Starting phenix.refine on Mon May 20 17:17:37 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/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 strategy=individual_sites+individual_adp ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4yei.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/4yei.pdb" 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" } 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 } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/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: 3.02, per 1000 atoms: 0.32 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: 8.60 Conformation dependent library (CDL) restraints added in 993.8 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: 2.05 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: 6.52 Time building geometry restraints manager: 4.82 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: 1124 1.32 - 1.49: 1726 1.49 - 1.66: 1935 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 ALA A 210 " pdb=" H ALA A 210 " 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 ALA A 228 " pdb=" H ALA A 228 " 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: 3987 15.79 - 31.57: 244 31.57 - 47.36: 121 47.36 - 63.15: 23 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: 1.27 - 1.94: 308 1.94 - 2.60: 9685 2.60 - 3.27: 30900 3.27 - 3.93: 40764 3.93 - 4.60: 59750 Nonbonded interactions: 141407 Sorted by model distance: 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=" HD3 ARG A 208 " pdb=" O ARG A 208 " model vdw sym.op. 1.352 2.620 -x+2,y,-z+2 nonbonded pdb=" O ARG A 208 " pdb=" HD3 ARG A 208 " model vdw sym.op. 1.352 2.620 -x+2,y,-z+2 nonbonded pdb=" HB3 ALA B 234 " pdb=" HE ARG C 216 " model vdw sym.op. 1.398 2.270 x,-y+2,-z+2 nonbonded pdb=" OXT ALA B 234 " pdb="HH21 ARG C 216 " model vdw sym.op. 1.425 1.850 x,-y+2,-z+2 ... (remaining 141402 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== 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 } } output { prefix = "4yei_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 4584 occupancy sum: 4584.00 (% of total atoms 49.12) Rotatable: count: 1419 occupancy sum: 1419.00 (% of total atoms 15.20) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.55 - 37.43 A, n_refl.=12716 (all), 4.90 % free)------------| | | | r_work= 0.4648 r_free= 0.3724 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 6.850734 | | target function (ml) not normalized (work): 82845.930745 | | target function (ml) not normalized (free): 4160.088940 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.4107 7.9301 7.1801| | 2: 5.64 - 4.48 0.97 3007 139 0.4270 0.3140 6.6996 6.8358| | 3: 4.48 - 3.91 0.98 2977 158 0.4835 0.3449 6.4646 6.5718| | 4: 3.91 - 3.55 0.98 2949 176 0.5523 0.4277 6.238 6.2191| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 44.13 0.74 0.59 276018.49| | 2: 5.64 - 4.48 3007 139 0.64 40.12 1.64 0.84 146839.46| | 3: 4.48 - 3.91 2977 158 0.77 28.52 1.84 0.98 70891.22| | 4: 3.91 - 3.55 2949 176 0.73 33.00 2.00 1.01 48173.76| |alpha: min = 0.59 max = 1.01 mean = 0.85| |beta: min = 48173.76 max = 276018.49 mean = 137837.78| |figures of merit: min = 0.00 max = 1.00 mean = 0.68| |phase err.