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/1u87.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u87/1u87.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/1u87.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u87.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u87/1u87.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u87/1u87.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 None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3506 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3471 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.45, per 1000 atoms: 0.41 Number of scatterers: 3506 At special positions: 0 Unit cell: (123.05, 123.05, 72.51, 90, 90, 120) Space group: P 63 2 2 (No. 182) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 316 8.00 N 282 7.00 C 1138 6.00 H 1756 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: 2.01 Conformation dependent library (CDL) restraints added in 616.5 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 8 helices and 1 sheets defined 56.0% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.093A pdb=" N ARG A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.265A pdb=" N HIS A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 110 removed outlier: 3.880A pdb=" N ILE A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 139 removed outlier: 4.783A pdb=" N VAL A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Proline residue: A 127 - end of helix removed outlier: 3.990A pdb=" N MET A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 133 " --> pdb=" O MET A 129 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N HIS A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 removed outlier: 4.289A pdb=" N TYR A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.716A pdb=" N LYS A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.849A pdb=" N TYR A 33 " --> pdb=" O PHE A 7 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 213 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: 1.76 Time building geometry restraints manager: 1.67 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: 1751 1.15 - 1.33: 431 1.33 - 1.50: 638 1.50 - 1.68: 707 1.68 - 1.85: 23 Bond restraints: 3550 Sorted by residual: bond pdb=" N3 GSH A 500 " pdb=" HN3 GSH A 500 " ideal model delta sigma weight residual 0.860 1.020 -0.160 1.00e-02 1.00e+04 2.57e+02 bond pdb=" N2 GSH A 500 " pdb=" HN2 GSH A 500 " ideal model delta sigma weight residual 0.860 1.020 -0.160 1.10e-02 8.26e+03 2.12e+02 bond pdb=" CA2 GSH A 500 " pdb=" HA2 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.45e+02 bond pdb=" CB2 GSH A 500 " pdb="HB23 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.45e+02 bond pdb=" CA1 GSH A 500 " pdb=" HA1 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.44e+02 ... (remaining 3545 not shown) Histogram of bond angle deviations from ideal: 99.31 - 107.06: 254 107.06 - 114.81: 4243 114.81 - 122.56: 1410 122.56 - 130.32: 522 130.32 - 138.07: 15 Bond angle restraints: 6444 Sorted by residual: angle pdb=" N TYR A 164 " pdb=" CA TYR A 164 " pdb=" C TYR A 164 " ideal model delta sigma weight residual 114.31 102.34 11.97 1.29e+00 6.01e-01 8.61e+01 angle pdb="HN11 GSH A 500 " pdb=" N1 GSH A 500 " pdb="HN12 GSH A 500 " ideal model delta sigma weight residual 111.04 138.07 -27.03 3.00e+00 1.11e-01 8.12e+01 angle pdb=" N ASP A 62 " pdb=" CA ASP A 62 " pdb=" C ASP A 62 " ideal model delta sigma weight residual 114.04 103.69 10.35 1.24e+00 6.50e-01 6.97e+01 angle pdb=" CA2 GSH A 500 " pdb=" C2 GSH A 500 " pdb=" O2 GSH A 500 " ideal model delta sigma weight residual 120.61 109.21 11.40 1.39e+00 5.18e-01 6.72e+01 angle pdb=" N GLY A 61 " pdb=" CA GLY A 61 " pdb=" C GLY A 61 " ideal model delta sigma weight residual 115.47 104.89 10.58 1.31e+00 5.83e-01 6.53e+01 ... (remaining 6439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.48: 1414 13.48 - 26.97: 129 26.97 - 40.45: 71 40.45 - 53.94: 33 53.94 - 67.42: 25 Dihedral angle restraints: 1672 sinusoidal: 918 harmonic: 754 Sorted by residual: dihedral pdb=" CA ASP A 190 " pdb=" CB ASP A 190 " pdb=" CG ASP A 190 " pdb=" OD1 ASP A 190 " ideal model delta sinusoidal sigma weight residual -30.00 -89.11 59.11 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" N HIS A 150 " pdb=" C HIS A 150 " pdb=" CA HIS A 150 " pdb=" CB HIS A 150 " ideal model delta harmonic sigma weight residual 122.80 130.92 -8.12 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CB MET A 132 " pdb=" CG MET A 132 " pdb=" SD MET A 132 " pdb=" CE MET A 132 " ideal model delta sinusoidal sigma weight residual 180.00 120.60 59.40 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1669 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 1.084: 254 1.084 - 2.167: 0 2.167 - 3.250: 0 3.250 - 4.334: 0 4.334 - 5.417: 1 Chirality restraints: 255 Sorted by residual: chirality pdb=" CA1 GSH A 500 " pdb=" CB1 GSH A 500 " pdb=" C1 GSH A 500 " pdb=" N1 GSH A 500 " both_signs ideal model delta sigma weight residual False -2.66 2.76 -5.42 2.00e-01 2.50e+01 7.34e+02 chirality pdb=" CA HIS A 150 " pdb=" N HIS A 150 " pdb=" C HIS A 150 " pdb=" CB HIS A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA ILE A 186 " pdb=" N ILE A 186 " pdb=" C ILE A 186 " pdb=" CB ILE A 186 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 252 not shown) Planarity restraints: 502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 GSH A 500 " 0.313 2.00e-02 2.50e+03 2.24e-01 7.49e+02 pdb=" CA2 GSH A 500 " 0.101 2.00e-02 2.50e+03 pdb=" CA3 GSH A 500 " 0.137 2.00e-02 2.50e+03 pdb=" N3 GSH A 500 " 0.034 2.00e-02 2.50e+03 pdb=" O2 GSH A 500 " -0.303 2.00e-02 2.50e+03 pdb=" HN3 GSH A 500 " -0.283 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 156 " -0.131 2.00e-02 2.50e+03 5.15e-02 7.95e+01 pdb=" CG TYR A 156 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 156 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 156 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 156 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 156 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 156 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 156 " -0.089 2.00e-02 2.50e+03 pdb=" HD1 TYR A 156 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 TYR A 156 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR A 156 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 156 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 201 " 0.100 2.00e-02 2.50e+03 3.02e-02 3.64e+01 pdb=" CG TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 201 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP A 201 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 201 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 201 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 201 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 201 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP A 201 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 TRP A 201 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 201 " -0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 201 " 0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 201 " -0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP A 201 " 0.021 2.00e-02 2.50e+03 ... (remaining 499 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.87: 132 1.87 - 2.55: 3303 2.55 - 3.23: 10888 3.23 - 3.92: 