Monomer Library directory: "/net/chevy/raid1/afonine/sources/chem_data/mon_lib" Total number of atoms: 3380 Number of models: 1 Model: "" Number of chains: 2 Chain: "L" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1700 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 207, 'PCIS': 3} Chain: "H" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1680 Classifications: {'peptide': 220} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 197, 'PCIS': 2} Chain breaks: 8 Time building chain proxies: 1.99, per 1000 atoms: 0.59 Number of scatterers: 3380 At special positions: 0 Unit cell: (72.24, 72.01, 86.99, 90, 90, 90) Space group: P 21 21 21 (No. 19) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 679 8.00 N 561 7.00 C 2126 6.00 sf(0) = scattering factor at diffraction angle 0. ================================== X-ray data ================================= F-obs: AutoBuild_run_1_/TEMP0/aniso_refinement_data_PHX.mtz:FP,SIGFP Miller array info: AutoBuild_run_1_/TEMP0/aniso_refinement_data_PHX.mtz:FP,SIGFP Observation type: xray.amplitude Type of data: double, size=27466 Type of sigmas: double, size=27466 Number of Miller indices: 27466 Anomalous flag: False Unit cell: (72.24, 72.01, 86.99, 90, 90, 90) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 2631 Resolution range: 43.9962 1.95007 Completeness in resolution range: 0.814049 Completeness with d_max=infinity: 0.813976 Wavelength: 1.0000 Number of F-obs in resolution range: 27465 Number of F-obs<0 (these reflections will be rejected): 0 Number of F-obs=0 (these reflections will be used in refinement): 0 Refinement resolution range: d_max = 43.9962 d_min = 1.9501 Fobs statistics after all cutoffs applied: Miller array info: None Observation type: xray.amplitude Type of data: double, size=27465 Type of sigmas: double, size=27465 Number of Miller indices: 27465 Anomalous flag: False Unit cell: (72.24, 72.01, 86.99, 90, 90, 90) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 2631 Resolution range: 43.9962 1.95013 Completeness in resolution range: 0.814091 Completeness with d_max=infinity: 0.814019 R-free flags: AutoBuild_run_1_/TEMP0/aniso_refinement_data_PHX.mtz:FreeR_flag Miller array info: AutoBuild_run_1_/TEMP0/aniso_refinement_data_PHX.mtz:FreeR_flag Observation type: None Type of data: int, size=28288 Type of sigmas: None Number of Miller indices: 28288 Anomalous flag: False Unit cell: (72.24, 72.01, 86.99, 90, 90, 90) Space group: P 21 21 21 (No. 19) Systematic absences: 0 Centric reflections: 2804 Resolution range: 43.9962 1.95007 Completeness in resolution range: 0.838411 Completeness with d_max=infinity: 0.838337 Wavelength: 1.0000 Test (R-free flags) flag value: 0 Number of work/free reflections by resolution: work free %free bin 1: 44.0074 - 4.2003 [3521/3575] 3180 341 9.7% bin 2: 4.2003 - 3.3343 [3340/3419] 3015 325 9.7% bin 3: 3.3343 - 2.9129 [3268/3381] 2949 319 9.8% bin 4: 2.9129 - 2.6466 [3225/3376] 2923 302 9.4% bin 5: 2.6466 - 2.4569 [3148/3355] 2809 339 10.8% bin 6: 2.4569 - 2.3121 [3075/3335] 2767 308 10.0% bin 7: 2.3121 - 2.1963 [3011/3344] 2716 295 9.8% bin 8: 2.1963 - 2.1007 [2194/3331] 1963 231 10.5% bin 9: 2.1007 - 2.0198 [1549/3308] 1393 156 10.1% bin 10: 2.0198 - 1.9501 [1134/3313] 1029 105 9.3% overall 24744 2721 9.9% ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 4 Type Number sf(0) Gaussians S 14 15.96 2 O 679 7.97 2 N 561 6.97 2 C 2126 5.97 2 sf(0) = scattering factor at diffraction angle 0. ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ======================== Summary of geometry restraints ======================= Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.02 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS L 219 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 220 " distance=2.03 Time building geometry restraints manager: 0.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 1176 1.39 - 1.55: 2235 1.55 - 1.71: 27 1.71 - 1.87: 18 1.87 - 2.04: 5 Bond restraints: 3461 Sorted by residual: bond pdb=" N GLY H 1 " pdb=" CA GLY H 1 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.74e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.00e+00 bond pdb=" CB ARG L 113 " pdb=" CG ARG L 113 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.86e+00 bond pdb=" SD MET L 180 " pdb=" CE MET L 180 " ideal model delta sigma weight residual 1.791 1.763 0.028 2.50e-02 1.60e+03 1.23e+00 bond pdb=" CG PRO H 163 " pdb=" CD PRO H 163 " ideal model delta sigma weight residual 1.503 1.541 -0.038 3.40e-02 8.65e+02 1.23e+00 ... (remaining 3456 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 4390 2.44 - 4.87: 248 4.87 - 7.31: 54 7.31 - 9.74: 19 9.74 - 12.18: 2 Bond angle restraints: 4713 Sorted by residual: angle pdb=" N ILE H 52 " pdb=" CA ILE H 52 " pdb=" C ILE H 52 " ideal model delta sigma weight residual 111.20 99.02 12.18 2.80e+00 1.28e-01 1.89e+01 angle pdb=" N THR L 119 " pdb=" CA THR L 119 " pdb=" C THR L 119 " ideal model delta sigma weight residual 111.20 101.45 9.75 2.80e+00 1.28e-01 1.21e+01 angle pdb=" N SER H 125 " pdb=" CA SER H 125 " pdb=" C SER H 125 " ideal model delta sigma weight residual 111.20 101.49 9.71 2.80e+00 1.28e-01 1.20e+01 angle pdb=" N ILE L 80 " pdb=" CA ILE L 80 " pdb=" C ILE L 80 " ideal model delta sigma weight residual 111.20 101.91 9.29 2.80e+00 1.28e-01 1.10e+01 angle pdb=" CA CYS H 96 " pdb=" CB CYS H 96 " pdb=" SG CYS H 96 " ideal model delta sigma weight residual 114.40 122.03 -7.63 2.30e+00 1.89e-01 1.10e+01 ... (remaining 4708 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 1115 17.39 - 34.77: 83 34.77 - 52.16: 17 52.16 - 69.55: 19 69.55 - 86.93: 3 Dihedral angle restraints: 1237 sinusoidal: 787 harmonic: 450 Sorted by residual: dihedral pdb=" CA ARG L 113 " pdb=" CB ARG L 113 " pdb=" CG ARG L 113 " pdb=" CD ARG L 113 " ideal model delta sinusoidal sigma weight residual 60.00 -123.00 -57.00 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" N ARG H 212 " pdb=" CA ARG H 212 " pdb=" CB ARG H 212 " pdb=" CG ARG H 212 " ideal model delta sinusoidal sigma weight residual 60.00 -114.14 54.14 3 1.50e+01 4.44e-03 9.26e+00 dihedral pdb=" N VAL H 222 " pdb=" CA VAL H 222 " pdb=" CB VAL H 222 " pdb=" CG2 VAL H 222 " ideal model delta sinusoidal sigma weight residual 180.00 133.90 46.10 3 1.50e+01 4.44e-03 8.28e+00 ... (remaining 1234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 244 0.059 - 0.117: 191 0.117 - 0.175: 76 0.175 - 0.233: 17 0.233 - 0.291: 11 Chirality restraints: 539 Sorted by residual: chirality pdb=" CA THR