Starting phenix.refine on Fri Aug 9 09:31:39 2024 by nigel =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, 4phenix_4yei.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4yei/4yei.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 amber.topology_file_name=4amber_4yei.prmtop amber.coordinate_file_name=4amber_4yei.rst7 amber.order_file_name=4amber_4yei.order use_amber=True strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Processing files from PHIL: ------------------------------------------------------------------------------- Files not used by program: -------------------------- 4amber_4yei.order 4amber_4yei.rst7 4amber_4yei.prmtop Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4yei/4yei.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/4yei/4yei.mtz" model { file = "4phenix_4yei.pdb" } default_model = "4phenix_4yei.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } amber { use_amber = True topology_file_name = 4amber_4yei.prmtop coordinate_file_name = 4amber_4yei.rst7 order_file_name = 4amber_4yei.order } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/bootstrap/modules/chem_data/mon_lib" Total number of atoms: 9333 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Chain: "B" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Chain: "C" Number of atoms: 3111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3111 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 213} Time building chain proxies: 1.12, per 1000 atoms: 0.12 Number of scatterers: 9333 At special positions: 0 Unit cell: (110.36, 115.96, 164.12, 90, 90, 90) Space group: I 2 2 2 (No. 23) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 966 8.00 N 909 7.00 C 2865 6.00 H 4584 1.00 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 - 3.50 Amino acid : False - 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: 1.63 Conformation dependent library (CDL) restraints added in 208.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 1200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 9 helices and 0 sheets defined 12.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.638A pdb=" N ARG A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'B' and resid 23 through 31 Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.570A pdb=" N ARG B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 229 Processing helix chain 'C' and resid 23 through 31 Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.592A pdb=" N ARG C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 229 39 hydrogen bonds defined for protein. 117 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: 1.42 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 4581 1.15 - 1.32: 1126 1.32 - 1.49: 1725 1.49 - 1.66: 1934 1.66 - 1.84: 15 Bond restraints: 9381 Sorted by residual: bond pdb=" N GLU A 44 " pdb=" H GLU A 44 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ARG A 186 " pdb=" H ARG A 186 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N LEU B 177 " pdb=" H LEU B 177 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ASP B 153 " pdb=" H ASP B 153 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N ALA C 165 " pdb=" H ALA C 165 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 9376 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.44: 223 105.44 - 112.60: 10348 112.60 - 119.75: 2632 119.75 - 126.90: 3592 126.90 - 134.06: 50 Bond angle restraints: 16845 Sorted by residual: angle pdb=" N LEU A 233 " pdb=" CA LEU A 233 " pdb=" C LEU A 233 " ideal model