Starting phenix.real_space_refine on Wed Sep 17 03:17:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oln_16959/09_2025/8oln_16959.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oln_16959/09_2025/8oln_16959.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oln_16959/09_2025/8oln_16959.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oln_16959/09_2025/8oln_16959.map" model { file = "/net/cci-nas-00/data/ceres_data/8oln_16959/09_2025/8oln_16959.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oln_16959/09_2025/8oln_16959.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.001 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 10 5.16 5 C 1800 2.51 5 N 510 2.21 5 O 510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2830 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 283 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Restraints were copied for chains: J, B, C, D, E, F, G, H, I Time building chain proxies: 0.52, per 1000 atoms: 0.18 Number of scatterers: 2830 At special positions: 0 Unit cell: (91.304, 89.688, 42.016, 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 10 16.00 O 510 8.00 N 510 7.00 C 1800 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: 0.20 Conformation dependent library (CDL) restraints added in 65.9 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 640 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.510A pdb=" N ALA A 2 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ARG C 5 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE A 4 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASP C 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 4 removed outlier: 6.510A pdb=" N ALA A 2 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ARG C 5 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE A 4 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASP C 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ALA C 2 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ARG E 5 " --> pdb=" O ALA C 2 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N PHE C 4 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ASP E 7 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N HIS C 6 " --> pdb=" O ASP E 7 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLY E 9 " --> pdb=" O HIS C 6 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N SER C 8 " --> pdb=" O GLY E 9 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N GLU E 11 " --> pdb=" O SER C 8 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TYR C 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N HIS E 13 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL C 12 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ALA E 2 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ARG G 5 " --> pdb=" O ALA E 2 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N PHE E 4 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP G 7 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N HIS E 6 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N GLY G 9 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER E 8 " --> pdb=" O GLY G 9 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLU G 11 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TYR E 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N HIS G 13 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL E 12 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU I 3 " --> pdb=" O ALA G 2 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS G 6 " --> pdb=" O ARG I 5 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 24 removed outlier: 6.783A pdb=" N ALA A 21 " --> pdb=" O GLN C 22 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL C 24 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ASN A 23 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA C 21 " --> pdb=" O GLN E 22 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL E 24 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ASN C 23 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ALA E 21 " --> pdb=" O GLN G 22 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL G 24 " --> pdb=" O ALA E 21 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ASN E 23 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA G 21 " --> pdb=" O GLN I 22 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL I 24 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ASN G 23 " --> pdb=" O VAL I 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA5, first strand: chain 'J' and resid 2 through 13 removed outlier: 6.711A pdb=" N