Starting phenix.real_space_refine on Sun Apr 27 08:25:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5fna_3241/04_2025/5fna_3241.cif Found real_map, /net/cci-nas-00/data/ceres_data/5fna_3241/04_2025/5fna_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_3241/04_2025/5fna_3241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5fna_3241/04_2025/5fna_3241.map" model { file = "/net/cci-nas-00/data/ceres_data/5fna_3241/04_2025/5fna_3241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5fna_3241/04_2025/5fna_3241.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: C, B, E, D, G, F, H Time building chain proxies: 2.23, per 1000 atoms: 0.42 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: 1.72 Conformation dependent library (CDL) restraints added in 961.2 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: 0.61 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: 1.41 Time building geometry restraints manager: 1.95 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' 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: 0.250 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: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 18.050 Find NCS groups from input model: 0.140 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:3.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (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 PHE 0.001 0.000 PHE A 12 TYR 0.001 0.000 TYR A 74 ARG 0.001 0.000 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.18376 ( 272) hydrogen bonds : angle 7.27710 ( 600) covalent geometry : bond 0.01279 ( 5352) covalent geometry : angle 1.51269 ( 7160) *********************** 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 : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.8447 (m-80) cc_final: 0.8245 (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: 0.7703 (pm20) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.4608 time to fit residues: 14.1756 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 : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 19 optimal weight: 0.3980 chunk 30 optimal weight: 0.3980 chunk 37 optimal weight: 5.9990 chunk 58 optimal weight: 30.0000 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.056366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048410 restraints weight = 5499.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.049010 restraints weight = 4620.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.049594 restraints weight = 4035.661| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.6468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5352 Z= 0.186 Angle : 0.820 5.394 7160 Z= 0.462 Chirality : 0.059 0.337 856 Planarity : 0.006 0.039 912 Dihedral : 9.861 65.734 736 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 18.77 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.34), residues: 664 helix: -1.40 (0.23), residues: 440 sheet: None (None), residues: 0 loop : 3.07 (0.45), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.002 PHE E 12 TYR 0.004 0.001 TYR E 74 ARG 0.007 0.002 ARG G 44 Details of bonding type rmsd hydrogen bonds : bond 0.05673 ( 272) hydrogen bonds : angle 5.33315 ( 600) covalent geometry : bond 0.00350 ( 5352) covalent geometry : angle 0.81967 ( 7160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: H 18 GLU cc_start: 0.8907 (pm20) cc_final: 0.8276 (pp20) REVERT: H 39 MET cc_start: 0.9198 (tmm) cc_final: 0.8922 (tmm) REVERT: H 44 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7934 (mpt180) REVERT: H 48 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7232 (p) REVERT: H 50 MET cc_start: 0.7892 (ppp) cc_final: 0.6751 (mmp) REVERT: H 58 ASP cc_start: 0.8204 (m-30) cc_final: 0.7952 (m-30) outliers start: 3 outliers final: 0 residues processed: 25 average time/residue: 0.1606 time to fit residues: 4.2843 Evaluate side-chains 16 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 26 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 27 optimal weight: 0.0050 chunk 28 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 33 optimal weight: 0.0470 chunk 8 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 51 optimal weight: 0.0050 overall best weight: 0.6708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.057706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.049565 restraints weight = 5510.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.050067 restraints weight = 4777.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.050568 restraints weight = 4240.383| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.8508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5352 Z= 0.172 Angle : 0.779 6.674 7160 Z= 0.413 Chirality : 0.043 0.130 856 Planarity : 0.004 0.026 912 Dihedral : 7.591 33.879 736 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.35), residues: 664 helix: -0.93 (0.26), residues: 392 sheet: None (None), residues: 0 loop : 2.28 (0.44), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE A 12 TYR 0.008 0.002 TYR D 81 ARG 0.006 0.001 ARG E 9 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 272) hydrogen bonds : angle 5.49469 ( 600) covalent geometry : bond 0.00378 ( 5352) covalent geometry : angle 0.77900 ( 7160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.098 Fit side-chains REVERT: H 18 GLU cc_start: 0.8845 (pm20) cc_final: 0.8399 (pp20) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.2115 time to fit residues: 3.8568 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 : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3279 r_free = 0.3279 target = 0.057832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.049120 restraints weight = 5333.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.049739 restraints weight = 4679.