L 119 " pdb=" N THR L 119 " pdb=" C THR L 119 " pdb=" CB THR L 119 " both_signs ideal model delta sigma weight residual False 2.52 2.81 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA CYS L 93 " pdb=" N CYS L 93 " pdb=" C CYS L 93 " pdb=" CB CYS L 93 " both_signs ideal model delta sigma weight residual False 2.50 2.79 -0.29 2.00e-01 2.50e+01 2.08e+00 chirality pdb=" CA ASN H 61 " pdb=" N ASN H 61 " pdb=" C ASN H 61 " pdb=" CB ASN H 61 " both_signs ideal model delta sigma weight residual False 2.47 2.74 -0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 536 not shown) Planarity restraints: 593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 35 " 0.078 2.00e-02 2.50e+03 3.54e-02 3.14e+01 pdb=" CG TRP H 35 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP H 35 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP H 35 " -0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP H 35 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP H 35 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 35 " -0.036 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 35 " 0.032 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 35 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 35 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 104 " 0.076 2.00e-02 2.50e+03 3.48e-02 3.03e+01 pdb=" CG TRP H 104 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP H 104 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP H 104 " -0.029 2.00e-02 2.50e+03 pdb=" NE1 TRP H 104 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP H 104 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP H 104 " -0.035 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 104 " 0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 104 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP H 104 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 145 " 0.066 2.00e-02 2.50e+03 3.36e-02 2.26e+01 pdb=" CG TYR L 145 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR L 145 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR L 145 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR L 145 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR L 145 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR L 145 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR L 145 " 0.041 2.00e-02 2.50e+03 ... (remaining 590 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 8 2.04 - 2.76: 457 2.76 - 3.47: 4651 3.47 - 4.19: 8963 4.19 - 4.90: 14883 Nonbonded interactions: 28962 Sorted by model distance: nonbonded pdb=" C VAL H 166 " pdb=" N THR H 168 " model vdw 1.327 3.350 nonbonded pdb=" C ILE H 235 " pdb=" N VAL H 238 " model vdw 1.328 3.350 nonbonded pdb=" C GLY H 181 " pdb=" N VAL H 183 " model vdw 1.328 3.350 nonbonded pdb=" C SER H 192 " pdb=" N ASP H 195 " model vdw 1.329 3.350 nonbonded pdb=" C TRP H 169 " pdb=" N ASN H 174 " model vdw 1.330 3.350 ... (remaining 28957 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* ====================== Modifying start model if requested ===================== ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = False (0 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = False (iso = 0 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 atoms) group_anomalous = False n_use = 3380 n_use_u_iso = 3380 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 = 3380 ==================== Process input NCS or/and find new NCS ==================== Using existing and finding new NCS is disabled. Use refinement.main.ncs=true to activate it. Look at refinement.ncs for more NCS related parameters. =================== Write initial parameters into .eff file =================== Writing effective parameters to file: /net/chevy/raid1/afonine/work/crom/final/fig_17_results_1F8T/autobuild/AutoBuild_run_1_/TEMP0/refine_001.eff ============================ 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 { input { pdb { file_name = "/net/chevy/raid1/afonine/work/crom/final/fig_17_results_1F8T/autobuild/AutoBuild_run_1_/TEMP0/EDITED_unrefined.pdb_1" } xray_data { file_name = "AutoBuild_run_1_/TEMP0/aniso_refinement_data_PHX.mtz" labels = "FP,SIGFP" high_resolution = 1.9501 low_resolution = 500 r_free_flags { file_name = "AutoBuild_run_1_/TEMP0/aniso_refinement_data_PHX.mtz" label = "FreeR_flag" test_flag_value = 0 } } } output { prefix = "AutoBuild_run_1_/TEMP0/refine" serial = 1 write_geo_file = False export_final_f_model = True } electron_density_maps { apply_default_maps = True map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True isotropize = False } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" isotropize = False } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" isotropize = False } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" isotropize = False } 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 } main { number_of_macro_cycles = 1 use_experimental_phases = False random_seed = 405897 } hydrogens { refine = individual *riding Auto } pdb_interpretation { clash_guard { nonbonded_distance_threshold = None } } mask { ignore_zero_occupancy_atoms = False } } #phil __OFF__ =============================== refinement start ============================== ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 1.95 - 44.00 A, n_refl.=27465 (all), 9.91 % free)------------| | | | r_work= 0.3658 r_free= 0.3906 coordinate error (max.-lik. estimate): 0.08 A | | | | x-ray target function (ml) for work reflections: 3.800852 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 44.0074 - 5.2010 0.99 1704 192 0.4337 0.4260 4.7639 4.7823| | 2: 5.2010 - 4.1292 0.98 1636 179 0.2528 0.2877 4.5719 4.6069| | 3: 4.1292 - 3.6075 0.98 1599 150 0.3210 0.3207 4.2818 4.2478| | 4: 3.6075 - 3.2778 0.98 1593 170 0.3596 0.3815 4.1479 4.2339| | 5: 3.2778 - 3.0429 0.96 1552 156 0.3649 0.3749 3.9935 3.9814| | 6: 3.0429 - 2.8635 0.96 1532 193 0.3744 0.4155 3.8804 4.0177| | 7: 2.8635 - 2.7202 0.95 1542 158 0.3853 0.4020 3.766 3.8965| | 8: 2.7202 - 2.6018 0.95 1524 157 0.3734 0.4090 3.6561 3.7376| | 9: 2.6018 - 2.5016 0.94 1464 179 0.3688 0.4178 3.588 3.7122| | 10: 2.5016 - 2.4153 0.94 1471 166 0.3696 0.4059 3.5175 3.6334| | 11: 2.4153 - 2.3398 0.92 1466 166 0.3847 0.4210 3.4675 3.5818| | 12: 2.3398 - 2.2729 0.92 1441 162 0.3869 0.4270 3.431 3.5335| | 13: 2.2729 - 2.2131 0.90 1412 167 0.4114 0.4597 3.402 3.5067| | 14: 2.2131 - 2.1591 0.78 1235 127 0.4285 0.4337 3.4231 3.5354| | 15: 2.1591 - 2.1100 0.62 987 118 0.4318 0.4508 3.4191 3.4126| | 16: 2.1100 - 2.0651 0.53 811 98 