GLU J 3 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N HIS H 6 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ARG J 5 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N SER H 8 " --> pdb=" O ARG J 5 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ASP J 7 " --> pdb=" O SER H 8 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N TYR H 10 " --> pdb=" O ASP J 7 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N GLY J 9 " --> pdb=" O TYR H 10 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL H 12 " --> pdb=" O GLY J 9 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU J 11 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA F 2 " --> pdb=" O GLU H 3 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ARG H 5 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE F 4 " --> pdb=" O ARG H 5 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASP H 7 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N HIS F 6 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLY H 9 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N SER F 8 " --> pdb=" O GLY H 9 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N GLU H 11 " --> pdb=" O SER F 8 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TYR F 10 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N HIS H 13 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL F 12 " --> pdb=" O HIS H 13 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA D 2 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ARG F 5 " --> pdb=" O ALA D 2 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N PHE D 4 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N ASP F 7 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N HIS D 6 " --> pdb=" O ASP F 7 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLY F 9 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N SER D 8 " --> pdb=" O GLY F 9 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLU F 11 " --> pdb=" O SER D 8 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR D 10 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N HIS F 13 " --> pdb=" O TYR D 10 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL D 12 " --> pdb=" O HIS F 13 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA B 2 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ARG D 5 " --> pdb=" O ALA B 2 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N PHE B 4 " --> pdb=" O ARG D 5 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASP D 7 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N HIS B 6 " --> pdb=" O ASP D 7 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N GLY D 9 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER B 8 " --> pdb=" O GLY D 9 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N GLU D 11 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR B 10 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N HIS D 13 " --> pdb=" O TYR B 10 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 12 " --> pdb=" O HIS D 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'J' and resid 21 through 24 removed outlier: 6.810A pdb=" N ALA F 21 " --> pdb=" O GLN H 22 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL H 24 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ASN F 23 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA D 21 " --> pdb=" O GLN F 22 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL F 24 " --> pdb=" O ALA D 21 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ASN D 23 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA B 21 " --> pdb=" O GLN D 22 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL D 24 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASN B 23 " --> pdb=" O VAL D 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 30 through 32 removed outlier: 6.179A pdb=" N ILE J 31 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 17 through 18 Processing sheet with id=AA9, first strand: chain 'C' and resid 17 through 18 removed outlier: 3.503A pdb=" N VAL C 18 " --> pdb=" O LEU E 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 17 through 18 36 hydrogen bonds defined for protein. 