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.050137 restraints weight = 4180.591| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.9467 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= 0.159 Angle : 0.698 5.843 7160 Z= 0.389 Chirality : 0.047 0.130 856 Planarity : 0.005 0.036 912 Dihedral : 6.727 21.498 736 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.34), residues: 664 helix: -0.68 (0.27), residues: 336 sheet: None (None), residues: 0 loop : 1.56 (0.39), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.007 0.002 PHE C 12 TYR 0.007 0.002 TYR F 81 ARG 0.006 0.001 ARG A 9 Details of bonding type rmsd hydrogen bonds : bond 0.03629 ( 272) hydrogen bonds : angle 5.13588 ( 600) covalent geometry : bond 0.00346 ( 5352) covalent geometry : angle 0.69784 ( 7160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 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 : 0.082 Fit side-chains REVERT: H 18 GLU cc_start: 0.8914 (pm20) cc_final: 0.8208 (pp20) REVERT: H 50 MET cc_start: 0.7718 (ppp) cc_final: 0.6959 (mpp) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.1491 time to fit residues: 2.0030 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 : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 4 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 38 optimal weight: 0.0030 chunk 26 optimal weight: 6.9990 chunk 59 optimal weight: 0.0970 chunk 49 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.057801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.048766 restraints weight = 5358.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.049200 restraints weight = 4827.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.049616 restraints weight = 4429.913| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 1.0187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5352 Z= 0.130 Angle : 0.633 5.545 7160 Z= 0.352 Chirality : 0.044 0.123 856 Planarity : 0.004 0.036 912 Dihedral : 6.334 20.152 736 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.35), residues: 664 helix: -1.18 (0.24), residues: 416 sheet: None (None), residues: 0 loop : 1.42 (0.47), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.003 0.001 PHE A 12 TYR 0.005 0.002 TYR F 81 ARG 0.006 0.001 ARG A 9 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 272) hydrogen bonds : angle 5.01012 ( 600) covalent geometry : bond 0.00267 ( 5352) covalent geometry : angle 0.63278 ( 7160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.092 Fit side-chains REVERT: H 18 GLU cc_start: 0.8861 (pm20) cc_final: 0.8072 (pp20) REVERT: H 40 GLU cc_start: 0.8977 (pm20) cc_final: 0.8686 (pm20) REVERT: H 50 MET cc_start: 0.7656 (ppp) cc_final: 0.6994 (mpp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1238 time to fit residues: 2.3200 Evaluate side-chains 10 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 4 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 22 optimal weight: 0.4980 chunk 41 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 35 optimal weight: 0.4980 chunk 40 optimal weight: 20.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.048960 restraints weight = 5386.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.049624 restraints weight = 4631.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.050053 restraints weight = 4108.770| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 1.0541 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= 0.130 Angle : 0.628 5.540 7160 Z= 0.351 Chirality : 0.043 0.122 856 Planarity : 0.006 0.048 912 Dihedral : 6.458 18.418 736 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.35), residues: 664 helix: -0.30 (0.27), residues: 352 sheet: None (None), residues: 0 loop : 1.13 (0.42), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.000 0.000 PHE G 12 TYR 0.004 0.001 TYR H 81 ARG 0.008 0.001 ARG G 44 Details of bonding type rmsd hydrogen bonds : bond 0.02578 ( 272) hydrogen bonds : angle 4.74801 ( 600) covalent geometry : bond 0.00275 ( 5352) covalent geometry : angle 0.62774 ( 7160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.077 Fit side-chains REVERT: H 18 GLU cc_start: 0.8722 (pm20) cc_final: 0.7969 (pp20) REVERT: H 40 GLU cc_start: 0.8760 (pm20) cc_final: 0.8212 (tm-30) REVERT: H 49 VAL cc_start: 0.6690 (m) cc_final: 0.5855 (t) REVERT: H 50 MET cc_start: 0.7442 (ppp) cc_final: 0.6987 (mpp) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1397 time to fit residues: 2.6238 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 : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 17 optimal weight: 6.9990 chunk 51 optimal weight: 0.0470 chunk 60 optimal weight: 20.0000 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 52 optimal weight: 20.0000 chunk 55 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 overall best weight: 5.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.057982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.049353 restraints weight = 5231.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.049925 restraints weight = 4752.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.050304 restraints weight = 4324.204| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 1.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5352 Z= 0.128 Angle : 0.662 5.599 7160 Z= 0.367 Chirality : 0.045 0.122 856 Planarity : 0.004 0.034 912 Dihedral : 6.265 17.175 736 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.35), residues: 664 helix: -0.49 (0.27), residues: 360 sheet: None (None), residues: 0 loop : 1.21 (0.42), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE C 12 TYR 0.005 0.001 TYR H 81 ARG 0.005 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.02466 ( 272) hydrogen bonds : angle 5.52255 ( 600) covalent geometry : bond 0.00262 ( 5352) covalent geometry : angle 0.66218 ( 7160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1162 Ramachandran restraints generated. 581 Oldfield, 0 Emsley, 581 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 : 0.171 Fit side-chains REVERT: H 18 GLU cc_start: 0.8835 (pm20) cc_final: 0.8400 (pp20) REVERT: H 39 MET cc_start: 0.8843 (tmm) cc_final: 0.8467 (tmm) REVERT: H 49 VAL cc_start: 0.6764 (m) cc_final: 0.6133 (t) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1529 time to fit residues: 2.7276 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 : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 60 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 16 optimal weight: 30.0000 chunk 6 optimal weight: 0.0570 overall best weight: 3.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.059417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.051196 restraints weight = 5322.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.051722 restraints weight = 4630.