cc_final: 0.7408 (tm-30) REVERT: Af 46 ARG cc_start: 0.9246 (mpt180) cc_final: 0.8919 (mpt180) REVERT: Af 69 HIS cc_start: 0.8060 (m-70) cc_final: 0.6484 (t70) REVERT: Af 95 GLU cc_start: 0.8343 (mp0) cc_final: 0.7977 (mp0) REVERT: Af 168 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7460 (mt-10) REVERT: Ag 108 MET cc_start: 0.8956 (tpt) cc_final: 0.8621 (tpt) REVERT: Ag 116 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8763 (tmm) REVERT: Ag 168 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7496 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7576 (mptt) REVERT: Ag 181 MET cc_start: 0.7490 (mmt) cc_final: 0.6970 (mtm) REVERT: Ah 46 ARG cc_start: 0.9276 (mpt180) cc_final: 0.9048 (mpt180) REVERT: Ah 76 GLN cc_start: 0.8571 (mt0) cc_final: 0.8170 (mt0) REVERT: Ah 77 GLN cc_start: 0.8185 (mt0) cc_final: 0.7317 (mp-120) REVERT: Ah 91 ASP cc_start: 0.8540 (m-30) cc_final: 0.8269 (m-30) REVERT: Ah 173 MET cc_start: 0.7741 (ttp) cc_final: 0.7233 (ttt) REVERT: Ah 177 LYS cc_start: 0.8203 (mtpp) cc_final: 0.7703 (mptt) REVERT: Ah 178 GLU cc_start: 0.7290 (pt0) cc_final: 0.7054 (pt0) REVERT: Ah 181 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6908 (mtm) REVERT: Ai 60 LYS cc_start: 0.8524 (mptm) cc_final: 0.8321 (mmtm) REVERT: Ai 99 LEU cc_start: 0.8579 (tt) cc_final: 0.8173 (tp) REVERT: Ai 108 MET cc_start: 0.9006 (tpt) cc_final: 0.8735 (mmm) REVERT: Ai 121 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7515 (tp30) REVERT: Ai 153 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7173 (mptp) REVERT: Ai 173 MET cc_start: 0.7953 (ttp) cc_final: 0.7533 (ttt) REVERT: Ai 177 LYS cc_start: 0.8248 (mtpm) cc_final: 0.7864 (mptt) REVERT: Aj 102 ASP cc_start: 0.8774 (t0) cc_final: 0.8526 (t0) REVERT: Aj 177 LYS cc_start: 0.8246 (mtpp) cc_final: 0.7761 (mptt) REVERT: Aj 181 MET cc_start: 0.7106 (mmt) cc_final: 0.6843 (mtm) REVERT: Ak 139 GLU cc_start: 0.7853 (tt0) cc_final: 0.7517 (tt0) REVERT: Ak 142 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7941 (mt-10) REVERT: Ak 173 MET cc_start: 0.7702 (ttp) cc_final: 0.7151 (ttt) REVERT: Ak 177 LYS cc_start: 0.8160 (mtpp) cc_final: 0.7557 (mptt) REVERT: Ak 181 MET cc_start: 0.7221 (mmt) cc_final: 0.6801 (mtt) REVERT: Al 177 LYS cc_start: 0.8137 (mtpm) cc_final: 0.7649 (mptt) REVERT: Am 121 GLU cc_start: 0.7967 (tp30) cc_final: 0.7522 (mt-10) REVERT: Am 168 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7637 (mt-10) REVERT: Am 177 LYS cc_start: 0.8213 (mtpp) cc_final: 0.7951 (mtmm) REVERT: An 67 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8381 (mp) REVERT: An 99 LEU cc_start: 0.8385 (tt) cc_final: 0.8023 (tp) REVERT: An 173 MET cc_start: 0.7641 (ttp) cc_final: 0.7251 (ttt) REVERT: An 181 MET cc_start: 0.7413 (tpt) cc_final: 0.7198 (mtm) REVERT: Ao 46 ARG cc_start: 0.9278 (mpt180) cc_final: 0.9051 (mpt180) REVERT: Ao 91 ASP cc_start: 0.8631 (m-30) cc_final: 0.8360 (m-30) REVERT: Ao 173 MET cc_start: 0.7656 (ttp) cc_final: 0.7152 (ttt) REVERT: Ao 177 LYS cc_start: 0.8262 (mtpm) cc_final: 0.7986 (mtmm) REVERT: Ap 116 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8685 (ttp) REVERT: Ap 173 MET cc_start: 0.7750 (ttp) cc_final: 0.7373 (ttt) REVERT: Ap 181 MET cc_start: 0.7359 (mmt) cc_final: 0.6971 (mtm) REVERT: Aq 60 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8127 (mmtm) REVERT: Aq 160 MET cc_start: 0.9127 (mmt) cc_final: 0.8684 (mmp) REVERT: Aq 181 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7140 (mtm) REVERT: Ar 77 GLN cc_start: 0.8345 (mt0) cc_final: 0.7462 (mp-120) REVERT: Ar 99 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8254 (tp) REVERT: Ar 135 MET cc_start: 0.9111 (mmm) cc_final: 0.8634 (mmm) REVERT: Ar 168 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7579 (mt-10) REVERT: Ar 173 MET cc_start: 0.7870 (ttp) cc_final: 0.7405 (ttt) REVERT: Ar 177 LYS cc_start: 0.8222 (mtpp) cc_final: 0.8005 (mtmm) REVERT: As 121 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7823 (tm-30) REVERT: As 181 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.7015 (mtm) outliers start: 84 outliers final: 23 residues processed: 772 average time/residue: 1.7304 time to fit residues: 1479.6345 Evaluate side-chains 781 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 746 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa 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 181 MET Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 139 GLU Chi-restraints excluded: chain Ad residue 181 MET Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 146 LYS Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 116 MET Chi-restraints excluded: chain Ag residue 80 ILE Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 153 LYS Chi-restraints excluded: chain Aj residue 54 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 71 LEU Chi-restraints excluded: chain An residue 67 LEU Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 116 MET 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 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 116 MET 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 180 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 121 optimal weight: 7.9990 chunk 249 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 243 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 158 GLN Ae 77 GLN Ah 113 ASN ** Al 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.157433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132207 restraints weight = 24543.537| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.03 r_work: 0.3325 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 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 = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 22914 Z= 0.377 Angle : 0.603 6.000 31103 Z= 0.306 Chirality : 0.044 0.182 3420 Planarity : 0.005 0.039 4009 Dihedral : 4.410 16.466 3040 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.67 % Allowed : 22.63 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2755 helix: 1.43 (0.15), residues: 988 sheet: 1.06 (0.32), residues: 228 loop : -1.37 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAf 132 HIS 0.003 0.001 HISAc 69 PHE 0.015 0.002 PHEAi 163 TYR 0.019 0.002 TYRAl 180 ARG 0.007 0.001 ARGAa 55 *********************** 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 914 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 774 time to evaluate : 2.521 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: 0.9115 (mmp) cc_final: 0.8803 (mmt) REVERT: Aa 177 LYS cc_start: 0.8219 (mtpm) cc_final: 0.7516 (mptt) REVERT: Aa 181 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6987 (mtt) REVERT: Ab 76 GLN cc_start: 0.8619 (mt0) cc_final: 0.8165 (mt0) REVERT: Ab 99 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8268 (tp) REVERT: Ab 108 MET cc_start: 0.9008 (tpt) cc_final: 0.8739 (mmp) REVERT: Ab 113 ASN cc_start: 0.9013 (m110) cc_final: 0.8792 (m-40) REVERT: Ab 121 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7712 (tm-30) REVERT: Ab 173 MET cc_start: 0.8118 (ttp) cc_final: 0.7809 (ttp) REVERT: Ac 69 HIS cc_start: 0.7848 (m170) cc_final: 0.7634 (m-70) REVERT: Ac 88 SER cc_start: 0.8788 (p) cc_final: 0.8494 (p) REVERT: Ac 99 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8270 (tp) REVERT: Ac 108 MET cc_start: 0.9065 (tpt) cc_final: 0.8753 (mmt) REVERT: Ac 139 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7515 (tt0) REVERT: Ac 