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/1xgo.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1xgo/1xgo.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1xgo/1xgo.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1xgo/1xgo.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1xgo.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1xgo.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 } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 4719 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 4719 Classifications: {'peptide': 295} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 280} Time building chain proxies: 1.65, per 1000 atoms: 0.35 Number of scatterers: 4719 At special positions: 0 Unit cell: (138.916, 138.916, 63.907, 90, 90, 120) Space group: P 62 (No. 171) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 O 423 8.00 N 390 7.00 C 1490 6.00 H 2407 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: 3.99 Conformation dependent library (CDL) restraints added in 698.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 7 helices and 4 sheets defined 32.5% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 3 through 21 removed outlier: 3.528A pdb=" N LYS A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 44 removed outlier: 3.848A pdb=" N LEU A 44 " --> pdb=" O MET A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 128 through 141 Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.536A pdb=" N PHE A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 240 No H-bonds generated for 'chain 'A' and resid 237 through 240' Processing helix chain 'A' and resid 246 through 259 removed outlier: 3.702A pdb=" N LEU A 251 " --> pdb=" O GLN A 248 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 78 through 84 Processing sheet with id= B, first strand: chain 'A' and resid 183 through 190 Processing sheet with id= C, first strand: chain 'A' and resid 197 through 200 Processing sheet with id= D, first strand: chain 'A' and resid 205 through 208 removed outlier: 3.941A pdb=" N ILE A 205 " --> pdb=" O TYR A 265 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 225 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: 3.66 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 2407 1.16 - 1.34: 725 1.34 - 1.52: 904 1.52 - 1.70: 706 1.70 - 1.88: 18 Bond restraints: 4760 Sorted by residual: bond pdb=" N GLU A 257 " pdb=" H GLU A 257 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH1 ARG A 123 " pdb="HH11 ARG A 123 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE ARG A 25 " pdb=" HE ARG A 25 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N MET A 7 " pdb=" H MET A 7 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH1 ARG A 215 " pdb="HH11 ARG A 215 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 4755 not shown) Histogram of bond angle deviations from ideal: 95.63 - 103.31: 128 103.31 - 110.98: 4961 110.98 - 118.66: 1711 118.66 - 126.34: 1854 126.34 - 134.02: 35 Bond angle restraints: 8689 Sorted by residual: angle pdb=" N GLY A 68 " pdb=" CA GLY A 68 " pdb=" C GLY A 68 " ideal model delta sigma weight residual 114.48 102.68 11.80 1.19e+00 7.06e-01 9.84e+01 angle pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" C LEU A 131 " ideal model delta sigma weight residual 111.03 100.14 10.89 1.11e+00 8.12e-01 9.62e+01 angle pdb=" N TYR A 237 " pdb=" CA TYR A 237 " pdb=" C TYR A 237 " ideal