Starting phenix.real_space_refine on Sun Sep 29 11:31:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opf_17051/09_2024/8opf_17051.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opf_17051/09_2024/8opf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opf_17051/09_2024/8opf_17051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opf_17051/09_2024/8opf_17051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opf_17051/09_2024/8opf_17051.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8opf_17051/09_2024/8opf_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 5.14, 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: 5.58 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: 2.35 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: 6.07 Time building geometry restraints manager: 6.53 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: 0.00 Found NCS groups: ncs_group { reference = chain 'Aa' selection = chain 'Ab' selection = chain 'Ac' selection = chain 'Ad' selection = chain 'Ae' selection = chain 'Af' selection = chain 'Ag' selection = chain 'Ah' selection = chain 'Ai' selection = chain 'Aj' selection = chain 'Ak' selection = chain 'Al' selection = chain 'Am' selection = chain 'An' selection = chain 'Ao' selection = chain 'Ap' selection = chain 'Aq' selection = chain 'Ar' selection = chain 'As' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 39.860 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.660 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 13 poor density : 736 time to evaluate : 2.467 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: 1.5403 time to fit residues: 1271.3591 Evaluate side-chains 694 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 693 time to evaluate : 2.566 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 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 fitting. rotamer outliers: 111 poor density : 748 time to evaluate : 2.639 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: 0.8657 (m-30) cc_final: 0.8396 (m-30) REVERT: Aa 134 MET cc_start: 0.9079 (ttt) cc_final: 0.8556 (ttt) REVERT: Aa 160 MET cc_start: 0.9134 (mmp) cc_final: 0.8749 (mmt) REVERT: Aa 168 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7455 (mt-10) REVERT: Ab 76 GLN cc_start: 0.8437 (mt0) cc_final: 0.7953 (mt0) REVERT: Ab 99 LEU cc_start: 0.8584 (tt) cc_final: 0.8272 (tp) REVERT: Ab 113 ASN cc_start: 0.8867 (m110) cc_final: 0.8667 (m110) REVERT: Ab 121 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7314 (tm-30) REVERT: Ab 127 ASN cc_start: 0.8437 (t0) cc_final: 0.8195 (t0) REVERT: Ab 173 MET cc_start: 0.7699 (ttp) cc_final: 0.7400 (ttp) REVERT: Ab 177 LYS cc_start: 0.8260 (mtpp) cc_final: 0.7921 (mptt) REVERT: Ac 121 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7412 (tm-30) REVERT: Ac 173 MET cc_start: 0.7637 (ttp) cc_final: 0.7344 (ttp) REVERT: Ac 177 LYS cc_start: 0.8170 (mtpp) cc_final: 0.7808 (mptt) REVERT: Ad 56 MET cc_start: 0.8776 (mmp) cc_final: 0.8475 (mmm) REVERT: Ad 168 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7535 (mt-10) REVERT: Ad 173 MET cc_start: 0.7813 (ttp) cc_final: 0.7549 (ttp) REVERT: Ae 56 MET cc_start: 0.8779 (mmp) cc_final: 0.8556 (mmt) REVERT: Ae 139 GLU cc_start: 0.7530 (pt0) cc_final: 0.6813 (pm20) REVERT: Ae 173 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7703 (ttp) REVERT: Af 46 ARG cc_start: 0.9257 (mpt180) cc_final: 0.8962 (mpt180) REVERT: Af 60 LYS cc_start: 0.8647 (mptm) cc_final: 0.8436 (mptt) REVERT: Af 69 HIS cc_start: 0.8160 (m-70) cc_final: 0.6851 (t-90) REVERT: Af 95 GLU cc_start: 0.8256 (mp0) cc_final: 0.7901 (mp0) REVERT: Af 153 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8483 (mmtt) REVERT: Af 168 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7470 (mt-10) REVERT: Af 173 MET cc_start: 0.7759 (ttp) cc_final: 0.7542 (ttp) REVERT: Af 177 LYS cc_start: 0.8211 (mtpp) cc_final: 0.7697 (mptt) REVERT: Ag 50 ILE cc_start: 0.8282 (mm) cc_final: 0.7982 (mm) REVERT: Ag 108 MET cc_start: 0.9026 (tpt) cc_final: 0.8819 (tpt) REVERT: Ag 116 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8859 (tmm) REVERT: Ag 139 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.6891 (pm20) REVERT: Ag 177 LYS cc_start: 0.8130 (mtpp) cc_final: 0.7711 (mptt) REVERT: Ag 181 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6766 (mtm) REVERT: Ah 71 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8521 (mt) REVERT: Ah 76 GLN cc_start: 0.8449 (mt0) cc_final: 0.8058 (mt0) REVERT: Ah 173 MET cc_start: 0.7757 (ttp) cc_final: 0.7280 (ttt) REVERT: Ah 177 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7634 (mptt) REVERT: Ah 181 MET cc_start: 0.7131 (OUTLIER) cc_final: 0.6823 (mtm) REVERT: Ai 67 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8642 (mp) REVERT: Ai 99 LEU cc_start: 0.8637 (tt) cc_final: 0.8243 (tp) REVERT: Ai 108 MET cc_start: 0.9008 (tpt) cc_final: 0.8788 (tpt) REVERT: Ai 153 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.7210 (mptp) REVERT: Ai 173 MET cc_start: 0.7832 (ttp) cc_final: 0.7473 (ttt) REVERT: Aj 67 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8426 (mp) REVERT: Aj 139 GLU cc_start: 0.7580 (pt0) cc_final: 0.7329 (pt0) REVERT: Aj 168 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7564 (mt-10) REVERT: Aj 177 LYS cc_start: 0.8191 (mtpp) cc_final: 0.7786 (mptt) REVERT: Aj 181 MET cc_start: 0.6996 (mmt) cc_final: 0.6788 (mtm) REVERT: Ak 173 MET cc_start: 0.7649 (ttp) cc_final: 0.7194 (ttt) REVERT: Ak 177 LYS cc_start: 0.8112 (mtpp) cc_final: 0.7724 (mptt) REVERT: Ak 181 MET cc_start: 0.7057 (OUTLIER) cc_final: 0.6771 (mtm) REVERT: Al 168 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7480 (mt-10) REVERT: Al 177 LYS cc_start: 0.8096 (mtpp) cc_final: 0.7757 (mptt) REVERT: Am 99 LEU cc_start: 0.8726 (tt) cc_final: 0.8316 (tp) REVERT: Am 108 MET cc_start: 0.9064 (tpt) cc_final: 0.8782 (tpt) REVERT: Am 139 GLU cc_start: 0.7600 (pt0) cc_final: 0.7249 (pt0) REVERT: Am 168 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7577 (mt-10) REVERT: An 67 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8539 (mp) REVERT: An 99 LEU cc_start: 0.8509 (tt) cc_final: 0.8104 (tp) REVERT: An 108 MET cc_start: 0.9003 (tpt) cc_final: 0.8382 (tpt) REVERT: An 135 MET cc_start: 0.9027 (mmm) cc_final: 0.8820 (mmm) REVERT: An 173 MET cc_start: 0.7747 (ttp) cc_final: 0.7282 (ttt) REVERT: Ao 56 MET cc_start: 0.8707 (mmp) cc_final: 0.8398 (mmt) REVERT: Ao 91 ASP cc_start: 0.8753 (m-30) cc_final: 0.8452 (m-30) REVERT: Ao 135 MET cc_start: 0.9101 (mmm) cc_final: 0.8834 (mmm) REVERT: Ao 153 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7624 (mptp) REVERT: Ao 173 MET cc_start: 0.7766 (ttp) cc_final: 0.7387 (ttt) REVERT: Ap 60 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.7509 (mptt) REVERT: Ap 91 ASP cc_start: 0.8714 (m-30) cc_final: 0.8510 (m-30) REVERT: Ap 116 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8862 (ttp) REVERT: Ap 168 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7373 (mt-10) REVERT: Ap 173 MET cc_start: 0.7791 (ttp) cc_final: 0.7429 (ttt) REVERT: Aq 60 LYS cc_start: 0.8462 (mmtt) cc_final: 0.8252 (mmtm) REVERT: Aq 91 ASP cc_start: 0.8690 (m-30) cc_final: 0.8286 (m-30) REVERT: Aq 112 MET cc_start: 0.9384 (mmp) cc_final: 0.9178 (mmp) REVERT: Aq 153 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.7478 (mptp) REVERT: Aq 160 MET cc_start: 0.9239 (mmt) cc_final: 0.8817 (mmt) REVERT: Aq 181 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6820 (mtm) REVERT: Ar 67 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8568 (mp) REVERT: Ar 91 ASP cc_start: 0.8742 (m-30) cc_final: 0.8512 (m-30) REVERT: Ar 168 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7405 (mt-10) REVERT: Ar 173 MET cc_start: 0.7771 (ttp) cc_final: 0.7324 (ttt) REVERT: As 56 MET cc_start: 0.8675 (mmt) cc_final: 0.8430 (mmt) outliers start: 111 outliers final: 15 residues processed: 769 average time/residue: 1.5816 time to fit residues: 1352.1007 Evaluate side-chains 779 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 746 time to evaluate : 3.