108 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: 0.27 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 960 1.34 - 1.46: 655 1.46 - 1.57: 1255 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 2890 Sorted by residual: bond pdb=" CA VAL J 12 " pdb=" CB VAL J 12 " ideal model delta sigma weight residual 1.548 1.539 0.009 1.13e-02 7.83e+03 5.93e-01 bond pdb=" CA VAL I 12 " pdb=" CB VAL I 12 " ideal model delta sigma weight residual 1.548 1.539 0.008 1.13e-02 7.83e+03 5.38e-01 bond pdb=" CA VAL G 18 " pdb=" CB VAL G 18 " ideal model delta sigma weight residual 1.548 1.539 0.008 1.13e-02 7.83e+03 5.36e-01 bond pdb=" CA VAL C 18 " pdb=" CB VAL C 18 " ideal model delta sigma weight residual 1.548 1.539 0.008 1.13e-02 7.83e+03 5.31e-01 bond pdb=" CA VAL F 12 " pdb=" CB VAL F 12 " ideal model delta sigma weight residual 1.548 1.540 0.008 1.13e-02 7.83e+03 5.00e-01 ... (remaining 2885 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.59: 3271 0.59 - 1.17: 440 1.17 - 1.76: 139 1.76 - 2.35: 0 2.35 - 2.94: 20 Bond angle restraints: 3870 Sorted by residual: angle pdb=" N ALA B 2 " pdb=" CA ALA B 2 " pdb=" C ALA B 2 " ideal model delta sigma weight residual 108.32 111.26 -2.94 1.64e+00 3.72e-01 3.20e+00 angle pdb=" N ALA F 2 " pdb=" CA ALA F 2 " pdb=" C ALA F 2 " ideal model delta sigma weight residual 108.32 111.24 -2.92 1.64e+00 3.72e-01 3.18e+00 angle pdb=" N ALA D 2 " pdb=" CA ALA D 2 " pdb=" C ALA D 2 " ideal model delta sigma weight residual 108.32 111.24 -2.92 1.64e+00 3.72e-01 3.17e+00 angle pdb=" N ALA J 2 " pdb=" CA ALA J 2 " pdb=" C ALA J 2 " ideal model delta sigma weight residual 108.32 111.23 -2.91 1.64e+00 3.72e-01 3.14e+00 angle pdb=" N ALA G 2 " pdb=" CA ALA G 2 " pdb=" C ALA G 2 " ideal model delta sigma weight residual 108.32 111.22 -2.90 1.64e+00 3.72e-01 3.14e+00 ... (remaining 3865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.02: 1270 6.02 - 12.05: 220 12.05 - 18.07: 80 18.07 - 24.09: 30 24.09 - 30.12: 40 Dihedral angle restraints: 1640 sinusoidal: 640 harmonic: 1000 Sorted by residual: dihedral pdb=" CA LYS B 28 " pdb=" CB LYS B 28 " pdb=" CG LYS B 28 " pdb=" CD LYS B 28 " ideal model delta sinusoidal sigma weight residual -180.00 -149.88 -30.12 3 1.50e+01 4.44e-03 4.77e+00 dihedral pdb=" CA LYS E 28 " pdb=" CB LYS E 28 " pdb=" CG LYS E 28 " pdb=" CD LYS E 28 " ideal model delta sinusoidal sigma weight residual -180.00 -149.91 -30.09 3 1.50e+01 4.44e-03 4.76e+00 dihedral pdb=" CA LYS I 28 " pdb=" CB LYS I 28 " pdb=" CG LYS I 28 " pdb=" CD LYS I 28 " ideal model delta sinusoidal sigma weight residual -180.00 -149.93 -30.07 3 1.50e+01 4.44e-03 4.76e+00 ... (remaining 1637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 187 0.025 - 0.049: 143 0.049 - 0.074: 20 0.074 - 0.099: 27 0.099 - 0.123: 23 Chirality restraints: 400 Sorted by residual: chirality pdb=" CA ILE I 31 " pdb=" N ILE I 31 " pdb=" C ILE I 31 " pdb=" CB ILE I 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE F 31 " pdb=" N ILE F 31 " pdb=" C ILE F 31 " pdb=" CB ILE F 31 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 chirality pdb=" CA ILE D 31 " pdb=" N ILE D 31 " pdb=" C ILE D 31 " pdb=" CB ILE D 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 397 not shown) Planarity restraints: 510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 5 " -0.002 2.00e-02 2.50e+03 3.88e-03 1.51e-01 pdb=" C ARG E 5 " 0.007 2.00e-02 2.50e+03 pdb=" O ARG E 5 " -0.003 2.00e-02 2.50e+03 pdb=" N HIS E 6 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 5 " -0.002 2.00e-02 2.50e+03 3.88e-03 1.50e-01 pdb=" C ARG H 5 " 0.007 2.00e-02 2.50e+03 pdb=" O ARG H 5 " -0.003 2.00e-02 2.50e+03 pdb=" N HIS H 6 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG J 5 " -0.002 2.00e-02 2.50e+03 3.68e-03 1.36e-01 pdb=" C ARG J 5 " 0.006 2.00e-02 2.50e+03 pdb=" O ARG J 5 " -0.002 2.00e-02 2.50e+03 pdb=" N HIS J 6 " -0.002 2.00e-02 2.50e+03 ... (remaining 507 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 611 2.80 - 3.32: 2443 3.32 - 3.85: 4757 3.85 - 4.37: 5160 4.37 - 4.90: 9774 Nonbonded interactions: 22745 Sorted by model distance: nonbonded pdb=" OD1 ASP F 1 " pdb=" N ASP H 1 " model vdw 2.271 3.120 nonbonded pdb=" OD1 ASP C 1 " pdb=" N ASP E 1 " model vdw 2.305 3.120 nonbonded pdb=" O ASN D 23 " pdb=" OH TYR F 10 " model vdw 2.430 3.040 nonbonded pdb=" OD1 ASP B 1 " pdb=" N ASP D 1 " model vdw 2.439 3.120 nonbonded pdb=" O ASN G 23 " pdb=" OH TYR I 10 " model vdw 2.455 3.040 ... (remaining 22740 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'J' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 3.590 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.002 0.009 2890 Z= 0.125 Angle : 0.479 2.936 3870 Z= 0.307 Chirality : 0.044 0.123 400 Planarity : 0.001 0.005 510 Dihedral : 9.035 30.117 1000 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 2.41 % Allowed : 4.48 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.24 (0.32), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 5 TYR 0.004 0.001 TYR