model delta sigma weight residual 111.36 101.53 9.83 1.09e+00 8.42e-01 8.13e+01 angle pdb=" N THR A 64 " pdb=" CA THR A 64 " pdb=" C THR A 64 " ideal model delta sigma weight residual 110.14 96.77 13.37 1.51e+00 4.39e-01 7.84e+01 angle pdb=" N ASP A 182 " pdb=" CA ASP A 182 " pdb=" C ASP A 182 " ideal model delta sigma weight residual 110.23 97.58 12.65 1.45e+00 4.76e-01 7.61e+01 ... (remaining 8684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 1843 17.47 - 34.93: 215 34.93 - 52.40: 90 52.40 - 69.86: 38 69.86 - 87.33: 12 Dihedral angle restraints: 2198 sinusoidal: 1234 harmonic: 964 Sorted by residual: dihedral pdb=" C HIS A 86 " pdb=" N HIS A 86 " pdb=" CA HIS A 86 " pdb=" CB HIS A 86 " ideal model delta harmonic sigma weight residual -122.60 -109.89 -12.71 0 2.50e+00 1.60e-01 2.58e+01 dihedral pdb=" C LEU A 150 " pdb=" N LEU A 150 " pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " ideal model delta harmonic sigma weight residual -122.60 -133.16 10.56 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" C LEU A 131 " pdb=" N LEU A 131 " pdb=" CA LEU A 131 " pdb=" CB LEU A 131 " ideal model delta harmonic sigma weight residual -122.60 -112.34 -10.26 0 2.50e+00 1.60e-01 1.68e+01 ... (remaining 2195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 200 0.107 - 0.215: 103 0.215 - 0.322: 47 0.322 - 0.429: 11 0.429 - 0.536: 4 Chirality restraints: 365 Sorted by residual: chirality pdb=" CA ASN A 53 " pdb=" N ASN A 53 " pdb=" C ASN A 53 " pdb=" CB ASN A 53 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.18e+00 chirality pdb=" CA LEU A 150 " pdb=" N LEU A 150 " pdb=" C LEU A 150 " pdb=" CB LEU A 150 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CA VAL A 212 " pdb=" N VAL A 212 " pdb=" C VAL A 212 " pdb=" CB VAL A 212 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 362 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 78 " 0.157 2.00e-02 2.50e+03 6.46e-02 1.25e+02 pdb=" CG TYR A 78 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 78 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 78 " -0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 78 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 78 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 78 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 78 " 0.125 2.00e-02 2.50e+03 pdb=" HD1 TYR A 78 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 78 " -0.049 2.00e-02 2.50e+03 pdb=" HE1 TYR A 78 " -0.024 2.00e-02 2.50e+03 pdb=" HE2 TYR A 78 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 265 " -0.144 2.00e-02 2.50e+03 5.64e-02 9.54e+01 pdb=" CG TYR A 265 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 265 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 265 " 0.033 2.00e-02 2.50e+03 pdb=" CE1 TYR A 265 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR A 265 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 265 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 265 " -0.095 2.00e-02 2.50e+03 pdb=" HD1 TYR A 265 " 0.044 2.00e-02 2.50e+03 pdb=" HD2 TYR A 265 " 0.054 2.00e-02 2.50e+03 pdb=" HE1 TYR A 265 " 0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR A 265 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 170 " 0.131 2.00e-02 2.50e+03 5.19e-02 8.08e+01 pdb=" CG TYR A 170 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 170 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR A 170 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 