14214 3.92 - 4.60: 22150 Nonbonded interactions: 50687 Sorted by model distance: nonbonded pdb="HG13 ILE A 109 " pdb=" H ALA A 110 " model vdw 1.183 2.270 nonbonded pdb="HH12 ARG A 103 " pdb="HE21 GLN A 204 " model vdw 1.249 2.100 nonbonded pdb=" HD2 PHE A 122 " pdb=" HE1 MET A 165 " model vdw 1.275 2.270 nonbonded pdb=" HA PHE A 7 " pdb="HD22 LEU A 55 " model vdw 1.279 2.440 nonbonded pdb=" HB3 GLU A 30 " pdb="HD11 LEU A 32 " model vdw 1.331 2.440 ... (remaining 50682 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 14 15.91 1 O 316 7.97 1 N 282 6.97 1 C 1138 5.97 1 H 1756 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: 1756 of 3506 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3506 n_use_u_iso = 3506 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 = 3506 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3506 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3506 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 15 through 24 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 38 through 47 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 68 through 79 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 86 through 110 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 115 through 139 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 150 through 165 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 174 through 185 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 187 through 193 } sheet { first_strand = chain 'A' and resid 29 through 33 sheet_id = " A" strand { selection = chain 'A' and resid 4 through 8 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 5 and name N bond_start_previous = chain 'A' and resid 29 and name O } strand { selection = chain 'A' and resid 57 through 59 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 59 and name N bond_start_previous = chain 'A' and resid 4 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1u87_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1756 occupancy sum: 1756.00 (% of total atoms 50.11) Rotatable: count: 466 occupancy sum: 466.00 (% of total atoms 13.30) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 29.97 A, n_refl.=4185 (all), 10.01 % free)-------------| | | | r_work= 0.3292 r_free= 0.3504 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 4.035015 | | target function (ml) not normalized (work): 15195.866676 | | target function (ml) not normalized (free): 1683.480726 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 29.97 - 5.04 0.97 1353 151 0.3689 0.3748 4.5706 4.5071| | 2: 5.04 - 4.01 0.96 1235 137 0.2801 0.3157 3.9206 3.9093| | 3: 4.00 - 3.50 0.92 1178 131 0.3184 0.3512 3.5398 3.5675| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 29.97 - 5.04 1353 151 0.58 43.57 0.90 0.05 1455.33| | 2: 5.04 - 4.01 1235 137 0.71 33.64 1.20 0.06 636.30| | 3: 4.00 - 3.50 1178 131 0.85 21.79 1.27 0.07 174.86| |alpha: min = 0.05 max = 0.07 mean = 0.06| |beta: min = 174.86 max = 1455.33 mean = 786.21| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.84 mean = 33.50| |phase err.(test): min = 0.00 max = 88.64 mean = 34.34| |-----------------------------------------------------------------------------| ----------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 : 0.011 0.121 1794 Z= 0.655 Angle : 1.713 19.034 2419 Z= 1.088 Chirality : 0.354 5.417 255 Planarity : 0.012 0.154 305 Dihedral : 17.263 67.421 697 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 38.80 Ramachandran Plot: Outliers : 8.70 % Allowed : 20.29 % Favored : 71.01 % Rotamer: Outliers : 9.57 % Allowed : 6.91 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: -6.40 (0.37), residues: 207 helix: -4.33 (0.27), residues: 