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ae residue 173 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 153 LYS Chi-restraints excluded: chain Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 181 MET Chi-restraints excluded: chain Ar residue 67 LEU Chi-restraints excluded: chain Ar residue 116 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 134 optimal weight: 6.9990 chunk 74 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 241 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 239 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 113 ASN Ad 113 ASN Ae 77 GLN Ae 113 ASN Af 113 ASN Ag 113 ASN ** Ah 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ai 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 113 ASN ** Al 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** An 175 ASN Aq 113 ASN Ar 113 ASN As 113 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22914 Z= 0.253 Angle : 0.551 5.911 31103 Z= 0.280 Chirality : 0.041 0.173 3420 Planarity : 0.005 0.036 4009 Dihedral : 4.063 15.738 3040 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.85 % Allowed : 23.85 % Favored : 72.31 % 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: -0.05 (0.16), residues: 2755 helix: 1.59 (0.15), residues: 988 sheet: 1.53 (0.34), residues: 228 loop : -1.47 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAf 132 HIS 0.001 0.000 HISAc 69 PHE 0.012 0.002 PHEAb 163 TYR 0.018 0.001 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 846 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 751 time to evaluate : 2.378 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 91 ASP cc_start: 0.8661 (m-30) cc_final: 0.8390 (m-30) REVERT: Aa 160 MET cc_start: 0.9135 (mmp) cc_final: 0.8749 (mmt) REVERT: Aa 168 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7427 (mt-10) REVERT: Aa 173 MET cc_start: 0.7776 (ttp) cc_final: 0.7341 (ttt) REVERT: Aa 177 LYS cc_start: 0.8105 (mtpm) cc_final: 0.7740 (mptt) REVERT: Ab 99 LEU cc_start: 0.8628 (tt) cc_final: 0.8278 (tp) REVERT: Ab 121 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: Ab 127 ASN cc_start: 0.8458 (t0) cc_final: 0.8204 (t0) REVERT: Ab 139 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: Ab 173 MET cc_start: 0.7659 (ttp) cc_final: 0.7258 (ttt) REVERT: Ac 173 MET cc_start: 0.7581 (ttp) cc_final: 0.7232 (ttp) REVERT: Ac 177 LYS cc_start: 0.8179 (mtpp) cc_final: 0.7757 (mptt) REVERT: Ad 56 MET cc_start: 0.8791 (mmp) cc_final: 0.8473 (mmm) REVERT: Ad 160 MET cc_start: 0.9295 (mmp) cc_final: 0.8983 (mmp) REVERT: Ad 168 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7535 (mt-10) REVERT: Ad 173 MET cc_start: 0.7793 (ttp) cc_final: 0.7587 (ttp) REVERT: Ae 56 MET cc_start: 0.8789 (mmp) cc_final: 0.8521 (mmt) REVERT: Ae 139 GLU cc_start: 0.7635 (pt0) cc_final: 0.6870 (pm20) REVERT: Af 46 ARG cc_start: 0.9266 (mpt180) cc_final: 0.9000 (mpt180) REVERT: Af 69 HIS cc_start: 0.8060 (m-70) cc_final: 0.6823 (t-90) REVERT: Af 168 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7514 (mt-10) REVERT: Ag 116 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8872 (tmm) REVERT: Ag 168 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7467 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8116 (mtpp) cc_final: 0.7603 (mptt) REVERT: Ag 181 MET cc_start: 0.7060 (mmt) cc_final: 0.6812 (mtm) REVERT: Ah 71 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8536 (mt) REVERT: Ah 76 GLN cc_start: 0.8465 (mt0) cc_final: 0.8057 (mt0) REVERT: Ah 116 MET cc_start: 0.9001 (ttp) cc_final: 0.8793 (ttp) REVERT: Ah 173 MET cc_start: 0.7682 (ttp) cc_final: 0.7257 (ttt) REVERT: Ah 177 LYS cc_start: 0.8123 (mtpp) cc_final: 0.7732 (mptt) REVERT: Ah 181 MET cc_start: 0.7109 (mmt) cc_final: 0.6772 (mtm) REVERT: Ai 67 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8661 (mp) REVERT: Ai 99 LEU cc_start: 0.8621 (tt) cc_final: 0.8249 (tp) REVERT: Ai 108 MET cc_start: 0.9066 (tpt) cc_final: 0.8723 (mmm) REVERT: Ai 153 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7113 (mptp) REVERT: Ai 173 MET cc_start: 0.7779 (ttp) cc_final: 0.7411 (ttt) REVERT: Ai 177 LYS cc_start: 0.8190 (mtpm) cc_final: 0.7819 (mptt) REVERT: Aj 69 HIS cc_start: 0.8165 (m170) cc_final: 0.7941 (m-70) REVERT: Aj 168 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7532 (mt-10) REVERT: Aj 177 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7803 (mptt) REVERT: Ak 173 MET cc_start: 0.7570 (ttp) cc_final: 0.7143 (ttt) REVERT: Ak 177 LYS cc_start: 0.8120 (mtpp) cc_final: 0.7733 (mptt) REVERT: Al 168 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7437 (mt-10) REVERT: Al 177 LYS cc_start: 0.8108 (mtpp) cc_final: 0.7790 (mptt) REVERT: Am 168 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7557 (mt-10) REVERT: An 67 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8436 (mp) REVERT: An 99 LEU cc_start: 0.8439 (tt) cc_final: 0.8086 (tp) REVERT: An 108 MET cc_start: 0.9031 (tpt) cc_final: 0.8205 (tpt) REVERT: An 135 MET cc_start: 0.9016 (mmm) cc_final: 0.8702 (mmm) REVERT: An 173 MET cc_start: 0.7477 (ttp) cc_final: 0.7115 (ttt) REVERT: Ao 56 MET cc_start: 0.8729 (mmp) cc_final: 0.8384 (mmt) REVERT: Ao 91 ASP cc_start: 0.8754 (m-30) cc_final: 0.8488 (m-30) REVERT: Ao 135 MET cc_start: 0.9084 (mmm) cc_final: 0.8795 (mmm) REVERT: Ao 173 MET cc_start: 0.7739 (ttp) cc_final: 0.7338 (ttt) REVERT: Ao 177 LYS cc_start: 0.8294 (mtpp) cc_final: 0.8068 (mtmm) REVERT: Ap 91 ASP cc_start: 0.8701 (m-30) cc_final: 0.8474 (m-30) REVERT: Ap 99 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8022 (mt) REVERT: Ap 108 MET cc_start: 0.9090 (tpt) cc_final: 0.8709 (tpt) REVERT: Ap 116 MET cc_start: 0.9081 (OUTLIER) cc_final: 0.8836 (ttp) REVERT: Ap 168 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7363 (mt-10) REVERT: Ap 173 MET cc_start: 0.7719 (ttp) cc_final: 0.7382 (ttt) REVERT: Aq 54 MET cc_start: 0.7690 (ttm) cc_final: 0.7435 (ttt) REVERT: Aq 91 ASP cc_start: 0.8708 (m-30) cc_final: 0.8496 (m-30) REVERT: Aq 160 MET cc_start: 0.9255 (mmt) cc_final: 0.8863 (mmt) REVERT: Ar 77 GLN cc_start: 0.8133 (mt0) cc_final: 0.7629 (mp-120) REVERT: Ar 91 ASP cc_start: 0.8760 (m-30) cc_final: 0.8478 (m-30) REVERT: Ar 135 MET cc_start: 0.9033 (mmm) cc_final: 0.8445 (mmm) REVERT: Ar 168 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7469 (mt-10) REVERT: Ar 173 MET cc_start: 0.7756 (ttp) cc_final: 0.7375 (ttt) outliers start: 95 outliers final: 32 residues processed: 772 average time/residue: 1.5920 time to fit residues: 1364.1353 Evaluate side-chains 792 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 751 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 121 GLU Chi-restraints excluded: chain Ab residue 139 GLU Chi-restraints excluded: chain Ac residue 116 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 110 THR Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ah residue 71 LEU 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 Ak residue 116 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 71 LEU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain 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 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 181 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 239 optimal weight: 8.9990 chunk 181 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 162 optimal weight: 7.9990 chunk 242 optimal weight: 3.9990 chunk 257 optimal weight: 0.6980 chunk 126 optimal weight: 8.9990 chunk 230 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 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 Am 113 ASN An 175 ASN Aq 113 ASN As 113 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 22914 Z= 0.394 Angle : 0.613 5.882 31103 Z= 0.312 Chirality : 0.045 0.181 3420 Planarity : 0.005 0.039 4009 Dihedral : 4.441 16.300 3040 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.45 % Allowed : 24.01 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.15), residues: 988 sheet: 1.26 (0.33), residues: 228 loop : -1.49 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRPAf 132 HIS 0.002 0.001 HISAs 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 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 885 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 775 time to evaluate : 2.483 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: 0.9105 (mmp) cc_final: 0.8855 (mmt) REVERT: Aa 177 LYS cc_start: 0.8152 (mtpm) cc_final: 0.7668 (mptt) REVERT: Ab 76 GLN cc_start: 0.8481 (mm110) cc_final: 0.7995 (mt0) REVERT: Ab 99 LEU cc_start: 0.8623 (tt) cc_final: 0.8298 (tp) REVERT: Ab 108 MET cc_start: 0.9046 (tpt) cc_final: 0.8809 (mmp) REVERT: Ab 113 ASN cc_start: 0.9022 (m110) cc_final: 0.8801 (m-40) REVERT: Ab 121 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7473 (tm-30) REVERT: Ab 168 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7435 (mt-10) REVERT: Ab 173 MET cc_start: 0.7693 (ttp) cc_final: 0.7438 (ttp) REVERT: Ac 88 SER cc_start: 0.8769 (p) cc_final: 0.8483 (p) REVERT: Ac 173 MET cc_start: 0.7700 (ttp) cc_final: 0.7373 (ttp) REVERT: Ac 177 LYS