delta sigma weight residual 110.80 119.87 -9.07 2.13e+00 2.20e-01 1.81e+01 angle pdb=" N THR B 209 " pdb=" CA THR B 209 " pdb=" C THR B 209 " ideal model delta sigma weight residual 113.88 119.07 -5.19 1.23e+00 6.61e-01 1.78e+01 angle pdb=" N SER A 211 " pdb=" CA SER A 211 " pdb=" CB SER A 211 " ideal model delta sigma weight residual 110.06 116.02 -5.96 1.51e+00 4.39e-01 1.56e+01 angle pdb=" CG ARG A 191 " pdb=" CD ARG A 191 " pdb=" NE ARG A 191 " ideal model delta sigma weight residual 112.00 103.57 8.43 2.20e+00 2.07e-01 1.47e+01 angle pdb=" CA ALA C 210 " pdb=" C ALA C 210 " pdb=" O ALA C 210 " ideal model delta sigma weight residual 121.47 117.12 4.35 1.15e+00 7.56e-01 1.43e+01 ... (remaining 16840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 3980 15.79 - 31.57: 246 31.57 - 47.36: 119 47.36 - 63.15: 30 63.15 - 78.93: 8 Dihedral angle restraints: 4383 sinusoidal: 2373 harmonic: 2010 Sorted by residual: dihedral pdb=" C ASP A 218 " pdb=" N ASP A 218 " pdb=" CA ASP A 218 " pdb=" CB ASP A 218 " ideal model delta harmonic sigma weight residual -122.60 -113.38 -9.22 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N ALA A 234 " pdb=" CA ALA A 234 " ideal model delta harmonic sigma weight residual -180.00 -162.17 -17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" C VAL C 205 " pdb=" N VAL C 205 " pdb=" CA VAL C 205 " pdb=" CB VAL C 205 " ideal model delta harmonic sigma weight residual -122.00 -130.88 8.88 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 4380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 559 0.093 - 0.186: 157 0.186 - 0.278: 32 0.278 - 0.371: 16 0.371 - 0.464: 1 Chirality restraints: 765 Sorted by residual: chirality pdb=" CA ARG A 208 " pdb=" N ARG A 208 " pdb=" C ARG A 208 " pdb=" CB ARG A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+00 chirality pdb=" CA MET B 171 " pdb=" N MET B 171 " pdb=" C MET B 171 " pdb=" CB MET B 171 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA GLU A 109 " pdb=" N GLU A 109 " pdb=" C GLU A 109 " pdb=" CB GLU A 109 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 762 not shown) Planarity restraints: 1539 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 208 " 0.046 9.50e-02 1.11e+02 3.78e-02 2.72e+01 pdb=" NE ARG A 208 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 208 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG A 208 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 208 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 208 " 0.058 2.00e-02 2.50e+03 pdb="HH12 ARG A 208 " -0.020 2.00e-02 2.50e+03 pdb="HH21 ARG A 208 " 0.056 2.00e-02 2.50e+03 pdb="HH22 ARG A 208 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 59 " -0.022 2.00e-02 2.50e+03 2.61e-02 2.05e+01 pdb=" CG TYR A 59 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR A 59 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 59 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 59 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 59 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 59 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 59 " 0.012 2.00e-02 2.50e+03 pdb=" HD1 TYR A 59 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 TYR A 59 " 0.062 2.00e-02 2.50e+03 pdb=" HE1 TYR A 59 " 0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 59 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 59 " -0.005 2.00e-02 2.50e+03 2.61e-02 2.05e+01 pdb=" CG TYR C 59 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR C 59 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR C 59 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR C 59 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR C 59 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR C 59 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 59 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 TYR C 59 " -0.023 2.00e-02 2.50e+03 pdb=" HD2 TYR C 59 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 TYR C 59 " 0.030 2.00e-02 2.50e+03 pdb=" HE2 TYR C 59 " -0.049 2.00e-02 2.50e+03 ... (remaining 1536 not shown) Histogram of nonbonded interaction distances: 0.97 - 1.70: 35 1.70 - 2.42: 3847 2.42 - 3.15: 30818 3.15 - 3.87: 42366 3.87 - 4.60: 64202 Warning: very small nonbonded interaction distances. Nonbonded interactions: 141268 Sorted by model distance: nonbonded pdb=" HG1 THR C 187 " pdb=" HG1 THR C 209 " model vdw 0.973 2.100 nonbonded pdb=" HG1 THR A 187 " pdb=" HG1 THR A 209 " model vdw 1.093 2.100 nonbonded pdb=" HE1 HIS A 198 " pdb=" HB3 ALA A 234 " model vdw sym.op. 1.270 2.270 x,-y+2,-z+2 nonbonded pdb=" HG1 THR B 187 " pdb=" HG1 THR B 209 " model vdw 1.316 2.100 nonbonded pdb=" HD3 ARG A 208 " pdb=" O ARG A 208 " model vdw sym.op. 1.352 2.620 -x+2,y,-z+2 ... (remaining 141263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Initializing Amber ============================= topology : 4amber_4yei.prmtop atom order : 4amber_4yei.order coordinates : 4amber_4yei.rst7 ===================================== ... ===================================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians S 9 15.91 1 O 966 7.97 1 N 909 6.97 1 C 2865 5.97 1 H 4584 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== Setting occupancies to: 1.000: selected atoms: 4584 of 9333 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 9333 n_use_u_iso = 4587 n_use_u_aniso = 4746 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 9333 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (9333 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4587 aniso = 4746) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous den } main { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 23 through 31 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 204 through 209 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 219 through 229 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'B' and resid 23 through 31 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'B' and resid 204 through 209 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'B' and resid 219 through 229 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'C' and resid 23 through 31 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'C' and resid 204 through 209 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'C' and resid 219 through 229 } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } amber { use_amber = True topology_file_name = "4amber_4yei.prmtop" coordinate_file_name = "4amber_4yei.rst7" order_file_name = "4amber_4yei.order" } } output { prefix = "4phenix_4yei_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== WARNING: failed to analyze molecule topology. Atomic model may be wrong. ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.55 - 37.43 A, n_refl.