Starting phenix.refine on Mon May 20 17:15:26 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+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { 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" 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" } 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 { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { 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: 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: 0.88, per 1000 atoms: 0.19 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: 1.09 Conformation dependent library (CDL) restraints added in 178.5 milliseconds 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. 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: 0.36 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: 1.07 Time building geometry restraints manager: 1.26 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 { 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 } ramachandran_plot_restraints { 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 ============================ Update phi&psi targets =========================== 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.1925 r_free=0.1997 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1925 r_free=0.1997 ========================= Local real-space refinement ========================= Before: r_work=0.1925 r_free=0.1997 153 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 87 time to evaluate : 0.185 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 42 residues processed: 66 average time/residue: 0.1754 time to fit residues: 14.4871 After: r_work=0.1995 r_free=0.2102 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.662908 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.515757 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 0.2427 0.2495 0.0068 0.004 0.9 17.2 0.7 17.7 0 0.125 0.2394 0.2490 0.0096 0.004 0.9 17.6 0.7 17.7 0 0.250 0.2301 0.2443 0.0142 0.004 0.9 18.2 0.7 18.9 0 0.500 0.2153 0.2287 0.0135 0.008 1.4 41.5 1.7 19.3 0 1.000 0.2099 0.2283 0.0184 0.009 1.4 43.2 1.7 19.8 0 2.000 0.2057 0.2283 0.0227 0.010 1.5 44.7 1.7 20.6 0 3.000 0.2012 0.2432 0.0420 0.009 1.2 38.4 1.0 23.9 0 4.000 0.1975 0.2408 0.0433 0.010 1.3 43.2 1.0 23.9 0 5.000 0.1967 0.2299 0.0332 0.013 1.6 49.2 1.7 20.2 0 6.000 0.1917 0.2417 0.0500 0.013 1.5 49.8 1.0 25.5 0 7.000 0.1895 0.2415 0.0520 0.014 1.6 52.6 1.0 26.7 0 8.000 0.1876 0.2400 0.0525 0.015 1.6 55.9 1.0 27.2 0 9.000 0.1860 0.2416 0.0556 0.016 1.7 58.7 1.0 28.0 0 10.000 0.1880 0.2409 0.0529 0.015 1.6 55.5 1.0 26.7 0 8.831 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2153 0.2287 0.0135 0.008 1.4 41.5 1.7 19.3 0 1.000 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2153 r_free=0.2287 138 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 91 time to evaluate : 0.357 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 6 residues processed: 47 average time/residue: 0.1511 time to fit residues: 10.8493 After: r_work=0.2310 r_free=0.2409 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.10 24.09 0.99 3.509 35.115 0.516 0.068 22.09 24.49 2.39 6.742 36.297 0.516 0.062 Individual atomic B min max mean iso aniso Overall: 6.48 117.90 37.55 6.43 2312 0 Protein: 6.48 117.90 37.55 6.43 2312 0 Chain A: 6.48 117.90 37.55 N/A 2312 0 Histogram: Values Number of atoms 6.48 - 17.62 229 17.62 - 28.76 620 28.76 - 39.90 610 39.90 - 51.05 380 51.05 - 62.19 231 62.19 - 