170 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 170 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A 170 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 170 " 0.092 2.00e-02 2.50e+03 pdb=" HD1 TYR A 170 " -0.045 2.00e-02 2.50e+03 pdb=" HD2 TYR A 170 " -0.043 2.00e-02 2.50e+03 pdb=" HE1 TYR A 170 " -0.014 2.00e-02 2.50e+03 pdb=" HE2 TYR A 170 " -0.016 2.00e-02 2.50e+03 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 190 1.80 - 2.50: 4320 2.50 - 3.20: 15994 3.20 - 3.90: 22021 3.90 - 4.60: 33386 Nonbonded interactions: 75911 Sorted by model distance: nonbonded pdb=" HE2 PHE A 221 " pdb=" HB3 LYS A 258 " model vdw sym.op. 1.102 2.270 -y+1,x-y,z-1/3 nonbonded pdb=" HA VAL A 285 " pdb="HG12 VAL A 290 " model vdw 1.137 2.440 nonbonded pdb="HH12 ARG A 123 " pdb=" HA ASP A 288 " model vdw 1.169 2.270 nonbonded pdb=" H GLY A 27 " pdb="HG13 VAL A 72 " model vdw 1.177 2.270 nonbonded pdb=" HB2 ALA A 60 " pdb="HG21 VAL A 197 " model vdw 1.192 2.440 ... (remaining 75906 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 423 7.97 1 N 390 6.97 1 C 1490 5.97 1 H 2407 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: 2407 of 4719 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 4719 n_use_u_iso = 4719 n_use_u_aniso = 0 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 = 4719 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (4719 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 4719 aniso = 0) 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 3 through 21 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 30 through 44 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 106 through 121 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 128 through 141 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 217 through 230 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 237 through 240 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 246 through 259 helix_type = alpha pi *3_10 unknown } sheet { first_strand = chain 'A' and resid 78 through 84 sheet_id = " A" strand { selection = chain 'A' and resid 93 through 99 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 98 and name N bond_start_previous = chain 'A' and resid 79 and name O } } sheet { first_strand = chain 'A' and resid 183 through 190 sheet_id = " B" strand { selection = chain 'A' and resid 277 through 285 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 283 and name N bond_start_previous = chain 'A' and resid 184 and name O } strand { selection = chain 'A' and resid 290 through 292 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 291 and name N bond_start_previous = chain 'A' and resid 284 and name O } } sheet { first_strand = chain 'A' and resid 197 through 200 sheet_id = " C" strand { selection = chain 'A' and resid 267 through 270 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 269 and name N bond_start_previous = chain 'A' and resid 198 and name O } } sheet { first_strand = chain 'A' and resid 205 through 208 sheet_id = " D" strand { selection = chain 'A' and resid 262 through 265 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 265 and name N bond_start_previous = chain 'A' and resid 205 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1xgo_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2407 occupancy sum: 2407.00 (% of total atoms 51.01) Rotatable: count: 742 occupancy sum: 742.00 (% of total atoms 15.72) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.51 - 47.03 A, n_refl.