Starting phenix.real_space_refine on Thu Sep 10 23:10:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5fna_3241/09_2026/5fna_3241.cif Found real_map, /net/cci-nas-00/data/ceres_data/5fna_3241/09_2026/5fna_3241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5fna_3241/09_2026/5fna_3241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5fna_3241/09_2026/5fna_3241.map" model { file = "/net/cci-nas-00/data/ceres_data/5fna_3241/09_2026/5fna_3241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5fna_3241/09_2026/5fna_3241.cif" } resolution = 4.8 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 ------------------------------------------------------------------------------- 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= 0.718 sd= 0.877 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 48 5.16 5 C 3312 2.51 5 N 920 2.21 5 O 1048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5328 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 0.96, per 1000 atoms: 0.18 Number of scatterers: 5328 At special positions: 0 Unit cell: (80.91, 83.52, 81.78, 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 48 16.00 O 1048 8.00 N 920 7.00 C 3312 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: 0.48 Conformation dependent library (CDL) restraints added in 194.8 milliseconds 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1280 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 82.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 1 through 8 Processing helix chain 'A' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE A 13 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG A 14 " --> pdb=" O LEU A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 31 removed outlier: 5.215A pdb=" N GLY A 23 " --> pdb=" O GLY A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 41 Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 48 through 50 No H-bonds generated for 'chain 'A' and resid 48 through 50' Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.805A pdb=" N ALA A 55 " --> pdb=" O ASP A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 66 No H-bonds generated for 'chain 'A' and resid 64 through 66' Processing helix chain 'A' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 8 Processing helix chain 'B' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE B 13 " --> pdb=" O LYS B 10 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 31 removed outlier: 5.215A pdb=" N GLY B 23 " --> pdb=" O GLY B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 41 Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 48 through 50 No H-bonds generated for 'chain 'B' and resid 48 through 50' Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.805A pdb=" N ALA B 55 " --> pdb=" O ASP B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 8 Processing helix chain 'C' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE C 13 " --> pdb=" O LYS C 10 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG C 14 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 31 removed outlier: 5.215A pdb=" N GLY C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 41 Processing helix chain 'C' and resid 42 through 45 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 51 through 59 removed outlier: 3.806A pdb=" N ALA C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing helix chain 'C' and resid 67 through 79 removed outlier: 3.588A pdb=" N CYS C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 1 through 8 Processing helix chain 'D' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE D 13 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG D 14 " --> pdb=" O LEU D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 31 removed outlier: 5.214A pdb=" N GLY D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 41 Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 48 through 50 No H-bonds generated for 'chain 'D' and resid 48 through 50' Processing helix chain 'D' and resid 51 through 59 removed outlier: 3.805A pdb=" N ALA D 55 " --> pdb=" O ASP D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 66 No H-bonds generated for 'chain 'D' and resid 64 through 66' Processing helix chain 'D' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 8 Processing helix chain 'E' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE E 13 " --> pdb=" O LYS E 10 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG E 14 " --> pdb=" O LEU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 31 removed outlier: 5.215A pdb=" N GLY E 23 " --> pdb=" O GLY E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 41 Processing helix chain 'E' and resid 42 through 45 Processing helix chain 'E' and resid 48 through 50 No H-bonds generated for 'chain 'E' and resid 48 through 50' Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.806A pdb=" N ALA E 55 " --> pdb=" O ASP E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 66 No H-bonds generated for 'chain 'E' and resid 64 through 66' Processing helix chain 'E' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 1 through 8 Processing helix chain 'F' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE F 13 " --> pdb=" O LYS F 10 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG F 14 " --> pdb=" O