173 MET cc_start: 0.8029 (ttp) cc_final: 0.7471 (ttp) REVERT: Ac 177 LYS cc_start: 0.8199 (mtpp) cc_final: 0.7634 (mptt) REVERT: Ac 181 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.6973 (mtm) REVERT: Ad 95 GLU cc_start: 0.8444 (mp0) cc_final: 0.7972 (mp0) REVERT: Ad 173 MET cc_start: 0.8012 (ttp) cc_final: 0.7741 (ttp) REVERT: Ad 181 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.7030 (mtt) REVERT: Ae 56 MET cc_start: 0.8769 (mmp) cc_final: 0.8439 (mmt) REVERT: Ae 121 GLU cc_start: 0.7937 (tp30) cc_final: 0.7639 (tm-30) REVERT: Ae 173 MET cc_start: 0.8307 (ttp) cc_final: 0.8061 (ttp) REVERT: Af 69 HIS cc_start: 0.8162 (m-70) cc_final: 0.6556 (t70) REVERT: Af 95 GLU cc_start: 0.8585 (mp0) cc_final: 0.8328 (mp0) REVERT: Af 168 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7983 (mt-10) REVERT: Af 181 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.6832 (mtm) REVERT: Ag 108 MET cc_start: 0.9036 (tpt) cc_final: 0.8613 (tpt) REVERT: Ag 116 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8878 (tmm) REVERT: Ag 168 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7829 (mt-10) REVERT: Ag 175 ASN cc_start: 0.8478 (m-40) cc_final: 0.8220 (m-40) REVERT: Ag 177 LYS cc_start: 0.8171 (mtpp) cc_final: 0.7543 (mptt) REVERT: Ag 181 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7141 (mtt) REVERT: Ah 48 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8433 (mtmm) REVERT: Ah 76 GLN cc_start: 0.8679 (mt0) cc_final: 0.8302 (mt0) REVERT: Ah 77 GLN cc_start: 0.8401 (mt0) cc_final: 0.7607 (mp-120) REVERT: Ah 91 ASP cc_start: 0.8837 (m-30) cc_final: 0.8633 (m-30) REVERT: Ah 178 GLU cc_start: 0.7545 (pt0) cc_final: 0.7246 (pt0) REVERT: Ah 181 MET cc_start: 0.7740 (OUTLIER) cc_final: 0.6962 (mtm) REVERT: Ai 99 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8271 (tp) REVERT: Ai 153 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.7069 (mptp) REVERT: Ai 168 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7728 (mt-10) REVERT: Ai 173 MET cc_start: 0.8280 (ttp) cc_final: 0.7846 (ttt) REVERT: Ai 177 LYS cc_start: 0.8325 (mtpm) cc_final: 0.7881 (mptt) REVERT: Ai 181 MET cc_start: 0.7469 (tpt) cc_final: 0.7186 (mtt) REVERT: Aj 102 ASP cc_start: 0.9058 (t0) cc_final: 0.8821 (t0) REVERT: Aj 172 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7310 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8302 (mtpp) cc_final: 0.7759 (mptt) REVERT: Aj 181 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6921 (mtm) REVERT: Ak 67 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8621 (mp) REVERT: Ak 99 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8228 (tp) REVERT: Ak 181 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6919 (mtt) REVERT: Al 172 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6783 (mt-10) REVERT: Am 121 GLU cc_start: 0.8187 (tp30) cc_final: 0.7539 (mt-10) REVERT: Am 139 GLU cc_start: 0.8167 (tt0) cc_final: 0.7823 (tt0) REVERT: Am 168 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7984 (mt-10) REVERT: An 60 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8276 (mptt) REVERT: An 67 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8582 (mp) REVERT: An 99 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8144 (tp) REVERT: An 102 ASP cc_start: 0.8738 (t0) cc_final: 0.8338 (t0) REVERT: An 108 MET cc_start: 0.9035 (tpt) cc_final: 0.8632 (tpt) REVERT: An 153 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8281 (mmpt) REVERT: An 173 MET cc_start: 0.8101 (ttp) cc_final: 0.7570 (ttt) REVERT: An 177 LYS cc_start: 0.8203 (mtpm) cc_final: 0.7912 (mtmm) REVERT: An 181 MET cc_start: 0.7669 (tpt) cc_final: 0.7201 (mtm) REVERT: Ao 91 ASP cc_start: 0.8840 (m-30) cc_final: 0.8578 (m-30) REVERT: Ao 139 GLU cc_start: 0.8113 (pt0) cc_final: 0.7788 (tt0) REVERT: Ao 153 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.7540 (mptp) REVERT: Ao 173 MET cc_start: 0.7999 (ttp) cc_final: 0.7457 (ttt) REVERT: Ao 177 LYS cc_start: 0.8306 (mtpm) cc_final: 0.7938 (mtmm) REVERT: Ap 46 ARG cc_start: 0.9175 (mpt180) cc_final: 0.8921 (mpt180) REVERT: Ap 60 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7256 (mptt) REVERT: Ap 116 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8883 (ttp) REVERT: Ap 173 MET cc_start: 0.8196 (ttp) cc_final: 0.7785 (ttt) REVERT: Ap 181 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7074 (mtm) REVERT: Aq 60 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8236 (mmtm) REVERT: Aq 67 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8105 (mp) REVERT: Aq 91 ASP cc_start: 0.8819 (m-30) cc_final: 0.8541 (m-30) REVERT: Aq 153 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.7543 (mptp) REVERT: Aq 177 LYS cc_start: 0.8225 (mtpm) cc_final: 0.7624 (mptt) REVERT: Aq 181 MET cc_start: 0.7542 (OUTLIER) cc_final: 0.7055 (mtm) REVERT: Ar 77 GLN cc_start: 0.8570 (mt0) cc_final: 0.7615 (mp-120) REVERT: Ar 99 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8347 (tp) REVERT: Ar 135 MET cc_start: 0.9229 (mmm) cc_final: 0.8773 (mmm) REVERT: Ar 168 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7810 (mt-10) REVERT: Ar 173 MET cc_start: 0.8200 (ttp) cc_final: 0.7690 (ttt) REVERT: Ar 177 LYS cc_start: 0.8301 (mtpp) cc_final: 0.8045 (mtmm) REVERT: As 153 LYS cc_start: 0.8748 (OUTLIER) cc_final: 0.7441 (mptp) REVERT: As 181 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.7014 (mtm) outliers start: 140 outliers final: 42 residues processed: 824 average time/residue: 1.6775 time to fit residues: 1533.4863 Evaluate side-chains 848 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 775 time to evaluate : 2.738 ------------------------------------------------------------------------------- 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 121 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 Ad residue 54 MET 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 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 Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 153 LYS Chi-restraints excluded: chain Aj residue 54 MET 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 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 181 MET Chi-restraints excluded: chain Al residue 54 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 Al residue 181 MET Chi-restraints excluded: chain Am residue 67 LEU Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 60 LYS 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 99 LEU Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 153 LYS Chi-restraints excluded: chain Ao residue 181 MET Chi-restraints excluded: chain Ao residue 187 VAL 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 209 optimal weight: 0.0050 chunk 249 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 206 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 19 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- 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 151 ASN Af 113 ASN Ag 113 ASN ** Ah 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 113 ASN Ak 113 ASN Ap 113 ASN Aq 113 ASN As 113 ASN As 175 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.161630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136839 restraints weight = 24480.065| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.03 r_work: 0.3378 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- 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: 19 