cc_start: 0.8189 (mtpp) cc_final: 0.7797 (mptt) REVERT: Ad 173 MET cc_start: 0.7827 (ttp) cc_final: 0.7543 (ttp) REVERT: Ae 56 MET cc_start: 0.8818 (mmp) cc_final: 0.8512 (mmt) REVERT: Ae 91 ASP cc_start: 0.8690 (m-30) cc_final: 0.8475 (m-30) REVERT: Ae 173 MET cc_start: 0.8008 (ttp) cc_final: 0.7756 (ttp) REVERT: Af 46 ARG cc_start: 0.9247 (mpt180) cc_final: 0.8952 (mpt180) REVERT: Af 69 HIS cc_start: 0.8164 (m-70) cc_final: 0.7026 (t70) REVERT: Af 168 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7490 (mt-10) REVERT: Ag 108 MET cc_start: 0.9088 (tpt) cc_final: 0.8727 (tpt) REVERT: Ag 168 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7479 (mt-10) REVERT: Ag 175 ASN cc_start: 0.8480 (m-40) cc_final: 0.8219 (m-40) REVERT: Ag 177 LYS cc_start: 0.8120 (mtpp) cc_final: 0.7660 (mptt) REVERT: Ag 181 MET cc_start: 0.7136 (OUTLIER) cc_final: 0.6870 (mtm) REVERT: Ah 76 GLN cc_start: 0.8524 (mt0) cc_final: 0.8134 (mt0) REVERT: Ah 116 MET cc_start: 0.9114 (ttp) cc_final: 0.8891 (ttp) REVERT: Ah 173 MET cc_start: 0.7755 (ttp) cc_final: 0.7390 (ttt) REVERT: Ah 177 LYS cc_start: 0.8202 (mtpp) cc_final: 0.7807 (mptt) REVERT: Ah 181 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6901 (mtm) REVERT: Ai 99 LEU cc_start: 0.8575 (tt) cc_final: 0.8230 (tp) REVERT: Ai 108 MET cc_start: 0.8980 (tpt) cc_final: 0.8777 (tpt) REVERT: Ai 121 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7615 (tp30) REVERT: Ai 153 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.7100 (mptp) REVERT: Ai 168 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7420 (mt-10) REVERT: Ai 173 MET cc_start: 0.7878 (ttp) cc_final: 0.7530 (ttt) REVERT: Ai 177 LYS cc_start: 0.8295 (mtpm) cc_final: 0.7964 (mptt) REVERT: Aj 177 LYS cc_start: 0.8234 (mtpp) cc_final: 0.7886 (mptt) REVERT: Ak 99 LEU cc_start: 0.8592 (tt) cc_final: 0.8196 (tp) REVERT: Ak 177 LYS cc_start: 0.8159 (mtpp) cc_final: 0.7775 (mptt) REVERT: Am 168 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7585 (mt-10) REVERT: An 67 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8568 (mp) REVERT: An 99 LEU cc_start: 0.8462 (tt) cc_final: 0.8105 (tp) REVERT: An 102 ASP cc_start: 0.8634 (t0) cc_final: 0.8223 (t0) REVERT: An 108 MET cc_start: 0.9026 (tpt) cc_final: 0.8293 (tpt) REVERT: An 173 MET cc_start: 0.7741 (ttp) cc_final: 0.7339 (ttt) REVERT: An 177 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7274 (mtmm) REVERT: Ao 67 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8550 (mp) REVERT: Ao 91 ASP cc_start: 0.8797 (m-30) cc_final: 0.8506 (m-30) REVERT: Ao 139 GLU cc_start: 0.7712 (pt0) cc_final: 0.7491 (tt0) REVERT: Ao 153 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.7516 (mptp) REVERT: Ao 160 MET cc_start: 0.9090 (tpt) cc_final: 0.8885 (mmt) REVERT: Ao 173 MET cc_start: 0.7764 (ttp) cc_final: 0.7418 (ttt) REVERT: Ap 60 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7582 (mptt) REVERT: Ap 91 ASP cc_start: 0.8761 (m-30) cc_final: 0.8528 (m-30) REVERT: Ap 116 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8971 (ttp) REVERT: Ap 173 MET cc_start: 0.7829 (ttp) cc_final: 0.7533 (ttt) REVERT: Aq 91 ASP cc_start: 0.8698 (m-30) cc_final: 0.8394 (m-30) REVERT: Aq 153 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.7476 (mptp) REVERT: Ar 77 GLN cc_start: 0.8126 (mt0) cc_final: 0.7539 (mp-120) REVERT: Ar 91 ASP cc_start: 0.8789 (m-30) cc_final: 0.8481 (m-30) REVERT: Ar 99 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8290 (tp) REVERT: Ar 135 MET cc_start: 0.9054 (mmm) cc_final: 0.8540 (mmm) REVERT: Ar 168 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7498 (mt-10) REVERT: Ar 173 MET cc_start: 0.7817 (ttp) cc_final: 0.7475 (ttt) REVERT: As 153 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.7433 (mptp) outliers start: 110 outliers final: 42 residues processed: 800 average time/residue: 1.6387 time to fit residues: 1454.2487 Evaluate side-chains 828 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 773 time to evaluate : 2.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 54 MET Chi-restraints excluded: chain Aa residue 99 LEU Chi-restraints excluded: chain Ab residue 116 MET Chi-restraints excluded: chain Ab residue 121 GLU Chi-restraints excluded: chain Ab residue 181 MET Chi-restraints excluded: chain Ac residue 116 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 Ae residue 116 MET Chi-restraints excluded: chain Af residue 54 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Ag residue 71 LEU Chi-restraints excluded: chain Ag residue 80 ILE 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 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 Ak residue 54 MET Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 116 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 Al residue 178 GLU 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 67 LEU Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 177 LYS 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 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 Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 153 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 214 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 191 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 177 optimal weight: 0.0470 chunk 0 optimal weight: 7.9990 chunk 131 optimal weight: 2.9990 chunk 230 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 overall best weight: 2.2086 ------------------------------------------------------------------------------- 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 77 GLN Ah 113 ASN Aj 113 ASN ** Ak 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Am 113 ASN Ap 113 ASN Aq 113 ASN As 113 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22914 Z= 0.279 Angle : 0.557 5.333 31103 Z= 0.282 Chirality : 0.042 0.166 3420 Planarity : 0.005 0.037 4009 Dihedral : 4.208 16.266 3040 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 5.14 % Allowed : 23.56 % Favored : 71.30 % 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: -0.03 (0.16), residues: 2755 helix: 1.55 (0.15), residues: 988 sheet: 1.07 (0.32), residues: 228 loop : -1.32 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRPAf 132 HIS 0.002 0.001 HISAc 69 PHE 0.013 0.002 PHEAi 163 TYR 0.018 0.002 TYRAl 180 ARG 0.007 0.001 ARGAg 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 886 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 759 time to evaluate : 2.774 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: symmetry clash REVERT: Aa 160 MET cc_start: 0.9110 (mmp) cc_final: 0.8754 (mmt) REVERT: Aa 173 MET cc_start: 0.7780 (ttp) cc_final: 0.7389 (ttt) REVERT: Aa 177 LYS cc_start: 0.8173 (mtpm) cc_final: 0.7728 (mptt) REVERT: Ab 99 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8286 (tp) REVERT: Ab 108 MET cc_start: 0.9045 (tpt) cc_final: 0.8757 (mmp) REVERT: Ab 113 ASN cc_start: 0.8847 (m110) cc_final: 0.8620 (m110) REVERT: Ab 173 MET cc_start: 0.7636 (ttp) cc_final: 0.7374 (ttp) REVERT: Ac 99 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8212 (tp) REVERT: Ac 108 MET cc_start: 0.9044 (tpt) cc_final: 0.8808 (mmp) REVERT: Ac 139 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: Ac 173 MET cc_start: 0.7642 (ttp) cc_final: 0.7184 (ttp) REVERT: Ac 177 LYS cc_start: 0.8166 (mtpp) cc_final: 0.7743 (mptt) REVERT: Ad 91 ASP cc_start: 0.8653 (m-30) cc_final: 0.8237 (m-30) REVERT: Ad 95 GLU cc_start: 0.8057 (mp0) cc_final: 0.7660 (mp0) REVERT: Ae 56 MET cc_start: 0.8793 (mmp) cc_final: 0.8480 (mmt) REVERT: Ae 91 ASP cc_start: 0.8614 (m-30) cc_final: 0.8390 (m-30) REVERT: Ae 134 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8818 (ttt) REVERT: Ae 173 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7719 (ttp) REVERT: Af 46 ARG cc_start: 0.9267 (mpt180) cc_final: 0.8955 (mpt180) REVERT: Af 69 HIS cc_start: 0.8146 (m-70) cc_final: 0.7017 (t70) REVERT: Af 168 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7610 (mt-10) REVERT: Ag 108 MET cc_start: 0.9100 (tpt) cc_final: 0.8782 (tpt) REVERT: Ag 116 MET cc_start: 0.9206 (OUTLIER) cc_final: 0.8916 (tmm) REVERT: Ag 168 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7439 (mt-10) REVERT: Ag 175 ASN cc_start: 0.8461 (m-40) cc_final: 0.8249 (m-40) REVERT: Ag 177 LYS cc_start: 0.8126 (mtpp) cc_final: 0.7660 (mptt) REVERT: Ah 76 GLN cc_start: 0.8482 (mt0) cc_final: 0.8085 (mt0) REVERT: Ah 116 MET cc_start: 0.9071 (ttp) cc_final: 0.8871 (ttp) REVERT: Ah 139 GLU cc_start: 0.7784 (tt0) cc_final: 0.7582 (tt0) REVERT: Ah 173 MET cc_start: 0.7696 (ttp) cc_final: 0.7321 (ttt) REVERT: Ah 177 LYS cc_start: 0.8099 (mtpp) cc_final: 0.7739 (mptt) REVERT: Ah 181 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6828 (mtm) REVERT: Ai 99 LEU cc_start: 0.8596 (tt) cc_final: 0.8234 (tp) REVERT: Ai 108 MET cc_start: 0.9082 (tpt) cc_final: 0.8868 (tpt) REVERT: Ai 121 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7568 (tp30) REVERT: Ai 153 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.7137 (mptp) REVERT: Ai 168 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7406 (mt-10) REVERT: Ai 173 MET cc_start: 0.7873 (ttp) cc_final: 0.7518 (ttt) REVERT: Ai 177 LYS cc_start: 0.8233 (mtpm) cc_final: 0.7875 (mptt) REVERT: Aj 172 GLU cc_start: 0.7404 (mm-30) cc_final: 0.7119 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7881 (mptt) REVERT: Ak 99 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8208 (tp) REVERT: Ak 177 LYS cc_start: 0.8146 (mtpp) cc_final: 0.7755 (mptt) REVERT: Al 177 LYS cc_start: 0.8159 (mtpm) cc_final: 0.7717 (mptt) REVERT: Am 168 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7559 (mt-10) REVERT: An 67 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8548 (mp) REVERT: An 99 LEU cc_start: 0.8468 (tt) cc_final: 0.8125 (tp) REVERT: An 102 ASP cc_start: 0.8621 (t0) cc_final: 0.8161 (t0) REVERT: An 108 MET cc_start: 0.9078 (tpt) cc_final: 0.8233 (tpt) REVERT: An 121 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7312 (tp30) REVERT: An 153 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8258 (mmpt) REVERT: An 173 MET cc_start: 0.7526 (ttp) cc_final: 0.7181 (ttt) REVERT: An 177 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7282 (mtmm) REVERT: Ao 91 ASP cc_start: 0.8768 (m-30) cc_final: 0.8526 (m-30) REVERT: Ao 139 GLU cc_start: 0.7775 (pt0) cc_final: 0.7521 (tt0) REVERT: Ao 153 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.7480 (mptp) REVERT: Ao 173 MET cc_start: 0.7683 (ttp) cc_final: 0.7279 (ttt) REVERT: Ap 46 ARG cc_start: 0.9251 (mpt180) cc_final: 0.8987 (mpt180) REVERT: Ap 60 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7479 (mptt) REVERT: Ap 91 ASP cc_start: 0.8752 (m-30) cc_final: 0.8506 (m-30) REVERT: Ap 116 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8894 (ttp) REVERT: Ap 173 MET cc_start: 0.7667 (ttp) cc_final: 0.7378 (ttt) REVERT: Aq 91 ASP cc_start: 0.8736 (m-30) cc_final: 0.8251 (m-30) REVERT: Aq 153 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.7481 (mptp) REVERT: Aq 177 LYS cc_start: 0.8112 (mtpm) cc_final: 0.7703 (mptt) REVERT: Ar 77 GLN cc_start: 0.8012 (mt0) cc_final: 0.7448 (mp-120) REVERT: Ar 91 ASP cc_start: 0.8763 (m-30) cc_final: 0.8448 (m-30) REVERT: Ar 99 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8289 (tp) REVERT: Ar 135 MET cc_start: 0.9056 (mmm) cc_final: 0.8582 (mmm) REVERT: Ar 168 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7442 (mt-10) REVERT: Ar 173 MET cc_start: 0.7785 (ttp) cc_final: 0.7514 (ttt) REVERT: As 121 GLU cc_start: 0.7981 (tm-30) cc_final: 0.7531 (tm-30) REVERT: As 153 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.7431 (mptp) outliers start: 127 outliers final: 43 residues processed: 812 average time/residue: 1.5802 time to fit residues: 1426.7959 Evaluate side-chains 819 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 758 time to evaluate : 2.419 ------------------------------------------------------------------------------- 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 Ac residue 99 LEU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 139 GLU Chi-restraints excluded: chain Ad residue 54 MET Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ad residue 181 MET Chi-restraints excluded: chain Ae residue 80 ILE Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 134 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 Ag residue 71 LEU 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 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 Ak residue 54 MET Chi-restraints excluded: chain Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 116 MET Chi-restraints excluded: chain Al residue 58 LYS Chi-restraints excluded: chain Al residue 95 GLU Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 95 GLU Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 67 LEU Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 153 LYS Chi-restraints excluded: chain An residue 177 LYS 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 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS 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 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 86 optimal weight: 3.9990 chunk 231 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 213 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ad 113 ASN Ae 77 GLN Af 113 ASN Ag 113 ASN Ah 113 ASN Aj 113 ASN Ap 175 ASN As 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22914 Z= 0.210 Angle : 0.521 5.212 31103 Z= 0.263 Chirality : 0.040 0.177 3420 Planarity : 0.005 0.037 4009 Dihedral : 3.977 16.338 3040 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.21 % Allowed : 24.09 % 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: 0.25 (0.16), residues: 2755 helix: 1.82 (0.15), residues: 988 sheet: 1.16 (0.32), residues: 228 loop : -1.16 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPAh 132 HIS 0.003 0.000 HISAg 69 PHE 0.010 0.002 PHEAr 163 TYR 0.016 0.001 TYRAl 180 ARG 0.007 0.000 ARGAp 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 850 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 746 time to evaluate : 2.401 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: 0.9141 (mmp) cc_final: 0.8788 (mmt) REVERT: Aa 173 MET cc_start: 0.7716 (ttp) cc_final: 0.7317 (ttt) REVERT: Aa 177 LYS cc_start: 0.8128 (mtpm) cc_final: 0.7649 (mptt) REVERT: Aa 181 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.7075 (mtt) REVERT: Ab 99 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8268 (tp) REVERT: Ab 127 ASN cc_start: 0.8463 (t0) cc_final: 0.8195 (t0) REVERT: Ab 173 MET cc_start: 0.7568 (ttp) cc_final: 0.7334 (ttp) REVERT: Ac 108 MET cc_start: 0.9042 (tpt) cc_final: 0.8800 (mmp) REVERT: Ac 142 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7969 (mp0) REVERT: Ac 173 MET cc_start: 0.7582 (ttp) cc_final: 0.7279 (ttp) REVERT: Ac 177 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7727 (mptt) REVERT: Ad 91 ASP cc_start: 0.8658 (m-30) cc_final: 0.8338 (m-30) REVERT: Ad 95 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: Ad 160 MET cc_start: 0.9282 (mmp) cc_final: 0.8861 (mmp) REVERT: Ae 91 ASP cc_start: 0.8659 (m-30) cc_final: 0.8401 (m-30) REVERT: Ae 134 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8798 (ttt) REVERT: Af 69 HIS cc_start: 0.8159 (m-70) cc_final: 0.7035 (t70) REVERT: Ag 116 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8932 (tmm) REVERT: Ag 168 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7416 (mt-10) REVERT: Ag 177 LYS cc_start: 0.8012 (mtpp) cc_final: 0.7605 (mptt) REVERT: Ah 77 GLN cc_start: 0.7933 (mt0) cc_final: 0.7453 (mp-120) REVERT: Ah 173 MET cc_start: 0.7687 (ttp) cc_final: 0.7334 (ttt) REVERT: Ah 177 LYS cc_start: 0.8024 (mtpp) cc_final: 0.7679 (mptt) REVERT: Ah 181 MET cc_start: 0.7121 (OUTLIER) cc_final: 0.6920 (mtt) REVERT: Ai 99 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8247 (tp) REVERT: Ai 108 MET cc_start: 0.9117 (tpt) cc_final: 0.8832 (mmm) REVERT: Ai 153 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.7106 (mptp) REVERT: Ai 168 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7399 (mt-10) REVERT: Ai 173 MET cc_start: 0.7837 (ttp) cc_final: 0.7480 (ttt) REVERT: Ai 177 LYS cc_start: 0.8225 (mtpm) cc_final: 0.7876 (mptt) REVERT: Aj 172 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7098 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8151 (mtpp) cc_final: 0.7858 (mptt) REVERT: Ak 99 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8203 (tp) REVERT: Ak 177 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7690 (mptt) REVERT: Al 177 LYS cc_start: 0.8049 (mtpm) cc_final: 0.7594 (mptt) REVERT: Am 71 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8348 (mt) REVERT: Am 113 ASN cc_start: 0.8480 (m-40) cc_final: 0.8278 (m110) REVERT: Am 168 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7550 (mt-10) REVERT: Am 177 LYS cc_start: 0.7771 (mtmm) cc_final: 0.7489 (mptt) REVERT: An 67 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8495 (mp) REVERT: An 91 ASP cc_start: 0.8448 (m-30) cc_final: 0.7993 (m-30) REVERT: An 95 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7638 (mp0) REVERT: An 