73.33 132 73.33 - 84.47 67 84.47 - 95.62 28 95.62 - 106.76 11 106.76 - 117.90 4 =========================== Idealize ADP of riding H ========================== r_work=0.2209 r_free=0.2449 r_work=0.2185 r_free=0.2444 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.2185 r_free= 0.2444 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ls_wunit_k1) (work): 0.060698 | | target function (ls_wunit_k1) not normalized (work): 414.019201 | | target function (ls_wunit_k1) not normalized (free): 56.502174 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2212 0.2185 0.2444 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3354 0.3350 0.3390 n_refl.: 7570 remove outliers: r(all,work,free)=0.3354 0.3350 0.3390 n_refl.: 7570 overall B=3.58 to atoms: r(all,work,free)=0.3480 0.3477 0.3504 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.2178 0.2151 0.2414 n_refl.: 7570 remove outliers: r(all,work,free)=0.2178 0.2151 0.2414 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 0.2530 973.560 944.988 1.815 1.001 0.379 15.935-12.710 100.00 89 10 0.1567 1080.027 1069.958 1.368 1.000 0.271 12.669-10.064 99.01 182 19 0.1471 984.487 969.055 1.336 1.000 0.260 10.054-8.008 99.48 344 37 0.1645 828.381 814.561 1.267 1.000 0.257 7.993-6.350 96.06 662 70 0.2156 525.406 506.780 1.143 0.999 0.255 6.344-5.045 94.20 1288 142 0.2318 444.383 419.082 0.928 0.996 0.136 5.041-4.007 88.19 2360 262 0.2123 459.085 428.447 0.937 0.992 0.086 4.004-3.512 68.84 1807 197 0.2440 419.418 383.195 1.103 0.983 0.066 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.2668 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2151 r_free=0.2414 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 GLN Total number of N/Q/H flips: 1 r_work=0.2152 r_free=0.2414 ========================= Local real-space refinement ========================= Before: r_work=0.2152 r_free=0.2414 91 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.648 outliers start: 6 outliers final: 5 residues processed: 6 average time/residue: 0.5575 time to fit residues: 4.9735 After: r_work=0.2156 r_free=0.2413 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.213541 wxc_scale = 0.026 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.169909 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 0.2216 0.2410 0.0194 0.005 1.0 22.0 0.7 2.5 0 0.011 0.2198 0.2400 0.0202 0.005 1.0 23.5 0.7 2.5 0 0.033 0.2183 0.2396 0.0214 0.005 1.0 23.9 0.7 2.5 0 0.067 0.2163 0.2387 0.0224 0.005 1.1 25.2 0.7 2.5 0 0.100 0.2149 0.2389 0.0240 0.005 1.1 26.3 0.7 2.5 0 0.133 0.2133 0.2378 0.0246 0.006 1.1 25.6 0.7 2.5 0 0.167 0.2178 0.2446 0.0268 0.004 0.9 18.2 0.7 4.5 0 0.200 0.2107 0.2368 0.0261 0.006 1.1 27.1 0.7 2.9 0 0.234 0.2151 0.2379 0.0228 0.005 1.1 25.9 0.7 2.5 0 0.111 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2178 0.2446 0.0268 0.004 0.9 18.2 0.7 4.5 0 0.200 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2178 r_free=0.2446 96 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.070 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 11 average time/residue: 0.6186 time to fit residues: 9.6755 After: r_work=0.2196 r_free=0.2449 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.96 24.49 2.52 7.561 45.749 0.170 6.285 23.68 25.07 1.39 8.281 48.014 0.005 6.324 23.09 24.91 1.82 7.908 47.609 0.021 6.309 21.63 24.67 3.04 8.040 47.393 0.085 6.272 20.91 24.63 3.71 9.225 47.382 0.170 6.256 20.55 24.68 4.13 10.605 47.725 0.255 6.249 20.32 24.72 