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22914 Z= 0.199 Angle : 0.522 6.678 31103 Z= 0.262 Chirality : 0.040 0.170 3420 Planarity : 0.005 0.036 4009 Dihedral : 3.956 16.341 3040 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 4.41 % Allowed : 23.40 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 2755 helix: 1.38 (0.15), residues: 1102 sheet: 2.22 (0.33), residues: 190 loop : -1.11 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAf 132 HIS 0.003 0.000 HISAg 69 PHE 0.010 0.002 PHEAn 163 TYR 0.017 0.001 TYRAl 180 ARG 0.007 0.001 ARGAe 55 *********************** 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 849 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 740 time to evaluate : 2.490 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: 0.9124 (mmp) cc_final: 0.8683 (mmt) REVERT: Aa 173 MET cc_start: 0.8018 (ttp) cc_final: 0.7554 (ttt) REVERT: Aa 177 LYS cc_start: 0.8213 (mtpm) cc_final: 0.7493 (mptt) REVERT: Aa 181 MET cc_start: 0.7599 (mmt) cc_final: 0.6987 (mtt) REVERT: Ab 76 GLN cc_start: 0.8524 (mt0) cc_final: 0.8052 (mt0) REVERT: Ab 99 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8282 (tp) REVERT: Ab 108 MET cc_start: 0.9021 (tpt) cc_final: 0.8739 (mmp) REVERT: Ab 121 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: Ab 127 ASN cc_start: 0.8600 (t0) cc_final: 0.8317 (t0) REVERT: Ab 173 MET cc_start: 0.7965 (ttp) cc_final: 0.7502 (ttt) REVERT: Ac 99 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8224 (tp) REVERT: Ac 108 MET cc_start: 0.9065 (tpt) cc_final: 0.8745 (mmp) REVERT: Ac 113 ASN cc_start: 0.8929 (m110) cc_final: 0.8692 (m-40) REVERT: Ac 139 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7532 (tt0) REVERT: Ac 173 MET cc_start: 0.7871 (ttp) cc_final: 0.7469 (ttp) REVERT: Ac 177 LYS cc_start: 0.8138 (mtpp) cc_final: 0.7556 (mptt) REVERT: Ac 181 MET cc_start: 0.7503 (mmt) cc_final: 0.6927 (mtm) REVERT: Ad 95 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.8003 (mp0) REVERT: Ad 160 MET cc_start: 0.9292 (mmp) cc_final: 0.8796 (mmt) REVERT: Ad 181 MET cc_start: 0.7434 (OUTLIER) cc_final: 0.7002 (mtt) REVERT: Ae 121 GLU cc_start: 0.7932 (tp30) cc_final: 0.7654 (tm-30) REVERT: Af 69 HIS cc_start: 0.8120 (m-70) cc_final: 0.6436 (t70) REVERT: Af 95 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: Af 181 MET cc_start: 0.7424 (mmt) cc_final: 0.6801 (mtm) REVERT: Ag 116 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8837 (tmm) REVERT: Ag 168 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7793 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8083 (mtpp) cc_final: 0.7500 (mptt) REVERT: Ag 181 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.7124 (mtt) REVERT: Ah 91 ASP cc_start: 0.8781 (m-30) cc_final: 0.8572 (m-30) REVERT: Ah 139 GLU cc_start: 0.7803 (tt0) cc_final: 0.7587 (tm-30) REVERT: Ah 173 MET cc_start: 0.8055 (ttp) cc_final: 0.7546 (ttt) REVERT: Ah 177 LYS cc_start: 0.8114 (mtpm) cc_final: 0.7572 (mptt) REVERT: Ah 181 MET cc_start: 0.7727 (OUTLIER) cc_final: 0.7001 (mtt) REVERT: Ai 121 GLU cc_start: 0.8245 (tp30) cc_final: 0.7700 (tp30) REVERT: Ai 153 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.6977 (mptp) REVERT: Ai 168 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7672 (mt-10) REVERT: Ai 173 MET cc_start: 0.8236 (ttp) cc_final: 0.7769 (ttt) REVERT: Ai 177 LYS cc_start: 0.8317 (mtpm) cc_final: 0.7860 (mptt) REVERT: Ai 181 MET cc_start: 0.7343 (tpt) cc_final: 0.6886 (mtt) REVERT: Aj 102 ASP cc_start: 0.8966 (t0) cc_final: 0.8674 (t0) REVERT: Aj 172 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7253 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7664 (mptt) REVERT: Aj 181 MET cc_start: 0.7366 (mmt) cc_final: 0.6928 (mtm) REVERT: Ak 99 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8233 (tp) REVERT: Ak 181 MET cc_start: 0.7587 (mmt) cc_final: 0.6931 (mtm) REVERT: Al 177 LYS cc_start: 0.8175 (mtpm) cc_final: 0.7595 (mptt) REVERT: Am 113 ASN cc_start: 0.8643 (m-40) cc_final: 0.8364 (m110) REVERT: Am 121 GLU cc_start: 0.8206 (tp30) cc_final: 0.7546 (mt-10) REVERT: Am 139 GLU cc_start: 0.8226 (tt0) cc_final: 0.7855 (tt0) REVERT: Am 168 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7897 (mt-10) REVERT: Am 177 LYS cc_start: 0.8147 (mtpm) cc_final: 0.7499 (mptt) REVERT: An 91 ASP cc_start: 0.8555 (m-30) cc_final: 0.8278 (m-30) REVERT: An 95 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7928 (mp0) REVERT: An 99 LEU cc_start: 0.8485 (tt) cc_final: 0.8138 (tp) REVERT: An 121 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7501 (tp30) REVERT: An 153 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8592 (mmtm) REVERT: An 173 MET cc_start: 0.7896 (ttp) cc_final: 0.7334 (ttt) REVERT: An 177 LYS cc_start: 0.8172 (mtpm) cc_final: 0.7644 (mptt) REVERT: An 181 MET cc_start: 0.7596 (tpt) cc_final: 0.7046 (mtm) REVERT: Ao 46 ARG cc_start: 0.9341 (mpt180) cc_final: 0.8999 (mpt180) REVERT: Ao 60 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7894 (mptt) REVERT: Ao 91 ASP cc_start: 0.8845 (m-30) cc_final: 0.8563 (m-30) REVERT: Ao 112 MET cc_start: 0.9226 (mmp) cc_final: 0.8616 (mmp) REVERT: Ao 139 GLU cc_start: 0.8124 (pt0) cc_final: 0.7745 (tt0) REVERT: Ao 173 MET cc_start: 0.7823 (ttp) cc_final: 0.7283 (ttt) REVERT: Ao 177 LYS cc_start: 0.8319 (mtpm) cc_final: 0.7764 (mptt) REVERT: Ap 60 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7359 (mptt) REVERT: Ap 116 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8733 (ttp) REVERT: Ap 173 MET cc_start: 0.8016 (ttp) cc_final: 0.7588 (ttt) REVERT: Ap 181 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7122 (mtm) REVERT: Aq 60 LYS cc_start: 0.8405 (mmtt) cc_final: 0.8034 (mmtm) REVERT: Aq 91 ASP cc_start: 0.8812 (m-30) cc_final: 0.8559 (m-30) REVERT: Aq 160 MET cc_start: 0.9140 (mmt) cc_final: 0.8766 (mmt) REVERT: Aq 177 LYS cc_start: 0.8239 (mtpm) cc_final: 0.7713 (mptt) REVERT: Aq 181 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.6954 (mtm) REVERT: Ar 77 GLN cc_start: 0.8553 (mt0) cc_final: 0.7513 (mp-120) REVERT: Ar 99 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8354 (tp) REVERT: Ar 139 GLU cc_start: 0.8021 (pt0) cc_final: 0.7812 (tt0) REVERT: Ar 168 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7761 (mt-10) REVERT: Ar 173 MET cc_start: 0.8096 (ttp) cc_final: 0.7595 (ttt) REVERT: Ar 177 LYS cc_start: 0.8229 (mtpp) cc_final: 0.7960 (mtmm) REVERT: As 121 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7856 (tm-30) REVERT: As 146 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8423 (ttpp) REVERT: As 153 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.7421 (mptp) REVERT: As 181 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.6990 (mtm) outliers start: 109 outliers final: 44 residues processed: 778 average time/residue: 1.7212 time to fit residues: 1484.9626 Evaluate side-chains 801 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 735 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 95 GLU 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 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 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 116 MET Chi-restraints excluded: chain Ae residue 146 LYS 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 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 153 LYS 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 Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Ak residue 168 GLU