99 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8111 (tp) REVERT: An 121 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7350 (tp30) REVERT: An 135 MET cc_start: 0.8994 (mmm) cc_final: 0.8681 (mmm) REVERT: An 153 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8558 (mmtm) REVERT: An 173 MET cc_start: 0.7495 (ttp) cc_final: 0.7286 (ttt) REVERT: Ao 46 ARG cc_start: 0.9297 (mpt180) cc_final: 0.8967 (mpt180) REVERT: Ao 91 ASP cc_start: 0.8777 (m-30) cc_final: 0.8496 (m-30) REVERT: Ao 121 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7416 (tm-30) REVERT: Ao 139 GLU cc_start: 0.7757 (pt0) cc_final: 0.7492 (tt0) REVERT: Ao 153 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.7453 (mptp) REVERT: Ao 173 MET cc_start: 0.7561 (ttp) cc_final: 0.7188 (ttt) REVERT: Ap 60 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7481 (mptt) REVERT: Ap 91 ASP cc_start: 0.8734 (m-30) cc_final: 0.8485 (m-30) REVERT: Ap 99 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8016 (mt) REVERT: Ap 116 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8818 (ttp) REVERT: Ap 173 MET cc_start: 0.7634 (ttp) cc_final: 0.7330 (ttt) REVERT: Aq 91 ASP cc_start: 0.8696 (m-30) cc_final: 0.8217 (m-30) REVERT: Aq 153 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.7485 (mptp) REVERT: Aq 160 MET cc_start: 0.9084 (mmp) cc_final: 0.8670 (mmt) REVERT: Aq 177 LYS cc_start: 0.8125 (mtpm) cc_final: 0.7766 (mptt) REVERT: Ar 77 GLN cc_start: 0.8067 (mt0) cc_final: 0.7503 (mp-120) REVERT: Ar 91 ASP cc_start: 0.8749 (m-30) cc_final: 0.8438 (m-30) REVERT: Ar 99 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8287 (tp) REVERT: Ar 135 MET cc_start: 0.9070 (mmm) cc_final: 0.8615 (mmm) REVERT: Ar 168 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7424 (mt-10) REVERT: Ar 173 MET cc_start: 0.7749 (ttp) cc_final: 0.7358 (ttt) REVERT: Ar 177 LYS cc_start: 0.8149 (mtmt) cc_final: 0.7737 (mptt) REVERT: As 121 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7523 (tm-30) REVERT: As 153 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.7419 (mptp) outliers start: 104 outliers final: 44 residues processed: 782 average time/residue: 1.6730 time to fit residues: 1461.6483 Evaluate side-chains 805 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 740 time to evaluate : 2.906 ------------------------------------------------------------------------------- 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 187 VAL Chi-restraints excluded: chain Ac residue 95 GLU Chi-restraints excluded: chain Ac residue 116 MET Chi-restraints excluded: chain Ac residue 187 VAL Chi-restraints excluded: chain Ad residue 95 GLU Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ad residue 110 THR Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 134 MET Chi-restraints excluded: chain Ae residue 173 MET 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 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 Ak residue 99 LEU Chi-restraints excluded: chain Ak residue 116 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 95 GLU Chi-restraints excluded: chain Am residue 116 MET Chi-restraints excluded: chain An residue 67 LEU Chi-restraints excluded: chain An residue 71 LEU Chi-restraints excluded: chain An residue 81 SER Chi-restraints excluded: chain An residue 95 GLU Chi-restraints excluded: chain An residue 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 Ap residue 60 LYS Chi-restraints excluded: chain Ap residue 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain 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 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 153 LYS Chi-restraints excluded: chain As residue 181 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 248 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 chunk 187 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 216 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 chunk 256 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 113 ASN Af 113 ASN Ag 113 ASN Ah 113 ASN Aj 113 ASN As 113 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22914 Z= 0.222 Angle : 0.523 5.529 31103 Z= 0.265 Chirality : 0.041 0.161 3420 Planarity : 0.005 0.036 4009 Dihedral : 3.956 16.479 3040 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.13 % Allowed : 23.89 % Favored : 71.98 % 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: 0.33 (0.16), residues: 2755 helix: 1.89 (0.15), residues: 988 sheet: 1.11 (0.32), residues: 228 loop : -1.10 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPAf 132 HIS 0.004 0.000 HISAg 69 PHE 0.011 0.002 PHEAi 163 TYR 0.018 0.001 TYRAg 180 ARG 0.007 0.001 ARGAa 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 825 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 723 time to evaluate : 2.666 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: 0.9141 (mmp) cc_final: 0.8774 (mmt) REVERT: Aa 173 MET cc_start: 0.7710 (ttp) cc_final: 0.7320 (ttt) REVERT: Aa 177 LYS cc_start: 0.8106 (mtpm) cc_final: 0.7636 (mptt) REVERT: Ab 99 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8263 (tp) REVERT: Ab 127 ASN cc_start: 0.8448 (t0) cc_final: 0.8177 (t0) REVERT: Ab 160 MET cc_start: 0.9085 (tpt) cc_final: 0.8829 (mmm) REVERT: Ab 173 MET cc_start: 0.7577 (ttp) cc_final: 0.7340 (ttp) REVERT: Ac 99 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8225 (tp) REVERT: Ac 108 MET cc_start: 0.9040 (tpt) cc_final: 0.8751 (mmp) REVERT: Ac 139 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: Ac 142 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8011 (mp0) REVERT: Ac 173 MET cc_start: 0.7584 (ttp) cc_final: 0.7281 (ttp) REVERT: Ac 177 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7679 (mptt) REVERT: Ad 91 ASP cc_start: 0.8650 (m-30) cc_final: 0.8318 (m-30) REVERT: Ad 95 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7657 (mp0) REVERT: Ad 121 GLU cc_start: 0.7902 (tm-30) cc_final: 0.7573 (tm-30) REVERT: Ad 160 MET cc_start: 0.9280 (mmp) cc_final: 0.8850 (mmp) REVERT: Ae 91 ASP cc_start: 0.8625 (m-30) cc_final: 0.8372 (m-30) REVERT: Af 69 HIS cc_start: 0.8167 (m-70) cc_final: 0.7040 (t70) REVERT: Ag 116 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8928 (tmm) REVERT: Ag 168 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7433 (mt-10) REVERT: Ag 177 LYS cc_start: 0.7979 (mtpp) cc_final: 0.7573 (mptt) REVERT: Ah 173 MET cc_start: 0.7738 (ttp) cc_final: 0.7378 (ttt) REVERT: Ah 177 LYS cc_start: 0.7988 (mtpp) cc_final: 0.7666 (mptt) REVERT: Ah 181 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6899 (mtt) REVERT: Ai 99 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8245 (tp) REVERT: Ai 108 MET cc_start: 0.9100 (tpt) cc_final: 0.8828 (mmm) REVERT: Ai 121 GLU cc_start: 0.7921 (tp30) cc_final: 0.7414 (tp30) REVERT: Ai 153 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.7078 (mptp) REVERT: Ai 168 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7393 (mt-10) REVERT: Ai 173 MET cc_start: 0.7823 (ttp) cc_final: 0.7458 (ttt) REVERT: Ai 177 LYS cc_start: 0.8288 (mtpm) cc_final: 0.7998 (mptt) REVERT: Aj 102 ASP cc_start: 0.8668 (t0) cc_final: 0.8464 (t0) REVERT: Aj 172 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7104 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8113 (mtpp) cc_final: 0.7813 (mptt) REVERT: Ak 99 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8200 (tp) REVERT: Ak 177 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7646 (mptt) REVERT: Al 177 LYS cc_start: 0.8031 (mtpm) cc_final: 0.7569 (mptt) REVERT: Am 71 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8344 (mt) REVERT: Am 113 ASN cc_start: 0.8456 (m-40) cc_final: 0.8251 (m110) REVERT: Am 168 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7570 (mt-10) REVERT: Am 177 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7440 (mptt) REVERT: An 91 ASP cc_start: 0.8466 (m-30) cc_final: 0.8085 (m-30) REVERT: An 95 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: An 99 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8162 (tp) REVERT: An 108 MET cc_start: 0.8928 (tpt) cc_final: 0.8289 (tpt) REVERT: An 121 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7362 (tp30) REVERT: An 153 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8589 (mmtm) REVERT: An 173 MET cc_start: 0.7537 (ttp) cc_final: 0.7276 (ttt) REVERT: Ao 91 ASP cc_start: 0.8775 (m-30) cc_final: 0.8527 (m-30) REVERT: Ao 139 GLU cc_start: 0.7781 (pt0) cc_final: 0.7478 (tt0) REVERT: Ao 153 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.7403 (mptp) REVERT: Ao 173 MET cc_start: 0.7536 (ttp) cc_final: 0.7176 (ttt) REVERT: Ap 60 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7455 (mptt) REVERT: Ap 99 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7995 (mt) REVERT: Ap 116 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8827 (ttp) REVERT: Ap 173 MET cc_start: 0.7669 (ttp) cc_final: 0.7378 (ttt) REVERT: Aq 91 ASP cc_start: 0.8737 (m-30) cc_final: 0.8257 (m-30) REVERT: Aq 153 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.7470 (mptp) REVERT: Aq 160 MET cc_start: 0.9138 (mmp) cc_final: 0.8838 (mmt) REVERT: Aq 177 LYS cc_start: 0.8095 (mtpm) cc_final: 0.7740 (mptt) REVERT: Ar 77 GLN cc_start: 0.8061 (mt0) cc_final: 0.7582 (mp-120) REVERT: Ar 91 ASP cc_start: 0.8768 (m-30) cc_final: 0.8518 (m-30) REVERT: Ar 99 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8288 (tp) REVERT: Ar 168 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7427 (mt-10) REVERT: Ar 173 MET cc_start: 0.7749 (ttp) cc_final: 0.7393 (ttt) REVERT: Ar 177 LYS cc_start: 0.8191 (mtmt) cc_final: 0.7819 (mptt) REVERT: As 153 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.7396 (mptp) outliers start: 102 outliers final: 47 residues processed: 761 average time/residue: 1.5699 time to fit residues: 1329.7274 Evaluate side-chains 788 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 721 time to evaluate : 2.451 ------------------------------------------------------------------------------- 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 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 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 Ae residue 116 MET Chi-restraints excluded: chain Ae residue 181 MET 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 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 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 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 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 95 GLU 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 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 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain 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 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 153 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 158 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 162 optimal weight: 10.0000 chunk 174 optimal weight: 0.0870 chunk 126 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 overall best weight: 2.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ae 77 GLN Af 113 ASN Ag 113 ASN Ah 113 ASN Aj 113 ASN As 113 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 22914 Z= 0.303 Angle : 0.569 6.711 31103 Z= 0.288 Chirality : 0.043 0.192 3420 Planarity : 0.005 0.038 4009 Dihedral : 4.202 16.436 3040 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.97 % Allowed : 24.13 % Favored : 71.90 % 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: 0.19 (0.16), residues: 2755 helix: 1.69 (0.15), residues: 988 sheet: 0.97 (0.31), residues: 228 loop : -1.11 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAf 132 HIS 0.005 0.001 HISAg 69 PHE 0.013 0.002 PHEAi 163 TYR 0.018 0.002 TYRAh 180 ARG 0.007 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 844 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 746 time to evaluate : 2.648 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: 0.9133 (mmp) cc_final: 0.8819 (mmt) REVERT: Aa 173 MET cc_start: 0.7713 (ttp) cc_final: 0.7300 (ttt) REVERT: Aa 177 LYS cc_start: 0.8149 (mtpm) cc_final: 0.7729 (mptt) REVERT: Ab 99 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8279 (tp) REVERT: Ab 108 MET cc_start: 0.9034 (tpt) cc_final: 0.8773 (mmp) REVERT: Ab 113 ASN cc_start: 0.8911 (m110) cc_final: 0.8675 (m110) REVERT: Ab 160 MET cc_start: 0.9063 (tpt) cc_final: 0.8798 (mmm) REVERT: Ab 173 MET cc_start: 0.7635 (ttp) cc_final: 0.7390 (ttp) REVERT: Ac 69 HIS cc_start: 0.8213 (m170) cc_final: 0.7946 (m-70) REVERT: Ac 99 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8196 (tp) REVERT: Ac 108 MET cc_start: 0.9049 (tpt) cc_final: 0.8816 (mmp) REVERT: Ac 139 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: Ad 91 ASP cc_start: 0.8649 (m-30) cc_final: 0.8319 (m-30) REVERT: Ad 95 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: Ad 177 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7639 (mptt) REVERT: Ae 99 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8203 (tp) REVERT: Af 69 HIS cc_start: 0.8203 (m-70) cc_final: 0.7065 (t70) REVERT: Ag 116 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8887 (tmm) REVERT: Ag 168 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7459 (mt-10) REVERT: Ag 177 LYS cc_start: 0.7967 (mtpp) cc_final: 0.7579 (mptt) REVERT: Ah 173 MET cc_start: 0.7806 (ttp) cc_final: 0.7440 (ttt) REVERT: Ah 177 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7683 (mptt) REVERT: Ai 69 HIS cc_start: 0.8049 (m-70) cc_final: 0.6843 (t-90) REVERT: Ai 99 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8250 (tp) REVERT: Ai 108 MET cc_start: 0.9064 (tpt) cc_final: 0.8704 (mmm) REVERT: Ai 121 GLU cc_start: 0.7926 (tp30) cc_final: 0.7449 (tp30) REVERT: Ai 153 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.7043 (mptp) REVERT: Ai 168 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7424 (mt-10) REVERT: Ai 173 MET cc_start: 0.7837 (ttp) cc_final: 0.7499 (ttt) REVERT: Ai 177 LYS cc_start: 0.8305 (mtpm) cc_final: 0.8012 (mptt) REVERT: Aj 172 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7140 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8088 (mtpp) cc_final: 0.7784 (mptt) REVERT: Ak 99 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8187 (tp) REVERT: Ak 177 LYS cc_start: 0.8025 (mtpp) cc_final: 0.7658 (mptt) REVERT: Al 172 GLU cc_start: 0.7384 (mm-30) cc_final: 0.6608 (mt-10) REVERT: Al 177 LYS cc_start: 0.8074 (mtpm) cc_final: 0.7632 (mptt) REVERT: Am 99 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8314 (tp) REVERT: Am 168 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7605 (mt-10) REVERT: An 91 ASP cc_start: 0.8538 (m-30) cc_final: 0.8159 (m-30) REVERT: An 95 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: An 99 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8135 (tp) REVERT: An 102 ASP cc_start: 0.8610 (t0) cc_final: 0.8197 (t0) REVERT: An 121 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7614 (tp30) REVERT: An 153 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8598 (mmtm) REVERT: An 173 MET cc_start: 0.7589 (ttp) cc_final: 0.7301 (ttt) REVERT: Ao 91 ASP cc_start: 0.8769 (m-30) cc_final: 0.8517 (m-30) REVERT: Ao 139 GLU cc_start: 0.7793 (pt0) cc_final: 0.7461 (tt0) REVERT: Ao 153 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.7464 (mptp) REVERT: Ao 173 MET cc_start: 0.7615 (ttp) cc_final: 0.7274 (ttt) REVERT: Ap 60 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.7444 (mptt) REVERT: Ap 116 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8896 (ttp) REVERT: Ap 173 MET cc_start: 0.7671 (ttp) cc_final: 0.7375 (ttt) REVERT: Aq 91 ASP cc_start: 0.8751 (m-30) cc_final: 0.8438 (m-30) REVERT: Aq 153 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.7486 (mptp) REVERT: Aq 177 LYS cc_start: 0.8095 (mtpm) cc_final: 0.7686 (mptt) REVERT: Ar 77 GLN cc_start: 0.8087 (mt0) cc_final: 0.7511 (mp-120) REVERT: Ar 91 ASP cc_start: 0.8793 (m-30) cc_final: 0.8572 (m-30) REVERT: Ar 99 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8265 (tp) REVERT: Ar 168 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7451 (mt-10) REVERT: Ar 173 MET cc_start: 0.7843 (ttp) cc_final: 0.7481 (ttt) REVERT: Ar 177 LYS cc_start: 0.8201 (mtmt) cc_final: 0.7828 (mptt) REVERT: As 153 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.7383 (mptp) outliers start: 98 outliers final: 50 residues processed: 782 average time/residue: 1.5063 time to fit residues: 1310.0702 Evaluate side-chains 814 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 745 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 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 54 MET Chi-restraints excluded: chain Ad residue 95 GLU Chi-restraints excluded: chain Ad residue 103 ILE Chi-restraints excluded: chain Ae residue 80 ILE 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 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 187 VAL 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 181 MET Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 95 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 120 ILE 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 