=7571 (all), 9.89 % free)-------------| | | | r_work= 0.3043 r_free= 0.2973 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 2.775446 | | target function (ml) not normalized (work): 18934.094254 | | target function (ml) not normalized (free): 2088.341598 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 47.03 - 6.00 0.97 1619 177 0.3308 0.3084 3.393 3.3877| | 2: 6.00 - 4.77 0.93 1498 166 0.2497 0.2533 2.7716 2.7743| | 3: 4.77 - 4.16 0.89 1443 156 0.2701 0.2738 2.6018 2.67| | 4: 4.16 - 3.78 0.76 1216 130 0.3199 0.3113 2.4611 2.5682| | 5: 3.78 - 3.51 0.66 1046 120 0.3548 0.3588 2.4301 2.3149| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 47.03 - 6.00 1619 177 0.62 42.01 0.85 0.01 129.62| | 2: 6.00 - 4.77 1498 166 0.55 48.28 1.19 0.01 106.43| | 3: 4.77 - 4.16 1443 156 0.78 30.68 1.27 0.02 57.82| | 4: 4.16 - 3.78 1216 130 0.86 22.43 1.34 0.02 31.93| | 5: 3.78 - 3.51 1046 120 0.93 16.40 1.42 0.02 18.56| |alpha: min = 0.01 max = 0.02 mean = 0.02| |beta: min = 18.56 max = 129.62 mean = 74.90| |figures of merit: min = 0.00 max = 1.00 mean = 0.73| |phase err.(work): min = 0.00 max = 89.99 mean = 33.57| |phase err.(test): min = 0.00 max = 85.41 mean = 33.49| |-----------------------------------------------------------------------------| ----------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 : 0.016 0.079 2353 Z= 1.034 Angle : 2.306 13.371 3178 Z= 1.460 Chirality : 0.158 0.536 365 Planarity : 0.016 0.129 405 Dihedral : 20.740 87.330 901 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 83.28 Ramachandran Plot: Outliers : 8.19 % Allowed : 22.18 % Favored : 69.62 % Rotamer: Outliers : 27.16 % Allowed : 18.52 % Favored : 54.32 % Cbeta Deviations : 0.73 % Peptide Plane: Cis-proline : 7.14 % 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: -6.45 (0.33), residues: 293 helix: -4.64 (0.26), residues: 96 sheet: -3.34 (0.65), residues: 50 loop : -4.43 (0.36), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.003 ARG A 25 TYR 0.131 0.025 TYR A 78 PHE 0.083 0.011 PHE A 221 TRP 0.019 0.007 TRP A 239 HIS 0.006 0.001 HIS A 281 Individual atomic B min max mean iso aniso Overall: 2.00 107.66 31.50 4.99 2312 0 Protein: 2.00 107.66 31.50 4.99 2312 0 Chain A: 2.00 107.66 31.50 N/A 2312 0 Histogram: Values Number of atoms 2.00 - 12.57 417 12.57 - 23.13 473 23.13 - 33.70 490 33.70 - 44.26 393 44.26 - 54.83 220 54.83 - 65.40 164 65.40 - 75.96 98 75.96 - 86.53 29 86.53 - 97.09 20 97.09 - 107.66 8 |-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: 3.51 - 47.03 A, n_refl.=7571 (all), 9.89 % free)-------------| | | | r_work= 0.3043 r_free= 0.2973 coordinate error (max.-lik. estimate): 0.35 A | | | | normalized target function (ml) (work): 2.775446 | | target function (ml) not normalized (work): 18934.094254 | | target function (ml) not normalized (free): 2088.341598 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3036 0.3043 0.2973 n_refl.: 7571 re-set all scales: r(all,work,free)=0.3036 0.3043 0.2973 n_refl.: 7571 remove outliers: r(all,work,free)=0.3036 0.3043 0.2973 n_refl.: 7570 overall B=3.64 to atoms: r(all,work,free)=0.3166 0.3173 0.3101 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1932 0.1925 0.1997 n_refl.: 7570 remove outliers: r(all,work,free)=0.1932 0.1925 0.1997 n_refl.: 7570 ======================== 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 