A 10 PHE 0.003 0.001 PHE G 4 HIS 0.002 0.001 HIS D 13 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 2890) covalent geometry : angle 0.47927 ( 3870) hydrogen bonds : bond 0.27277 ( 36) hydrogen bonds : angle 10.22662 ( 108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 177 time to evaluate : 0.113 Fit side-chains REVERT: A 5 ARG cc_start: 0.5642 (ptm-80) cc_final: 0.5275 (ptt90) REVERT: J 5 ARG cc_start: 0.7146 (ptm-80) cc_final: 0.5757 (mmm160) REVERT: J 10 TYR cc_start: 0.8407 (t80) cc_final: 0.5764 (p90) REVERT: J 19 PHE cc_start: 0.8262 (t80) cc_final: 0.7969 (t80) REVERT: B 5 ARG cc_start: 0.6090 (ptm-80) cc_final: 0.5215 (ptt-90) REVERT: B 19 PHE cc_start: 0.8523 (t80) cc_final: 0.8210 (t80) REVERT: B 22 GLN cc_start: 0.8531 (mt0) cc_final: 0.7526 (pm20) REVERT: C 19 PHE cc_start: 0.8513 (t80) cc_final: 0.7936 (t80) REVERT: D 19 PHE cc_start: 0.8452 (t80) cc_final: 0.7850 (t80) REVERT: E 19 PHE cc_start: 0.8587 (t80) cc_final: 0.8080 (t80) REVERT: F 19 PHE cc_start: 0.8532 (t80) cc_final: 0.8112 (t80) REVERT: G 19 PHE cc_start: 0.8557 (t80) cc_final: 0.8194 (t80) REVERT: H 5 ARG cc_start: 0.7493 (ptm-80) cc_final: 0.7143 (ttp-110) REVERT: H 19 PHE cc_start: 0.8602 (t80) cc_final: 0.8347 (t80) REVERT: I 10 TYR cc_start: 0.8295 (t80) cc_final: 0.5903 (p90) REVERT: I 19 PHE cc_start: 0.8176 (t80) cc_final: 0.7526 (t80) REVERT: I 23 ASN cc_start: 0.8235 (m-40) cc_final: 0.7873 (m-40) outliers start: 7 outliers final: 5 residues processed: 183 average time/residue: 0.0786 time to fit residues: 16.5516 Evaluate side-chains 139 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 134 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 12 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 20.0000 chunk 12 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 HIS J 14 HIS J 22 GLN ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 HIS ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 HIS C 14 HIS D 14 HIS D 22 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 HIS E 22 GLN F 14 HIS F 22 GLN G 14 HIS H 13 HIS H 14 HIS H 22 GLN I 13 HIS I 14 HIS I 22 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.170297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.147213 restraints weight = 4589.771| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 4.82 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2890 Z= 0.119 Angle : 0.461 4.890 3870 Z= 0.263 Chirality : 0.050 0.139 400 Planarity : 0.002 0.017 510 Dihedral : 4.412 15.781 375 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.48 % Allowed : 16.90 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.32 (0.34), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.26), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 5 TYR 0.009 0.001 TYR G 10 PHE 0.011 0.001 PHE C 4 HIS 0.004 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2890) covalent geometry : angle 0.46148 ( 3870) hydrogen bonds : bond 0.04964 ( 36) hydrogen bonds : angle 6.71325 ( 108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.144 Fit side-chains REVERT: A 32 ILE cc_start: 0.7995 (mm) cc_final: 0.7670 (mm) REVERT: J 10 TYR cc_start: 0.8318 (t80) cc_final: 0.5638 (p90) REVERT: J 19 PHE cc_start: 0.8481 (t80) cc_final: 0.7747 (t80) REVERT: B 32 ILE cc_start: 0.7652 (mm) cc_final: 0.7366 (mm) REVERT: B 36 VAL cc_start: 0.7979 (m) cc_final: 0.7773 (t) REVERT: C 19 PHE cc_start: 0.8542 (t80) cc_final: 0.7958 (t80) REVERT: D 19 PHE cc_start: 0.8316 (t80) cc_final: 0.7899 (t80) REVERT: E 19 PHE cc_start: 0.8606 (t80) cc_final: 0.8145 (t80) REVERT: F 19 PHE cc_start: 0.8541 (t80) cc_final: 0.8183 (t80) REVERT: G 10 TYR cc_start: 0.8925 (t80) cc_final: 0.8290 (t80) REVERT: H 10 TYR cc_start: 0.8973 (t80) cc_final: 0.8497 (t80) REVERT: H 35 MET cc_start: 0.8482 (ptm) cc_final: 0.8277 (ptp) REVERT: I 10 TYR cc_start: 0.8433 (t80) cc_final: 0.5961 (p90) REVERT: I 16 LYS cc_start: 0.4860 (mmtt) cc_final: 0.3914 (mttt) outliers start: 13 outliers final: 10 residues processed: 146 average time/residue: 0.0750 time to fit residues: 12.7960 Evaluate side-chains 124 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 114 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain H residue 8 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 28 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 HIS ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 HIS ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 HIS E 22 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 HIS ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 HIS H 22 GLN ** I 