Al residue 58 LYS Chi-restraints excluded: chain Al residue 80 ILE Chi-restraints excluded: chain Al residue 116 MET Chi-restraints excluded: chain Al residue 120 ILE Chi-restraints excluded: chain Am residue 67 LEU Chi-restraints excluded: chain Am residue 71 LEU Chi-restraints excluded: chain Am residue 81 SER Chi-restraints excluded: chain Am residue 95 GLU 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 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 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 110 THR Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 153 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 233 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 238 optimal weight: 8.9990 chunk 143 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 187 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 225 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Ac 113 ASN Ae 77 GLN Af 113 ASN Ag 113 ASN ** Ah 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Aj 113 ASN An 69 HIS ** An 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** As 113 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2895 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= 0.338 Angle : 0.594 7.755 31103 Z= 0.301 Chirality : 0.044 0.198 3420 Planarity : 0.005 0.042 4009 Dihedral : 4.332 16.615 3040 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.52 % Allowed : 24.90 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.09 (0.16), residues: 2755 helix: 1.53 (0.15), residues: 988 sheet: 0.87 (0.31), residues: 228 loop : -1.11 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAf 132 HIS 0.005 0.001 HISAg 69 PHE 0.014 0.002 PHEAi 163 TYR 0.019 0.002 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 838 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 751 time to evaluate : 2.495 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: 0.9126 (mmp) cc_final: 0.8874 (mmt) REVERT: Aa 173 MET cc_start: 0.7746 (ttp) cc_final: 0.7324 (ttt) REVERT: Aa 177 LYS cc_start: 0.8154 (mtpm) cc_final: 0.7724 (mptt) REVERT: Ab 99 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8268 (tp) REVERT: Ab 108 MET cc_start: 0.9045 (tpt) cc_final: 0.8794 (mmp) REVERT: Ab 113 ASN cc_start: 0.8935 (m110) cc_final: 0.8727 (m-40) REVERT: Ab 173 MET cc_start: 0.7693 (ttp) cc_final: 0.7462 (ttp) REVERT: Ac 69 HIS cc_start: 0.8224 (m170) cc_final: 0.8001 (m-70) REVERT: Ac 99 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8199 (tp) REVERT: Ac 108 MET cc_start: 0.9044 (tpt) cc_final: 0.8809 (mmp) REVERT: Ac 139 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7626 (mt-10) REVERT: Ac 173 MET cc_start: 0.7766 (ttp) cc_final: 0.7333 (ttt) REVERT: Ac 177 LYS cc_start: 0.8045 (mtpm) cc_final: 0.7562 (mptt) REVERT: Ad 91 ASP cc_start: 0.8657 (m-30) cc_final: 0.8287 (m-30) REVERT: Ad 95 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: Ae 99 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8173 (tp) REVERT: Af 69 HIS cc_start: 0.8193 (m-70) cc_final: 0.7061 (t70) REVERT: Ag 116 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8871 (tmm) REVERT: Ag 168 GLU cc_start: 0.7823 (mt-10) cc_final: 0.7464 (mt-10) REVERT: Ag 177 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7621 (mptt) REVERT: Ah 108 MET cc_start: 0.9082 (mmm) cc_final: 0.8794 (tpt) REVERT: Ah 173 MET cc_start: 0.7820 (ttp) cc_final: 0.7474 (ttt) REVERT: Ah 177 LYS cc_start: 0.8050 (mtpp) cc_final: 0.7718 (mptt) REVERT: Ah 181 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6918 (mtt) REVERT: Ai 69 HIS cc_start: 0.8033 (m-70) cc_final: 0.6850 (t-90) REVERT: Ai 99 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8241 (tp) REVERT: Ai 108 MET cc_start: 0.9068 (tpt) cc_final: 0.8713 (mmm) REVERT: Ai 121 GLU cc_start: 0.7905 (tp30) cc_final: 0.7440 (tp30) REVERT: Ai 153 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7004 (mptp) REVERT: Ai 168 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7428 (mt-10) REVERT: Ai 173 MET cc_start: 0.7855 (ttp) cc_final: 0.7527 (ttt) REVERT: Ai 177 LYS cc_start: 0.8322 (mtpm) cc_final: 0.8031 (mptt) REVERT: Aj 69 HIS cc_start: 0.8304 (m90) cc_final: 0.8042 (m-70) REVERT: Aj 172 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7175 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8109 (mtpp) cc_final: 0.7801 (mptt) REVERT: Ak 99 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8181 (tp) REVERT: Al 172 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6616 (mt-10) REVERT: Al 177 LYS cc_start: 0.8087 (mtpm) cc_final: 0.7646 (mptt) REVERT: Am 99 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8307 (tp) REVERT: Am 168 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7613 (mt-10) REVERT: An 95 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: An 99 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8139 (tp) REVERT: An 102 ASP cc_start: 0.8569 (t0) cc_final: 0.8157 (t0) REVERT: An 108 MET cc_start: 0.8889 (tpt) cc_final: 0.8368 (tpt) REVERT: An 121 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7538 (tp30) REVERT: An 153 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8603 (mmtm) REVERT: An 173 MET cc_start: 0.7594 (ttp) cc_final: 0.7301 (ttt) REVERT: Ao 91 ASP cc_start: 0.8783 (m-30) cc_final: 0.8561 (m-30) REVERT: Ao 153 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7424 (mptp) REVERT: Ao 173 MET cc_start: 0.7646 (ttp) cc_final: 0.7305 (ttt) REVERT: Ap 60 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.7439 (mptt) REVERT: Ap 116 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8950 (ttp) REVERT: Ap 173 MET cc_start: 0.7723 (ttp) cc_final: 0.7425 (ttt) REVERT: Aq 91 ASP cc_start: 0.8755 (m-30) cc_final: 0.8441 (m-30) REVERT: Aq 153 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.7459 (mptp) REVERT: Aq 177 LYS cc_start: 0.8108 (mtpm) cc_final: 0.7703 (mptt) REVERT: Ar 77 GLN cc_start: 0.8094 (mt0) cc_final: 0.7545 (mp-120) REVERT: Ar 91 ASP cc_start: 0.8781 (m-30) cc_final: 0.8513 (m-30) REVERT: Ar 99 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8292 (tp) REVERT: Ar 168 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7448 (mt-10) REVERT: Ar 173 MET cc_start: 0.7859 (ttp) cc_final: 0.7488 (ttt) REVERT: Ar 177 LYS cc_start: 0.8225 (mtmt) cc_final: 0.7839 (mptt) REVERT: As 153 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.7404 (mptp) outliers start: 87 outliers final: 54 residues processed: 782 average time/residue: 1.5850 time to fit residues: 1376.7017 Evaluate side-chains 819 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 745 time to evaluate : 2.457 ------------------------------------------------------------------------------- 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 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 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 Ae residue 80 ILE 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 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 187 VAL Chi-restraints excluded: chain Ah residue 67 LEU Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ah residue 181 MET Chi-restraints excluded: chain Ai residue 99 LEU Chi-restraints excluded: chain Ai residue 153 LYS Chi-restraints excluded: chain Ai residue 181 MET Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 54 MET Chi-restraints excluded: chain Aj residue 95 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Aj residue 120 ILE 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 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 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 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 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 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 103 ILE Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain Aq residue 181 MET Chi-restraints excluded: chain Ar residue 95 GLU Chi-restraints excluded: chain Ar residue 99 LEU Chi-restraints excluded: chain Ar residue 116 MET Chi-restraints excluded: chain As residue 67 LEU Chi-restraints excluded: chain As residue 71 LEU Chi-restraints excluded: chain As residue 103 ILE Chi-restraints excluded: chain As residue 116 MET Chi-restraints excluded: chain As residue 153 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 252 optimal weight: 0.0970 chunk 154 optimal weight: 10.0000 chunk 119 optimal weight: 0.5980 chunk 175 optimal weight: 4.9990 chunk 265 optimal weight: 0.9980 chunk 243 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 129 optimal weight: 7.9990 chunk 167 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Af 