4.40 11.869 48.088 0.340 6.245 20.12 24.77 4.65 13.342 48.527 0.425 6.241 20.01 24.82 4.81 14.404 48.841 0.510 6.239 19.92 24.87 4.96 15.330 49.117 0.595 6.237 19.93 24.87 4.94 15.137 49.076 0.680 6.238 19.85 24.92 5.07 16.064 49.363 0.765 6.236 19.80 24.96 5.16 16.748 49.577 0.850 6.235 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.170 Accepted refinement result: 20.91 24.63 3.71 9.225 47.382 0.170 6.256 Individual atomic B min max mean iso aniso Overall: 7.57 125.57 44.46 10.11 2312 0 Protein: 7.57 125.57 44.46 10.11 2312 0 Chain A: 7.57 125.57 44.46 N/A 2312 0 Histogram: Values Number of atoms 7.57 - 19.37 145 19.37 - 31.17 490 31.17 - 42.97 605 42.97 - 54.77 479 54.77 - 66.57 260 66.57 - 78.37 182 78.37 - 90.17 82 90.17 - 101.97 48 101.97 - 113.77 17 113.77 - 125.57 4 =========================== Idealize ADP of riding H ========================== r_work=0.2091 r_free=0.2463 r_work=0.2077 r_free=0.2456 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.2077 r_free= 0.2456 coordinate error (max.-lik. estimate): 0.50 A | | | | normalized target function (ml) (work): 6.251366 | | target function (ml) not normalized (work): 42640.568536 | | target function (ml) not normalized (free): 4766.664858 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2115 0.2077 0.2456 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3523 0.3514 0.3603 n_refl.: 7570 remove outliers: r(all,work,free)=0.3523 0.3514 0.3603 n_refl.: 7570 overall B=3.60 to atoms: r(all,work,free)=0.3656 0.3648 0.3725 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.2102 0.2065 0.2433 n_refl.: 7570 remove outliers: r(all,work,free)=0.2102 0.2065 0.2433 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 0.2162 973.560 958.889 1.884 1.000 0.379 15.935-12.710 100.00 89 10 0.1242 1080.027 1075.058 1.487 0.999 0.309 12.669-10.064 99.01 182 19 0.1207 984.487 974.222 1.346 0.999 0.285 10.054-8.008 99.48 344 37 0.1445 828.381 816.522 1.271 0.999 0.280 7.993-6.350 96.06 662 70 0.1904 525.406 507.767 1.128 0.998 0.245 6.344-5.045 94.20 1288 142 0.2207 444.383 415.594 0.946 0.996 0.185 5.041-4.007 88.19 2360 262 0.2105 459.085 426.268 0.916 0.992 0.096 4.004-3.512 68.84 1807 197 0.2503 419.418 380.050 1.119 0.983 0.068 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.2987 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 586 Ramachandran restraints generated. 293 Oldfield, 0 Emsley, 293 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2065 r_free=0.2433 After: r_work=0.2065 r_free=0.2433 ================================== NQH flips ================================== r_work=0.2065 r_free=0.2433 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 r_work=0.2065 r_free=0.2433 ========================= Local real-space refinement ========================= Before: r_work=0.2065 r_free=0.2433 101 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 96 time to evaluate : 1.210 outliers start: 5 outliers final: 5 residues processed: 5 average time/residue: 0.9587 time to fit residues: 7.4077 After: r_work=0.2065 r_free=0.2433 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.839927 wxc_scale = 0.032 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.141784 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 0.2061 0.2429 0.0368 0.004 0.9 20.1 0.7 2.1 0 0.016 0.2060 0.2429 0.0368 0.004 0.9 20.1 0.7 2.1 0 0.047 0.2059 0.2428 0.0369 0.004 0.9 20.1 0.7 2.1 0 0.094 0.2059 0.2428 0.0370 0.004 0.9 20.1 0.7 