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.157476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.136671 restraints weight = 5067.440| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 4.88 r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.043 2890 Z= 0.441 Angle : 0.709 5.828 3870 Z= 0.405 Chirality : 0.052 0.150 400 Planarity : 0.004 0.021 510 Dihedral : 5.667 31.130 373 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 7.59 % Allowed : 23.10 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.48 (0.33), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 5 TYR 0.007 0.002 TYR G 10 PHE 0.016 0.002 PHE E 4 HIS 0.005 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00975 ( 2890) covalent geometry : angle 0.70885 ( 3870) hydrogen bonds : bond 0.05644 ( 36) hydrogen bonds : angle 7.42829 ( 108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 0.118 Fit side-chains REVERT: A 19 PHE cc_start: 0.8527 (t80) cc_final: 0.8278 (t80) REVERT: A 32 ILE cc_start: 0.8568 (mm) cc_final: 0.8345 (mm) REVERT: J 22 GLN cc_start: 0.8849 (mt0) cc_final: 0.8579 (mt0) REVERT: D 19 PHE cc_start: 0.8282 (t80) cc_final: 0.7821 (t80) REVERT: F 19 PHE cc_start: 0.8605 (t80) cc_final: 0.8160 (t80) REVERT: G 19 PHE cc_start: 0.8686 (t80) cc_final: 0.8450 (t80) REVERT: H 17 LEU cc_start: 0.8823 (mp) cc_final: 0.8512 (mp) REVERT: I 19 PHE cc_start: 0.8569 (t80) cc_final: 0.8058 (t80) outliers start: 22 outliers final: 16 residues processed: 141 average time/residue: 0.0661 time to fit residues: 11.0557 Evaluate side-chains 131 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 36 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN C 23 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.166959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.145724 restraints weight = 4865.906| |-----------------------------------------------------------------------------| r_work (start): 0.4118 rms_B_bonded: 4.83 r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.5148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2890 Z= 0.116 Angle : 0.471 5.629 3870 Z= 0.264 Chirality : 0.050 0.148 400 Planarity : 0.002 0.010 510 Dihedral : 4.620 17.896 373 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 5.52 % Allowed : 26.90 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.46 (0.33), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 5 TYR 0.008 0.001 TYR J 10 PHE 0.008 0.001 PHE J 4 HIS 0.002 0.001 HIS G 13 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2890) covalent geometry : angle 0.47103 ( 3870) hydrogen bonds : bond 0.03449 ( 36) hydrogen bonds : angle 6.18951 ( 108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.134 Fit side-chains REVERT: A 19 PHE cc_start: 0.8634 (t80) cc_final: 0.8318 (t80) REVERT: A 32 ILE cc_start: 0.7854 (mm) cc_final: 0.7568 (mm) REVERT: J 19 PHE cc_start: 0.8656 (t80) cc_final: 0.8303 (t80) REVERT: J 22 GLN cc_start: 0.8825 (mt0) cc_final: 0.8537 (mt0) REVERT: B 35 MET cc_start: 0.8438 (ptp) cc_final: 0.8200 (ptp) REVERT: B 36 VAL cc_start: 0.7932 (m) cc_final: 0.7701 (t) REVERT: C 19 PHE cc_start: 0.8557 (t80) cc_final: 0.8138 (t80) REVERT: D 19 PHE cc_start: 0.8288 (t80) cc_final: 0.7759 (t80) REVERT: F 19 PHE cc_start: 0.8586 (t80) cc_final: 0.7985 (t80) REVERT: F 20 PHE cc_start: 0.8754 (m-80) cc_final: 0.8467 (m-80) REVERT: G 19 PHE cc_start: 0.8560 (t80) cc_final: 0.8306 (t80) REVERT: I 19 PHE cc_start: 0.8655 (t80) cc_final: 0.8330 (t80) outliers start: 16 outliers final: 13 residues processed: 134 average time/residue: 0.0637 time to fit residues: 10.1923 Evaluate side-chains 123 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 110 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain I residue 23 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 8 optimal weight: 0.3980 chunk 19 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN B 22 GLN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.158108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.138995 restraints weight = 4983.634| |-----------------------------------------------------------------------------| r_work (start): 0.4037 rms_B_bonded: 4.66 r_work (final): 0.4037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 2890 Z= 0.291 Angle : 0.584 5.855 3870 Z= 0.334 Chirality : 0.050 0.144 400 Planarity : 0.003 0.018 510 Dihedral : 5.080 25.157 372 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 10.00 % Allowed : 23.10 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.56 (0.33), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 5 TYR 0.007 0.001 TYR