=12716 (all), 4.90 % free)------------| | | | r_work= 0.4647 r_free= 0.3729 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 6.851712 | | target function (ml) not normalized (work): 82857.747217 | | target function (ml) not normalized (free): 4161.080737 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 37.43 - 5.64 0.98 3160 150 0.4377 0.4111 7.9312 7.1804| | 2: 5.64 - 4.48 0.97 3007 139 0.4268 0.3151 6.7002 6.8388| | 3: 4.48 - 3.91 0.98 2977 158 0.4832 0.3448 6.4662 6.5734| | 4: 3.91 - 3.55 0.98 2949 176 0.5522 0.4281 6.2386 6.2206| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 37.43 - 5.64 3160 150 0.58 44.10 0.74 0.59 275701.06| | 2: 5.64 - 4.48 3007 139 0.64 40.14 1.64 0.84 147075.61| | 3: 4.48 - 3.91 2977 158 0.77 28.60 1.84 0.98 71301.77| | 4: 3.91 - 3.55 2949 176 0.73 33.09 2.00 1.01 48379.55| |alpha: min = 0.59 max = 1.01 mean = 0.85| |beta: min = 48379.55 max = 275701.06 mean = 137964.80| |figures of merit: min = 0.00 max = 1.00 mean = 0.68| |phase err.(work): min = 0.00 max = 89.98 mean = 36.61| |phase err.(test): min = 0.00 max = 89.48 mean = 35.86| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.091 4797 Z= 1.134 Angle : 1.564 10.417 6522 Z= 0.950 Chirality : 0.097 0.464 765 Planarity : 0.008 0.044 900 Dihedral : 14.850 78.933 1683 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 1.49 % Allowed : 5.94 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.25), residues: 639 helix: -0.76 (0.52), residues: 93 sheet: None (None), residues: 0 loop : -1.42 (0.19), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG A 208 TYR 0.030 0.009 TYR C 30 PHE 0.030 0.007 PHE B 225 TRP 0.026 0.009 TRP C 207 HIS 0.015 0.004 HIS A 198 Individual atomic B min max mean iso aniso Overall: 49.64 289.79 106.35 4.55 4749 0 Protein: 49.64 289.79 106.35 4.55 4749 0 Chain A: 49.64 180.30 105.90 N/A 1583 0 Chain B: 56.85 174.83 98.34 N/A 1583 0 Chain C: 58.38 289.79 114.82 N/A 1583 0 Histogram: Values Number of atoms 49.64 - 73.66 630 73.66 - 97.67 1454 97.67 - 121.69 1256 121.69 - 145.70 892 145.70 - 169.72 426 169.72 - 193.73 50 193.73 - 217.74 22 217.74 - 241.76 11 241.76 - 265.77 5 265.77 - 289.79 3 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.55 - 37.43 A, n_refl.=12716 (all), 4.90 % free)------------| | | | r_work= 0.4647 r_free= 0.3729 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 6.851712 | | target function (ml) not normalized (work): 82857.747217 | | target function (ml) not normalized (free): 4161.080737 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 7.9871 percent. r_work = 0.5445 r_free = 0.4725 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.5419 0.5445 0.4725 n_refl.: 12716 re-set all scales: r(all,work,free)=0.5419 0.5445 0.4725 n_refl.: 12716 remove outliers: r(all,work,free)=0.5325 0.5348 0.4725 n_refl.: 12706 overall B=-20.73 to atoms: r(all,work,free)=0.4727 0.4746 0.4302 n_refl.: 12706 bulk-solvent and scaling: r(all,work,free)=0.2836 0.2826 0.3041 n_refl.: 12706 remove outliers: r(all,work,free)=0.2835 0.2825 0.3041 n_refl.: 12705 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.244-17.658 90.00 95 4 0.2362 2887.955 2807.951 1.435 1.061 0.425 17.650-14.285 98.02 94 5 0.1432 3044.642 2999.565 1.111 1.060 0.378 14.282-11.568 95.90 180 7 0.1415 3014.321 2942.158 1.211 1.047 0.367 11.530-9.354 97.49 335 14 0.2118 1632.869 1594.067 1.196 1.038 0.368 9.349-7.570 98.64 624 29 0.2501 1223.344 1166.330 0.945 1.021 0.313 7.566-6.123 98.85 1143 56 0.2825 950.322 892.588 0.936 0.998 0.269 6.123-4.955 97.48 2111 97 0.3012 843.723 798.620 1.024 0.958 0.262 4.954-4.009 97.40 3921 193 0.2757 1174.241 1155.276 1.213 0.903 0.196 4.009-3.554 97.79 3579 218 0.3570 708.293 634.089 1.137 0.849 0.159 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0608 b_overall=5.8308 