(work): min = 0.00 max = 89.82 mean = 36.58| |phase err.(test): min = 0.00 max = 89.91 mean = 35.81| |-----------------------------------------------------------------------------| ----------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: 49.64 180.30 105.91 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= 0.4648 r_free= 0.3724 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 6.850734 | | target function (ml) not normalized (work): 82845.930745 | | target function (ml) not normalized (free): 4160.088940 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 7.9863 percent. r_work = 0.5447 r_free = 0.4722 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.5420 0.5447 0.4722 n_refl.: 12716 re-set all scales: r(all,work,free)=0.5420 0.5447 0.4722 n_refl.: 12716 remove outliers: r(all,work,free)=0.5326 0.5350 0.4722 n_refl.: 12706 overall B=-19.52 to atoms: r(all,work,free)=0.4761 0.4780 0.4317 n_refl.: 12706 bulk-solvent and scaling: r(all,work,free)=0.2831 0.2821 0.3031 n_refl.: 12706 remove outliers: r(all,work,free)=0.2830 0.2820 0.3031 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 0.2361 2888.741 2836.860 1.377 1.103 0.425 17.650-14.285 98.02 94 5 0.1437 3045.471 3027.032 1.043 1.100 0.372 14.282-11.568 95.90 180 7 0.1422 3015.142 2972.767 1.162 1.084 0.366 11.530-9.354 97.49 335 14 0.2123 1633.314 1609.041 1.151 1.071 0.367 9.349-7.570 98.64 624 29 0.2492 1223.678 1175.786 0.914 1.049 0.311 7.566-6.123 98.85 1143 56 0.2819 950.581 897.392 0.914 1.017 0.268 6.123-4.955 97.48 2111 97 0.3017 843.953 800.215 1.013 0.964 0.260 4.954-4.009 97.40 3921 193 0.2745 1174.560 1150.097 1.226 0.888 0.193 4.009-3.554 97.79 3579 218 0.3563 708.485 625.652 1.175 0.814 0.156 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0608 b_overall=6.4247 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 12.892776 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.141170 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 0.2908 0.3152 0.0243 0.002 0.4 0.4 0.0 0.2 0 0.125 0.2841 0.3127 0.0286 0.002 0.4 0.4 0.0 0.2 0 0.250 0.2748 0.3116 0.0368 0.002 0.5 0.4 0.0 0.4 0 0.500 0.2662 0.3112 0.0450 0.003 0.6 1.5 0.0 0.8 0 1.000 0.2604 0.3077 0.0474 0.005 0.8 2.7 0.0 0.8 0 2.000 0.2580 0.3072 0.0493 0.007 1.0 3.5 0.0 1.3 0 3.000 0.2550 0.3057 0.0506 0.009 1.2 4.1 0.0 1.3 0 4.000 0.2409 0.3170 0.0762 0.009 1.0 13.1 3.6 6.8 0 5.000 0.2382 0.3169 0.0787 0.010 1.1 16.2 4.4 7.0 0 6.000 0.2361 0.3144 0.0783 0.011 1.2 18.6 5.3 7.6 0 7.000 0.2344 0.3131 0.0787 0.012 1.3 19.7 5.8 7.6 0 8.000 0.2327 0.3146 0.0819 0.013 1.3 23.7 7.0 9.6 0 9.000 0.2311 0.3144 0.0832 0.014 1.4 25.2 7.5 11.7 0 10.000 0.2373 0.3147 0.0774 0.010 1.2 17.1 4.9 7.2 0 6.446 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2841 0.3127 0.0286 0.002 0.4 0.4 0.0 0.2 0 0.250 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 28.41 31.27 2.86 3.255 86.699 0.141 0.082 28.30 31.26 2.96 3.524 86.938 0.004 0.081 28.03 31.12 3.09 3.571 86.941 0.018 0.079 26.80 30.61 3.81 6.021 87.563 0.071 0.071 26.18 30.36 4.18 7.130 87.719 0.141 0.068 25.84 30.18 4.34 8.118 87.934 0.212 0.066 25.68 30.14 4.45 8.704 88.066 0.282 0.065 