LEU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 31 removed outlier: 5.215A pdb=" N GLY F 23 " --> pdb=" O GLY F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 41 Processing helix chain 'F' and resid 42 through 45 Processing helix chain 'F' and resid 48 through 50 No H-bonds generated for 'chain 'F' and resid 48 through 50' Processing helix chain 'F' and resid 51 through 59 removed outlier: 3.806A pdb=" N ALA F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS F 71 " --> pdb=" O ALA F 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 1 through 8 Processing helix chain 'G' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE G 13 " --> pdb=" O LYS G 10 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ARG G 14 " --> pdb=" O LEU G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 31 removed outlier: 5.214A pdb=" N GLY G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 41 Processing helix chain 'G' and resid 42 through 45 Processing helix chain 'G' and resid 48 through 50 No H-bonds generated for 'chain 'G' and resid 48 through 50' Processing helix chain 'G' and resid 51 through 59 removed outlier: 3.806A pdb=" N ALA G 55 " --> pdb=" O ASP G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 66 No H-bonds generated for 'chain 'G' and resid 64 through 66' Processing helix chain 'G' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 1 through 8 Processing helix chain 'H' and resid 9 through 16 removed outlier: 3.662A pdb=" N ILE H 13 " --> pdb=" O LYS H 10 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ARG H 14 " --> pdb=" O LEU H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 17 through 31 removed outlier: 5.215A pdb=" N GLY H 23 " --> pdb=" O GLY H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 41 Processing helix chain 'H' and resid 42 through 45 Processing helix chain 'H' and resid 48 through 50 No H-bonds generated for 'chain 'H' and resid 48 through 50' Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.805A pdb=" N ALA H 55 " --> pdb=" O ASP H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing helix chain 'H' and resid 67 through 79 removed outlier: 3.587A pdb=" N CYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 600 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: 0.66 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1143 1.32 - 1.44: 1112 1.44 - 1.57: 3025 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 5352 Sorted by residual: bond pdb=" CA VAL B 42 " pdb=" C VAL B 42 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.46e-02 4.69e+03 1.47e+01 bond pdb=" CA VAL C 42 " pdb=" C VAL C 42 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.46e-02 4.69e+03 1.45e+01 bond pdb=" CA VAL F 42 " pdb=" C VAL F 42 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.46e-02 4.69e+03 1.43e+01 bond pdb=" CA VAL D 42 " pdb=" C VAL D 42 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.46e-02 4.69e+03 1.43e+01 bond pdb=" CA VAL H 42 " pdb=" C VAL H 42 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.46e-02 4.69e+03 1.42e+01 ... (remaining 5347 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 6588 2.38 - 4.75: 449 4.75 - 7.13: 83 7.13 - 9.51: 24 9.51 - 11.88: 16 Bond angle restraints: 7160 Sorted by residual: angle pdb=" N LYS E 8 " pdb=" CA LYS E 8 " pdb=" C LYS E 8 " ideal model delta sigma weight residual 111.36 123.24 -11.88 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N LYS H 8 " pdb=" CA LYS H 8 " pdb=" C LYS H 8 " ideal model delta sigma weight residual 111.36 123.24 -11.88 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N LYS C 8 " pdb=" CA LYS C 8 " pdb=" C LYS C 8 " ideal model delta sigma weight residual 111.36 123.23 -11.87 1.09e+00 8.42e-01 1.18e+02 angle pdb=" N LYS A 8 " pdb=" CA LYS A 8 " pdb=" C LYS A 8 " ideal model delta sigma weight residual 111.36 123.22 -11.86 1.09e+00 8.42e-01 1.18e+02 angle pdb=" N LYS B 8 " pdb=" CA LYS B 8 " pdb=" C LYS B 8 " ideal model delta sigma weight residual 111.36 123.21 -11.85 1.09e+00 8.42e-01 1.18e+02 ... (remaining 7155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 3184 17.63 - 35.26: 192 35.26 - 52.89: 24 52.89 - 70.52: 8 70.52 - 88.16: 8 Dihedral angle restraints: 3416 sinusoidal: 1448 harmonic: 1968 Sorted by residual: dihedral pdb=" CA LYS D 8 " pdb=" C LYS D 8 " pdb=" N ARG D 9 " pdb=" CA ARG D 9 " ideal model delta harmonic sigma weight residual 0.00 15.63 -15.63 0 5.00e+00 4.00e-02 9.77e+00 dihedral pdb=" CA LYS B 8 " pdb=" C LYS B 8 " pdb=" N ARG B 9 " pdb=" CA ARG B 9 " ideal model delta harmonic sigma weight residual 0.00 15.61 -15.61 0 5.00e+00 4.00e-02 9.75e+00 dihedral pdb=" CA LYS H 8 " pdb=" C LYS H 8 " pdb=" N ARG H 9 " pdb=" CA ARG H 9 " ideal model delta harmonic sigma weight residual 0.00 15.56 -15.56 0 5.00e+00 4.00e-02 9.69e+00 ... (remaining 3413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 595 0.077 - 0.154: 226 0.154 - 0.231: 19 0.231 - 0.308: 8 0.308 - 0.385: 8 Chirality restraints: 856 Sorted by residual: chirality pdb=" CA LYS H 8 " pdb=" N LYS H 8 " pdb=" C LYS H 8 " pdb=" CB LYS H 8 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA LYS B 8 " pdb=" N LYS B 8 " pdb=" C LYS B 8 " pdb=" CB LYS B 8 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA LYS A 8 " pdb=" N LYS A 8 " pdb=" C LYS A 8 " pdb=" CB LYS A 8 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 853 not shown) Planarity restraints: 912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET F 50 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C MET F 50 " -0.047 2.00e-02 2.50e+03 pdb=" O MET F 50 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP F 51 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET H 50 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C MET H 50 " -0.047 2.00e-02 2.50e+03 pdb=" O MET H 50 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP H 51 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET G 50 " -0.013 2.00e-02 2.50e+03 2.68e-02 7.17e+00 pdb=" C MET G 50 " 0.046 2.00e-02 2.50e+03 pdb=" O MET G 50 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP G 51 " -0.016 2.00e-02 2.50e+03 ... (remaining 909 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1092 2.76 - 3.29: 6049 3.29 - 3.83: 8159 3.83 - 4.36: 11768 4.36 - 4.90: 15435 Nonbonded interactions: 42503 Sorted by model distance: nonbonded pdb=" CB ALA D 83 " pdb=" CD LYS H 63 " model vdw 2.219 3.860 nonbonded pdb=" CB ALA A 83 " pdb=" CD LYS E 63 " model vdw 2.256 3.860 nonbonded pdb=" CB ALA C 83 " pdb=" CD LYS G 63 " model vdw 2.299 3.860 nonbonded pdb=" CB ALA B 83 " pdb=" CD LYS F 63 " model vdw 2.318 3.860 nonbonded pdb=" CB ALA D 83 " pdb=" CG LYS H 63 " model vdw 2.354 3.860 ... (remaining 42498 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 0.420 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: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.000 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 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 : 0.013 0.056 5352 Z= 0.837 Angle : 1.513 11.882 7160 Z= 1.126 Chirality : 0.078 0.385 856 Planarity : 0.006 0.027 912 Dihedral : 12.323 88.156 2136 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 36.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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 are not related in a simple way. whole: -1.83 (0.32), residues: 664 helix: -2.44 (0.21), residues: 432 sheet: None (None), residues: 0 loop : 1.96 (0.44), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 32 TYR 0.001 0.000 TYR A 74 PHE 0.001 0.000 PHE A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.01279 / 0.84 ( 5352) covalent geometry : angle 1.51269 / 1.13 ( 7160) hydrogen bonds : bond 0.18376 / 11.24 ( 272) hydrogen bonds : angle 7.27710 / 5.04 ( 600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8447 (m-80) cc_final: 0.8246 (m-80) REVERT: A 18 GLU cc_start: 0.8770 (pm20) cc_final: 0.8143 (pp20) REVERT: A 41 LYS cc_start: 0.8697 (mttm) cc_final: 0.8312 (ttpt) REVERT: A 66 GLN cc_start: 0.7935 (pm20) cc_final: 0.7702 (pm20) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0984 time to fit residues: 2.9827 Evaluate side-chains 16 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 49 optimal weight: 20.0000 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.0040 chunk 17 optimal weight: 20.0000 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.057460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048934 restraints weight = 5468.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.049633 restraints weight = 4643.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050205 restraints weight = 4031.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.050658 restraints weight = 3573.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.050980 restraints weight = 3226.957| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5352 Z= 0.187 Angle : 0.823 5.586 7160 Z= 0.464 Chirality : 0.061 0.377 856 Planarity : 0.005 0.037 912 Dihedral : 9.854 66.525 736 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.05 % Allowed : 4.05 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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 are not related in a simple way. whole: -0.15 (0.34), residues: 664 helix: -1.29 (0.24), residues: 440 sheet: None (None), residues: 0 loop : 3.16 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 44 TYR 0.006 0.001 TYR A 74 PHE 0.002 0.001 PHE H 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.19 ( 5352) covalent geometry : angle 0.82269 / 0.46 ( 7160) hydrogen bonds : bond 0.05747 / 3.20 ( 272) hydrogen bonds : angle 5.24484 / 3.67 ( 600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8714 (pm20) cc_final: 0.8257 (pp20) REVERT: H 39 MET cc_start: 0.9119 (tmm) cc_final: 0.8811 (tmm) REVERT: H 58 ASP cc_start: 0.8123 (m-30) cc_final: 0.7872 (m-30) outliers start: 3 outliers final: 0 residues processed: 26 average time/residue: 0.0606 time to fit residues: 1.6914 Evaluate side-chains 15 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.057860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049529 restraints weight = 5331.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.050102 restraints weight = 4702.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.050595 restraints weight = 4201.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.050913 restraints weight = 3800.