47.029-15.950 98.06 89 12 0.3007 1414.453 1341.492 1.574 0.993 0.369 15.935-12.710 100.00 89 10 0.1574 1569.136 1549.736 1.335 0.993 0.254 12.669-10.064 98.05 182 19 0.1369 1430.329 1407.075 1.246 0.994 0.228 10.054-8.008 99.48 344 37 0.1287 1203.527 1188.791 1.191 0.995 0.227 7.993-6.350 95.81 662 70 0.1846 763.345 742.669 1.113 0.996 0.216 6.344-5.045 94.08 1288 142 0.2012 645.629 615.645 0.984 0.996 0.155 5.041-4.007 88.08 2360 262 0.1884 666.989 633.520 0.957 0.995 0.067 4.004-3.512 68.80 1807 197 0.2244 609.358 569.198 1.052 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.3659 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.316843 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.524469 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 0.1865 0.2389 0.0524 0.015 1.6 63.1 10.9 25.5 0 9.158 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.65 23.89 5.24 3.509 35.115 0.524 0.044 19.51 24.81 5.30 4.289 35.648 0.016 0.048 19.34 24.78 5.44 4.253 35.659 0.066 0.047 18.81 24.71 5.90 4.551 35.760 0.262 0.045 18.32 24.65 6.33 5.369 35.894 0.524 0.042 17.99 24.60 6.62 6.313 36.068 0.787 0.041 17.73 24.57 6.84 7.440 36.355 1.049 0.040 17.58 24.53 6.95 8.144 36.495 1.311 0.039 17.47 24.49 7.02 8.657 36.593 1.573 0.039 17.38 24.45 7.07 9.106 36.686 1.836 0.039 17.32 24.43 7.11 9.471 36.762 2.098 0.038 17.24 24.43 7.19 10.070 36.924 2.360 0.038 17.10 24.47 7.37 11.353 37.335 2.622 0.037 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.262 Accepted refinement result: 18.81 24.71 5.90 4.551 35.760 0.262 0.045 Individual atomic B min max mean iso aniso Overall: 10.64 107.09 36.45 4.48 2312 0 Protein: 10.64 107.09 36.45 4.48 2312 0 Chain A: 10.64 107.09 36.45 N/A 2312 0 Histogram: Values Number of atoms 10.64 - 20.28 401 20.28 - 29.93 592 29.93 - 39.57 515 39.57 - 49.22 334 49.22 - 58.86 183 58.86 - 68.51 147 68.51 - 78.16 86 78.16 - 87.80 26 87.80 - 97.45 17 97.45 - 107.09 11 =========================== Idealize ADP of riding H ========================== r_work=0.1881 r_free=0.2471 r_work=0.1875 r_free=0.2472 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.1875 r_free= 0.2472 coordinate error (max.-lik. estimate): 0.45 A | | | | normalized target function (ls_wunit_k1) (work): 0.044430 | | target function (ls_wunit_k1) not normalized (work): 303.056299 | | target function (ls_wunit_k1) not normalized (free): 57.259962 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1936 0.1875 0.2472 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3224 0.3200 0.3431 n_refl.: 7570 remove outliers: r(all,work,free)=0.3224 0.3200 0.3431 n_refl.: 7570 overall B=1.47 to atoms: r(all,work,free)=0.3277 0.3253 0.3476 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1913 0.1852 0.2441 n_refl.: 7570 remove outliers: r(all,work,free)=0.1913 0.1852 0.2441 n_refl.: 7570 ======================== 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 47.029-15.950 99.02 89 12 0.2256 979.114 956.231 1.825 0.991 0.380 15.935-12.710 100.00 89 10 0.1176 1086.189 1082.861 1.393 0.992 0.280 12.669-10.064 99.01 182 19 0.1112 990.104 977.550 1.290 0.992 0.254 10.054-8.008 99.48 344 37 0.1216 833.106 825.820 1.220 0.993 0.249 7.993-6.350 96.06 662 70 0.1680 528.403 516.542 1.128 0.994 0.248 6.344-5.045 94.20 1288 142 0.1966 446.918 425.085 0.969 0.994 0.188 5.041-4.007 88.19 2360 262 0.1892 461.704 436.584 0.928 0.993 0.069 4.004-3.512 68.84 