25.48 30.02 4.55 9.590 88.335 0.353 0.064 25.20 29.97 4.77 10.782 88.799 0.424 0.063 25.09 29.91 4.82 11.408 88.969 0.494 0.062 25.01 29.89 4.88 11.844 89.095 0.565 0.062 24.95 29.88 4.93 12.234 89.204 0.635 0.062 24.89 29.84 4.94 12.580 89.300 0.706 0.061 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.706 Accepted refinement result: 24.89 29.84 4.94 12.580 89.300 0.706 0.061 Individual atomic B min max mean iso aniso Overall: 25.42 265.26 91.94 11.96 4749 0 Protein: 25.42 265.26 91.94 11.96 4749 0 Chain A: 25.42 167.03 90.76 N/A 1583 0 Chain B: 33.11 162.91 84.68 N/A 1583 0 Chain C: 35.83 265.26 100.38 N/A 1583 0 Histogram: Values Number of atoms 25.42 - 49.41 210 49.41 - 73.39 1196 73.39 - 97.37 1470 97.37 - 121.36 1061 121.36 - 145.34 650 145.34 - 169.33 120 169.33 - 193.31 23 193.31 - 217.29 11 217.29 - 241.28 5 241.28 - 265.26 3 =========================== Idealize ADP of riding H ========================== r_work=0.2489 r_free=0.2984 r_work=0.2458 r_free=0.2960 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2458 r_free= 0.2960 coordinate error (max.-lik. estimate): 0.49 A | | | | normalized target function (ls_wunit_k1) (work): 0.059684 | | target function (ls_wunit_k1) not normalized (work): 721.102973 | | target function (ls_wunit_k1) not normalized (free): 52.699434 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2482 0.2458 0.2960 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4822 0.4837 0.4468 n_refl.: 12705 remove outliers: r(all,work,free)=0.4822 0.4837 0.4468 n_refl.: 12705 overall B=-0.02 to atoms: r(all,work,free)=0.4821 0.4836 0.4467 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2464 0.2439 0.2953 n_refl.: 12705 remove outliers: r(all,work,free)=0.2464 0.2439 0.2953 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 0.2340 1602.625 1595.190 1.335 1.074 0.430 17.650-14.285 98.02 94 5 0.1479 1689.576 1671.273 1.084 1.073 0.383 14.282-11.568 95.90 180 7 0.1362 1672.750 1657.368 1.169 1.059 0.363 11.530-9.354 97.49 335 14 0.2007 906.135 896.109 1.135 1.049 0.350 9.349-7.570 98.64 624 29 0.2349 678.876 659.524 0.916 1.032 0.310 7.566-6.123 98.85 1143 56 0.2556 527.366 507.416 0.911 1.007 0.263 6.123-4.955 97.48 2111 97 0.2642 468.211 452.486 1.011 0.966 0.250 4.954-4.009 97.40 3921 193 0.2197 651.626 646.356 1.227 0.908 0.180 4.009-3.554 97.79 3579 218 0.3145 393.056 360.327 1.211 0.852 0.130 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=-0.0421 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.439655 wxc_scale = 0.028 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.034594 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 0.2579 0.3069 0.0490 0.001 0.4 0.9 0.0 0.2 0 0.010 0.2501 0.3040 0.0540 0.001 0.4 1.1 0.0 0.2 0 0.029 0.2420 0.2987 0.0568 0.001 0.4 0.8 0.0 0.2 0 0.057 0.2374 0.2975 0.0601 0.001 0.4 0.8 0.0 0.2 0 0.086 0.2349 0.2958 0.0609 0.002 0.4 0.6 0.0 0.4 0 0.115 0.2333 0.2957 0.0624 0.002 0.4 1.2 0.0 0.2 0 0.143 0.2320 0.2950 0.0630 0.002 0.5 1.0 0.0 0.2 0 0.172 0.2307 0.2936 0.0629 0.002 0.5 1.2 0.0 1.1 0 0.201 0.2367 0.2967 0.0600 0.001 0.4 0.5 0.0 0.4 0 0.096 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2579 0.3069 0.0490 0.001 