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.051392 restraints weight = 3502.802| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.8665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5352 Z= 0.178 Angle : 0.788 5.900 7160 Z= 0.428 Chirality : 0.050 0.260 856 Planarity : 0.004 0.024 912 Dihedral : 7.994 37.562 736 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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 are not related in a simple way. whole: 0.25 (0.35), residues: 664 helix: -0.78 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 2.14 (0.45), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 44 TYR 0.007 0.002 TYR F 81 PHE 0.004 0.001 PHE A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 ( 5352) covalent geometry : angle 0.78768 / 0.43 ( 7160) hydrogen bonds : bond 0.04985 / 2.88 ( 272) hydrogen bonds : angle 5.51011 / 3.81 ( 600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 16 MET cc_start: 0.7584 (tpt) cc_final: 0.7369 (tpt) REVERT: H 18 GLU cc_start: 0.8803 (pm20) cc_final: 0.8360 (pp20) REVERT: H 39 MET cc_start: 0.8951 (tmm) cc_final: 0.8729 (tmm) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0695 time to fit residues: 1.3346 Evaluate side-chains 11 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 20.0000 chunk 5 optimal weight: 8.9990 chunk 15 optimal weight: 20.0000 chunk 52 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 30 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.059423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.050544 restraints weight = 5200.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.051317 restraints weight = 4379.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.051955 restraints weight = 3784.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.052408 restraints weight = 3336.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.052891 restraints weight = 3012.802| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.9313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5352 Z= 0.161 Angle : 0.698 5.378 7160 Z= 0.385 Chirality : 0.044 0.129 856 Planarity : 0.006 0.036 912 Dihedral : 6.924 20.680 736 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 18.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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 are not related in a simple way. whole: 0.69 (0.34), residues: 664 helix: -0.43 (0.28), residues: 336 sheet: None (None), residues: 0 loop : 1.81 (0.39), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 9 TYR 0.006 0.002 TYR F 81 PHE 0.002 0.001 PHE C 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 ( 5352) covalent geometry : angle 0.69822 / 0.38 ( 7160) hydrogen bonds : bond 0.03975 / 2.34 ( 272) hydrogen bonds : angle 5.62535 / 3.91 ( 600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8828 (pm20) cc_final: 0.8047 (pp20) REVERT: H 39 MET cc_start: 0.8938 (tmm) cc_final: 0.8609 (tmm) REVERT: H 50 MET cc_start: 0.7574 (ppp) cc_final: 0.6696 (mpp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0660 time to fit residues: 1.1362 Evaluate side-chains 12 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 39 optimal weight: 20.0000 chunk 30 optimal weight: 0.0040 chunk 48 optimal weight: 20.0000 chunk 44 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 overall best weight: 5.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.058935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.049497 restraints weight = 5107.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.050183 restraints weight = 4418.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.050667 restraints weight = 3916.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.051118 restraints weight = 3550.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.051626 restraints weight = 3232.489| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.9808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5352 Z= 0.145 Angle : 0.682 5.392 7160 Z= 0.379 Chirality : 0.044 0.126 856 Planarity : 0.007 0.055 912 Dihedral : 6.607 19.746 736 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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 are not related in a simple way. whole: -0.48 (0.35), residues: 664 helix: -1.05 (0.25), residues: 416 sheet: None (None), residues: 0 loop : 1.51 (0.46), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG D 44 TYR 0.006 0.002 TYR D 74 PHE 0.002 0.001 PHE E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 ( 5352) covalent geometry : angle 0.68157 / 0.38 ( 7160) hydrogen bonds : bond 0.03473 / 2.11 ( 272) hydrogen bonds : angle 5.63057 / 3.94 ( 600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.031 Fit side-chains REVERT: H 18 GLU cc_start: 0.8899 (pm20) cc_final: 0.8179 (pp20) REVERT: H 39 MET cc_start: 0.8970 (tmm) cc_final: 0.8565 (tmm) REVERT: H 40 GLU cc_start: 0.8799 (pm20) cc_final: 0.8377 (pm20) REVERT: H 49 VAL cc_start: 0.6859 (m) cc_final: 0.6145 (t) REVERT: H 50 MET cc_start: 0.7614 (ppp) cc_final: 0.7040 (mpp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0667 time to fit residues: 1.1464 Evaluate side-chains 9 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 31 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 35 optimal weight: 0.0370 chunk 28 optimal weight: 20.0000 chunk 32 optimal weight: 30.0000 overall best weight: 4.