Monomer Library directory: "/net/chevy/raid1/afonine/sources/chem_data/mon_lib" Total number of atoms: 6157 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2958 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 33, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 3087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3087 Classifications: {'peptide': 402} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 33, 'TRANS': 368} Unresolved chain link angles: 1 Unresolved chain link planarities: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 69 Unusual residues: {'HEM': 1, 'SPK': 1, 'MES': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2558 SG CYS A 353 -4.150 38.367 63.156 1.00 10.76 S ATOM 5645 SG CYS B 353 86.504 12.317 62.930 1.00 11.22 S Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N GLU A 36 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A 36 " occ=0.50 residue: pdb=" N GLU A 130 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU A 130 " occ=0.50 residue: pdb=" N ARG B 77 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG B 77 " occ=0.50 residue: pdb=" N GLN B 176 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN B 176 " occ=0.50 residue: pdb=" O1 MES A 632 " occ=0.50 ... (10 atoms not shown) pdb=" O3S MES A 632 " occ=0.50 Time building chain proxies: 3.28, per 1000 atoms: 0.53 Number of scatterers: 6157 At special positions: 0 Unit cell: (59.554, 79.206, 87.43, 90, 92.26, 90) Space group: P 1 21 1 (No. 4) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 22 16.00 O 1127 8.00 N 1118 7.00 C 3888 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=84260 Type of sigmas: double, size=84260 Number of Miller indices: 84260 Anomalous flag: False Unit cell: (59.554, 79.206, 87.43, 90, 92.26, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 2332 Resolution range: 35.8944 1.6096 Completeness in resolution range: 0.802293 Completeness with d_max=infinity: 0.802201 Wavelength: 1.0000 Number of F-obs in resolution range: 84260 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 = 35.8944 d_min = 1.6096 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=86913 Type of sigmas: None Number of Miller indices: 86913 Anomalous flag: False Unit cell: (59.554, 79.206, 87.43, 90, 92.26, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 2421 Resolution range: 35.8944 1.60959 Completeness in resolution range: 0.827491 Completeness with d_max=infinity: 0.827396 Wavelength: 1.0000 Test (R-free flags) flag value: 0 Number of work/free reflections by resolution: work free %free bin 1: 35.9033 - 3.4668 [ 8907/10684] 8025 882 9.9% bin 2: 3.4668 - 2.7520 [10515/10539] 9436 1079 10.3% bin 3: 2.7520 - 2.4043 [10496/10532] 9429 1067 10.2% bin 4: 2.4043 - 2.1845 [ 7402/10496] 6696 706 9.5% bin 5: 2.1845 - 2.0279 [10371/10477] 9347 1024 9.9% bin 6: 2.0279 - 1.9084 [ 8851/10484] 7957 894 10.1% bin 7: 1.9084 - 1.8128 [ 8347/10453] 7497 850 10.2% bin 8: 1.8128 - 1.7339 [ 8309/10465] 7491 818 9.8% bin 9: 1.7339 - 1.6671 [ 6383/10482] 5745 638 10.0% bin 10: 1.6671 - 1.6096 [ 4679/10412] 4215 464 9.9% overall 75838 8422 10.0% ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 25.90 2 S 22 15.96 2 O 1127 7.97 2 N 1118 6.97 2 C 3888 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=0, symmetry=0 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.36: 2147 1.36 - 1.53: 2838 1.53 - 1.70: 1276 1.70 - 1.87: 39 1.87 - 2.04: 8 Bond restraints: 6308 Sorted by residual: bond pdb=" CAB HEM A 430 " pdb=" CBB HEM A 430 " ideal model delta sigma weight residual 1.337 1.544 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C SER B 182 " pdb=" N HIS B 183 " ideal model delta sigma weight residual 1.329 1.185 0.144 1.40e-02 5.10e+03 1.06e+02 bond pdb=" CAC HEM A 430 " pdb=" CBC HEM A 430 " ideal model delta sigma weight residual 1.337 1.541 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" CAC HEM B 430 " pdb=" CBC HEM B 430 " ideal model delta sigma weight residual 1.337 1.538 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" CAB HEM B 430 " pdb=" CBB HEM B 430 " ideal model delta sigma weight residual 1.337 1.538 -0.201 2.00e-02 2.50e+03 1.01e+02 ... (remaining 6303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 11.13: 8607 11.13 - 22.27: 10 22.27 - 33.40: 0 33.40 - 44.54: 0 44.54 - 55.67: 2 Bond angle restraints: 8619 Sorted by residual: angle pdb=" C SER A 339 " pdb=" N PRO A 340 " pdb=" CD PRO A 340 " ideal model delta sigma weight residual 125.00 76.08 48.92 4.10e+00 5.95e-02 1.42e+02 angle pdb=" C SER A 339 " pdb=" N PRO A 340 " pdb=" CA PRO A 340 " ideal model delta sigma weight residual 122.60 178.27 -55.67 5.00e+00 4.00e-02 1.24e+02 angle pdb=" N SER B 180 " pdb=" CA SER B 180 " pdb=" C SER B 180 " ideal model delta sigma weight residual 111.20 132.12 -20.92 2.80e+00 1.28e-01 5.58e+01 angle pdb=" C SER B 180 " pdb=" N SER B 181 " pdb=" CA SER B 181 " ideal model delta sigma weight residual 121.70 134.92 -13.22 1.80e+00 3.09e-01 5.39e+01 angle pdb=" CA SER B 180 " pdb=" C SER B 180 " pdb=" N SER B 181 " ideal model delta sigma weight residual 116.20 102.84 13.36 2.00e+00 2.50e-01 4.46e+01 ... (remaining 8614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.97: 2211 27.97 - 55.94: 107 55.94 - 83.91: 27 83.91 - 111.88: 4 111.88 - 139.85: 1 Dihedral angle restraints: 2350 sinusoidal: 1559 harmonic: 791 Sorted by residual: dihedral pdb=" C2C HEM B 430 " pdb=" C3C HEM B 430 " pdb=" CAC HEM B 430 " pdb=" CBC HEM B 430 " ideal model delta sinusoidal sigma weight residual 180.00 73.06 -73.06 2 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" C7 MES A 632 " pdb=" C8 MES A 632 " pdb=" S MES A 632 " pdb=" O3S MES A 632 " ideal model delta sinusoidal sigma weight residual 180.00 40.15 139.85 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" C2C