F 10 PHE 0.013 0.002 PHE E 4 HIS 0.004 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00653 ( 2890) covalent geometry : angle 0.58357 ( 3870) hydrogen bonds : bond 0.04417 ( 36) hydrogen bonds : angle 6.76795 ( 108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.117 Fit side-chains REVERT: A 19 PHE cc_start: 0.8505 (t80) cc_final: 0.8210 (t80) REVERT: A 32 ILE cc_start: 0.8294 (mm) cc_final: 0.8056 (mm) REVERT: J 19 PHE cc_start: 0.8619 (t80) cc_final: 0.8203 (t80) REVERT: J 20 PHE cc_start: 0.8625 (m-80) cc_final: 0.8124 (m-80) REVERT: J 22 GLN cc_start: 0.8847 (mt0) cc_final: 0.8531 (mt0) REVERT: C 19 PHE cc_start: 0.8547 (t80) cc_final: 0.8035 (t80) REVERT: F 19 PHE cc_start: 0.8659 (t80) cc_final: 0.7971 (t80) REVERT: F 20 PHE cc_start: 0.8783 (m-80) cc_final: 0.8027 (m-80) REVERT: G 19 PHE cc_start: 0.8684 (t80) cc_final: 0.8404 (t80) REVERT: I 7 ASP cc_start: 0.7301 (t0) cc_final: 0.7000 (t70) REVERT: I 19 PHE cc_start: 0.8642 (t80) cc_final: 0.8282 (t80) outliers start: 29 outliers final: 25 residues processed: 141 average time/residue: 0.0606 time to fit residues: 10.3532 Evaluate side-chains 142 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 HIS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 23 ASN Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 23 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN F 22 GLN F 23 ASN H 23 ASN I 22 GLN I 23 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.157522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.138969 restraints weight = 5116.764| |-----------------------------------------------------------------------------| r_work (start): 0.4045 rms_B_bonded: 4.50 r_work: 0.3899 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 2890 Z= 0.310 Angle : 0.589 6.094 3870 Z= 0.336 Chirality : 0.050 0.143 400 Planarity : 0.003 0.018 510 Dihedral : 5.119 23.019 372 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 10.34 % Allowed : 25.17 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.57 (0.33), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 5 TYR 0.013 0.002 TYR I 10 PHE 0.013 0.002 PHE H 4 HIS 0.004 0.001 HIS A 13 Details of bonding type rmsd covalent geometry : bond 0.00693 ( 2890) covalent geometry : angle 0.58936 ( 3870) hydrogen bonds : bond 0.04283 ( 36) hydrogen bonds : angle 6.65206 ( 108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.115 Fit side-chains REVERT: A 19 PHE cc_start: 0.8626 (t80) cc_final: 0.8378 (t80) REVERT: J 19 PHE cc_start: 0.8663 (t80) cc_final: 0.8271 (t80) REVERT: J 20 PHE cc_start: 0.8661 (m-80) cc_final: 0.8269 (m-80) REVERT: J 22 GLN cc_start: 0.9129 (mt0) cc_final: 0.8855 (mt0) REVERT: C 19 PHE cc_start: 0.8535 (t80) cc_final: 0.8167 (t80) REVERT: D 19 PHE cc_start: 0.8316 (t80) cc_final: 0.7807 (t80) REVERT: E 19 PHE cc_start: 0.8519 (t80) cc_final: 0.8138 (t80) REVERT: F 19 PHE cc_start: 0.8693 (t80) cc_final: 0.7995 (t80) REVERT: F 20 PHE cc_start: 0.8879 (m-80) cc_final: 0.8044 (m-80) REVERT: G 19 PHE cc_start: 0.8655 (t80) cc_final: 0.8411 (t80) REVERT: I 7 ASP cc_start: 0.7224 (t0) cc_final: 0.6764 (t70) REVERT: I 19 PHE cc_start: 0.8659 (t80) cc_final: 0.8359 (t80) outliers start: 30 outliers final: 26 residues processed: 136 average time/residue: 0.0586 time to fit residues: 9.6910 Evaluate side-chains 140 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 HIS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain B residue 6 HIS Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 23 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN C 23 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN I 22 GLN I 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.164615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.145640 restraints weight = 4884.512| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 4.48 r_work: 0.3953 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2890 Z= 0.176 Angle : 0.501 6.415 3870 Z= 0.285 Chirality : 0.050 0.146 400 Planarity : 0.002 0.012 510 Dihedral : 4.806 19.893 372 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 7.93 % Allowed : 26.90 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.57 (0.33), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 5 TYR 0.013 0.002 TYR F 10 PHE 0.008 0.001 PHE E 4 HIS 0.003 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 2890) covalent geometry : angle 0.50111 ( 3870) hydrogen bonds : bond 0.03552 ( 36) hydrogen bonds : angle 6.40685 ( 108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.121 Fit side-chains REVERT: A 19 PHE cc_start: 0.8687 (t80) cc_final: 