Chi-restraints excluded: chain Al residue 58 LYS 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 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 116 MET Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain Ao residue 60 LYS Chi-restraints excluded: chain Ao residue 71 LEU 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 116 MET Chi-restraints excluded: chain Ap residue 181 MET Chi-restraints excluded: chain Aq residue 95 GLU 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 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 2 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 249 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 219 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 256 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 158 GLN Ac 113 ASN Ae 77 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.157688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132362 restraints weight = 24405.056| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.03 r_work: 0.3326 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 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 = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22914 Z= 0.352 Angle : 0.592 6.023 31103 Z= 0.299 Chirality : 0.044 0.180 3420 Planarity : 0.005 0.044 4009 Dihedral : 4.309 16.242 3040 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.86 % Allowed : 23.32 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2755 helix: 1.61 (0.15), residues: 988 sheet: 0.96 (0.31), residues: 228 loop : -1.21 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAf 132 HIS 0.003 0.001 HISAc 69 PHE 0.014 0.002 PHEAi 163 TYR 0.019 0.002 TYRAd 180 ARG 0.008 0.001 ARGAm 55 *********************** 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 872 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 752 time to evaluate : 2.325 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: 0.9119 (mmp) cc_final: 0.8856 (mmt) REVERT: Aa 173 MET cc_start: 0.8138 (ttp) cc_final: 0.7692 (ttt) REVERT: Aa 177 LYS cc_start: 0.8243 (mtpm) cc_final: 0.7614 (mptt) REVERT: Aa 181 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.6944 (mtt) REVERT: Ab 76 GLN cc_start: 0.8594 (mt0) cc_final: 0.8181 (mt0) REVERT: Ab 99 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8285 (tp) REVERT: Ab 108 MET cc_start: 0.9000 (tpt) cc_final: 0.8706 (mmp) REVERT: Ab 113 ASN cc_start: 0.9009 (m110) cc_final: 0.8782 (m-40) REVERT: Ab 121 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: Ab 173 MET cc_start: 0.8086 (ttp) cc_final: 0.7795 (ttp) REVERT: Ac 69 HIS cc_start: 0.7947 (m170) cc_final: 0.7739 (m-70) REVERT: Ac 88 SER cc_start: 0.8820 (p) cc_final: 0.8533 (p) REVERT: Ac 99 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8189 (tp) REVERT: Ac 108 MET cc_start: 0.9088 (tpt) cc_final: 0.8793 (mmp) REVERT: Ac 139 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: Ac 173 MET cc_start: 0.8005 (ttp) cc_final: 0.7619 (ttp) REVERT: Ac 177 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7551 (mptt) REVERT: Ac 181 MET cc_start: 0.7566 (OUTLIER) cc_final: 0.6968 (mtm) REVERT: Ad 91 ASP cc_start: 0.8698 (m-30) cc_final: 0.8489 (m-30) REVERT: Ad 95 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: Ad 181 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6993 (mtt) REVERT: Ae 99 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8194 (tp) REVERT: Ae 121 GLU cc_start: 0.7980 (tp30) cc_final: 0.7681 (tm-30) REVERT: Ae 173 MET cc_start: 0.8307 (ttp) cc_final: 0.8050 (ttp) REVERT: Ae 181 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6996 (mtt) REVERT: Af 69 HIS cc_start: 0.8185 (m-70) cc_final: 0.6528 (t70) REVERT: Af 95 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8237 (mp0) REVERT: Af 181 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.6855 (mtm) REVERT: Ag 116 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8845 (tmm) REVERT: Ag 168 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7826 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8099 (mtpp) cc_final: 0.7535 (mptt) REVERT: Ag 181 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7174 (mtt) REVERT: Ah 91 ASP cc_start: 0.8822 (m-30) cc_final: 0.8600 (m-30) REVERT: Ah 139 GLU cc_start: 0.7829 (tt0) cc_final: 0.7604 (tm-30) REVERT: Ah 173 MET cc_start: 0.8235 (ttp) cc_final: 0.7746 (ttt) REVERT: Ah 177 LYS cc_start: 0.8166 (mtpm) cc_final: 0.7648 (mptt) REVERT: Ah 181 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7008 (mtt) REVERT: Ai 69 HIS cc_start: 0.7928 (m-70) cc_final: 0.6212 (t-90) REVERT: Ai 99 LEU cc_start: 0.8619 (tt) cc_final: 0.8295 (tp) REVERT: Ai 108 MET cc_start: 0.8987 (mmm) cc_final: 0.8347 (tpt) REVERT: Ai 121 GLU cc_start: 0.8314 (tp30) cc_final: 0.7783 (tp30) REVERT: Ai 153 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.7073 (mptp) REVERT: Ai 168 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7727 (mt-10) REVERT: Ai 173 MET cc_start: 0.8247 (ttp) cc_final: 0.7815 (ttt) REVERT: Ai 177 LYS cc_start: 0.8402 (mtpm) cc_final: 0.7920 (mptt) REVERT: Ai 181 MET cc_start: 0.7413 (tpt) cc_final: 0.6947 (mtt) REVERT: Aj 102 ASP cc_start: 0.9009 (t0) cc_final: 0.8788 (t0) REVERT: Aj 172 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7302 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8197 (mtpp) cc_final: 0.7701 (mptt) REVERT: Aj 181 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6938 (mtm) REVERT: Ak 99 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8221 (tp) REVERT: Ak 181 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6924 (mtm) REVERT: Al 177 LYS cc_start: 0.8159 (mtpm) cc_final: 0.7602 (mptt) REVERT: Am 99 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8249 (tp) REVERT: Am 121 GLU cc_start: 0.8174 (tp30) cc_final: 0.7519 (mt-10) REVERT: Am 139 GLU cc_start: 0.8183 (tt0) cc_final: 0.7785 (tm-30) REVERT: Am 168 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7953 (mt-10) REVERT: Am 177 LYS cc_start: 0.8191 (mtpm) cc_final: 0.7629 (mppt) REVERT: An 91 ASP cc_start: 0.8685 (m-30) cc_final: 0.8363 (m-30) REVERT: An 95 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7974 (mp0) REVERT: An 99 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8165 (tp) REVERT: An 102 ASP cc_start: 0.8731 (t0) cc_final: 0.8321 (t0) REVERT: An 121 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7806 (tp30) REVERT: An 153 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8583 (mmtm) REVERT: An 173 MET cc_start: 0.8056 (ttp) cc_final: 0.7511 (ttt) REVERT: An 177 LYS cc_start: 0.8211 (mtpm) cc_final: 0.7622 (mptt) REVERT: An 181 MET cc_start: 0.7674 (tpt) cc_final: 0.7159 (mtm) REVERT: Ao 60 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8231 (mptt) REVERT: Ao 91 ASP cc_start: 0.8840 (m-30) cc_final: 0.8569 (m-30) REVERT: Ao 139 GLU cc_start: 0.8157 (pt0) cc_final: 0.7763 (tt0) REVERT: Ao 153 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.7525 (mptp) REVERT: Ao 173 MET cc_start: 0.7983 (ttp) cc_final: 0.7394 (ttt) REVERT: Ao 177 LYS cc_start: 0.8320 (mtpm) cc_final: 0.7931 (mtmm) REVERT: Ap 60 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.7187 (mptt) REVERT: Ap 116 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8857 (ttp) REVERT: Ap 173 MET cc_start: 0.8160 (ttp) cc_final: 0.7727 (ttt) REVERT: Ap 181 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7112 (mtt) REVERT: Aq 60 LYS cc_start: 0.8428 (mmtt) cc_final: 