104 sheet: None (None), residues: 0 loop : -4.22 (0.45), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 103 TYR 0.107 0.013 TYR A 156 PHE 0.039 0.010 PHE A 179 TRP 0.068 0.013 TRP A 201 HIS 0.001 0.001 HIS A 139 Individual atomic B min max mean iso aniso Overall: 15.03 98.11 43.96 1.66 1750 0 Protein: 15.03 98.11 43.87 1.66 1730 0 Other: 41.47 63.03 52.15 N/A 20 0 Chain A: 15.03 98.11 43.96 N/A 1750 0 Histogram: Values Number of atoms 15.03 - 23.34 283 23.34 - 31.65 247 31.65 - 39.95 311 39.95 - 48.26 195 48.26 - 56.57 287 56.57 - 64.88 141 64.88 - 73.19 115 73.19 - 81.49 109 81.49 - 89.80 54 89.80 - 98.11 8 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4185 (all), 10.01 % free)-------------| | | | r_work= 0.3292 r_free= 0.3504 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 4.035015 | | target function (ml) not normalized (work): 15195.866676 | | target function (ml) not normalized (free): 1683.480726 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3311 0.3292 0.3504 n_refl.: 4185 re-set all scales: r(all,work,free)=0.3311 0.3292 0.3504 n_refl.: 4185 remove outliers: r(all,work,free)=0.3322 0.3304 0.3504 n_refl.: 4182 overall B=13.94 to atoms: r(all,work,free)=0.3719 0.3690 0.3993 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.2220 0.2217 0.2255 n_refl.: 4182 remove outliers: r(all,work,free)=0.2220 0.2217 0.2255 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2919 1104.388 1001.047 1.273 0.998 0.352 12.881-10.207 97.06 88 11 0.2180 1533.577 1475.189 1.351 0.999 0.334 10.181-8.045 98.52 181 19 0.1853 1232.177 1220.067 1.249 0.998 0.325 8.023-6.324 96.77 350 40 0.2505 756.993 729.392 1.028 0.996 0.298 6.311-4.969 96.87 696 77 0.2091 690.006 669.251 0.952 0.990 0.241 4.967-3.908 95.56 1374 153 0.2087 652.071 626.849 1.012 0.981 0.158 3.907-3.500 91.76 983 109 0.2468 480.180 456.614 1.052 0.972 0.077 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.6244 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.833074 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.257357 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 0.1855 0.2416 0.0561 0.013 1.4 20.3 3.9 9.0 0 7.417 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.55 24.16 5.61 1.179 57.497 0.257 0.040 18.58 24.16 5.58 2.521 57.663 0.008 0.041 18.34 24.11 5.78 2.403 57.667 0.032 0.040 17.72 24.00 6.28 2.994 57.775 0.129 0.037 17.07 24.04 6.97 5.084 58.151 0.257 0.035 16.85 24.02 7.17 5.750 58.287 0.386 0.034 16.70 24.00 7.29 6.350 58.436 0.515 0.033 16.61 23.95 7.34 6.758 58.536 0.643 0.033 16.44 23.87 7.43 7.702 58.853 0.772 0.033 16.38 23.85 7.46 8.058 58.951 0.901 0.032 16.34 23.86 7.52 8.383 59.044 1.029 0.032 16.30 23.85 7.54 8.678 59.128 1.158 0.032 16.28 23.85 7.56 8.835 59.167 1.287 0.032 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.032 Accepted refinement result: 18.34 24.11 5.78 2.403 57.667 0.032 0.040 Individual atomic B min max mean iso aniso Overall: 29.83 111.83 58.24 1.89 1750 0 Protein: 29.83 111.83 58.19 1.88 1730 0 Other: 50.41 75.00 62.88 N/A 20 0 Chain A: 29.83 111.83 58.24 N/A 1750 0 Histogram: Values Number of atoms 29.83 - 38.03 236 38.03 - 46.23 274 46.23 - 54.43 342 54.43 - 62.63 242 62.63 - 70.83 242 70.83 - 79.03 142 79.03 - 87.23 120 87.23 - 95.43 97 95.43 - 103.63 48 103.63 - 111.83 7 =========================== Idealize ADP of riding H ========================== r_work=0.1834 r_free=0.2411 r_work=0.1829 r_free=0.2401 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1829 r_free= 0.2401 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ls_wunit_k1) (work): 0.039459 | | target function (ls_wunit_k1) not normalized (work): 148.482695 | | target function (ls_wunit_k1) not