HEM A 430 " pdb=" C3C HEM A 430 " pdb=" CAC HEM A 430 " pdb=" CBC HEM A 430 " ideal model delta sinusoidal sigma weight residual 180.00 68.86 -68.86 2 1.00e+01 1.00e-02 4.18e+01 ... (remaining 2347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 807 0.131 - 0.261: 129 0.261 - 0.392: 8 0.392 - 0.522: 2 0.522 - 0.653: 4 Chirality restraints: 950 Sorted by residual: chirality pdb=" CA SER B 180 " pdb=" N SER B 180 " pdb=" C SER B 180 " pdb=" CB SER B 180 " both_signs ideal model delta sigma weight residual False 2.50 1.85 0.65 2.00e-01 2.50e+01 1.07e+01 chirality pdb=" CA SER B 207 " pdb=" N SER B 207 " pdb=" C SER B 207 " pdb=" CB SER B 207 " both_signs ideal model delta sigma weight residual False 2.50 1.93 0.57 2.00e-01 2.50e+01 8.20e+00 chirality pdb=" CA PRO A 140 " pdb=" N PRO A 140 " pdb=" C PRO A 140 " pdb=" CB PRO A 140 " both_signs ideal model delta sigma weight residual False 2.73 2.19 0.54 2.00e-01 2.50e+01 7.21e+00 ... (remaining 947 not shown) Planarity restraints: 1138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 318 " 0.071 2.00e-02 2.50e+03 4.05e-02 3.27e+01 pdb=" CG TYR A 318 " -0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR A 318 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 318 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 318 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 318 " -0.023 2.00e-02 2.50e+03 pdb=" CZ TYR A 318 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR A 318 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 318 " -0.054 2.00e-02 2.50e+03 3.07e-02 1.88e+01 pdb=" CG TYR B 318 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR B 318 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR B 318 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 TYR B 318 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR B 318 " 0.018 2.00e-02 2.50e+03 pdb=" CZ TYR B 318 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR B 318 " -0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 266 " -0.036 2.00e-02 2.50e+03 3.43e-02 1.47e+01 pdb=" NE ARG A 266 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 266 " 0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG A 266 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 266 " -0.039 2.00e-02 2.50e+03 ... (remaining 1135 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 82 2.59 - 3.17: 5862 3.17 - 3.75: 10302 3.75 - 4.32: 15119 4.32 - 4.90: 22754 Nonbonded interactions: 54119 Sorted by model distance: nonbonded pdb=" CD1 LEU A 202 " pdb=" NH2 ARG A 206 " model vdw 2.013 3.540 nonbonded pdb=" O ARG A 206 " pdb=" CG ARG A 206 " model vdw 2.134 3.440 nonbonded pdb=" O ASP B 66 " pdb=" O ARG B 68 " model vdw 2.156 3.040 nonbonded pdb=" O SER A 339 " pdb=" CD PRO A 340 " model vdw 2.189 2.752 nonbonded pdb=" OG SER B 207 " pdb=" O SER B 216 " model vdw 2.201 2.440 ... (remaining 54114 