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.721325 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.143354 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2849 0.3267 0.0418 0.013 2.0 0.1 0.3 2.5 0 0.125 0.2696 0.3235 0.0539 0.013 2.0 0.2 0.0 2.8 0 0.250 0.2567 0.3158 0.0590 0.014 2.2 0.4 0.2 1.9 0 0.500 0.2434 0.3102 0.0668 0.016 2.5 1.1 0.5 2.8 2 1.000 0.2369 0.3044 0.0675 0.021 3.1 2.3 0.3 1.5 8 2.000 0.2329 0.3018 0.0689 0.026 3.5 3.9 0.3 1.7 10 3.000 0.2355 0.2974 0.0619 0.029 3.5 3.4 0.3 1.5 9 4.000 0.2780 0.3022 0.0242 0.018 1.8 1.5 0.0 1.5 0 5.000 0.2524 0.2961 0.0437 0.029 2.9 1.2 0.0 1.5 1 6.000 0.2550 0.2961 0.0411 0.030 2.8 1.1 0.0 1.5 1 7.000 0.2562 0.2963 0.0401 0.031 2.8 1.1 0.0 1.5 1 8.000 0.2550 0.2962 0.0412 0.033 2.9 1.3 0.0 1.5 1 9.000 0.2588 0.2969 0.0381 0.032 2.7 1.5 0.0 1.5 0 10.000 0.2384 0.3052 0.0668 0.021 3.1 1.9 0.3 1.5 7 1.861 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2550 0.2961 0.0411 0.030 2.8 1.1 0.0 1.5 1 7.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.50 29.61 4.11 3.255 85.491 0.143 0.065 25.41 29.56 4.14 3.598 85.762 0.004 0.064 25.18 29.44 4.26 3.623 85.765 0.018 0.063 24.21 28.88 4.68 5.591 86.303 0.072 0.058 23.67 28.67 5.00 6.345 86.357 0.143 0.055 23.42 28.57 5.15 6.994 86.455 0.215 0.054 23.27 28.52 5.26 7.501 86.548 0.287 0.053 23.11 28.48 5.37 8.107 86.727 0.358 0.053 22.90 28.37 5.47 9.094 87.086 0.430 0.052 22.83 28.36 5.54 9.487 87.184 0.502 0.051 22.77 28.34 5.57 9.823 87.267 0.573 0.051 22.72 28.33 5.61 10.109 87.340 0.645 0.051 22.68 28.33 5.66 10.391 87.415 0.717 0.051 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.717 Accepted refinement result: 22.68 28.33 5.66 10.391 87.415 0.717 0.051 Individual atomic B min max mean iso aniso Overall: 23.91 264.06 89.41 10.16 4749 0 Protein: 23.91 264.06 89.41 10.16 4749 0 Chain A: 23.91 161.38 88.12 N/A 1583 0 Chain B: 31.85 154.40 82.14 N/A 1583 0 Chain C: 34.62 264.06 97.96 N/A 1583 0 Histogram: Values Number of atoms 23.91 - 47.93 207 47.93 - 71.94 1277 71.94 - 95.96 1464 95.96 - 119.97 1031 119.97 - 143.99 636 143.99 - 168.00 92 168.00 - 192.01 22 192.01 - 216.03 12 216.03 - 240.04 5 240.04 - 264.06 3 =========================== Idealize ADP of riding H ========================== r_work=0.2268 r_free=0.2833 r_work=0.2245 r_free=0.2824 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2245 r_free= 0.2824 coordinate error (max.-lik. estimate): 0.48 A | | | | normalized target function (ls_wunit_k1) (work): 0.049786 | | target function (ls_wunit_k1) not normalized (work): 601.515057 | | target function (ls_wunit_k1) not normalized (free): 48.099290 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2273 0.2245 0.2824 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4709 0.4725 0.4368 n_refl.: 12705 remove outliers: r(all,work,free)=0.4709 0.4725 0.4368 n_refl.: 12705 overall B=0.35 to atoms: r(all,work,free)=0.4720 0.4736 0.4375 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2257 0.2228 0.2838 n_refl.: 12705 remove outliers: r(all,work,free)=0.2257 0.2228 0.2838 n_refl.: 12705 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.244-17.658 90.00 95 4 0.2413 1625.009 1602.584 1.367 1.076 0.430 17.650-14.285 98.02 94 5 0.1352 1713.174 1712.746 1.076 1.075 0.380 14.282-11.568 95.90 180 7 0.1160 1696.113 1681.751 1.179 1.061 0.370 11.530-9.354 97.49 335 14 0.1784 918.791 910.318 1.162 1.051 0.369 9.349-7.570 98.64 624 29 0.2165 688.358 671.636 0.903 1.033 0.300 7.566-6.123 98.85 1143 56 0.2299 534.732 519.806 0.907 1.009 0.256 6.123-4.955 