0.4276 0.4603 3.3807 3.3682| | 17: 2.0651 - 2.0238 0.43 682 74 0.4478 0.4769 3.3615 3.2669| | 18: 2.0238 - 1.9856 0.39 609 60 0.4568 0.4462 3.3145 3.3046| | 19: 1.9856 - 1.9501 0.31 484 49 0.4585 0.4798 3.2269 3.2764| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 44.0074 - 5.2010 1704 192 0.56 45.74 0.59 0.06 2652.43| | 2: 5.2010 - 4.1292 1636 179 0.79 27.13 1.20 0.12 1506.31| | 3: 4.1292 - 3.6075 1599 150 0.85 22.12 1.37 0.15 820.58| | 4: 3.6075 - 3.2778 1593 170 0.84 22.51 1.45 0.16 616.84| | 5: 3.2778 - 3.0429 1552 156 0.83 24.20 1.45 0.17 494.99| | 6: 3.0429 - 2.8635 1532 193 0.80 26.49 1.44 0.17 424.70| | 7: 2.8635 - 2.7202 1542 158 0.76 30.25 1.45 0.17 392.06| | 8: 2.7202 - 2.6018 1524 157 0.77 30.11 1.44 0.16 339.71| | 9: 2.6018 - 2.5016 1464 179 0.76 30.31 1.41 0.16 292.60| | 10: 2.5016 - 2.4153 1471 166 0.77 30.17 1.42 0.16 244.33| | 11: 2.4153 - 2.3398 1466 166 0.77 29.75 1.48 0.16 224.71| | 12: 2.3398 - 2.2729 1441 162 0.77 29.66 1.49 0.16 206.64| | 13: 2.2729 - 2.2131 1412 167 0.78 29.15 1.55 0.16 190.81| | 14: 2.2131 - 2.1591 1235 127 0.77 29.90 1.58 0.17 180.49| | 15: 2.1591 - 2.1100 987 118 0.76 31.43 1.53 0.17 173.03| | 16: 2.1100 - 2.0651 811 98 0.77 30.64 1.54 0.18 163.76| | 17: 2.0651 - 2.0238 682 74 0.77 30.34 1.57 0.18 146.65| | 18: 2.0238 - 1.9856 609 60 0.78 29.79 1.61 0.18 131.76| | 19: 1.9856 - 1.9501 484 49 0.76 31.49 1.63 0.17 121.79| |alpha: min = 0.06 max = 0.18 mean = 0.15| |beta: min = 121.79 max = 2652.43 mean = 576.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.77| |phase err.(work): min = 0.00 max = 89.96 mean = 29.40| |phase err.(test): min = 0.00 max = 89.91 mean = 28.87| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Restraints library geostd + mon.lib. deviations from ideal values. rmsd max count bond : 0.005 0.041 3461 angle : 1.352 12.175 4713 chirality : 0.092 0.291 539 planarity : 0.007 0.051 593 dihedral : 12.904 86.934 1237 min nonbonded distance : 1.327 Molprobity statistics. all-atom clashscore : 7.96 ramachandran plot: outliers : 0.72 % allowed : 3.58 % favored : 95.70 % rotamer outliers : 2.82 % cbeta deviations : 0 |-ADP statistics (Wilson B = 19.500)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 3380 0 7.48 100.80 27.46 None None None | | all(noH): 3380 0 7.48 100.80 27.46 None None None | | Sol. : 0 0 None None None None None None | | Mac. : 3380 0 7.48 100.80 27.46 None None None | | Hyd. : 0 0 None None None None None None | | - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - | | Distribution of isotropic (or equivalent) ADP for non-H atoms: | | Bin# value range #atoms | Bin# value range #atoms | | 0: 7.480 - 16.812: 440 | 5: 54.140 - 63.472: 56 | | 1: 16.812 - 26.144: 1655 | 6: 63.472 - 72.804: 33 | | 2: 26.144 - 35.476: 715 | 7: 72.804 - 82.136: 10 | | 3: 35.476 - 44.808: 259 | 8: 82.136 - 91.468: 22 | | 4: 44.808 - 54.140: 150 | 9: 91.468 - 100.800: 40 | | =>continue=> | |-----------------------------------------------------------------------------| |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 1 OF 1 ************************* |--(resolution: 1.95 - 44.00 A, n_refl.=27465 (all), 9.91 % free)------------| | | | r_work= 0.3658 r_free= 0.3906 coordinate error (max.