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 = 6157 n_use_u_iso = 6157 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 = 6157 ==================== 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_22_bad_lig_1SE6/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_22_bad_lig_1SE6/autobuild/AutoBuild_run_1_/TEMP0/LIG_EDITED_EDITED_unrefined.pdb_1" } xray_data { file_name = "AutoBuild_run_1_/TEMP0/aniso_refinement_data_PHX.mtz" labels = "FP,SIGFP" high_resolution = 1.6096 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: 1.61 - 35.89 A, n_refl.=84260 (all), 10.00 % free)------------| | | | r_work= 0.3684 r_free= 0.3841 coordinate error (max.-lik. estimate): 0.05 A | | | | x-ray target function (ml) for work reflections: 5.113741 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 35.9033 - 4.9971 0.97 3124 358 0.6623 0.6351 5.7917 5.8065| | 2: 4.9971 - 3.9679 0.98 3080 334 0.2577 0.2748 5.7931 5.7866| | 3: 3.9679 - 3.4668 0.62 1821 190 0.2969 0.3156 5.7581 5.8061| | 4: 3.4668 - 3.1501 1.00 3136 374 0.3379 0.3625 5.6917 5.7336| | 5: 3.1501 - 2.9244 1.00 3181 336 0.3426 0.3527 5.5518 5.586| | 6: 2.9244 - 2.7520 1.00 3119 369 0.3212 0.3229 5.3777 5.3634| | 7: 2.7520 - 2.6143 1.00 3150 356 0.3314 0.3645 5.3235 5.4078| | 8: 2.6143 - 2.5005 1.00 3154 338 0.3168 0.3307 5.2492 5.3044| | 9: 2.5005 - 2.4043 1.00 3125 373 0.3192 0.3563 5.2071 5.2731| | 10: 2.4043 - 2.3213 0.99 3159 317 0.3358 0.3447 5.1884 5.2158| | 11: 2.3213 - 2.2487 0.57 1792 206 0.3739 0.4025 5.4681 5.6415| | 12: 2.2487 - 2.1845 0.55 1745 183 0.4292 0.4662 5.7698 6.0795| | 13: 2.1845 - 2.1270 0.99 3099 346 0.3655 0.3680 5.1402 5.165| | 14: 2.1270 - 2.0751 0.99 3141 336 0.3710 0.3843 5.0713 5.1391| | 15: 2.0751 - 2.0279 0.99 3107 342 0.3689 0.3829 4.9726 5.0506| | 16: 2.0279 - 1.9848 0.98 3062 353 0.3631 0.4051 4.9312 5.0187| | 17: 1.9848 - 1.9451 0.96 3011 334 0.3416 0.3694 4.8608 4.8836| | 18: 1.9451 - 1.9084 0.60 1884 207 0.5236 0.5476 5.9572 6.0327| | 19: 1.9084 - 1.8743 0.59 1859 202 0.3349 0.3428 4.7383 4.8262| | 20: 1.8743 - 1.8425 0.92 2863 333 0.3312 0.3675 4.8315 4.9078| | 21: 1.8425 - 1.8128 0.89 2775 315 0.3397 0.3460 4.722 4.7525| | 22: 1.8128 - 1.7849 0.85 2690 307 0.3505 0.3427 4.5554 4.5789| | 23: 1.7849 - 1.7586 0.79 2470 268 0.3726 0.3980 4.5237 4.6344| | 24: 1.7586 - 1.7339 0.74 2331 243 0.3940 0.4224 4.5349 4.5575| | 25: 1.7339 - 1.7104 0.67 2106 226 0.4146 0.4133 4.5737 4.5819| | 26: 1.7104 - 1.6882 0.61 1927 221 0.4312 0.4327 4.5637 4.5313| | 27: 1.6882 - 1.6671 0.54 1712 191 0.4387 0.4184 4.5416 4.5125| | 28: 1.6671 - 1.6470 0.51 1580 181 0.4474 0.4224 4.531 4.5693| | 29: 1.6470 - 1.6279 0.44 1397 145 0.4514 0.4065 4.4932 4.4762| | 30: 1.6279 - 1.6096 0.40 1238 138 0.4604 0.4661 4.5311 4.627| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 35.9033 - 4.9971 3124 358 0.57 46.70 0.55 0.23 26053.41| | 2: 4.9971 - 3.9679 3080 334 0.80 26.83 0.94 0.37 13970.54| | 