1807 197 0.2241 421.811 392.619 1.084 0.987 0.010 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.6118 ============================ 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 = 4.328705 wxc_scale = 0.154 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.185994 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 0.2189 0.2542 0.0353 0.004 0.9 21.0 8.5 23.5 0 0.067 0.2112 0.2526 0.0415 0.005 0.9 22.9 7.8 24.3 0 0.200 0.2051 0.2524 0.0473 0.006 1.0 27.1 8.5 24.3 0 0.401 0.2010 0.2518 0.0508 0.007 1.0 33.5 9.6 24.7 0 0.601 0.1971 0.2523 0.0551 0.008 1.1 37.5 9.6 24.7 0 0.801 0.1944 0.2525 0.0581 0.009 1.2 41.1 11.6 25.5 0 1.001 0.1917 0.2538 0.0621 0.011 1.3 45.8 12.3 29.2 0 1.202 0.1897 0.2530 0.0633 0.012 1.4 51.1 13.3 30.0 0 1.402 0.1998 0.2522 0.0525 0.007 1.1 35.4 9.2 24.7 0 0.668 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2189 0.2542 0.0353 0.004 0.9 21.0 8.5 23.5 0 0.067 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.89 25.42 3.53 6.592 41.845 0.186 6.294 22.92 25.87 2.95 7.506 43.431 0.006 6.320 22.38 25.71 3.33 7.193 43.149 0.023 6.306 21.07 25.32 4.25 7.554 43.066 0.093 6.272 20.52 25.24 4.72 8.866 43.262 0.186 6.260 20.22 25.20 4.98 10.307 43.688 0.279 6.254 20.06 25.18 5.12 11.306 43.966 0.372 6.251 19.94 25.16 5.22 12.235 44.246 0.465 6.248 19.82 25.15 5.33 13.307 44.573 0.558 6.246 19.75 25.14 5.39 14.093 44.806 0.651 6.244 19.69 25.15 5.46 14.767 45.008 0.744 6.243 19.63 25.16 5.53 15.504 45.227 0.837 6.242 19.60 25.16 5.56 15.889 45.351 0.930 6.242 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.651 Accepted refinement result: 19.75 25.14 5.39 14.093 44.806 0.651 6.244 Individual atomic B min max mean iso aniso Overall: 7.11 132.71 43.97 15.52 2312 0 Protein: 7.11 132.71 43.97 15.52 2312 0 Chain A: 7.11 132.71 43.97 N/A 2312 0 Histogram: Values Number of atoms 7.11 - 19.67 359 19.67 - 32.23 460 32.23 - 44.79 513 44.79 - 57.35 394 57.35 - 69.91 241 69.91 - 82.47 157 82.47 - 95.03 110 95.03 - 107.59 56 107.59 - 120.15 17 120.15 - 132.71 5 =========================== Idealize ADP of riding H ========================== r_work=0.1975 r_free=0.2514 r_work=0.1958 r_free=0.2510 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.1958 r_free= 0.2510 coordinate error (max.-lik. estimate): 0.57 A | | | | normalized target function (ml) (work): 6.239327 | | target function (ml) not normalized (work): 42558.447180 | | target function (ml) not normalized (free): 4784.207765 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2014 0.1958 0.2510 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3394 0.3376 0.3551 n_refl.: 7570 remove outliers: r(all,work,free)=0.3394 0.3376 0.3551 n_refl.: 7570 overall B=3.99 to atoms: r(all,work,free)=0.3542 0.3527 0.3672 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.1998 0.1944 0.2482 n_refl.: 7570 remove outliers: r(all,work,free)=0.1998 0.1944 0.2482 n_refl.: 7570 ======================== 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 47.029-15.950 99.02 89 12 0.2044 979.114 965.285 1.882 0.998 0.379 15.935-12.710 100.00 89 10 0.1246 1086.189 1086.030 1.482 0.999 0.308 12.669-10.064 99.01 182 19 0.1192 990.104 980.460 1.287 0.999 0.266 10.054-8.008 99.48 344 37 0.1299 833.106 824.199 1.230 0.999 0.263 7.993-6.350 96.06 662 70 0.1767 528.403 512.931 1.115 0.998 0.235 6.344-5.045 94.20 1288 142 0.2066 446.918 419.583 0.965 0.996 0.184 5.041-4.007 88.19 2360 262 