0.8205 (mmtm) REVERT: Aq 153 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.7529 (mptp) REVERT: Aq 177 LYS cc_start: 0.8192 (mtpm) cc_final: 0.7566 (mptt) REVERT: Aq 181 MET cc_start: 0.7516 (OUTLIER) cc_final: 0.7006 (mtm) REVERT: Ar 77 GLN cc_start: 0.8556 (mt0) cc_final: 0.7572 (mp10) REVERT: Ar 99 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8320 (tp) REVERT: Ar 168 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7782 (mt-10) REVERT: Ar 173 MET cc_start: 0.8188 (ttp) cc_final: 0.7665 (ttt) REVERT: Ar 177 LYS cc_start: 0.8259 (mtpp) cc_final: 0.7986 (mtmm) REVERT: As 153 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.7421 (mptp) REVERT: As 181 MET cc_start: 0.7422 (OUTLIER) cc_final: 0.6951 (mtm) outliers start: 120 outliers final: 51 residues processed: 796 average time/residue: 1.6754 time to fit residues: 1477.8298 Evaluate side-chains 835 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 751 time to evaluate : 2.793 ------------------------------------------------------------------------------- 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 121 GLU Chi-restraints excluded: chain Ab residue 181 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 54 MET 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 99 LEU 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 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 48 LYS Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 153 LYS 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 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 71 LEU Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 99 LEU 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 60 LYS Chi-restraints excluded: chain Ao residue 71 LEU 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 Ap residue 181 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 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 257 optimal weight: 5.9990 chunk 253 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 225 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 216 optimal weight: 0.5980 chunk 223 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Ac 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ad 113 ASN Ae 77 GLN Af 113 ASN Ag 113 ASN Ah 113 ASN Aj 113 ASN ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** An 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3858 r_free = 0.3858 target = 0.158711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.133559 restraints weight = 24287.426| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.03 r_work: 0.3340 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 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 = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22914 Z= 0.297 Angle : 0.573 6.170 31103 Z= 0.289 Chirality : 0.042 0.185 3420 Planarity : 0.005 0.038 4009 Dihedral : 4.248 16.477 3040 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 4.25 % Allowed : 23.72 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.16), residues: 2755 helix: 1.59 (0.15), residues: 988 sheet: 0.90 (0.31), residues: 228 loop : -1.15 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAf 132 HIS 0.003 0.001 HISAg 69 PHE 0.013 0.002 PHEAi 163 TYR 0.018 0.002 TYRAg 180 ARG 0.008 0.001 ARGAe 55 *********************** 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 849 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 744 time to evaluate : 2.494 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: 0.9103 (mmp) cc_final: 0.8772 (mmt) REVERT: Aa 173 MET cc_start: 0.8000 (ttp) cc_final: 0.7541 (ttt) REVERT: Aa 177 LYS cc_start: 0.8271 (mtpm) cc_final: 0.7607 (mptt) REVERT: Aa 181 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.6984 (mtt) REVERT: Ab 76 GLN cc_start: 0.8578 (mt0) cc_final: 0.8116 (mt0) REVERT: Ab 99 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8285 (tp) REVERT: Ab 108 MET cc_start: 0.9025 (tpt) cc_final: 0.8741 (mmp) REVERT: Ab 113 ASN cc_start: 0.8929 (m110) cc_final: 0.8613 (m110) REVERT: Ab 121 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: Ab 173 MET cc_start: 0.8106 (ttp) cc_final: 0.7796 (ttp) REVERT: Ac 69 HIS cc_start: 0.7945 (m170) cc_final: 0.7736 (m-70) REVERT: Ac 99 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8200 (tp) REVERT: Ac 108 MET cc_start: 0.9095 (tpt) cc_final: 0.8789 (mmp) REVERT: Ac 139 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7596 (mt-10) REVERT: Ac 142 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8293 (mp0) REVERT: Ac 173 MET cc_start: 0.7969 (ttp) cc_final: 0.7595 (ttp) REVERT: Ac 177 LYS cc_start: 0.8161 (mtpp) cc_final: 0.7566 (mptt) REVERT: Ac 181 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.6956 (mtm) REVERT: Ad 91 ASP cc_start: 0.8672 (m-30) cc_final: 0.8450 (m-30) REVERT: Ad 95 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: Ad 181 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6952 (mtt) REVERT: Ae 121 GLU cc_start: 0.7953 (tp30) cc_final: 0.7659 (tm-30) REVERT: Ae 173 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8052 (ttp) REVERT: Ae 181 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.6950 (mtt) REVERT: Af 69 HIS cc_start: 0.8194 (m-70) cc_final: 0.6526 (t70) REVERT: Af 95 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8348 (mp0) REVERT: Af 181 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6819 (mtm) REVERT: Ag 116 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8838 (tmm) REVERT: Ag 168 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7818 (mt-10) REVERT: Ah 91 ASP cc_start: 0.8810 (m-30) cc_final: 0.8589 (m-30) REVERT: Ah 173 MET cc_start: 0.8174 (ttp) cc_final: 0.7692 (ttt) REVERT: Ah 177 LYS cc_start: 0.8152 (mtpm) cc_final: 0.7646 (mptt) REVERT: Ai 69 HIS cc_start: 0.7906 (m-70) cc_final: 0.6197 (t-90) REVERT: Ai 99 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8270 (tp) REVERT: Ai 153 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.7006 (mptp) REVERT: Ai 168 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7729 (mt-10) REVERT: Ai 173 MET cc_start: 0.8262 (ttp) cc_final: 0.7830 (ttt) REVERT: Ai 177 LYS cc_start: 0.8398 (mtpm) cc_final: 0.7931 (mptt) REVERT: Ai 181 MET cc_start: 0.7436 (tpt) cc_final: 0.6962 (mtt) REVERT: Aj 102 ASP cc_start: 0.8974 (t0) cc_final: 0.8748 (t0) REVERT: Aj 172 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7332 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8187 (mtpp) cc_final: 0.7672 (mptt) REVERT: Aj 181 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6950 (mtm) REVERT: Ak 99 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8223 (tp) REVERT: Ak 181 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.6899 (mtm) REVERT: Al 172 GLU cc_start: 0.7597 (mm-30) cc_final: 0.6687 (mt-10) REVERT: Al 177 LYS cc_start: 0.8155 (mtpm) cc_final: 0.7601 (mptt) REVERT: Am 99 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8259 (tp) REVERT: Am 121 GLU cc_start: 0.8160 (tp30) cc_final: 0.7511 (mt-10) REVERT: Am 139 GLU cc_start: 0.8179 (tt0) cc_final: 0.7773 (tm-30) REVERT: Am 168 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7933 (mt-10) REVERT: Am 177 LYS cc_start: 0.8162 (mtpm) cc_final: 0.7627 (mppt) REVERT: An 95 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8026 (mp0) REVERT: An 99 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8164 (tp) REVERT: An 102 ASP cc_start: 0.8785 (t0) cc_final: 0.8366 (t0) REVERT: An 121 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7782 (tp30) REVERT: An 153 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8599 (mmtm) REVERT: An 173 MET cc_start: 0.7951 (ttp) cc_final: 0.7315 (ttt) REVERT: An 177 LYS cc_start: 0.8188 (mtpm) cc_final: 0.7584 (mptt) REVERT: An 181 MET cc_start: 0.7716 (tpt) cc_final: 0.7158 (mtm) REVERT: Ao 60 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8206 (mptt) REVERT: Ao 91 ASP cc_start: 0.8824 (m-30) cc_final: 0.8562 (m-30) REVERT: Ao 99 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8165 (tp) REVERT: Ao 153 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.7505 (mptp) REVERT: Ao 173 MET cc_start: 0.7938 (ttp) cc_final: 0.7339 (ttt) REVERT: Ao 177 LYS cc_start: 0.8326 (mtpm) cc_final: 0.7923 (mtmm) REVERT: Ap 60 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.7231 (mptt) REVERT: Ap 116 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8816 (ttp) REVERT: Ap 173 MET cc_start: 0.8135 (ttp) cc_final: 0.7691 (ttt) REVERT: Ap 181 MET cc_start: 0.7592 (OUTLIER) cc_final: 0.7082 (mtt) REVERT: Aq 60 LYS cc_start: 0.8408 (mmtt) cc_final: 0.8188 (mmtm) REVERT: Aq 99 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8234 (tp) REVERT: Aq 153 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.7527 (mptp) REVERT: Aq 177 LYS cc_start: 0.8178 (mtpm) cc_final: 0.7579 (mptt) REVERT: Aq 181 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.6978 (mtm) REVERT: Ar 77 GLN cc_start: 0.8528 (mt0) cc_final: 0.7480 (mp10) REVERT: Ar 99 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8318 (tp) REVERT: Ar 173 MET cc_start: 0.8176 (ttp) cc_final: 0.7656 (ttt) REVERT: Ar 177 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7977 (mtmm) REVERT: As 121 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7455 (tp30) REVERT: As 153 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.7426 (mptp) outliers start: 105 outliers final: 52 residues processed: 781 average time/residue: 1.7258 time to fit residues: 1496.4679 Evaluate side-chains 827 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 742 time to evaluate : 2.587 ------------------------------------------------------------------------------- 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 121 GLU 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 146 LYS Chi-restraints excluded: chain Ae residue 173 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 116 MET 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 187 VAL Chi-restraints excluded: chain Ah residue 48 LYS Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 153 LYS 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 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 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 99 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 99 LEU Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain An residue 187 VAL Chi-restraints excluded: chain Ao residue 60 LYS Chi-restraints excluded: chain Ao residue 71 LEU Chi-restraints excluded: chain Ao residue 99 LEU 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 99 LEU 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 116 MET Chi-restraints excluded: chain As residue 71 LEU 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 37 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 253 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 69 HIS Aj 113 ASN An 69 HIS 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 = 0.3882 r_free = 0.3882 target = 0.161107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136091 restraints weight = 24307.350| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.03 r_work: 0.3369 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 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 = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22914 Z= 0.209 Angle : 0.534 5.706 31103 Z= 0.270 Chirality : 0.040 0.160 3420 Planarity : 0.005 0.039 4009 Dihedral : 4.025 16.602 3040 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.44 % Allowed : 24.94 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2755 helix: 1.82 (0.16), residues: 988 sheet: 1.00 (0.31), residues: 228 loop : -1.05 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAf 132 HIS 0.003 0.000 HISAg 69 PHE 0.011 0.002 PHEAi 163 TYR 0.018 0.001 TYRAh 180 ARG 0.008 0.001 ARGAe 55 *********************** 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 808 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 723 time to evaluate : 2.496 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 160 MET cc_start: 0.9089 (mmp) cc_final: 0.8610 (mmt) REVERT: Aa 173 MET cc_start: 0.7940 (ttp) cc_final: 0.7500 (ttt) REVERT: Aa 177 LYS cc_start: 0.8273 (mtpm) cc_final: 0.7501 (mptt) REVERT: Aa 181 MET cc_start: 0.7580 (mmt) cc_final: 0.7016 (mtt) REVERT: Ab 76 GLN cc_start: 0.8520 (mt0) cc_final: 0.8055 (mt0) REVERT: Ab 99 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8284 (tp) REVERT: Ab 108 MET cc_start: 0.9036 (tpt) cc_final: 0.8744 (mmp) REVERT: Ab 121 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7555 (tm-30) REVERT: Ab 160 MET cc_start: 0.9112 (tpt) cc_final: 0.8855 (mmm) REVERT: Ab 173 MET cc_start: 0.7978 (ttp) cc_final: 0.7661 (ttp) REVERT: Ac 69 HIS cc_start: 0.7933 (m170) cc_final: 0.7733 (m-70) REVERT: Ac 108 MET cc_start: 0.9076 (tpt) cc_final: 0.8692 (mmp) REVERT: Ac 139 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7604 (mt-10) REVERT: Ac 142 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8316 (mp0) REVERT: Ac 173 MET cc_start: 0.7858 (ttp) cc_final: 0.7445 (ttp) REVERT: Ac 177 LYS cc_start: 0.8175 (mtpp) cc_final: 0.7558 (mptt) REVERT: Ac 181 MET cc_start: 0.7511 (mmt) cc_final: 0.6935 (mtm) REVERT: Ad 91 ASP cc_start: 0.8687 (m-30) cc_final: 0.8471 (m-30) REVERT: Ad 95 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8011 (mp0) REVERT: Ad 160 MET cc_start: 0.9281 (mmp) cc_final: 0.8796 (mmp) REVERT: Ad 177 LYS cc_start: 0.8281 (mtmt) cc_final: 0.7465 (mptt) REVERT: Ad 181 MET cc_start: 0.7312 (mmt) cc_final: 0.6923 (mtt) REVERT: Ae 99 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8240 (tp) REVERT: Ae 121 GLU cc_start: 0.7965 (tp30) cc_final: 0.7671 (tm-30) REVERT: Ae 139 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7614 (pt0) REVERT: Ae 173 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7929 (ttp) REVERT: Ae 181 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6935 (mtt) REVERT: Af 69 HIS cc_start: 0.8179 (m-70) cc_final: 0.6508 (t70) REVERT: Af 95 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: Af 181 MET cc_start: 0.7392 (mmt) cc_final: 0.6791 (mtm) REVERT: Ag 116 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.8851 (tmm) REVERT: Ag 168 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7795 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8197 (mtpm) cc_final: 0.7507 (mptt) REVERT: Ag 181 MET cc_start: 0.7785 (mmt) cc_final: 0.7493 (tpp) REVERT: Ah 91 ASP cc_start: 0.8779 (m-30) cc_final: 0.8569 (m-30) REVERT: Ah 99 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8268 (tp) REVERT: Ah 139 GLU cc_start: 0.7860 (tt0) cc_final: 0.7652 (tm-30) REVERT: Ah 173 MET cc_start: 0.8102 (ttp) cc_final: 0.7581 (ttt) REVERT: Ah 177 LYS cc_start: 0.8102 (mtpm) cc_final: 0.7560 (mptt) REVERT: Ah 181 MET cc_start: 0.7742 (mmt) cc_final: 0.6974 (mpp) REVERT: Ai 69 HIS cc_start: 0.7876 (m-70) cc_final: 