3: 3.9679 - 3.4668 1821 190 0.80 27.06 1.20 0.50 15615.35| | 4: 3.4668 - 3.1501 3136 374 0.76 31.06 1.25 0.54 15569.50| | 5: 3.1501 - 2.9244 3181 336 0.72 34.20 1.19 0.54 12494.62| | 6: 2.9244 - 2.7520 3119 369 0.74 33.22 1.16 0.51 9190.38| | 7: 2.7520 - 2.6143 3150 356 0.74 32.59 1.15 0.50 7293.80| | 8: 2.6143 - 2.5005 3154 338 0.72 34.83 1.16 0.48 7375.12| | 9: 2.5005 - 2.4043 3125 373 0.72 34.81 1.19 0.50 7030.74| | 10: 2.4043 - 2.3213 3159 317 0.71 35.10 1.24 0.51 6445.82| | 11: 2.3213 - 2.2487 1792 206 0.75 32.12 1.31 0.51 5399.89| | 12: 2.2487 - 2.1845 1745 183 0.76 31.15 1.44 0.55 5348.17| | 13: 2.1845 - 2.1270 3099 346 0.68 37.89 1.36 0.62 7147.00| | 14: 2.1270 - 2.0751 3141 336 0.69 36.93 1.35 0.60 5802.16| | 15: 2.0751 - 2.0279 3107 342 0.74 33.25 1.36 0.59 4092.80| | 16: 2.0279 - 1.9848 3062 353 0.72 34.74 1.34 0.59 4153.48| | 17: 1.9848 - 1.9451 3011 334 0.71 35.32 1.29 0.60 3858.84| | 18: 1.9451 - 1.9084 1884 207 0.79 28.96 1.70 0.59 3580.04| | 19: 1.9084 - 1.8743 1859 202 0.70 36.08 1.23 0.56 2915.77| | 20: 1.8743 - 1.8425 2863 333 0.63 42.26 1.26 0.62 4309.54| | 21: 1.8425 - 1.8128 2775 315 0.62 43.42 1.29 0.57 3885.97| | 22: 1.8128 - 1.7849 2690 307 0.74 33.50 1.34 0.51 2010.70| | 23: 1.7849 - 1.7586 2470 268 0.77 30.43 1.40 0.55 1639.88| | 24: 1.7586 - 1.7339 2331 243 0.79 28.84 1.42 0.59 1467.26| | 25: 1.7339 - 1.7104 2106 226 0.80 28.23 1.46 0.63 1454.99| | 26: 1.7104 - 1.6882 1927 221 0.79 28.77 1.49 0.65 1502.29| | 27: 1.6882 - 1.6671 1712 191 0.77 30.44 1.52 0.64 1538.79| | 28: 1.6671 - 1.6470 1580 181 0.78 29.54 1.55 0.67 1473.99| | 29: 1.6470 - 1.6279 1397 145 0.78 29.78 1.58 0.67 1383.08| | 30: 1.6279 - 1.6096 1238 138 0.78 29.97 1.60 0.69 1543.28| |alpha: min = 0.19 max = 0.71 mean = 0.54| |beta: min = 1378.86 max = 32236.30 mean = 6830.73| |figures of merit: min = 0.00 max = 1.00 mean = 0.73| |phase err.(work): min = 0.00 max = 89.98 mean = 33.88| |phase err.(test): min = 0.00 max = 89.89 mean = 33.68| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Restraints library geostd + mon.lib. deviations from ideal values. rmsd max count bond : 0.009 0.207 6308 angle : 1.689 55.669 8619 chirality : 0.101 0.653 950 planarity : 0.007 0.061 1138 dihedral : 14.289 139.847 2350 min nonbonded distance : 2.013 Molprobity statistics. all-atom clashscore : 16.88 ramachandran plot: outliers : 3.08 % allowed : 3.97 % favored : 92.95 % rotamer outliers : 5.31 % cbeta deviations : 1 |-ADP statistics (Wilson B = 7.420)-------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 6157 0 4.36 62.98 17.35 None None None | | all(noH): 6157 0 4.36 62.98 17.35 None None None | | Sol. : 0 0 None None None None None None | | Mac. : 6157 0 4.36 62.98 17.35 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: 4.360 - 10.222: 1512 | 5: 33.670 - 39.532: 236 | | 1: 10.222 - 16.084: 2256 | 6: 39.532 - 45.394: 131 | | 2: 16.084 - 21.946: 992 | 7: 45.394 - 51.256: 134 | | 3: 21.946 - 27.808: 548 | 8: 51.256 - 57.118: 53 | | 4: 27.808 - 33.670: 275 | 9: 57.118 - 62.980: 20 | | =>continue=> | |-----------------------------------------------------------------------------| |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 1 OF 1 ************************* |--(resolution: 1.61 - 35.89 A, n_refl.