0.8446 (t80) REVERT: J 19 PHE cc_start: 0.8657 (t80) cc_final: 0.8190 (t80) REVERT: J 20 PHE cc_start: 0.8713 (m-80) cc_final: 0.8127 (m-80) REVERT: J 22 GLN cc_start: 0.9110 (mt0) cc_final: 0.8854 (mt0) REVERT: C 19 PHE cc_start: 0.8499 (t80) cc_final: 0.8153 (t80) REVERT: D 19 PHE cc_start: 0.8332 (t80) cc_final: 0.7899 (t80) REVERT: F 19 PHE cc_start: 0.8689 (t80) cc_final: 0.8201 (t80) REVERT: F 20 PHE cc_start: 0.8852 (m-80) cc_final: 0.8450 (m-80) REVERT: G 19 PHE cc_start: 0.8653 (t80) cc_final: 0.8399 (t80) REVERT: I 7 ASP cc_start: 0.7103 (t0) cc_final: 0.6670 (t70) REVERT: I 19 PHE cc_start: 0.8694 (t80) cc_final: 0.8430 (t80) outliers start: 23 outliers final: 21 residues processed: 138 average time/residue: 0.0597 time to fit residues: 9.9894 Evaluate side-chains 137 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 HIS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain B residue 6 HIS Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain H residue 8 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 6 optimal weight: 30.0000 chunk 22 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN F 23 ASN I 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.157253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.137885 restraints weight = 5163.786| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 4.73 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 2890 Z= 0.299 Angle : 0.585 6.481 3870 Z= 0.332 Chirality : 0.050 0.145 400 Planarity : 0.003 0.013 510 Dihedral : 5.174 24.235 372 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 9.66 % Allowed : 25.86 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.64 (0.33), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 5 TYR 0.016 0.002 TYR F 10 PHE 0.011 0.002 PHE H 4 HIS 0.004 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00671 ( 2890) covalent geometry : angle 0.58531 ( 3870) hydrogen bonds : bond 0.04183 ( 36) hydrogen bonds : angle 6.73078 ( 108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.142 Fit side-chains REVERT: A 19 PHE cc_start: 0.8642 (t80) cc_final: 0.8399 (t80) REVERT: J 19 PHE cc_start: 0.8629 (t80) cc_final: 0.8214 (t80) REVERT: J 20 PHE cc_start: 0.8657 (m-80) cc_final: 0.8220 (m-10) REVERT: J 22 GLN cc_start: 0.8856 (mt0) cc_final: 0.8541 (mt0) REVERT: C 19 PHE cc_start: 0.8393 (t80) cc_final: 0.7997 (t80) REVERT: D 19 PHE cc_start: 0.8300 (t80) cc_final: 0.7758 (t80) REVERT: F 19 PHE cc_start: 0.8652 (t80) cc_final: 0.7965 (t80) REVERT: F 20 PHE cc_start: 0.8810 (m-80) cc_final: 0.7903 (m-80) REVERT: G 19 PHE cc_start: 0.8678 (t80) cc_final: 0.8341 (t80) REVERT: I 7 ASP cc_start: 0.7100 (t0) cc_final: 0.6675 (t70) REVERT: I 19 PHE cc_start: 0.8674 (t80) cc_final: 0.8274 (t80) outliers start: 28 outliers final: 25 residues processed: 139 average time/residue: 0.0604 time to fit residues: 10.1626 Evaluate side-chains 143 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 HIS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain B residue 6 HIS Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 16 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 23 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.165724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.145867 restraints weight = 4978.724| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 4.67 r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2890 Z= 0.138 Angle : 0.474 6.895 3870 Z= 0.266 Chirality : 0.050 0.146 400 Planarity : 0.002 0.009 510 Dihedral : 4.706 17.586 372 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 8.62 % Allowed : 26.21 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.64 (0.32), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 5 TYR 0.016 0.002 TYR F 10 PHE 0.009 0.001 PHE C 20 HIS 0.002 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 2890) covalent geometry : angle 0.47449 ( 3870) hydrogen bonds : bond 0.03289 ( 36) hydrogen bonds : angle 6.35999 ( 108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.135 Fit side-chains REVERT: A 19 PHE cc_start: 0.8674 (t80) cc_final: 0.8464 (t80) REVERT: J 19 PHE cc_start: 0.8638 (t80) cc_final: 0.8070 (t80) REVERT: J 20 PHE cc_start: 0.8623 (m-80) cc_final: 0.7944 (m-80) REVERT: J 22 GLN cc_start: 0.8817 (mt0) cc_final: 0.8507 (mt0) REVERT: C 19 PHE cc_start: 0.8404 (t80) cc_final: 0.8023 (t80) REVERT: D 19 PHE cc_start: 0.8217 (t80) cc_final: 0.7795 (t80) REVERT: F 19 PHE cc_start: 0.8676 (t80) cc_final: 0.8171 (t80) REVERT: F 20 PHE cc_start: 0.8766 (m-80) cc_final: 0.8251 (m-80) REVERT: G 19 PHE cc_start: 0.8525 (t80) cc_final: 0.7944 (t80) REVERT: G 20 PHE cc_start: 0.8831 (m-80) cc_final: 0.8003 (m-80) REVERT: I 7 ASP cc_start: 0.6979 (t0) cc_final: 0.6593 (t70) REVERT: I 19 PHE cc_start: 0.8676 (t80) cc_final: 0.8427 (t80) outliers start: 25 outliers final: 23 residues processed: 137 average time/residue: 0.0561 time to fit residues: 9.4080 Evaluate side-chains 137 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 HIS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain B residue 6 HIS Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 23 ASN Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain I residue 8 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN I 23 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.161285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.141805 restraints weight = 5086.029| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 4.60 r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.5888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2890 Z= 0.226 Angle : 0.525 6.658 3870 Z= 0.298 Chirality : 0.051 0.164 400 Planarity : 0.002 0.010 510 Dihedral : 4.888 20.733 372 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 8.62 % Allowed : 26.55 % Favored : 64.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.68 (0.33), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 5 TYR 0.018 0.002 TYR F 10 PHE 0.014 0.002 PHE C 20 HIS 0.004 0.001 HIS C 13 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 2890) covalent geometry : angle 0.52496 ( 3870) hydrogen bonds : bond 0.04124 ( 36) hydrogen bonds : angle 6.71778 ( 108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 680 Ramachandran restraints generated. 340 Oldfield, 0 Emsley, 340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.115 Fit side-chains REVERT: A 19 PHE cc_start: 0.8645 (t80) cc_final: 0.8420 (t80) REVERT: J 19 PHE cc_start: 0.8658 (t80) cc_final: 0.8145 (t80) REVERT: J 20 PHE cc_start: 0.8647 (m-80) cc_final: 0.8004 (m-80) REVERT: J 22 GLN cc_start: 0.8833 (mt0) cc_final: 0.8520 (mt0) REVERT: C 19 PHE cc_start: 0.8428 (t80) cc_final: 0.8019 (t80) REVERT: D 19 PHE cc_start: 0.8294 (t80) cc_final: 0.7966 (t80) REVERT: F 19 PHE cc_start: 0.8607 (t80) cc_final: 0.8340 (t80) REVERT: G 19 PHE cc_start: 0.8563 (t80) cc_final: 0.8001 (t80) REVERT: G 20 PHE cc_start: 0.8797 (m-80) cc_final: 0.8036 (m-80) REVERT: I 7 ASP cc_start: 0.7008 (t0) cc_final: 0.6605 (t70) REVERT: I 19 PHE cc_start: 0.8685 (t80) cc_final: 0.8415 (t80) outliers start: 25 outliers final: 22 residues processed: 137 average time/residue: 0.0584 time to fit residues: 9.7137 Evaluate side-chains 140 residues out of total 290 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 HIS Chi-restraints excluded: chain A residue 8 SER Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain B residue 6 HIS Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 23 ASN Chi-restraints excluded: chain D residue 8 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 23 ASN Chi-restraints excluded: chain F residue 8 SER Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 18 VAL Chi-restraints excluded: chain G residue 8 SER Chi-restraints excluded: chain H residue 8 SER Chi-restraints excluded: chain I residue 8 SER Chi-restraints excluded: chain I residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 chunk 1 optimal weight: 0.0070 chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 23 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN I 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.165793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.146067 restraints weight = 4940.292| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 4.65 r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.6007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2890 Z= 0.143 Angle : 0.477 7.193 3870 Z= 0.268 Chirality : 0.051 0.159 400 Planarity : 0.002 0.009 510 Dihedral : 4.665 17.993 372 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 8.97 % Allowed : 25.86 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.64 (0.32), residues: 340 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.25), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 5 TYR 0.021 0.003 TYR G 10 PHE 0.012 0.001 PHE C 20 HIS 0.003 0.001 HIS G 13 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 2890) covalent geometry : angle 0.47654 ( 3870) hydrogen bonds : bond 0.03618 ( 36) hydrogen bonds : angle 6.59104 ( 108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 806.61 seconds wall clock time: 14 minutes 34.86 seconds (874.86 seconds total)