0.1975 461.704 430.942 0.910 0.993 0.076 4.004-3.512 68.84 1807 197 0.2384 421.811 385.252 1.093 0.985 0.028 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.9856 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1944 r_free=0.2482 After: r_work=0.1944 r_free=0.2482 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 5.254247 wxc_scale = 0.023 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.150009 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 0.1945 0.2481 0.0536 0.004 0.9 21.6 7.8 23.0 0 0.012 0.1945 0.2481 0.0536 0.004 0.9 21.8 7.8 23.0 0 0.037 0.1944 0.2482 0.0537 0.004 0.9 21.8 7.8 23.0 0 0.074 0.1944 0.2481 0.0538 0.004 0.9 21.8 7.8 23.0 0 0.110 0.1943 0.2481 0.0538 0.004 0.9 21.4 7.8 23.0 0 0.147 0.1942 0.2481 0.0539 0.004 0.9 21.4 7.8 23.0 0 0.184 0.1941 0.2481 0.0540 0.004 0.9 21.4 7.8 23.0 0 0.221 0.1940 0.2481 0.0541 0.004 0.9 21.4 7.8 23.0 0 0.257 0.1943 0.2481 0.0538 0.004 0.9 21.6 7.8 23.0 0 0.123 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1943 0.2481 0.0538 0.004 0.9 21.4 7.8 23.0 0 0.147 0.1942 0.2481 0.0539 0.004 0.9 21.4 7.8 23.0 0 0.184 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.43 24.81 5.38 13.148 53.700 0.150 6.233 22.32 25.59 3.27 12.532 57.906 0.005 6.276 21.58 25.24 3.66 11.972 56.893 0.019 6.264 20.40 24.84 4.44 11.920 55.156 0.075 6.245 19.73 24.76 5.03 12.256 54.075 0.150 6.235 19.49 24.83 5.34 12.688 54.054 0.225 6.232 19.27 24.90 5.62 13.267 54.231 0.300 6.228 19.14 24.88 5.74 13.695 54.198 0.375 6.226 19.06 24.91 5.84 14.139 54.292 0.450 6.225 18.98 24.94 5.96 14.698 54.536 0.525 6.223 18.92 24.98 6.06 15.192 54.739 0.600 6.223 18.88 25.02 6.14 15.639 54.919 0.675 6.222 18.84 25.05 6.21 16.092 55.104 0.750 6.222 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.150 Accepted refinement result: 19.73 24.76 5.03 12.256 54.075 0.150 6.235 Individual atomic B min max mean iso aniso Overall: 6.88 147.74 48.72 12.00 2312 0 Protein: 6.88 147.74 48.72 12.00 2312 0 Chain A: 6.88 147.74 48.72 N/A 2312 0 Histogram: Values Number of atoms 6.88 - 20.97 113 20.97 - 35.05 556 35.05 - 49.14 684 49.14 - 63.22 458 63.22 - 77.31 250 77.31 - 91.39 142 91.39 - 105.48 75 105.48 - 119.56 28 119.56 - 133.65 5 133.65 - 147.74 1 =========================== Idealize ADP of riding H ========================== r_work=0.1973 r_free=0.2476 r_work=0.1980 r_free=0.2483 ----------X-ray data---------- |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.1980 r_free= 0.2483 coordinate error (max.-lik. estimate): 0.51 A | | | | normalized target function (ml) (work): 6.237345 | | target function (ml) not normalized (work): 42544.930231 | | target function (ml) not normalized (free): 4778.564937 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 47.03 - 6.00 0.97 1618 177 0.1559 0.1927 6.3335 6.5036| | 2: 6.00 - 4.77 0.93 1498 166 0.2050 0.2438 6.1808 6.2693| | 3: 4.77 - 4.16 0.89 1443 156 0.1987 0.2631 6.196 6.4245| | 4: 4.16 - 3.78 0.76 1216 130 0.2351 0.3106 6.2128 6.3716| | 5: 3.78 - 3.51 0.66 1046 120 0.2496 0.2981 6.2553 6.3015| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 47.03 - 6.00 1618 177 0.90 16.12 1.00 1.09 52204.89| | 2: 6.00 - 4.77 1498 166 0.86 22.79 0.99 1.07 54574.31| | 3: 4.77 - 4.16 1443 156 0.86 22.67 0.99 1.02 59538.36| | 4: 4.16 - 3.78 1216 130 0.82 26.99 1.00 0.98 65771.53| | 5: 3.78 - 3.51 1046 120 0.80 28.71 1.04 0.96 68989.15| |alpha: min = 0.96 max = 1.09 mean = 1.03| |beta: min = 52204.89 max = 68989.15 mean = 59269.10| |figures of merit: min = 0.01 max = 1.00 mean = 0.85| |phase err.