2.1 0 0.142 0.2057 0.2428 0.0370 0.004 0.9 20.1 0.7 2.1 0 0.189 0.2056 0.2427 0.0371 0.004 0.9 20.1 0.7 2.1 0 0.236 0.2055 0.2427 0.0372 0.004 0.9 20.1 0.7 2.1 0 0.283 0.2053 0.2428 0.0375 0.004 0.9 19.9 0.7 2.1 0 0.330 0.2058 0.2428 0.0370 0.004 0.9 20.1 0.7 2.1 0 0.157 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2053 0.2428 0.0375 0.004 0.9 19.9 0.7 2.1 0 0.330 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2053 r_free=0.2428 100 residues out of total 243 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 1.008 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 5 average time/residue: 0.4019 time to fit residues: 3.8624 After: r_work=0.2053 r_free=0.2428 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.53 24.28 3.75 10.084 53.795 0.142 6.237 23.36 24.96 1.61 10.073 57.373 0.004 6.294 22.94 24.86 1.92 9.991 56.915 0.018 6.287 21.24 24.44 3.20 9.534 54.684 0.071 6.254 20.34 24.35 4.01 9.937 54.785 0.142 6.232 19.87 24.39 4.52 11.162 54.976 0.213 6.223 19.66 24.45 4.79 12.084 55.137 0.284 6.219 19.53 24.51 4.98 12.856 55.367 0.354 6.217 19.44 24.56 5.12 13.563 55.611 0.425 6.215 19.38 24.59 5.21 14.172 55.832 0.496 6.214 19.33 24.61 5.28 14.711 56.029 0.567 6.213 19.30 24.64 5.35 15.199 56.213 0.638 6.213 19.27 24.67 5.40 15.627 56.373 0.709 6.212 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.142 Accepted refinement result: 20.34 24.35 4.01 9.937 54.785 0.142 6.232 Individual atomic B min max mean iso aniso Overall: 10.24 143.80 50.08 10.77 2312 0 Protein: 10.24 143.80 50.08 10.77 2312 0 Chain A: 10.24 143.80 50.08 N/A 2312 0 Histogram: Values Number of atoms 10.24 - 23.59 133 23.59 - 36.95 537 36.95 - 50.31 668 50.31 - 63.66 469 63.66 - 77.02 254 77.02 - 90.37 141 90.37 - 103.73 65 103.73 - 117.09 35 117.09 - 130.44 7 130.44 - 143.80 3 =========================== Idealize ADP of riding H ========================== r_work=0.2034 r_free=0.2435 r_work=0.2031 r_free=0.2435 ----------X-ray data---------- |--(resolution: 3.51 - 47.03 A, n_refl.=7570 (all), 9.89 % free)-------------| | | | r_work= 0.2031 r_free= 0.2435 coordinate error (max.-lik. estimate): 0.48 A | | | | normalized target function (ml) (work): 6.231821 | | target function (ml) not normalized (work): 42507.247718 | | target function (ml) not normalized (free): 4757.594060 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1601 0.1878 6.334 6.4718| | 2: 6.00 - 4.77 0.93 1498 166 0.2112 0.2382 6.1836 6.2509| | 3: 4.77 - 4.16 0.89 1443 156 0.2052 0.2527 6.184 6.3779| | 4: 4.16 - 3.78 0.76 1216 130 0.2381 0.3120 6.1972 6.3511| | 5: 3.78 - 3.51 0.66 1046 120 0.2558 0.2969 6.2491 6.2821| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 16.07 1.00 1.11 50778.04| | 2: 6.00 - 4.77 1498 166 0.86 22.37 0.99 1.09 52408.65| | 3: 4.77 - 4.16 1443 156 0.87 21.78 0.99 1.04 55824.85| | 4: 4.16 - 3.78 1216 130 0.83 26.29 1.01 1.00 61294.03| | 5: 3.78 - 3.51 1046 120 0.81 27.56 1.03 0.97 64117.27| |alpha: min = 0.97 max = 1.11 mean = 1.05| |beta: min = 50778.04 max = 64117.27 mean = 56124.10| |figures of merit: min = 0.02 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 88.21 mean = 22.25| |phase err.