=84260 (all), 10.00 % free)------------| | | | r_work= 0.3684 r_free= 0.3841 coordinate error (max.-lik. estimate): 0.05 A | | | | x-ray target function (ml) for work reflections: 5.113741 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r_work=0.3684 r_free=0.3841 n_reflections: 84260 start: r_work=0.3684 r_free=0.3841 (reset all scales to undefined) bulk-solvent and scaling: r_work=0.2868 r_free=0.3066 remove outliers: r_work=0.2868 r_free=0.3066 correct solvent mask: r_work=0.2847 r_free=0.3053 final: r_work=0.2847 r_free=0.3053 n_reflections: 84256 overall anisotropic scale matrix: V0: -0.2225,0.1983,0.1371,-0.2266,-0.0487,-0.0364 V1: 0.0174,-0.0089,-0.0081,0.0046,0.0036,-0.0002 ======================== 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 35.894-14.758 73.72 89 12 0.2764 165.317 159.139 0.485 1.006 0.347 14.720-12.123 85.34 85 14 0.2660 195.737 182.800 0.464 1.007 0.345 12.119-9.959 82.52 153 17 0.1720 244.411 242.558 0.460 1.007 0.344 9.943-8.172 93.14 317 36 0.1718 234.553 232.710 0.453 1.008 0.348 8.166-6.713 99.40 589 69 0.2106 186.482 182.599 0.440 1.007 0.361 6.710-5.511 100.00 1079 120 0.2315 164.258 157.764 0.426 1.007 0.364 5.509-4.525 99.35 1910 221 0.2058 221.357 217.112 0.465 1.006 0.367 4.524-3.726 78.95 2718 267 0.2052 254.727 246.861 0.519 1.005 0.324 3.703-3.051 89.60 5498 639 0.2816 214.096 202.184 0.595 1.002 0.079 3.051-2.506 99.73 11166 1243 0.3032 147.233 138.228 0.561 1.001 0.000 2.505-2.057 85.79 17343 1899 0.3036 121.372 113.766 0.627 0.997 0.000 2.057-1.610 71.11 34887 3885 0.3037 79.018 73.289 0.683 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.4865 b_overall=-4.4863 ============================ Set refinement target ============================ using refinement target ml ----------X-ray data---------- |--(resolution: 1.61 - 35.89 A, n_refl.=84256 (all), 10.00 % free)------------| | | | r_work= 0.2847 r_free= 0.3053 coordinate error (max.-lik. estimate): 0.22 A | | | | x-ray target function (ml) for work reflections: 5.075713 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 35.9033 - 4.9971 0.97 3122 358 0.2158 0.2199 5.31 5.3492| | 2: 4.9971 - 3.9679 0.98 3080 334 0.1982 0.2074 5.4927 5.5448| | 3: 3.9679 - 3.4668 0.62 1821 190 0.2398 0.2718 5.6636 5.7681| | 4: 3.4668 - 3.1501 1.00 3136 374 0.2802 0.3215 5.6655 5.7291| | 5: 3.1501 - 2.9244 1.00 3180 336 0.3142 0.3115 5.5341 5.563| | 6: 2.9244 - 2.7520 1.00 3119 369 0.2978 0.3071 5.3738 5.3588| | 7: 2.7520 - 2.6143 1.00 3150 356 0.3119 0.3533 5.3216 5.4083| | 8: 2.6143 - 2.5005 1.00 3154 338 