normalized (free): 29.123311 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1887 0.1829 0.2401 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3598 0.3542 0.4076 n_refl.: 4182 remove outliers: r(all,work,free)=0.3598 0.3542 0.4076 n_refl.: 4182 overall B=0.00 to atoms: r(all,work,free)=0.3598 0.3542 0.4076 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1868 0.1810 0.2385 n_refl.: 4182 remove outliers: r(all,work,free)=0.1868 0.1810 0.2385 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2282 686.445 650.597 1.251 1.014 0.354 12.881-10.207 97.06 88 11 0.1552 953.212 926.119 1.354 1.012 0.334 10.181-8.045 98.52 181 19 0.1366 765.874 767.805 1.268 1.008 0.327 8.023-6.324 96.77 350 40 0.1997 470.517 463.236 1.081 1.002 0.320 6.311-4.969 96.87 696 77 0.1777 428.881 419.989 0.974 0.988 0.240 4.967-3.908 95.56 1374 153 0.1691 405.302 397.023 1.029 0.967 0.150 3.907-3.500 91.76 983 109 0.2153 298.461 285.924 1.088 0.947 0.057 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.6524 ============================ 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 = 3.409934 wxc_scale = 0.104 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049039 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 0.2131 0.2433 0.0302 0.002 0.8 2.9 1.9 4.8 0 0.035 0.2045 0.2404 0.0358 0.003 0.8 5.1 1.9 5.9 0 0.106 0.1985 0.2403 0.0418 0.004 0.8 8.6 2.4 6.4 0 0.212 0.1928 0.2402 0.0474 0.005 0.9 9.1 2.9 6.4 0 0.318 0.1893 0.2391 0.0498 0.006 1.0 11.4 2.4 8.0 0 0.424 0.1876 0.2405 0.0529 0.007 1.1 12.0 2.4 8.5 0 0.529 0.1855 0.2400 0.0545 0.008 1.1 14.0 2.4 9.0 0 0.635 0.1831 0.2400 0.0569 0.009 1.2 15.4 2.9 9.6 0 0.741 0.1921 0.2400 0.0479 0.005 0.9 10.0 2.9 6.9 0 0.353 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2131 0.2433 0.0302 0.002 0.8 2.9 1.9 4.8 0 0.035 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.31 24.33 3.02 8.593 63.667 0.049 6.100 21.98 25.19 3.21 9.359 64.616 0.001 6.124 21.15 24.75 3.59 9.163 64.272 0.006 6.094 19.70 24.27 4.58 9.544 64.514 0.025 6.045 19.29 24.12 4.83 10.109 64.679 0.049 6.033 19.11 24.13 5.02 10.621 64.875 0.074 6.028 18.99 24.15 5.16 11.093 65.067 0.098 6.025 18.91 24.18 5.27 11.447 65.206 0.123 6.023 18.81 24.20 5.40 12.079 65.461 0.147 6.021 18.75 24.23 5.49 12.469 65.606 0.172 6.019 18.70 24.25 5.56 12.822 65.733 0.196 6.019 18.67 24.28 5.62 13.076 65.822 0.221 6.018 18.64 24.31 5.67 13.352 65.918 0.245 6.018 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.049 Accepted refinement result: 19.29 24.12 4.83 10.109 64.679 0.049 6.033 Individual atomic B min max mean iso aniso Overall: 25.63 129.32 60.27 7.40 1750 0 Protein: 25.63 129.32 60.27 7.40 1730 0 Other: 45.41 78.29 60.57 N/A 20 0 Chain A: 25.63 129.32 60.27 N/A 1750 0 Histogram: Values Number of atoms 25.63 - 35.99 155 35.99 - 46.36 329 46.36 - 56.73 371 56.73 - 67.10 316 67.10 - 77.47 192 77.47 - 87.84 183 87.84 - 98.21 129 98.21 - 108.58 61 108.58 - 118.95 12 118.95 - 129.32 2 =========================== Idealize ADP of riding H ========================== r_work=0.1929 r_free=0.2412 r_work=0.1910 r_free=0.2415 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1910 r_free= 0.2415 coordinate error (max.