0.6146 (t-90) REVERT: Ai 121 GLU cc_start: 0.8251 (tp30) cc_final: 0.7783 (tp30) REVERT: Ai 153 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.6952 (mptp) REVERT: Ai 168 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7690 (mt-10) REVERT: Ai 173 MET cc_start: 0.8223 (ttp) cc_final: 0.7780 (ttt) REVERT: Ai 177 LYS cc_start: 0.8377 (mtpm) cc_final: 0.7915 (mptt) REVERT: Ai 181 MET cc_start: 0.7477 (tpt) cc_final: 0.6992 (mtt) REVERT: Aj 69 HIS cc_start: 0.7916 (m90) cc_final: 0.7715 (m-70) REVERT: Aj 102 ASP cc_start: 0.8930 (t0) cc_final: 0.8726 (t0) REVERT: Aj 172 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7297 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8168 (mtpp) cc_final: 0.7661 (mptt) REVERT: Aj 181 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6888 (mtm) REVERT: Ak 99 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8230 (tp) REVERT: Ak 181 MET cc_start: 0.7646 (mmt) cc_final: 0.6916 (mtm) REVERT: Al 177 LYS cc_start: 0.8072 (mtpm) cc_final: 0.7481 (mptt) REVERT: Am 99 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8261 (tp) REVERT: Am 113 ASN cc_start: 0.8623 (m-40) cc_final: 0.8366 (m110) REVERT: Am 121 GLU cc_start: 0.8214 (tp30) cc_final: 0.7517 (mt-10) REVERT: Am 139 GLU cc_start: 0.8181 (tt0) cc_final: 0.7817 (tt0) REVERT: Am 168 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7904 (mt-10) REVERT: Am 177 LYS cc_start: 0.8102 (mtpm) cc_final: 0.7514 (mptt) REVERT: An 95 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8035 (mp0) REVERT: An 99 LEU cc_start: 0.8488 (tt) cc_final: 0.8157 (tp) REVERT: An 102 ASP cc_start: 0.8774 (t0) cc_final: 0.8346 (t0) REVERT: An 121 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7803 (tp30) REVERT: An 153 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8606 (mmtm) REVERT: An 173 MET cc_start: 0.7884 (ttp) cc_final: 0.7287 (ttt) REVERT: An 177 LYS cc_start: 0.8190 (mtpm) cc_final: 0.7576 (mptt) REVERT: An 181 MET cc_start: 0.7674 (tpt) cc_final: 0.7142 (mtm) REVERT: Ao 46 ARG cc_start: 0.9357 (mpt180) cc_final: 0.8985 (mpt180) REVERT: Ao 91 ASP cc_start: 0.8816 (m-30) cc_final: 0.8562 (m-30) REVERT: Ao 99 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8152 (tp) REVERT: Ao 121 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7459 (tm-30) REVERT: Ao 139 GLU cc_start: 0.8171 (pt0) cc_final: 0.7771 (tt0) REVERT: Ao 153 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.7471 (mptp) REVERT: Ao 173 MET cc_start: 0.7847 (ttp) cc_final: 0.7322 (ttt) REVERT: Ao 177 LYS cc_start: 0.8319 (mtpm) cc_final: 0.7777 (mptt) REVERT: Ap 60 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.7298 (mptt) REVERT: Ap 116 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8736 (ttp) REVERT: Ap 173 MET cc_start: 0.8034 (ttp) cc_final: 0.7599 (ttt) REVERT: Ap 181 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7104 (mtt) REVERT: Aq 60 LYS cc_start: 0.8413 (mmtt) cc_final: 0.8017 (mmtm) REVERT: Aq 177 LYS cc_start: 0.8215 (mtpm) cc_final: 0.7613 (mptt) REVERT: Aq 181 MET cc_start: 0.7478 (OUTLIER) cc_final: 0.6962 (mtm) REVERT: Ar 77 GLN cc_start: 0.8511 (mt0) cc_final: 0.7475 (mp-120) REVERT: Ar 99 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8348 (tp) REVERT: Ar 139 GLU cc_start: 0.8060 (pt0) cc_final: 0.7797 (tt0) REVERT: Ar 173 MET cc_start: 0.8113 (ttp) cc_final: 0.7600 (ttt) REVERT: Ar 177 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7988 (mtmm) REVERT: As 121 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7650 (tm-30) REVERT: As 153 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.7396 (mptp) outliers start: 85 outliers final: 50 residues processed: 757 average time/residue: 1.6775 time to fit residues: 1407.3537 Evaluate side-chains 795 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 721 time to evaluate : 2.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Aa residue 99 LEU 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 181 MET 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 139 GLU 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 99 LEU Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 146 LYS Chi-restraints excluded: chain Ae residue 173 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 116 MET Chi-restraints excluded: chain Af residue 160 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 48 LYS Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ai residue 95 GLU Chi-restraints excluded: chain Ai residue 153 LYS 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 Al residue 58 LYS Chi-restraints excluded: chain Al residue 80 ILE 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 99 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 116 MET 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 99 LEU 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 116 MET 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 71 LEU 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 93 optimal weight: 3.9990 chunk 210 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 247 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 Af 113 ASN Ag 113 ASN Ah 113 ASN ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Al 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 69 HIS ** An 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.157721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132471 restraints weight = 24369.573| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.02 r_work: 0.3328 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22914 Z= 0.353 Angle : 0.609 8.542 31103 Z= 0.308 Chirality : 0.044 0.210 3420 Planarity : 0.005 0.041 4009 Dihedral : 4.363 16.617 3040 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.52 % Allowed : 25.02 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2755 helix: 1.51 (0.15), residues: 988 sheet: 0.83 (0.31), residues: 228 loop : -1.09 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAf 132 HIS 0.004 0.001 HISAg 69 PHE 0.015 0.002 PHEAi 163 TYR 0.020 0.002 TYRAh 180 ARG 0.009 0.001 ARGAe 55 ********************** 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 841 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 754 time to evaluate : 2.567 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: 0.9130 (mmp) cc_final: 0.8863 (mmt) REVERT: Aa 173 MET cc_start: 0.8016 (ttp) cc_final: 0.7561 (ttt) REVERT: Aa 177 LYS cc_start: 0.8260 (mtpm) cc_final: 0.7489 (mptt) REVERT: Aa 181 MET cc_start: 0.7602 (mmt) cc_final: 0.7027 (mtt) REVERT: Ab 76 GLN cc_start: 0.8588 (mt0) cc_final: 0.8114 (mt0) REVERT: Ab 88 SER cc_start: 0.8789 (p) cc_final: 0.8529 (p) REVERT: Ab 99 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8268 (tp) REVERT: Ab 108 MET cc_start: 0.9010 (tpt) cc_final: 0.8737 (mmp) REVERT: Ab 113 ASN cc_start: 0.9016 (m110) cc_final: 0.8799 (m-40) REVERT: Ab 121 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7591 (tm-30) REVERT: Ab 172 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7034 (mm-30) REVERT: Ab 173 MET cc_start: 0.8097 (ttp) cc_final: 0.7793 (ttp) REVERT: Ac 88 SER cc_start: 0.8824 (p) cc_final: 0.8537 (p) REVERT: Ac 108 MET cc_start: 0.9072 (tpt) cc_final: 0.8768 (mmp) REVERT: Ac 139 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: Ac 173 MET cc_start: 0.7995 (ttp) cc_final: 0.7771 (ttp) REVERT: Ac 181 MET cc_start: 0.7506 (mmt) cc_final: 0.6924 (mtm) REVERT: Ad 95 GLU cc_start: 0.8492 (mp0) cc_final: 