0.4 0.9 0.0 0.2 0 0.010 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.79 30.69 4.90 16.044 101.226 0.035 6.586 29.07 31.56 2.49 14.139 106.207 0.001 6.662 28.65 31.22 2.57 14.040 106.171 0.004 6.645 26.97 30.32 3.35 15.302 103.206 0.017 6.592 26.25 30.28 4.03 16.136 102.437 0.035 6.566 25.69 30.09 4.41 16.362 101.771 0.052 6.555 25.49 30.19 4.70 16.888 102.361 0.069 6.545 25.33 30.26 4.93 17.289 102.493 0.086 6.540 25.23 30.24 5.01 17.428 102.367 0.104 6.538 25.14 30.28 5.14 17.758 102.543 0.121 6.536 25.06 30.30 5.24 18.071 102.699 0.138 6.534 25.00 30.32 5.32 18.377 102.853 0.156 6.532 24.95 30.35 5.40 18.653 102.986 0.173 6.530 max suggested for this run: 20.25 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.052 Accepted refinement result: 25.69 30.09 4.41 16.362 101.771 0.052 6.555 Individual atomic B min max mean iso aniso Overall: 32.09 260.25 93.00 11.43 4749 0 Protein: 32.09 260.25 93.00 11.43 4749 0 Chain A: 32.09 166.84 91.13 N/A 1583 0 Chain B: 33.50 163.73 85.79 N/A 1583 0 Chain C: 38.35 260.25 102.07 N/A 1583 0 Histogram: Values Number of atoms 32.09 - 54.90 274 54.90 - 77.72 1395 77.72 - 100.54 1364 100.54 - 123.35 934 123.35 - 146.17 589 146.17 - 168.98 155 168.98 - 191.80 19 191.80 - 214.62 11 214.62 - 237.43 5 237.43 - 260.25 3 =========================== Idealize ADP of riding H ========================== r_work=0.2569 r_free=0.3009 r_work=0.2575 r_free=0.3004 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2575 r_free= 0.3004 coordinate error (max.-lik. estimate): 0.58 A | | | | normalized target function (ml) (work): 6.553722 | | target function (ml) not normalized (work): 79182.065063 | | target function (ml) not normalized (free): 4145.195856 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2596 0.2575 0.3004 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4908 0.4924 0.4535 n_refl.: 12705 remove outliers: r(all,work,free)=0.4908 0.4924 0.4535 n_refl.: 12705 overall B=0.63 to atoms: r(all,work,free)=0.4926 0.4942 0.4548 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2588 0.2566 0.3012 n_refl.: 12705 remove outliers: r(all,work,free)=0.2588 0.2566 0.3012 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 0.2414 1602.625 1598.532 1.246 1.093 0.430 17.650-14.285 98.02 94 5 0.1521 1689.576 1655.215 1.015 1.092 0.380 14.282-11.568 95.90 180 7 0.1493 1672.750 1633.480 1.152 1.076 0.375 11.530-9.354 97.49 335 14 0.2122 906.135 888.176 1.124 1.065 0.369 9.349-7.570 98.64 624 29 0.2374 678.876 651.630 0.892 1.045 0.309 7.566-6.123 98.85 1143 56 0.2662 527.366 499.239 0.891 1.016 0.259 6.123-4.955 97.48 2111 97 0.2833 468.211 444.067 1.033 0.969 0.259 4.954-4.009 97.40 3921 193 0.2356 651.626 642.496 1.226 0.901 0.169 4.009-3.554 97.79 3579 218 0.3234 393.056 356.204 1.218 0.836 0.138 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0047 b_overall=0.2421 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2566 r_free=0.3012 After: r_work=0.2566 r_free=0.3012 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.661953 wxc_scale = 0.022 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.035054 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 0.2566 0.3010 