97.48 2111 97 0.2383 474.750 460.735 1.010 0.968 0.249 4.954-4.009 97.40 3921 193 0.1985 660.728 655.629 1.214 0.910 0.179 4.009-3.554 97.79 3579 218 0.2944 398.546 370.099 1.204 0.854 0.119 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.1366 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.998161 wxc_scale = 0.144 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.034789 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2610 0.3103 0.0493 0.013 2.0 0.1 0.0 1.9 0 0.014 0.2435 0.3045 0.0610 0.013 2.0 0.1 0.2 2.8 0 0.043 0.2319 0.2983 0.0664 0.013 2.1 0.1 0.2 2.8 0 0.086 0.2262 0.2975 0.0714 0.014 2.2 0.3 0.3 3.2 0 0.129 0.2222 0.2933 0.0711 0.015 2.4 0.6 0.3 1.7 2 0.172 0.2196 0.2911 0.0716 0.015 2.6 0.8 0.9 1.5 4 0.216 0.2171 0.2902 0.0731 0.016 2.7 1.2 0.8 2.8 5 0.259 0.2164 0.2906 0.0742 0.017 2.9 1.4 0.6 1.5 6 0.302 0.2244 0.2975 0.0730 0.014 2.3 0.3 0.3 3.4 1 0.144 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2171 0.2902 0.0731 0.016 2.7 1.2 0.8 2.8 5 0.259 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.71 29.02 7.31 15.047 98.546 0.035 6.460 24.38 29.60 5.22 13.600 102.668 0.001 6.525 24.23 29.58 5.35 13.710 103.017 0.004 6.515 22.63 28.83 6.20 14.901 99.783 0.017 6.465 21.84 28.71 6.87 15.393 98.592 0.035 6.443 21.66 28.75 7.09 15.761 98.888 0.052 6.435 21.47 28.80 7.33 16.014 98.906 0.070 6.430 21.36 28.84 7.49 16.269 99.034 0.087 6.427 21.28 28.88 7.60 16.377 98.952 0.104 6.426 21.21 28.91 7.70 16.558 99.042 0.122 6.424 21.16 28.92 7.76 16.715 99.121 0.139 6.423 21.12 28.97 7.85 16.852 99.189 0.157 6.423 21.09 28.98 7.89 16.973 99.253 0.174 6.422 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.004 Accepted refinement result: 24.23 29.58 5.35 13.710 103.017 0.004 6.515 Individual atomic B min max mean iso aniso Overall: 55.67 259.41 98.55 4.72 4749 0 Protein: 55.67 259.41 98.55 4.72 4749 0 Chain A: 55.67 156.73 97.51 N/A 1583 0 Chain B: 61.54 149.76 90.63 N/A 1583 0 Chain C: 59.12 259.41 107.51 N/A 1583 0 Histogram: Values Number of atoms 55.67 - 76.04 911 76.04 - 96.41 1698 96.41 - 116.79 988 116.79 - 137.16 829 137.16 - 157.54 226 157.54 - 177.91 65 177.91 - 198.29 18 198.29 - 218.66 8 218.66 - 239.04 3 239.04 - 259.41 3 =========================== Idealize ADP of riding H ========================== r_work=0.2423 r_free=0.2958 r_work=0.2460 r_free=0.2954 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2460 r_free= 0.2954 coordinate error (max.-lik. estimate): 0.51 A | | | | normalized target function (ml) (work): 6.523744 | | target function (ml) not normalized (work): 78819.872260 | | target function (ml) not normalized (free): 4148.966345 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2484 0.2460 0.2954 n_refl.: 12705 re-set all scales: r(all,work,free)=0.5114 0.5136 0.4659 n_refl.: 12705 remove outliers: r(all,work,free)=0.5114 0.5136 0.4659 n_refl.: 12705 overall B=-12.56 to atoms: r(all,work,free)=0.4721 0.4739 0.4404 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2449 0.2424 0.2938 n_refl.: 12705 remove outliers: r(all,work,free)=0.2449 0.2424 0.2938 n_refl.: 12705 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.244-17.658 90.00 95 4 0.2057 1458.032 1473.716 1.343 1.108 0.433 17.650-14.285 98.02 94 5 0.1250 1537.138 1532.474 1.071 1.107 0.383 14.282-11.568 95.90 180 7 0.1137 1521.830 1502.343 1.184 1.090 0.374 11.530-9.354 97.49 335 14 0.1618 824.381 815.195 1.198 1.077 0.371 9.349-7.570 98.64 624 29 0.2062 617.626 601.703 0.940 1.054 0.335 7.566-6.123 98.85 1143 56 0.2484 479.786 