0.8047 (mp0) REVERT: Ad 177 LYS cc_start: 0.8294 (mtmt) cc_final: 0.7515 (mptt) REVERT: Ad 181 MET cc_start: 0.7311 (mmt) cc_final: 0.6962 (mtt) REVERT: Ae 99 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8213 (tp) REVERT: Ae 121 GLU cc_start: 0.7975 (tp30) cc_final: 0.7667 (tm-30) REVERT: Ae 173 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8070 (ttp) REVERT: Ae 181 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.6936 (mtt) REVERT: Af 69 HIS cc_start: 0.8221 (m-70) cc_final: 0.6644 (t70) REVERT: Af 95 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: Af 181 MET cc_start: 0.7461 (mmt) cc_final: 0.6826 (mtm) REVERT: Ag 116 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8853 (tmm) REVERT: Ag 168 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7840 (mt-10) REVERT: Ah 91 ASP cc_start: 0.8814 (m-30) cc_final: 0.8605 (m-30) REVERT: Ah 99 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8284 (tp) REVERT: Ah 173 MET cc_start: 0.8189 (ttp) cc_final: 0.7703 (ttt) REVERT: Ah 177 LYS cc_start: 0.8140 (mtpm) cc_final: 0.7612 (mptt) REVERT: Ai 69 HIS cc_start: 0.7962 (m-70) cc_final: 0.6237 (t-90) REVERT: Ai 99 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8288 (tp) REVERT: Ai 121 GLU cc_start: 0.8269 (tp30) cc_final: 0.7797 (tp30) REVERT: Ai 153 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.6996 (mptp) REVERT: Ai 168 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7732 (mt-10) REVERT: Ai 173 MET cc_start: 0.8267 (ttp) cc_final: 0.7826 (ttt) REVERT: Ai 177 LYS cc_start: 0.8374 (mtpm) cc_final: 0.7914 (mptt) REVERT: Ai 181 MET cc_start: 0.7434 (tpt) cc_final: 0.7009 (mtt) REVERT: Aj 69 HIS cc_start: 0.7967 (m90) cc_final: 0.7736 (m-70) REVERT: Aj 102 ASP cc_start: 0.8969 (t0) cc_final: 0.8754 (t0) REVERT: Aj 172 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7336 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7652 (mptt) REVERT: Aj 181 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.6960 (mtm) REVERT: Ak 60 LYS cc_start: 0.8584 (mmtt) cc_final: 0.8328 (mmtm) REVERT: Ak 99 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8218 (tp) REVERT: Ak 181 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6939 (mtm) REVERT: Al 172 GLU cc_start: 0.7617 (mm-30) cc_final: 0.6686 (mt-10) REVERT: Al 177 LYS cc_start: 0.8115 (mtpm) cc_final: 0.7536 (mptt) REVERT: Am 99 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8261 (tp) REVERT: Am 116 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8652 (ttm) REVERT: Am 121 GLU cc_start: 0.8173 (tp30) cc_final: 0.7510 (mt-10) REVERT: Am 139 GLU cc_start: 0.8162 (tt0) cc_final: 0.7761 (tm-30) REVERT: Am 168 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7960 (mt-10) REVERT: Am 177 LYS cc_start: 0.8157 (mtpm) cc_final: 0.7622 (mppt) REVERT: An 95 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8251 (mm-30) REVERT: An 99 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8176 (tp) REVERT: An 102 ASP cc_start: 0.8778 (t0) cc_final: 0.8356 (t0) REVERT: An 121 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7808 (tp30) REVERT: An 153 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8617 (mmtm) REVERT: An 173 MET cc_start: 0.8002 (ttp) cc_final: 0.7375 (ttt) REVERT: An 177 LYS cc_start: 0.8233 (mtpm) cc_final: 0.7651 (mptt) REVERT: An 181 MET cc_start: 0.7724 (tpt) cc_final: 0.7198 (mtm) REVERT: Ao 91 ASP cc_start: 0.8803 (m-30) cc_final: 0.8538 (m-30) REVERT: Ao 99 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8172 (tp) REVERT: Ao 153 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.7557 (mptp) REVERT: Ao 173 MET cc_start: 0.7999 (ttp) cc_final: 0.7408 (ttt) REVERT: Ao 177 LYS cc_start: 0.8343 (mtpm) cc_final: 0.7926 (mtmm) REVERT: Ap 60 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7221 (mptt) REVERT: Ap 116 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8846 (ttp) REVERT: Ap 153 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8418 (mmtt) REVERT: Ap 173 MET cc_start: 0.8146 (ttp) cc_final: 0.7717 (ttt) REVERT: Ap 181 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7130 (OUTLIER) REVERT: Aq 60 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8237 (mmtm) REVERT: Aq 153 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.7533 (mptp) REVERT: Aq 177 LYS cc_start: 0.8220 (mtpm) cc_final: 0.7624 (mptt) REVERT: Aq 181 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.7029 (mtt) REVERT: Ar 77 GLN cc_start: 0.8560 (mt0) cc_final: 0.7579 (mp10) REVERT: Ar 99 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8344 (tp) REVERT: Ar 173 MET cc_start: 0.8205 (ttp) cc_final: 0.7696 (ttt) REVERT: Ar 177 LYS cc_start: 0.8332 (mtpp) cc_final: 0.8040 (mtmm) REVERT: As 153 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.7395 (mptp) outliers start: 87 outliers final: 52 residues processed: 783 average time/residue: 1.7361 time to fit residues: 1507.5380 Evaluate side-chains 830 residues out of total 2470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 751 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Aa residue 99 LEU 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 95 GLU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 139 GLU Chi-restraints excluded: chain Ac residue 187 VAL Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ae residue 77 GLN Chi-restraints excluded: chain Ae residue 99 LEU Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 146 LYS Chi-restraints excluded: chain Ae residue 173 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 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 67 LEU Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 99 LEU Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 153 LYS 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 80 ILE 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 Al residue 181 MET 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 99 LEU 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 99 LEU 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 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 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 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 84 optimal weight: 7.9990 chunk 225 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 233 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 158 optimal weight: 4.9990 chunk 199 optimal weight: 0.8980 chunk 227 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 An 69 HIS Ap 113 ASN As 113 ASN As 151 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.160178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135227 restraints weight = 24236.863| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.00 r_work: 0.3361 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22914 Z= 0.241 Angle : 0.561 7.662 31103 Z= 0.283 Chirality : 0.042 0.178 3420 Planarity : 0.005 0.040 4009 Dihedral : 4.168 16.719 3040 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.60 % Allowed : 25.34 % Favored : 71.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2755 helix: 1.66 (0.15), residues: 988 sheet: 0.87 (0.31), residues: 228 loop : -1.00 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAf 132 HIS 0.005 0.001 HISAg 69 PHE 0.012 0.002 PHEAq 163 TYR 0.017 0.001 TYRAh 180 ARG 0.008 0.001 ARGAe 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24336.66 seconds wall clock time: 429 minutes 44.11 seconds (25784.11 seconds total)