-lik. estimate): 0.08 A | | | | x-ray target function (ml) for work reflections: 3.800852 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r_work=0.3658 r_free=0.3906 n_reflections: 27465 start: r_work=0.3658 r_free=0.3906 (reset all scales to undefined) bulk-solvent and scaling: r_work=0.2139 r_free=0.2357 remove outliers: r_work=0.2139 r_free=0.2357 correct solvent mask: r_work=0.2128 r_free=0.2347 final: r_work=0.2128 r_free=0.2347 n_reflections: 27463 overall anisotropic scale matrix: V0: 0.2477,0.0998,-0.2921,-0.1994,-0.1491,-0.1078 V1: -0.0067,0.0012,0.0026,0.0089,0.0067,-0.0044 ======================== 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 43.996-14.237 96.15 88 12 0.1468 95.259 93.202 0.147 1.012 0.288 14.224-11.370 98.06 94 7 0.1328 85.201 84.501 0.156 1.013 0.305 11.321-9.092 98.90 156 23 0.1218 86.634 86.508 0.153 1.013 0.310 9.082-7.268 97.97 305 33 0.1615 62.151 61.031 0.144 1.012 0.310 7.264-5.810 98.96 601 63 0.1668 56.565 55.142 0.142 1.010 0.310 5.806-4.642 98.67 1134 127 0.1456 75.390 74.337 0.152 1.008 0.310 4.642-3.711 97.88 2198 203 0.1590 73.503 72.360 0.163 1.004 0.266 3.710-2.966 97.16 4129 462 0.2126 52.426 51.228 0.176 0.998 0.077 2.966-2.371 94.27 7737 874 0.2506 30.791 29.392 0.178 0.989 0.000 2.371-1.950 62.52 8300 917 0.2679 22.947 21.528 0.193 0.975 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.1519 b_overall=-4.1719 ============================ Set refinement target ============================ using refinement target ml ----------X-ray data---------- |--(resolution: 1.95 - 44.00 A, n_refl.=27463 (all), 9.91 % free)------------| | | | r_work= 0.2128 r_free= 0.2347 coordinate error (max.-lik. estimate): 0.23 A | | | | x-ray target function (ml) for work reflections: 3.689970 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 44.0074 - 5.2010 0.98 1702 192 0.1516 0.1476 3.9158 3.9426| | 2: 5.2010 - 4.1292 0.98 1636 179 0.1467 0.1644 4.0779 4.156| | 3: 4.1292 - 3.6075 0.98 1599 150 0.1693 0.1941 4.0567 4.1302| | 4: 3.6075 - 3.2778 0.98 1593 170 0.2070 0.2221 4.0688 4.1766| | 5: 3.2778 - 3.0429 0.96 1552 156 0.2220 0.2070 3.962 3.9642| | 6: 3.0429 - 2.8635 0.96 1532 193 0.2496 0.3035 3.8812 4.0189| | 7: 2.8635 - 2.7202 0.95 1542 158 0.2603 0.2785 3.7667 3.8996| | 8: 2.7202 - 2.6018 0.95 1524 157 0.2397 0.2800 3.6589 3.7383| | 9: 2.6018 - 2.5016 0.94 1464 179 0.2530 0.3079 3.5996 3.7204| | 10: 2.5016 - 2.4153 0.94 1471 166 0.2519 0.2826 3.522 3.6425| | 11: 2.4153 - 2.3398 0.92 1466 166 0.2397 0.2959 3.4662 3.5854| | 12: 2.3398 - 2.2729 0.92 1441 162 0.2420 0.2862 3.4323 3.5348| | 13: 2.2729 - 2.2131 0.90 1412 167 0.2412 0.2837 3.4011 3.5104| | 14: 2.2131 - 2.1591 0.78 1235 127 0.2710 0.3026 3.4179 3.545| | 15: 2.1591 - 2.1100 0.62 987 118 0.3020 0.2687 3.4272 3.4089| | 16: 2.1100 - 2.0651 0.53 811 98 0.2903 0.2637 3.3925 3.362| | 17: 2.0651 - 2.0238 0.43 682 74 0.3050 0.2701 3.3698 3.2717| | 18: 2.0238 - 1.9856 0.39 609 60 0.2949 0.3460 3.3145 3.3207| | 19: 1.9856 - 1.9501 0.31 484 49 0.2940 0.2834 3.2254 3.2695| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 44.0074 - 5.2010 1702 192 0.92 12.13 0.99 1.00 293.18| | 2: 5.2010 - 4.1292 1636 179 0.94 10.94 0.99 0.99 383.35| | 3: 4.1292 - 3.6075 1599 150 0.91 15.27 1.01 0.98 451.33| | 4: 3.6075 - 3.2778 1593 170 0.88 19.01 1.02 0.97 