(work): min = 0.00 max = 89.20 mean = 22.84| |phase err.(test): min = 0.00 max = 89.86 mean = 23.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2030 0.1980 0.2483 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3621 0.3607 0.3737 n_refl.: 7570 remove outliers: r(all,work,free)=0.3621 0.3607 0.3737 n_refl.: 7570 overall B=1.29 to atoms: r(all,work,free)=0.3670 0.3657 0.3781 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.2027 0.1976 0.2485 n_refl.: 7570 remove outliers: r(all,work,free)=0.2027 0.1976 0.2485 n_refl.: 7570 ======================== 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 47.029-15.950 98.06 89 12 0.2003 868.739 847.182 1.843 0.997 0.380 15.935-12.710 100.00 89 10 0.1218 963.744 961.369 1.505 0.998 0.319 12.669-10.064 98.05 182 19 0.1187 878.490 871.232 1.278 0.999 0.269 10.054-8.008 99.48 344 37 0.1293 739.191 731.074 1.226 0.999 0.269 7.993-6.350 95.81 662 70 0.1707 468.837 454.664 1.140 0.999 0.268 6.344-5.045 94.08 1288 142 0.2083 396.537 373.940 0.970 0.998 0.198 5.041-4.007 88.08 2360 262 0.2024 409.656 382.878 0.919 0.996 0.098 4.004-3.512 68.80 1807 197 0.2482 374.260 337.020 1.112 0.989 0.039 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.8028 ================= 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 : 0.3043 0.2973 0.016 2.306 2.0 107.7 31.5 0 0.000 1_bss: 0.1925 0.1997 0.016 2.306 5.6 111.3 35.1 0 0.000 1_settarget: 0.1925 0.1997 0.016 2.306 5.6 111.3 35.1 0 0.000 1_weight: 0.1925 0.1997 0.016 2.306 5.6 111.3 35.1 0 0.000 1_xyzrec: 0.1865 0.2389 0.015 1.619 5.6 111.3 35.1 0 0.253 1_adp: 0.1881 0.2471 0.015 1.619 10.6 107.1 36.5 0 0.253 1_regHadp: 0.1875 0.2472 0.015 1.619 10.6 107.1 36.5 0 0.253 2_bss: 0.1852 0.2441 0.015 1.619 12.1 108.6 37.9 0 0.253 2_settarget: 0.1852 0.2441 0.015 1.619 12.1 108.6 37.9 0 0.253 2_updatecdl: 0.1852 0.2441 0.015 1.649 12.1 108.6 37.9 0 0.253 2_weight: 0.1852 0.2441 0.015 1.649 12.1 108.6 37.9 0 0.253 2_xyzrec: 0.2189 0.2542 0.004 0.897 12.1 108.6 37.9 0 0.315 2_adp: 0.1975 0.2514 0.004 0.897 7.1 132.7 44.0 0 0.315 2_regHadp: 0.1958 0.2510 0.004 0.897 7.1 132.7 44.0 0 0.315 3_bss: 0.1944 0.2482 0.004 0.897 11.1 136.7 48.0 0 0.315 3_settarget: 0.1944 0.2482 0.004 0.897 11.1 136.7 48.0 0 0.315 3_updatecdl: 0.1944 0.2482 0.004 0.945 11.1 136.7 48.0 0 0.315 3_setrh: 0.1944 0.2482 0.004 0.945 11.1 136.7 48.0 0 0.315 3_weight: 0.1944 0.2482 0.004 0.945 11.1 136.7 48.0 0 0.315 3_xyzrec: 0.1943 0.2481 0.004 0.905 11.1 136.7 48.0 0 0.315 3_adp: 0.1973 0.2476 0.004 0.905 6.9 147.7 48.7 0 0.315 3_regHadp: 0.1980 0.2483 0.004 0.905 6.9 147.7 48.7 0 0.315 end: 0.1976 0.2485 0.004 0.905 8.2 149.0 50.0 0 0.315 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1xgo_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1xgo_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 6.9800 Refinement macro-cycles (run) : 207.9500 Write final files (write_after_run_outputs) : 21.2900 Total : 236.2200 Total CPU time: 4.50 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:31:45 PDT -0700 (1716251505.89 s) Start R-work = 0.1925, R-free = 0.1997 Final R-work = 0.1976, R-free = 0.2485 =============================================================================== Job complete usr+sys time: 289.89 seconds wall clock time: 14 minutes 42.04 seconds (882.04 seconds total)