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.052315 restraints weight = 4146.477| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 1.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 5352 Z= 0.117 Angle : 0.648 5.644 7160 Z= 0.350 Chirality : 0.043 0.119 856 Planarity : 0.004 0.034 912 Dihedral : 5.897 16.428 736 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.35), residues: 664 helix: -0.94 (0.26), residues: 416 sheet: None (None), residues: 0 loop : 1.13 (0.46), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE H 12 TYR 0.002 0.001 TYR G 81 ARG 0.002 0.000 ARG F 9 Details of bonding type rmsd hydrogen bonds : bond 0.02466 ( 272) hydrogen bonds : angle 5.21447 ( 600) covalent geometry : bond 0.00236 ( 5352) covalent geometry : angle 0.64786 ( 7160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 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 : 0.272 Fit side-chains REVERT: E 16 MET cc_start: 0.7789 (tpt) cc_final: 0.7349 (tpt) REVERT: E 39 MET cc_start: 0.8953 (tmm) cc_final: 0.8567 (tmm) REVERT: E 50 MET cc_start: 0.8609 (mpp) cc_final: 0.7993 (ptt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1544 time to fit residues: 2.6163 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 : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 21 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 24 optimal weight: 30.0000 chunk 4 optimal weight: 30.0000 chunk 50 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.058191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049768 restraints weight = 5250.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.050159 restraints weight = 4675.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.050597 restraints weight = 4243.607| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 1.1461 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= 0.125 Angle : 0.676 5.637 7160 Z= 0.368 Chirality : 0.043 0.119 856 Planarity : 0.004 0.033 912 Dihedral : 5.681 15.640 736 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.35), residues: 664 helix: 0.03 (0.28), residues: 352 sheet: None (None), residues: 0 loop : 1.34 (0.42), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE A 12 TYR 0.003 0.001 TYR H 81 ARG 0.001 0.000 ARG E 9 Details of bonding type rmsd hydrogen bonds : bond 0.02498 ( 272) hydrogen bonds : angle 5.25743 ( 600) covalent geometry : bond 0.00264 ( 5352) covalent geometry : angle 0.67606 ( 7160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 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 : 0.086 Fit side-chains REVERT: H 39 MET cc_start: 0.8877 (tmm) cc_final: 0.8527 (tmm) REVERT: H 41 LYS cc_start: 0.9267 (tptp) cc_final: 0.8924 (tppp) REVERT: H 50 MET cc_start: 0.8581 (mpp) cc_final: 0.7996 (mpp) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1588 time to fit residues: 2.6037 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 : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 60 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 55 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 overall best weight: 7.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.057757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.048760 restraints weight = 5370.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049203 restraints weight = 4890.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.049507 restraints weight = 4488.408| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 1.1673 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= 0.134 Angle : 0.666 5.338 7160 Z= 0.367 Chirality : 0.042 0.117 856 Planarity : 0.004 0.033 912 Dihedral : 5.497 16.392 736 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.07 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.35), residues: 664 helix: -0.20 (0.28), residues: 360 sheet: None (None), residues: 0 loop : 1.35 (0.42), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.002 0.001 PHE G 12 TYR 0.003 0.001 TYR H 81 ARG 0.002 0.000 ARG D 9 Details of bonding type rmsd hydrogen bonds : bond 0.02331 ( 272) hydrogen bonds : angle 5.15900 ( 600) covalent geometry : bond 0.00279 ( 5352) covalent geometry : angle 0.66590 ( 7160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 996 Ramachandran restraints generated. 498 Oldfield, 0 Emsley, 498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 74 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.094 Fit side-chains REVERT: H 16 MET cc_start: 0.7447 (tpt) cc_final: 0.7094 (tpt) REVERT: H 39 MET cc_start: 0.8918 (tmm) cc_final: 0.8537 (tmm) REVERT: H 41 LYS cc_start: 0.9277 (tptp) cc_final: 0.8972 (tppp) REVERT: H 50 MET cc_start: 0.8746 (mpp) cc_final: 0.8140 (ptt) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.1828 time to fit residues: 2.6398 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 : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 27 optimal weight: 0.0370 chunk 45 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 36 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 overall best weight: 5.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.057962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.048789 restraints weight = 5285.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.049164 restraints weight = 4816.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.049576 restraints weight = 4464.998| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 1.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5352 Z= 0.118 Angle : 0.643 5.464 7160 Z= 0.351 Chirality : 0.042 0.118 856 Planarity : 0.004 0.034 912 Dihedral : 5.318 16.545 736 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 9.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.35), residues: 664 helix: -0.83 (0.26), residues: 416 sheet: None (None), residues: 0 loop : 1.15 (0.48), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.001 0.000 PHE A 12 TYR 0.003 0.001 TYR H 81 ARG 0.002 0.000 ARG G 9 Details of bonding type rmsd hydrogen bonds : bond 0.02107 ( 272) hydrogen bonds : angle 4.99279 ( 600) covalent geometry : bond 0.00248 ( 5352) covalent geometry : angle 0.64255 ( 7160) =============================================================================== Job complete usr+sys time: 1630.72 seconds wall clock time: 31 minutes 26.71 seconds (1886.71 seconds total)