0.0444 0.001 0.4 0.9 0.0 0.2 0 0.008 0.2564 0.3011 0.0447 0.001 0.4 0.9 0.0 0.2 0 0.024 0.2562 0.3009 0.0447 0.001 0.4 1.0 0.0 0.2 0 0.049 0.2558 0.3008 0.0450 0.002 0.4 0.9 0.0 0.2 0 0.073 0.2553 0.3009 0.0456 0.002 0.4 0.9 0.0 0.2 0 0.097 0.2545 0.3004 0.0459 0.002 0.4 1.0 0.0 0.2 0 0.122 0.2534 0.2997 0.0463 0.003 0.5 1.0 0.0 0.2 0 0.146 0.2518 0.2986 0.0468 0.003 0.5 1.1 0.0 0.0 0 0.170 0.2556 0.3007 0.0450 0.002 0.4 0.9 0.0 0.2 0 0.081 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2518 0.2986 0.0468 0.003 0.5 1.1 0.0 0.0 0 0.170 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 25.18 29.86 4.68 15.927 102.988 0.035 6.541 29.40 32.06 2.66 14.275 109.445 0.001 6.670 28.58 31.46 2.87 13.565 109.380 0.004 6.643 26.74 30.03 3.29 14.907 104.974 0.018 6.589 25.70 29.67 3.96 15.536 103.705 0.035 6.555 24.90 29.37 4.47 16.086 103.430 0.053 6.529 24.52 29.48 4.96 16.851 103.490 0.070 6.517 24.35 29.54 5.19 17.403 103.652 0.088 6.512 24.25 29.57 5.32 17.828 103.809 0.105 6.508 24.18 29.58 5.40 18.181 103.963 0.123 6.506 24.12 29.59 5.47 18.492 104.112 0.140 6.504 24.08 29.61 5.53 18.763 104.252 0.158 6.503 24.04 29.62 5.58 19.015 104.378 0.175 6.502 max suggested for this run: 20.60 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.053 Accepted refinement result: 24.90 29.37 4.47 16.086 103.430 0.053 6.529 Individual atomic B min max mean iso aniso Overall: 34.23 255.87 94.49 12.05 4749 0 Protein: 34.23 255.87 94.49 12.05 4749 0 Chain A: 34.23 179.57 91.28 N/A 1583 0 Chain B: 35.68 165.81 87.55 N/A 1583 0 Chain C: 37.71 255.87 104.65 N/A 1583 0 Histogram: Values Number of atoms 34.23 - 56.40 295 56.40 - 78.56 1353 78.56 - 100.73 1387 100.73 - 122.89 842 122.89 - 145.05 571 145.05 - 167.22 245 167.22 - 189.38 39 189.38 - 211.55 10 211.55 - 233.71 4 233.71 - 255.87 3 =========================== Idealize ADP of riding H ========================== r_work=0.2490 r_free=0.2937 r_work=0.2489 r_free=0.2932 ----------X-ray data---------- |--(resolution: 3.55 - 32.24 A, n_refl.=12705 (all), 4.90 % free)------------| | | | r_work= 0.2489 r_free= 0.2932 coordinate error (max.-lik. estimate): 0.58 A | | | | normalized target function (ml) (work): 6.528553 | | target function (ml) not normalized (work): 78877.977881 | | target function (ml) not normalized (free): 4135.614277 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2261 0.2538 6.6761 6.7927| | 2: 5.63 - 4.48 0.97 3003 139 0.2341 0.2769 6.5633 6.7377| | 3: 4.48 - 3.91 0.98 2973 158 0.2403 0.2789 6.5504 6.7317| | 4: 3.91 - 3.55 0.98 2947 176 0.3339 0.4067 6.3129 6.3441| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.76 28.93 0.99 1.01 110342.60| | 2: 5.63 - 4.48 3003 139 0.69 35.11 1.05 1.00 101660.75| | 3: 4.48 - 3.91 2973 158 0.73 32.22 0.96 0.92 88806.43| | 4: 3.91 - 3.55 2947 176 0.61 43.50 0.97 0.78 71779.65| |alpha: min = 0.78 max = 1.01 mean = 0.93| |beta: min = 71779.65 max = 110342.60 mean = 93479.20| |figures of merit: min = 0.00 max = 1.00 mean = 0.70| |phase err.(work): min = 0.00 max = 89.89 mean = 34.83| |phase err.