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.058976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.050443 restraints weight = 5415.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.051138 restraints weight = 4673.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.051452 restraints weight = 4163.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.051953 restraints weight = 3828.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.052377 restraints weight = 3503.867| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 1.0431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5352 Z= 0.127 Angle : 0.625 5.521 7160 Z= 0.350 Chirality : 0.043 0.128 856 Planarity : 0.004 0.026 912 Dihedral : 6.221 18.960 736 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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 are not related in a simple way. whole: 0.75 (0.37), residues: 664 helix: -0.00 (0.29), residues: 360 sheet: None (None), residues: 0 loop : 1.47 (0.44), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG G 44 TYR 0.008 0.002 TYR D 74 PHE 0.001 0.000 PHE A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 ( 5352) covalent geometry : angle 0.62450 / 0.35 ( 7160) hydrogen bonds : bond 0.02591 / 1.59 ( 272) hydrogen bonds : angle 5.13637 / 3.58 ( 600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.036 Fit side-chains REVERT: E 18 GLU cc_start: 0.8970 (pm20) cc_final: 0.8205 (pp20) REVERT: E 39 MET cc_start: 0.9046 (tmm) cc_final: 0.8545 (tmm) REVERT: E 50 MET cc_start: 0.7473 (ppp) cc_final: 0.6777 (mpp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0566 time to fit residues: 0.8728 Evaluate side-chains 8 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 38 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 44 optimal weight: 20.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.057539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.049424 restraints weight = 5307.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049888 restraints weight = 4682.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.050410 restraints weight = 4233.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.050870 restraints weight = 3866.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.051170 restraints weight = 3534.264| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 1.0764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5352 Z= 0.145 Angle : 0.655 5.499 7160 Z= 0.365 Chirality : 0.045 0.125 856 Planarity : 0.004 0.026 912 Dihedral : 6.158 17.576 736 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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 are not related in a simple way. whole: 0.85 (0.36), residues: 664 helix: 0.18 (0.29), residues: 360 sheet: None (None), residues: 0 loop : 1.38 (0.43), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 44 TYR 0.008 0.002 TYR D 74 PHE 0.008 0.002 PHE G 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 ( 5352) covalent geometry : angle 0.65460 / 0.36 ( 7160) hydrogen bonds : bond 0.03028 / 1.96 ( 272) hydrogen bonds : angle 5.56073 / 3.91 ( 600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.030 Fit side-chains revert: symmetry clash REVERT: E 18 GLU cc_start: 0.8908 (pm20) cc_final: 0.8183 (pp20) REVERT: E 39 MET cc_start: 0.9108 (tmm) cc_final: 0.8629 (tmm) REVERT: E 50 MET cc_start: 0.7476 (ppp) cc_final: 0.6944 (mpp) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0651 time to fit residues: 1.0679 Evaluate side-chains 9 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 38 optimal weight: 30.0000 chunk 60 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.058257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.047549 restraints weight = 4600.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.048350 restraints weight = 3867.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.049113 restraints weight = 3360.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.049709 restraints weight = 2969.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.050115 restraints weight = 2676.152| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 1.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5352 Z= 0.152 Angle : 0.673 5.490 7160 Z= 0.381 Chirality : 0.044 0.119 856 Planarity : 0.004 0.030 912 Dihedral : 6.257 16.958 736 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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 are not related in a simple way. whole: 0.70 (0.36), residues: 664 helix: -0.08 (0.28), residues: 360 sheet: None (None), residues: 0 loop : 1.50 (0.43), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 9 TYR 0.008 0.002 TYR D 74 PHE 0.005 0.001 PHE D 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 ( 5352) covalent geometry : angle 0.67279 / 0.38 ( 7160) hydrogen bonds : bond 0.02792 / 1.80 ( 272) hydrogen bonds : angle 5.61248 / 3.93 ( 600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.028 Fit side-chains REVERT: E 16 MET cc_start: 0.7791 (tpt) cc_final: 0.7506 (tpt) REVERT: E 18 GLU cc_start: 0.8907 (pm20) cc_final: 0.8555 (pp20) REVERT: E 39 MET cc_start: 0.9059 (tmm) cc_final: 0.8601 (tmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0725 time to fit residues: 1.1762 Evaluate side-chains 8 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 17 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 24 optimal weight: 20.0000 chunk 8 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 22 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.057321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.048561 restraints weight = 5410.