0.2951 0.3020 5.2457 5.298| | 9: 2.5005 - 2.4043 1.00 3125 373 0.2880 0.3427 5.2039 5.2738| | 10: 2.4043 - 2.3213 0.99 3159 317 0.2922 0.3030 5.182 5.2069| | 11: 2.3213 - 2.2487 0.57 1792 206 0.3252 0.3526 5.4521 5.6268| | 12: 2.2487 - 2.1845 0.55 1745 183 0.3702 0.3969 5.7569 6.0604| | 13: 2.1845 - 2.1270 0.99 3099 346 0.2903 0.3099 5.1512 5.1794| | 14: 2.1270 - 2.0751 0.99 3141 336 0.2983 0.3219 5.076 5.1433| | 15: 2.0751 - 2.0279 0.99 3106 342 0.2969 0.3148 4.9724 5.0588| | 16: 2.0279 - 1.9848 0.98 3062 353 0.2964 0.3426 4.9286 5.0206| | 17: 1.9848 - 1.9451 0.96 3011 334 0.2834 0.3100 4.8643 4.887| | 18: 1.9451 - 1.9084 0.60 1884 207 0.4327 0.4574 5.9217 6.0033| | 19: 1.9084 - 1.8743 0.59 1859 202 0.3042 0.3602 4.7498 4.8528| | 20: 1.8743 - 1.8425 0.92 2863 333 0.2914 0.3563 4.8537 4.9336| | 21: 1.8425 - 1.8128 0.89 2775 315 0.2828 0.3065 4.7313 4.7633| | 22: 1.8128 - 1.7849 0.85 2690 307 0.2632 0.2747 4.5418 4.5669| | 23: 1.7849 - 1.7586 0.79 2470 268 0.2638 0.2974 4.5054 4.6134| | 24: 1.7586 - 1.7339 0.74 2331 243 0.2889 0.2888 4.5245 4.5424| | 25: 1.7339 - 1.7104 0.67 2106 226 0.3046 0.2932 4.5706 4.5768| | 26: 1.7104 - 1.6882 0.61 1927 221 0.3045 0.3024 4.5632 4.5288| | 27: 1.6882 - 1.6671 0.54 1712 191 0.3066 0.2679 4.5369 4.5034| | 28: 1.6671 - 1.6470 0.51 1580 181 0.3063 0.2923 4.5308 4.5731| | 29: 1.6470 - 1.6279 0.44 1397 145 0.3051 0.2900 4.4925 4.4813| | 30: 1.6279 - 1.6096 0.40 1238 138 0.2993 0.3063 4.5283 4.6275| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 35.9033 - 4.9971 3122 358 0.85 22.11 0.99 0.97 6551.14| | 2: 4.9971 - 3.9679 3080 334 0.89 17.91 0.99 0.95 7702.35| | 3: 3.9679 - 3.4668 1821 190 0.84 23.22 1.04 0.96 12405.07| | 4: 3.4668 - 3.1501 3136 374 0.77 29.79 1.00 0.92 14516.29| | 5: 3.1501 - 2.9244 3180 336 0.72 34.33 1.00 0.91 12073.58| | 6: 2.9244 - 2.7520 3119 369 0.74 33.15 1.01 0.91 9084.69| | 7: 2.7520 - 2.6143 3150 356 0.75 32.18 0.98 0.90 7252.09| | 8: 2.6143 - 2.5005 3154 338 0.72 34.31 0.97 0.86 7322.30| | 9: 2.5005 - 2.4043 3125 373 0.73 34.11 0.97 0.88 6968.29| | 10: 2.4043 - 2.3213 3159 317 0.72 34.43 0.98 0.87 6404.57| | 11: 2.3213 - 2.2487 1792 206 0.76 31.48 1.02 0.86 5354.90| | 12: 2.2487 - 2.1845 1745 183 0.77 30.59 1.10 0.90 5338.03| | 13: 2.1845 - 2.1270 3099 346 0.69 37.34 1.02 1.00 7142.07| | 14: 2.1270 - 2.0751 3141 336 0.70 36.39 1.00 0.94 5778.51| | 15: 2.0751 - 2.0279 3106 342 0.73 33.73 1.03 0.91 4085.05| | 16: 2.0279 - 1.9848 3062 353 0.71 35.52 1.04 0.91 4137.68| | 17: 1.9848 - 1.9451 3011 334 0.71 35.30 0.98 0.96 3874.20| | 18: 1.9451 - 1.9084 1884 207 0.79 28.49 1.28 0.95 3583.87| | 19: 1.9084 - 1.8743 1859 202 0.71 35.43 0.91 0.89 2909.04| | 20: 1.8743 - 1.8425 2863 333 0.64 41.62 0.92 0.98 4310.23| | 21: 1.8425 - 1.8128 2775 315 0.62 42.93 0.93 0.88 3900.33| | 22: 1.8128 - 1.7849 2690 307 0.74 32.94 0.95 0.78 2003.28| | 23: 1.7849 - 1.7586 2470 268 0.78 29.82 0.98 0.82 1629.61| | 