(test): min = 0.00 max = 89.62 mean = 35.76| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2511 0.2489 0.2932 n_refl.: 12705 re-set all scales: r(all,work,free)=0.4935 0.4952 0.4525 n_refl.: 12705 remove outliers: r(all,work,free)=0.4935 0.4952 0.4525 n_refl.: 12705 overall B=0.10 to atoms: r(all,work,free)=0.4938 0.4955 0.4527 n_refl.: 12705 bulk-solvent and scaling: r(all,work,free)=0.2512 0.2490 0.2941 n_refl.: 12705 remove outliers: r(all,work,free)=0.2512 0.2490 0.2941 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 0.2450 1602.625 1606.896 1.185 1.111 0.430 17.650-14.285 98.02 94 5 0.1470 1689.576 1671.830 0.965 1.109 0.380 14.282-11.568 95.90 180 7 0.1435 1672.750 1647.913 1.064 1.092 0.365 11.530-9.354 97.49 335 14 0.2068 906.135 895.494 1.056 1.079 0.360 9.349-7.570 98.64 624 29 0.2317 678.876 656.688 0.853 1.056 0.310 7.566-6.123 98.85 1143 56 0.2605 527.366 503.198 0.852 1.024 0.249 6.123-4.955 97.48 2111 97 0.2759 468.211 445.085 0.987 0.971 0.226 4.954-4.009 97.40 3921 193 0.2235 651.626 640.010 1.193 0.895 0.170 4.009-3.554 97.79 3579 218 0.3192 393.056 353.600 1.193 0.821 0.130 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9645 b_overall=0.0111 ================= 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 : 0.4648 0.3724 0.017 1.564 49.6 289.8 106.4 0 0.000 1_bss: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_settarget: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_weight: 0.2820 0.3031 0.017 1.564 30.1 270.3 86.8 0 0.000 1_xyzrec: 0.2841 0.3127 0.002 0.444 30.1 270.3 86.8 0 0.156 1_adp: 0.2489 0.2984 0.002 0.444 25.4 265.3 91.9 0 0.156 1_regHadp: 0.2458 0.2960 0.002 0.444 25.4 265.3 91.9 0 0.156 2_bss: 0.2439 0.2953 0.002 0.444 25.4 265.2 91.9 0 0.156 2_settarget: 0.2439 0.2953 0.002 0.444 25.4 265.2 91.9 0 0.156 2_updatecdl: 0.2439 0.2953 0.002 0.484 25.4 265.2 91.9 0 0.156 2_weight: 0.2439 0.2953 0.002 0.484 25.4 265.2 91.9 0 0.156 2_xyzrec: 0.2579 0.3069 0.001 0.382 25.4 265.2 91.9 0 0.209 2_adp: 0.2569 0.3009 0.001 0.382 32.1 260.2 93.0 0 0.209 2_regHadp: 0.2575 0.3004 0.001 0.382 32.1 260.2 93.0 0 0.209 3_bss: 0.2566 0.3012 0.001 0.382 32.7 260.9 93.6 0 0.209 3_settarget: 0.2566 0.3012 0.001 0.382 32.7 260.9 93.6 0 0.209 3_updatecdl: 0.2566 0.3012 0.001 0.424 32.7 260.9 93.6 0 0.209 3_setrh: 0.2566 0.3012 0.001 0.424 32.7 260.9 93.6 0 0.209 3_weight: 0.2566 0.3012 0.001 0.424 32.7 260.9 93.6 0 0.209 3_xyzrec: 0.2518 0.2986 0.003 0.508 32.7 260.9 93.6 0 0.207 3_adp: 0.2490 0.2937 0.003 0.508 34.2 255.9 94.5 0 0.207 3_regHadp: 0.2489 0.2932 0.003 0.508 34.2 255.9 94.5 0 0.207 end: 0.2490 0.2941 0.003 0.508 34.3 256.0 94.6 0 0.207 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/4yei_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/4yei_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 13.5000 Refinement macro-cycles (run) : 295.3100 Write final files (write_after_run_outputs) : 16.8000 Total : 325.6100 Total CPU time: 6.28 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:36:04 PDT -0700 (1716251764.18 s) Start R-work = 0.2820, R-free = 0.3031 Final R-work = 0.2490, R-free = 0.2941 =============================================================================== Job complete usr+sys time: 396.55 seconds wall clock time: 18 minutes 50.94 seconds (1130.94 seconds total)