457.738 0.913 1.021 0.268 6.123-4.955 97.48 2111 97 0.2742 425.968 402.536 1.023 0.967 0.256 4.954-4.009 97.40 3921 193 0.2248 592.835 581.397 1.198 0.890 0.188 4.009-3.554 97.79 3579 218 0.3213 357.593 320.902 1.192 0.813 0.112 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=5.6731 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== Setting wxc_scale using amber.wxc_factor : 0.500 * 1.000 = 0.500 |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.924710 wxc_scale = 0.339 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.037614 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2746 0.3130 0.0385 0.013 2.1 0.4 0.8 3.8 0 0.031 0.2506 0.3073 0.0567 0.014 2.2 0.5 0.3 3.6 1 0.094 0.2393 0.3016 0.0622 0.016 2.6 1.0 0.5 3.4 3 0.188 0.2415 0.2934 0.0519 0.016 2.7 1.2 0.8 2.8 5 0.282 0.2424 0.2938 0.0514 0.016 2.7 1.2 0.8 2.8 5 0.377 0.2424 0.2938 0.0514 0.016 2.7 1.2 0.8 2.8 5 0.471 0.2424 0.2938 0.0514 0.016 2.7 1.2 0.8 2.8 5 0.565 0.2424 0.2938 0.0514 0.016 2.7 1.2 0.8 2.8 5 0.659 0.2421 0.2936 0.0516 0.016 2.7 1.2 0.8 2.8 5 0.314 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2415 0.2934 0.0519 0.016 2.7 1.2 0.8 2.8 5 0.282 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 24.15 29.34 5.19 14.655 95.779 0.038 6.418 26.01 30.58 4.57 10.881 101.883 0.001 6.461 24.64 29.75 5.11 13.083 100.844 0.005 6.419 23.63 29.09 5.45 14.816 95.655 0.019 6.401 22.16 28.41 6.25 15.551 96.924 0.038 6.348 22.21 28.49 6.28 15.579 96.447 0.056 6.352 21.89 28.39 6.49 16.081 97.225 0.075 6.341 21.85 28.40 6.55 16.322 97.325 0.094 6.339 21.87 28.41 6.54 16.246 97.194 0.113 6.340 21.81 28.40 6.60 16.468 97.369 0.132 6.338 21.76 28.39 6.63 16.673 97.516 0.150 6.337 21.72 28.39 6.67 16.862 97.645 0.169 6.336 21.66 28.41 6.74 16.983 97.816 0.188 6.336 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.019 Accepted refinement result: 23.63 29.09 5.45 14.816 95.655 0.019 6.401 Individual atomic B min max mean iso aniso Overall: 43.43 243.36 85.74 4.37 4749 0 Protein: 43.43 243.36 85.74 4.37 4749 0 Chain A: 43.43 142.31 84.46 N/A 1583 0 Chain B: 49.87 136.77 77.93 N/A 1583 0 Chain C: 46.27 243.36 94.84 N/A 1583 0 Histogram: Values Number of atoms 43.43 - 63.43 935 63.43 - 83.42 1651 83.42 - 103.41 994 103.41 - 123.40 812 123.40 - 143.39 257 143.39 - 163.39 68 163.39 - 183.38 18 183.38 - 203.37 8 203.37 - 223.36 3 223.36 - 243.36 3 =========================== Idealize ADP of riding H ========================== r_work=0.2363 r_free=0.2909 r_work=0.2359 r_free=0.2910 ----------X-ray data---------- |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2359 r_free= 0.2910 coordinate error (max.-lik. estimate): 0.55 A | | | | normalized target function (ml) (work): 6.400203 | | target function (ml) not normalized (work): 77327.247076 | | target function (ml) not normalized (free): 4085.016628 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.24 - 5.63 0.98 3159 150 0.2027 0.2540 6.5155 6.7229| | 2: 5.63 - 4.48 0.97 3003 139 0.2232 0.2906 6.4435 6.6649| | 3: 4.48 - 3.91 0.98 2973 158 0.2351 0.2688 6.436 6.6529| | 4: 3.91 - 3.55 0.98 2947 176 0.3261 0.3911 6.1964 6.2443| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.24 - 5.63 3159 150 0.75 29.83 0.99 0.88 95037.18| | 2: 5.63 - 4.48 3003 139 0.69 35.26 1.05 0.88 85858.80| | 3: 4.48 - 3.91 2973 158 0.73 32.17 0.97 0.82 73468.95| | 4: 3.91 - 3.55 2947 176 0.62 42.41 0.98 0.71 57867.64| |alpha: min = 0.71 max = 0.88 mean = 0.83| |beta: min = 57867.64 max = 95037.18 mean = 78382.