468.90| | 5: 3.2778 - 3.0429 1552 156 0.84 22.70 0.99 0.95 447.19| | 6: 3.0429 - 2.8635 1532 193 0.80 26.38 1.01 0.94 409.93| | 7: 2.8635 - 2.7202 1542 158 0.76 30.52 1.04 0.95 389.76| | 8: 2.7202 - 2.6018 1524 157 0.77 30.05 1.01 0.95 342.37| | 9: 2.6018 - 2.5016 1464 179 0.77 29.91 0.96 0.95 294.32| | 10: 2.5016 - 2.4153 1471 166 0.77 29.57 0.95 0.92 243.47| | 11: 2.4153 - 2.3398 1466 166 0.77 29.50 0.99 0.90 223.39| | 12: 2.3398 - 2.2729 1441 162 0.77 29.83 1.01 0.89 206.26| | 13: 2.2729 - 2.2131 1412 167 0.78 29.11 1.04 0.90 191.75| | 14: 2.2131 - 2.1591 1235 127 0.78 29.63 1.03 0.94 182.39| | 15: 2.1591 - 2.1100 987 118 0.76 30.97 0.98 0.95 174.92| | 16: 2.1100 - 2.0651 811 98 0.77 30.10 0.97 0.95 164.74| | 17: 2.0651 - 2.0238 682 74 0.78 29.77 0.97 0.94 146.97| | 18: 2.0238 - 1.9856 609 60 0.78 29.25 0.98 0.92 131.28| | 19: 1.9856 - 1.9501 484 49 0.76 31.00 0.97 0.87 120.32| |alpha: min = 0.87 max = 1.00 mean = 0.94| |beta: min = 120.32 max = 468.90 mean = 302.89| |figures of merit: min = 0.00 max = 1.00 mean = 0.81| |phase err.(work): min = 0.00 max = 89.82 mean = 25.10| |phase err.(test): min = 0.00 max = 89.91 mean = 24.78| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r_work=0.2128 r_free=0.2347 n_reflections: 27463 start: r_work=0.3657 r_free=0.3906 (reset all scales to undefined) bulk-solvent and scaling: r_work=0.2139 r_free=0.2357 remove outliers: r_work=0.2139 r_free=0.2357 correct solvent mask: r_work=0.2128 r_free=0.2347 final: r_work=0.2128 r_free=0.2347 n_reflections: 27463 overall anisotropic scale matrix: V0: 0.2477,0.0998,-0.2921,-0.1994,-0.1491,-0.1078 V1: -0.0067,0.0012,0.0026,0.0089,0.0067,-0.0044 ======================== 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 43.996-14.237 96.15 88 12 0.1468 95.259 93.202 0.147 1.012 0.288 14.224-11.370 98.06 94 7 0.1328 85.201 84.501 0.156 1.013 0.305 11.321-9.092 98.90 156 23 0.1218 86.634 86.508 0.153 1.013 0.310 9.082-7.268 97.97 305 33 0.1615 62.151 61.031 0.144 1.012 0.310 7.264-5.810 98.96 601 63 0.1668 56.565 55.142 0.142 1.010 0.310 5.806-4.642 98.67 1134 127 0.1456 75.390 74.337 0.152 1.008 0.310 4.642-3.711 97.88 2198 203 0.1590 73.503 72.360 0.163 1.004 0.266 3.710-2.966 97.16 4129 462 0.2126 52.426 51.228 0.176 0.998 0.077 2.966-2.371 94.27 7737 874 0.2506 30.791 29.392 0.178 0.989 0.000 2.371-1.950 62.52 8300 917 0.2679 22.947 21.528 0.193 0.975 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.1519 b_overall=-4.1719 ================= 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 ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3658 0.3906 0.005 1.35 7.5 100.8 27.5 0 0.000 1_bss: 0.2128 0.2347 0.005 1.35 7.5 100.8 27.5 0 0.000 1_settarget: 0.2128 0.2347 0.005 1.35 7.5 100.8 27.5 0 0.000 end: 0.2128 0.2347 0.005 1.35 7.5 100.8 27.5 0 0.000 ------------------------------------------------------------------------ Writing refined structure to PDB file: AutoBuild_run_1_/TEMP0/refine.pdb_1 n_use = 3380 n_use_u_iso = 3380 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 = 3380 Writing refined fmodel to MTZ file: /net/chevy/raid1/afonine/work/crom/final/fig_17_results_1F8T/autobuild/AutoBuild_run_1_/TEMP0/refine_001_f_model.mtz # Date 2014/10/07 13:51:53 Final R(work) = 0.2128, R(free) = 0.2347