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049299 restraints weight = 4515.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.049837 restraints weight = 3870.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050178 restraints weight = 3451.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.050588 restraints weight = 3162.973| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 1.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5352 Z= 0.146 Angle : 0.660 5.482 7160 Z= 0.375 Chirality : 0.043 0.118 856 Planarity : 0.004 0.030 912 Dihedral : 6.018 16.835 736 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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 are not related in a simple way. whole: 0.58 (0.35), residues: 664 helix: -0.10 (0.28), residues: 352 sheet: None (None), residues: 0 loop : 1.29 (0.42), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 44 TYR 0.009 0.002 TYR D 74 PHE 0.004 0.001 PHE D 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 5352) covalent geometry : angle 0.65967 / 0.38 ( 7160) hydrogen bonds : bond 0.02601 / 1.66 ( 272) hydrogen bonds : angle 5.52529 / 3.87 ( 600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.029 Fit side-chains REVERT: H 16 MET cc_start: 0.7790 (tpt) cc_final: 0.7469 (tpt) REVERT: H 39 MET cc_start: 0.8879 (tmm) cc_final: 0.8119 (tmm) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0464 time to fit residues: 0.7727 Evaluate side-chains 6 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 33 optimal weight: 0.3980 chunk 8 optimal weight: 30.0000 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 56 optimal weight: 30.0000 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 10.0000 chunk 32 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.058010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.047882 restraints weight = 4919.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.048588 restraints weight = 4273.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.049096 restraints weight = 3803.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.049597 restraints weight = 3467.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.049922 restraints weight = 3179.117| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 1.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5352 Z= 0.133 Angle : 0.673 5.588 7160 Z= 0.371 Chirality : 0.043 0.118 856 Planarity : 0.004 0.032 912 Dihedral : 5.858 17.478 736 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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 are not related in a simple way. whole: 0.25 (0.35), residues: 664 helix: -0.22 (0.28), residues: 360 sheet: None (None), residues: 0 loop : 0.96 (0.42), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 9 TYR 0.007 0.001 TYR D 74 PHE 0.005 0.001 PHE A 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 5352) covalent geometry : angle 0.67279 / 0.37 ( 7160) hydrogen bonds : bond 0.02414 / 1.54 ( 272) hydrogen bonds : angle 5.14184 / 3.60 ( 600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1328 Ramachandran restraints generated. 664 Oldfield, 0 Emsley, 664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.031 Fit side-chains REVERT: E 39 MET cc_start: 0.9010 (tmm) cc_final: 0.8540 (tmm) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0648 time to fit residues: 0.8643 Evaluate side-chains 7 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 26 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 21 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.059370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.049811 restraints weight = 5262.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050239 restraints weight = 4682.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.050844 restraints weight = 4289.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.051200 restraints weight = 3929.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.051721 restraints weight = 3654.639| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 1.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5352 Z= 0.130 Angle : 0.706 6.534 7160 Z= 0.374 Chirality : 0.043 0.119 856 Planarity : 0.004 0.033 912 Dihedral : 5.600 16.257 736 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % 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 are not related in a simple way. whole: -0.09 (0.35), residues: 664 helix: -0.47 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 0.77 (0.42), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 9 TYR 0.005 0.001 TYR C 74 PHE 0.004 0.001 PHE E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 5352) covalent geometry : angle 0.70634 / 0.37 ( 7160) hydrogen bonds : bond 0.02489 / 1.59 ( 272) hydrogen bonds : angle 4.97892 / 3.48 ( 600) =============================================================================== Job complete usr+sys time: 589.64 seconds wall clock time: 11 minutes 2.79 seconds (662.79 seconds total)