-lik. estimate): 0.39 A | | | | normalized target function (ml) (work): 6.028485 | | target function (ml) not normalized (work): 22685.188218 | | target function (ml) not normalized (free): 2591.004346 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1961 0.1910 0.2415 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3672 0.3617 0.4148 n_refl.: 4182 remove outliers: r(all,work,free)=0.3672 0.3617 0.4148 n_refl.: 4182 overall B=3.32 to atoms: r(all,work,free)=0.3784 0.3728 0.4262 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1937 0.1887 0.2384 n_refl.: 4182 remove outliers: r(all,work,free)=0.1937 0.1887 0.2384 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2531 686.445 640.647 1.161 1.077 0.356 12.881-10.207 97.06 88 11 0.1613 953.212 932.204 1.251 1.066 0.336 10.181-8.045 98.52 181 19 0.1582 765.874 761.654 1.169 1.052 0.327 8.023-6.324 96.77 350 40 0.2122 470.517 461.477 1.063 1.030 0.315 6.311-4.969 96.87 696 77 0.2010 428.881 415.460 0.968 0.992 0.243 4.967-3.908 95.56 1374 153 0.1701 405.302 391.939 1.053 0.930 0.163 3.907-3.500 91.76 983 109 0.2067 298.461 282.717 1.177 0.872 0.078 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0913 b_overall=5.8070 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1887 r_free=0.2384 After: r_work=0.1887 r_free=0.2383 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.787275 wxc_scale = 0.023 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.047422 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 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.009 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.026 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.052 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.078 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.104 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.130 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.156 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.182 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.086 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.009 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.026 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.052 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.078 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.104 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.130 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.156 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.182 0.1887 0.2383 0.0496 0.003 0.8 2.9 1.9 4.8 0 0.086 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.87 23.83 4.96 10.342 69.504 0.047 6.018 21.53 24.97 3.44 9.733 72.699 0.001 6.088 20.93 24.67 3.74 9.926 71.860 0.006 6.074 19.06 23.77 4.71 10.219 69.415 0.024 6.021 18.77 23.82 5.05 10.431 69.436 0.047 6.014 18.44 23.76 5.33 10.918 69.370 0.071 6.006 18.05 23.79 5.74 11.829 69.825 0.095 6.000 17.93 23.85 5.91 12.250 70.015 0.119 5.999 17.86 23.90 6.04 12.614 70.174 0.142 5.999 17.80 23.96 6.16 12.935 70.314 0.166 5.998 17.76 23.99 6.23 13.216 70.434 0.190 5.998 17.73 24.03 6.30 13.463 70.539 0.213 5.998 17.71 24.06 6.35 13.685 70.629 0.237 5.998 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.071 Accepted refinement result: 18.44 23.76 5.33 10.918 69.370 0.071 6.006 Individual atomic B min max mean iso aniso Overall: 24.73 136.57 63.32 8.59 1750 0 Protein: 24.73 136.57 63.32 8.58 1730 0 Other: 45.83 82.05 63.22 N/A 20 0 Chain A: 24.73 136.57 63.32 N/A 1750 0 Histogram: Values Number of atoms 24.73 - 35.92 101 35.92 - 47.10 308 47.10 - 58.29 412 58.29 - 69.47 340 69.47 - 80.65 218 80.65 - 91.84 165 91.84 - 103.02 128 103.02 - 114.20 63 114.20 - 125.39 13 125.39 - 136.57 2 =========================== Idealize ADP of riding H ========================== r_work=0.1844 r_free=0.2376 r_work=0.1838 r_free=0.2376 ----------X-ray data---------- |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1838 r_free= 0.2376 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ml) (work): 6.004622 | | target function (ml) not normalized (work): 22595.393051 | | target function (ml) not normalized (free): 2586.123046 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 29.97 - 5.04 