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.70| |phase err.(work): min = 0.00 max = 89.94 mean = 34.82| |phase err.(test): min = 0.00 max = 89.73 mean = 35.23| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2386 0.2359 0.2910 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4703 0.4721 0.4389 n_refl.: 12705 remove outliers: r(all,work,free)=0.4703 0.4721 0.4389 n_refl.: 12705 overall B=0.00 to atoms: r(all,work,free)=0.4703 0.4721 0.4389 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2371 0.2344 0.2912 n_refl.: 12705 remove outliers: r(all,work,free)=0.2371 0.2344 0.2912 n_refl.: 12705 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.244-17.658 90.00 95 4 0.2034 1458.032 1467.187 1.250 1.174 0.430 17.650-14.285 98.02 94 5 0.1215 1537.138 1530.809 0.982 1.170 0.380 14.282-11.568 95.90 180 7 0.1130 1521.830 1500.235 1.123 1.149 0.380 11.530-9.354 97.49 335 14 0.1597 824.381 814.390 1.133 1.130 0.380 9.349-7.570 98.64 624 29 0.2041 617.626 600.217 0.882 1.098 0.330 7.566-6.123 98.85 1143 56 0.2441 479.786 458.075 0.872 1.051 0.270 6.123-4.955 97.48 2111 97 0.2658 425.968 403.831 1.005 0.977 0.260 4.954-4.009 97.40 3921 193 0.2139 592.835 582.390 1.210 0.868 0.190 4.009-3.554 97.79 3579 218 0.3116 357.593 322.375 1.253 0.758 0.120 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=6.7479 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.4647 0.3729 0.017 1.564 49.6 289.8 106.4 0 0.000 1_bss: 0.2825 0.3041 0.017 1.564 28.9 269.1 85.6 0 0.000 1_settarget: 0.2825 0.3041 0.017 1.564 28.9 269.1 85.6 0 0.000 1_weight: 0.2825 0.3041 0.017 1.564 28.9 269.1 85.6 0 0.000 1_xyzrec: 0.2550 0.2961 0.030 2.822 28.9 269.1 85.6 0 0.047 1_adp: 0.2268 0.2833 0.030 2.822 23.9 264.1 89.4 0 0.047 1_regHadp: 0.2245 0.2824 0.030 2.822 23.9 264.1 89.4 0 0.047 2_bss: 0.2228 0.2838 0.030 2.822 24.3 264.4 89.8 0 0.047 2_settarget: 0.2228 0.2838 0.030 2.822 24.3 264.4 89.8 0 0.047 2_updatecdl: 0.2228 0.2838 0.030 2.824 24.3 264.4 89.8 0 0.047 2_weight: 0.2228 0.2838 0.030 2.824 24.3 264.4 89.8 0 0.047 2_xyzrec: 0.2171 0.2902 0.016 2.673 24.3 264.4 89.8 0 0.271 2_adp: 0.2423 0.2958 0.016 2.673 55.7 259.4 98.5 0 0.271 2_regHadp: 0.2460 0.2954 0.016 2.673 55.7 259.4 98.5 0 0.271 3_bss: 0.2424 0.2938 0.016 2.673 43.1 246.9 86.0 0 0.271 3_settarget: 0.2424 0.2938 0.016 2.673 43.1 246.9 86.0 0 0.271 3_updatecdl: 0.2424 0.2938 0.016 2.707 43.1 246.9 86.0 0 0.271 3_setrh: 0.2424 0.2938 0.016 2.707 43.1 246.9 86.0 0 0.271 3_weight: 0.2424 0.2938 0.016 2.707 43.1 246.9 86.0 0 0.271 3_xyzrec: 0.2415 0.2934 0.016 2.719 43.1 246.9 86.0 0 0.272 3_adp: 0.2363 0.2909 0.016 2.719 43.4 243.4 85.7 0 0.272 3_regHadp: 0.2359 0.2910 0.016 2.719 43.4 243.4 85.7 0 0.272 end: 0.2344 0.2912 0.016 2.719 43.4 243.4 85.7 0 0.272 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_4yei_refine_001.cif Writing default parameters for subsequent refinement: /net/cci-filer3/home/nigel/work/ANI/result/xray/pairs/4phenix_4yei_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.5400 Refinement macro-cycles (run) : 334.9000 Write final files (write_after_run_outputs) : 13.3100 Total : 353.7500 Total CPU time: 6.74 minutes =========================== phenix.refine: finished =========================== # Date 2024-08-09 Time 09:43:23 PDT -0700 (1723221803.64 s) Start R-work = 0.2825, R-free = 0.3041 Final R-work = 0.2344, R-free = 0.2912 =============================================================================== Job complete usr+sys time: 416.87 seconds wall clock time: 11 minutes 59.53 seconds (719.53 seconds total)