(test): min = 0.00 max = 82.26 mean = 22.62| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2071 0.2031 0.2435 n_refl.: 7570 re-set all scales: r(all,work,free)=0.3703 0.3694 0.3780 n_refl.: 7570 remove outliers: r(all,work,free)=0.3703 0.3694 0.3780 n_refl.: 7570 overall B=1.23 to atoms: r(all,work,free)=0.3750 0.3742 0.3824 n_refl.: 7570 bulk-solvent and scaling: r(all,work,free)=0.2067 0.2026 0.2437 n_refl.: 7570 remove outliers: r(all,work,free)=0.2067 0.2026 0.2437 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 0.2066 861.286 839.832 1.856 0.997 0.380 15.935-12.710 100.00 89 10 0.1167 955.476 946.566 1.501 0.997 0.320 12.669-10.064 98.05 182 19 0.1149 870.954 869.934 1.337 0.998 0.284 10.054-8.008 99.48 344 37 0.1370 732.850 720.828 1.254 0.998 0.279 7.993-6.350 95.81 662 70 0.1757 464.815 448.971 1.156 0.998 0.278 6.344-5.045 94.08 1288 142 0.2150 393.135 369.597 0.953 0.997 0.198 5.041-4.007 88.08 2360 262 0.2102 406.142 378.451 0.918 0.996 0.108 4.004-3.512 68.80 1807 197 0.2505 371.050 333.464 1.127 0.990 0.078 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.5495 ================= 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_updatephipsi: 0.1925 0.1997 0.016 2.306 5.6 111.3 35.1 0 0.000 1_nqh: 0.1925 0.1997 0.016 2.306 5.6 111.3 35.1 0 0.000 1_realsrl: 0.1995 0.2102 0.017 2.315 5.6 111.3 35.1 0 0.053 1_weight: 0.1995 0.2102 0.017 2.315 5.6 111.3 35.1 0 0.053 1_xyzrec: 0.2153 0.2287 0.008 1.397 5.6 111.3 35.1 0 0.200 1_realsrl2: 0.2310 0.2409 0.008 1.397 5.6 111.3 35.1 0 0.260 1_adp: 0.2209 0.2449 0.008 1.397 6.5 117.9 37.5 0 0.260 1_regHadp: 0.2185 0.2444 0.008 1.397 6.5 117.9 37.5 0 0.260 2_bss: 0.2151 0.2414 0.008 1.397 10.1 121.5 41.1 0 0.260 2_settarget: 0.2151 0.2414 0.008 1.397 10.1 121.5 41.1 0 0.260 2_updatephipsi: 0.2151 0.2414 0.008 1.397 10.1 121.5 41.1 0 0.260 2_updatecdl: 0.2151 0.2414 0.008 1.422 10.1 121.5 41.1 0 0.260 2_nqh: 0.2152 0.2414 0.008 1.422 10.1 121.5 41.1 0 0.261 2_realsrl: 0.2156 0.2413 0.008 1.422 10.1 121.5 41.1 0 0.263 2_weight: 0.2156 0.2413 0.008 1.422 10.1 121.5 41.1 0 0.263 2_xyzrec: 0.2178 0.2446 0.004 0.869 10.1 121.5 41.1 0 0.385 2_realsrl2: 0.2196 0.2449 0.004 0.869 10.1 121.5 41.1 0 0.388 2_adp: 0.2091 0.2463 0.004 0.869 7.6 125.6 44.5 0 0.388 2_regHadp: 0.2077 0.2456 0.004 0.869 7.6 125.6 44.5 0 0.388 3_bss: 0.2065 0.2433 0.004 0.869 11.2 129.2 48.1 0 0.388 3_settarget: 0.2065 0.2433 0.004 0.869 11.2 129.2 48.1 0 0.388 3_updatephipsi: 0.2065 0.2433 0.004 0.869 11.2 129.2 48.1 0 0.388 3_updatecdl: 0.2065 0.2433 0.004 0.899 11.2 129.2 48.1 0 0.388 3_setrh: 0.2065 0.2433 0.004 0.899 11.2 129.2 48.1 0 0.388 3_nqh: 0.2065 0.2433 0.004 0.899 11.2 129.2 48.1 0 0.388 3_realsrl: 0.2065 0.2433 0.004 0.899 11.2 129.2 48.1 0 0.388 3_weight: 0.2065 0.2433 0.004 0.899 11.2 129.2 48.1 0 0.388 3_xyzrec: 0.2053 0.2428 0.004 0.879 11.2 129.2 48.1 0 0.388 3_realsrl2: 0.2053 0.2428 0.004 0.879 11.2 129.2 48.1 0 0.388 3_adp: 0.2034 0.2435 0.004 0.879 10.2 143.8 50.1 0 0.388 3_regHadp: 0.2031 0.2435 0.004 0.879 10.2 143.8 50.1 0 0.388 end: 0.2026 0.2437 0.004 0.879 11.5 145.0 51.3 0 0.388 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1xgo_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1xgo_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7300 Refinement macro-cycles (run) : 278.7800 Write final files (write_after_run_outputs) : 22.3500 Total : 304.8600 Total CPU time: 5.41 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:30:31 PDT -0700 (1716251431.68 s) Start R-work = 0.1925, R-free = 0.1997 Final R-work = 0.2026, R-free = 0.2437 =============================================================================== Job complete usr+sys time: 346.26 seconds wall clock time: 15 minutes 45.09 seconds (945.09 seconds total)