113 ASN Ag 113 ASN Ah 113 ASN Ai 151 ASN Aj 113 ASN As 113 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22914 Z= 0.174 Angle : 0.513 8.684 31103 Z= 0.259 Chirality : 0.040 0.152 3420 Planarity : 0.005 0.038 4009 Dihedral : 3.842 16.437 3040 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.47 % Allowed : 26.40 % Favored : 71.13 % 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: 0.51 (0.16), residues: 2755 helix: 1.52 (0.15), residues: 1102 sheet: 2.15 (0.32), residues: 190 loop : -0.86 (0.16), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRPAf 132 HIS 0.003 0.000 HISAg 69 PHE 0.009 0.001 PHEAi 163 TYR 0.014 0.001 TYRAg 180 ARG 0.007 0.000 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 766 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 705 time to evaluate : 2.429 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: 0.9073 (mmp) cc_final: 0.8551 (mmt) REVERT: Aa 173 MET cc_start: 0.7632 (ttp) cc_final: 0.7219 (ttt) REVERT: Aa 177 LYS cc_start: 0.8167 (mtpm) cc_final: 0.7716 (mptt) REVERT: Ab 48 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8419 (mtmt) REVERT: Ab 99 LEU cc_start: 0.8577 (tt) cc_final: 0.8231 (tp) REVERT: Ab 127 ASN cc_start: 0.8397 (t0) cc_final: 0.8154 (t0) REVERT: Ab 173 MET cc_start: 0.7458 (ttp) cc_final: 0.7138 (ttt) REVERT: Ac 69 HIS cc_start: 0.8204 (m170) cc_final: 0.7107 (t-90) REVERT: Ac 108 MET cc_start: 0.9060 (tpt) cc_final: 0.8772 (mmp) REVERT: Ac 139 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7646 (mt-10) REVERT: Ac 142 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7992 (mp0) REVERT: Ac 173 MET cc_start: 0.7691 (ttp) cc_final: 0.7306 (ttt) REVERT: Ac 177 LYS cc_start: 0.7994 (mtpm) cc_final: 0.7513 (mptt) REVERT: Ad 91 ASP cc_start: 0.8611 (m-30) cc_final: 0.8245 (m-30) REVERT: Ad 95 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7685 (mp0) REVERT: Ad 121 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7467 (tm-30) REVERT: Ad 160 MET cc_start: 0.9282 (mmp) cc_final: 0.8708 (mmt) REVERT: Ae 177 LYS cc_start: 0.8167 (mtpm) cc_final: 0.7616 (mptt) REVERT: Af 69 HIS cc_start: 0.8153 (m-70) cc_final: 0.7029 (t70) REVERT: Af 99 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8317 (tp) REVERT: Af 160 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8738 (mmm) REVERT: Ag 48 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8405 (mtmt) REVERT: Ag 116 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8866 (tmm) REVERT: Ag 177 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7624 (mptt) REVERT: Ah 48 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8267 (mtmm) REVERT: Ah 173 MET cc_start: 0.7677 (ttp) cc_final: 0.7311 (ttt) REVERT: Ah 177 LYS cc_start: 0.7879 (mtpp) cc_final: 0.7562 (mptt) REVERT: Ah 181 MET cc_start: 0.7051 (mmt) cc_final: 0.6779 (mpp) REVERT: Ai 69 HIS cc_start: 0.8049 (m-70) cc_final: 0.6842 (t-90) REVERT: Ai 108 MET cc_start: 0.9165 (tpt) cc_final: 0.8832 (mmm) REVERT: Ai 139 GLU cc_start: 0.7818 (tt0) cc_final: 0.7516 (pt0) REVERT: Ai 173 MET cc_start: 0.7803 (ttp) cc_final: 0.7449 (ttt) REVERT: Ai 177 LYS cc_start: 0.8296 (mtpm) cc_final: 0.8023 (mptt) REVERT: Aj 69 HIS cc_start: 0.8269 (m90) cc_final: 0.8029 (m-70) REVERT: Aj 172 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7102 (mm-30) REVERT: Aj 177 LYS cc_start: 0.8055 (mtpp) cc_final: 0.7765 (mptt) REVERT: Al 177 LYS cc_start: 0.7984 (mtpm) cc_final: 0.7577 (mptt) REVERT: Am 71 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8246 (mt) REVERT: Am 99 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8306 (tp) REVERT: Am 113 ASN cc_start: 0.8278 (m-40) cc_final: 0.8076 (m110) REVERT: Am 168 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7527 (mt-10) REVERT: Am 177 LYS cc_start: 0.7655 (mppt) cc_final: 0.7427 (mptt) REVERT: An 99 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8141 (tp) REVERT: An 108 MET cc_start: 0.8873 (tpt) cc_final: 0.8266 (tpt) REVERT: An 121 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7258 (tp30) REVERT: An 135 MET cc_start: 0.8988 (mmm) cc_final: 0.8714 (mmm) REVERT: An 153 LYS cc_start: 0.8802 (mmpt) cc_final: 0.8589 (mmtm) REVERT: An 173 MET cc_start: 0.7390 (ttp) cc_final: 0.7144 (ttt) REVERT: Ao 91 ASP cc_start: 0.8762 (m-30) cc_final: 0.8513 (m-30) REVERT: Ao 112 MET cc_start: 0.9312 (mmp) cc_final: 0.8620 (mmp) REVERT: Ao 121 GLU cc_start: 0.7733 (tm-30) cc_final: 0.7333 (tm-30) REVERT: Ao 139 GLU cc_start: 0.7791 (pt0) cc_final: 0.7452 (tt0) REVERT: Ao 153 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.7304 (mptp) REVERT: Ao 173 MET cc_start: 0.7451 (ttp) cc_final: 0.7183 (ttt) REVERT: Ap 60 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7435 (mptt) REVERT: Ap 99 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8045 (mt) REVERT: Ap 116 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8776 (ttp) REVERT: Ap 173 MET cc_start: 0.7527 (ttp) cc_final: 0.7254 (ttt) REVERT: Aq 153 LYS cc_start: 0.8773 (OUTLIER) cc_final: 0.7529 (mptp) REVERT: Aq 177 LYS cc_start: 0.8067 (mtpm) cc_final: 0.7715 (mptt) REVERT: Ar 69 HIS cc_start: 0.8198 (m-70) cc_final: 0.7052 (t-90) REVERT: Ar 91 ASP cc_start: 0.8739 (m-30) cc_final: 0.8496 (m-30) REVERT: Ar 99 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8265 (tp) REVERT: Ar 173 MET cc_start: 0.7727 (ttp) cc_final: 0.7364 (ttt) REVERT: Ar 177 LYS cc_start: 0.8155 (mtmt) cc_final: 0.7752 (mptt) REVERT: As 121 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7529 (tm-30) REVERT: As 146 LYS cc_start: 0.8689 (ttpt) cc_final: 0.8445 (ttpp) REVERT: As 153 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.7356 (mptp) outliers start: 61 outliers final: 32 residues processed: 730 average time/residue: 1.6101 time to fit residues: 1306.4585 Evaluate side-chains 747 residues out of total 2470 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 700 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Aa residue 95 GLU Chi-restraints excluded: chain Ab residue 116 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 110 THR Chi-restraints excluded: chain Ae residue 116 MET Chi-restraints excluded: chain Ae residue 181 MET Chi-restraints excluded: chain Af residue 99 LEU Chi-restraints excluded: chain Af residue 160 MET Chi-restraints excluded: chain Ag residue 95 GLU Chi-restraints excluded: chain Ag residue 116 MET Chi-restraints excluded: chain Ag residue 187 VAL Chi-restraints excluded: chain Ah residue 95 GLU Chi-restraints excluded: chain Ai residue 103 ILE Chi-restraints excluded: chain Ai residue 187 VAL Chi-restraints excluded: chain Aj residue 95 GLU Chi-restraints excluded: chain Aj residue 99 LEU Chi-restraints excluded: chain Ak residue 71 LEU Chi-restraints excluded: chain Ak residue 116 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 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 99 LEU Chi-restraints excluded: chain An residue 187 VAL 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 95 GLU Chi-restraints excluded: chain Ap residue 99 LEU Chi-restraints excluded: chain Ap residue 116 MET Chi-restraints excluded: chain Aq residue 116 MET Chi-restraints excluded: chain Aq residue 153 LYS Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 224 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 211 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 217 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Aa 140 GLN Ac 113 ASN Ah 113 ASN An 69 HIS ** An 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134269 restraints weight = 24158.983| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.01 r_work: 0.3353 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 57 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3208 r_free = 0.3208 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| r_final: 0.3208 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2934 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= 0.299 Angle : 0.582 10.618 31103 Z= 0.295 Chirality : 0.043 0.181 3420 Planarity : 0.005 0.041 4009 Dihedral : 4.168 16.863 3040 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.43 % Allowed : 26.36 % Favored : 71.21 % 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: 1.73 (0.16), residues: 988 sheet: 0.95 (0.31), residues: 228 loop : -0.95 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRPAh 132 HIS 0.005 0.001 HISAg 69 PHE 0.014 0.002 PHEAb 163 TYR 0.017 0.002 TYRAk 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: 16674.07 seconds wall clock time: 289 minutes 49.28 seconds (17389.28 seconds total)