0.97 1352 151 0.1941 0.2309 6.274 6.4079| | 2: 5.04 - 4.01 0.96 1235 137 0.1647 0.2295 5.949 6.1108| | 3: 4.00 - 3.50 0.92 1176 131 0.1904 0.2619 5.7534 5.9646| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 29.97 - 5.04 1352 151 0.83 21.25 1.00 1.01 44148.18| | 2: 5.04 - 4.01 1235 137 0.85 21.15 1.00 0.99 31309.64| | 3: 4.00 - 3.50 1176 131 0.83 23.95 1.01 0.96 21104.64| |alpha: min = 0.96 max = 1.01 mean = 0.99| |beta: min = 21104.64 max = 44148.18 mean = 32733.14| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.78 mean = 22.06| |phase err.(test): min = 0.00 max = 88.98 mean = 21.36| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1893 0.1838 0.2376 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3753 0.3696 0.4244 n_refl.: 4182 remove outliers: r(all,work,free)=0.3753 0.3696 0.4244 n_refl.: 4182 overall B=0.00 to atoms: r(all,work,free)=0.3753 0.3696 0.4244 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1901 0.1846 0.2394 n_refl.: 4182 remove outliers: r(all,work,free)=0.1901 0.1846 0.2394 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2526 686.445 641.774 1.221 1.030 0.355 12.881-10.207 97.06 88 11 0.1607 953.212 933.942 1.312 1.024 0.335 10.181-8.045 98.52 181 19 0.1583 765.874 762.927 1.220 1.017 0.327 8.023-6.324 96.77 350 40 0.2117 470.517 462.096 1.107 1.006 0.320 6.311-4.969 96.87 696 77 0.1980 428.881 415.517 0.985 0.984 0.250 4.967-3.908 95.56 1374 153 0.1656 405.302 391.991 1.033 0.951 0.160 3.907-3.500 91.76 983 109 0.1961 298.461 283.523 1.122 0.920 0.076 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.9307 ================= 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 : 0.3292 0.3504 0.011 1.713 15.0 98.1 44.0 0 0.000 1_bss: 0.2217 0.2255 0.011 1.713 29.0 112.0 57.9 0 0.000 1_settarget: 0.2217 0.2255 0.011 1.713 29.0 112.0 57.9 0 0.000 1_weight: 0.2217 0.2255 0.011 1.713 29.0 112.0 57.9 0 0.000 1_xyzrec: 0.1855 0.2416 0.013 1.423 29.0 112.0 57.9 0 0.283 1_adp: 0.1834 0.2411 0.013 1.423 29.8 111.8 58.2 0 0.283 1_regHadp: 0.1829 0.2401 0.013 1.423 29.8 111.8 58.2 0 0.283 2_bss: 0.1810 0.2385 0.013 1.423 29.8 111.8 58.2 0 0.283 2_settarget: 0.1810 0.2385 0.013 1.423 29.8 111.8 58.2 0 0.283 2_updatecdl: 0.1810 0.2385 0.013 1.444 29.8 111.8 58.2 0 0.283 2_weight: 0.1810 0.2385 0.013 1.444 29.8 111.8 58.2 0 0.283 2_xyzrec: 0.2131 0.2433 0.002 0.759 29.8 111.8 58.2 0 0.316 2_adp: 0.1929 0.2412 0.002 0.759 25.6 129.3 60.3 0 0.316 2_regHadp: 0.1910 0.2415 0.002 0.759 25.6 129.3 60.3 0 0.316 3_bss: 0.1887 0.2384 0.002 0.759 28.9 132.6 63.6 0 0.316 3_settarget: 0.1887 0.2384 0.002 0.759 28.9 132.6 63.6 0 0.316 3_updatecdl: 0.1887 0.2384 0.003 0.819 28.9 132.6 63.6 0 0.316 3_setrh: 0.1887 0.2383 0.003 0.819 28.9 132.6 63.6 0 0.316 3_weight: 0.1887 0.2383 0.003 0.819 28.9 132.6 63.6 0 0.316 3_xyzrec: 0.1887 0.2383 0.003 0.819 28.9 132.6 63.6 0 0.316 3_adp: 0.1844 0.2376 0.003 0.819 24.7 136.6 63.3 0 0.316 3_regHadp: 0.1838 0.2376 0.003 0.819 24.7 136.6 63.3 0 0.316 end: 0.1846 0.2394 0.003 0.819 24.7 136.6 63.3 0 0.316 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1u87_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1u87_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 5.1100 Refinement macro-cycles (run) : 150.6500 Write final files (write_after_run_outputs) : 16.4700 Total : 172.2300 Total CPU time: 3.34 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:28:54 PDT -0700 (1716251334.61 s) Start R-work = 0.2217, R-free = 0.2255 Final R-work = 0.1846, R-free = 0.2394 =============================================================================== Job complete usr+sys time: 213.58 seconds wall clock time: 11 minutes 53.03 seconds (713.03 seconds total)