24: 1.7586 - 1.7339 2331 243 0.80 28.26 0.98 0.87 1459.44| | 25: 1.7339 - 1.7104 2106 226 0.80 27.67 0.99 0.91 1447.62| | 26: 1.7104 - 1.6882 1927 221 0.80 28.20 1.00 0.93 1493.80| | 27: 1.6882 - 1.6671 1712 191 0.78 29.88 1.00 0.91 1528.99| | 28: 1.6671 - 1.6470 1580 181 0.79 29.06 1.01 0.92 1464.61| | 29: 1.6470 - 1.6279 1397 145 0.78 29.48 1.01 0.91 1380.83| | 30: 1.6279 - 1.6096 1238 138 0.78 29.99 1.01 0.91 1553.47| |alpha: min = 0.77 max = 1.01 mean = 0.91| |beta: min = 1374.78 max = 14687.12 mean = 5617.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.75| |phase err.(work): min = 0.00 max = 89.98 mean = 32.06| |phase err.(test): min = 0.00 max = 89.82 mean = 31.84| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r_work=0.2847 r_free=0.3053 n_reflections: 84256 start: r_work=0.3682 r_free=0.3841 (reset all scales to undefined) bulk-solvent and scaling: r_work=0.2868 r_free=0.3066 remove outliers: r_work=0.2868 r_free=0.3066 correct solvent mask: r_work=0.2847 r_free=0.3053 final: r_work=0.2847 r_free=0.3053 n_reflections: 84256 overall anisotropic scale matrix: V0: -0.2225,0.1983,0.1371,-0.2266,-0.0487,-0.0364 V1: 0.0174,-0.0089,-0.0081,0.0046,0.0036,-0.0002 ======================== 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 35.894-14.758 73.72 89 12 0.2764 165.317 159.139 0.485 1.006 0.347 14.720-12.123 85.34 85 14 0.2660 195.737 182.800 0.464 1.007 0.345 12.119-9.959 82.52 153 17 0.1720 244.411 242.558 0.460 1.007 0.344 9.943-8.172 93.14 317 36 0.1718 234.553 232.710 0.453 1.008 0.348 8.166-6.713 99.40 589 69 0.2106 186.482 182.599 0.440 1.007 0.361 6.710-5.511 100.00 1079 120 0.2315 164.258 157.764 0.426 1.007 0.364 5.509-4.525 99.35 1910 221 0.2058 221.357 217.112 0.465 1.006 0.367 4.524-3.726 78.95 2718 267 0.2052 254.727 246.861 0.519 1.005 0.324 3.703-3.051 89.60 5498 639 0.2816 214.096 202.184 0.595 1.002 0.079 3.051-2.506 99.73 11166 1243 0.3032 147.233 138.228 0.561 1.001 0.000 2.505-2.057 85.79 17343 1899 0.3036 121.372 113.766 0.627 0.997 0.000 2.057-1.610 71.11 34887 3885 0.3037 79.018 73.289 0.683 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.4865 b_overall=-4.4863 ================= 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 : 0.3684 0.3841 0.009 1.69 4.4 63.0 17.4 0 0.000 1_bss: 0.2847 0.3053 0.009 1.69 4.4 63.0 17.4 0 0.000 1_settarget: 0.2847 0.3053 0.009 1.69 4.4 63.0 17.4 0 0.000 end: 0.2847 0.3053 0.009 1.69 4.4 63.0 17.4 0 0.000 ------------------------------------------------------------------------ Writing refined structure to PDB file: AutoBuild_run_1_/TEMP0/refine.pdb_1 n_use = 6157 n_use_u_iso = 6157 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 = 6157 Writing refined fmodel to MTZ file: /net/chevy/raid1/afonine/work/crom/final/fig_22_bad_lig_1SE6/autobuild/AutoBuild_run_1_/TEMP0/refine_001_f_model.mtz # Date 2014/10/08 18:23:20 Final R(work) = 0.2847, R(free) = 0.3053