The structure factors that I downloaded from the PDB for my little MR project contains both reflections behind the beam stop and reflections of higher resolution than even the original authors would use. When setting up the MR I entered the more restrictive resolution limits into the Wizard and Phaser appears to have obeyed. As near as I can tell from the log files, however, Resolve is using all the data in the rebuild. I am including a copy of the log file from the "best" refinement. I would prefer that only data between 30 and 2.2A were used but it is clear that the refinement is, at least, monitoring the fit to all the data. I am presuming that the program is refining against the same data it is monitoring. I would like to suggest that either the log file be clearer about the resolution limits it is actually refining to, or the plumbing that passes the resolution limits from the AutoMR wizard to the AutoBuild wizard be checked. Dale Tronrud P.S. That's all my problems... For now. The project I'm working on is cursed and brings out the worst in all the software I have used. AutoBuild_run_3_/TEMP0/LIG_EDITED_EDITED_edit_model.pdb Monomer Library directory: "/usr/local/phenix-1.3b-rc6/ext_ref_files/mon_lib" Total number of atoms: 6255 Number of models: 1 Model: 0 Number of conformers: 1 Conformer: " " Number of atoms: 6255 Number of chains: 4 Number of residues, atoms: 352, 2697 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 333, 'PCIS': 2} Chain breaks: 8 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLN:plan2': 2, 'GLN%COO:plan2': 1, 'GLN%COO:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 26 Number of residues, atoms: 352, 2694 Classifications: {'peptide': 352} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 333, 'PCIS': 1} Chain breaks: 5 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLN:plan2': 2, 'GLN%COO:plan2': 1, 'GLN%COO:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 34 Number of residues, atoms: 7, 432 Unusual residues: {'BCL': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 12 Number of residues, atoms: 7, 432 Unusual residues: {'BCL': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 146 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 8.94, per 1000 atoms: 1.43 ================================== X-ray data ================================= F-obs: AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP R-free flags: AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FreeR_flag Miller array info: AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FP,SIGFP Observation type: xray.amplitude Type of data: double, size=38159 Type of sigmas: double, size=38159 Number of Miller indices: 38159 Anomalous flag: False Unit cell: (169.1, 169.1, 169.1, 90, 90, 90) Space group: P 43 3 2 (No. 212) Systematic absences: 0 Centric reflections: 4505 Resolution range: 75.6238 2.14896 Completeness in resolution range: 0.839637 Completeness with d_max=infinity: 0.8396 Number of F-obs in resolution range: 38159 Number of F-obs <= 0: 0 Refinement resolution range: d_max = 75.6238 d_min = 2.1490 Miller array info: AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz:FreeR_flag Observation type: None Type of data: int, size=38159 Type of sigmas: None Number of Miller indices: 38159 Anomalous flag: False Unit cell: (169.1, 169.1, 169.1, 90, 90, 90) Space group: P 43 3 2 (No. 212) Systematic absences: 0 Centric reflections: 4505 Resolution range: 75.6238 2.14896 Completeness in resolution range: 0.839637 Completeness with d_max=infinity: 0.8396 Test (R-free flags) flag value: 0 Number of work/free reflections by resolution: work free %free bin 1: 75.6707 - 4.6295 [4755/4893] 4536 219 4.6% bin 2: 4.6295 - 3.6746 [4493/4607] 4248 245 5.5% bin 3: 3.6746 - 3.2101 [4414/4577] 4178 236 5.3% bin 4: 3.2101 - 2.9166 [4232/4498] 4007 225 5.3% bin 5: 2.9166 - 2.7075 [4221/4533] 4026 195 4.6% bin 6: 2.7075 - 2.5479 [4005/4483] 3792 213 5.3% bin 7: 2.5479 - 2.4203 [3811/4480] 3637 174 4.6% bin 8: 2.4203 - 2.3149 [3223/4472] 3066 157 4.9% bin 9: 2.3149 - 2.2258 [2846/4459] 2702 144 5.1% bin 10: 2.2258 - 2.1490 [2159/4445] 2042 117 5.4% overall 36234 1925 5.0% No array of experimental phases found. ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ========================== Set up restraints manager ========================== Number of disulfides: simple=0, symmetry=0 Time building geometry restraints manager: 0.40 seconds Histogram of bond lengths: 1.12 - 1.26: 957 1.26 - 1.40: 1621 1.40 - 1.55: 3702 1.55 - 1.69: 131 1.69 - 1.83: 23 Bond restraints sorted by residual: atom i - atom j ideal model delta weight residual " O1A BCL B 6 " - " CGA BCL B 6 " 1.212 1.117 0.095 2.50e+03 2.25e+01 " O1A BCL D 6 " - " CGA BCL D 6 " 1.212 1.118 0.094 2.50e+03 2.22e+01 " C15 BCL D 6 " - " C16 BCL D 6 " 1.540 1.459 0.081 2.50e+03 1.63e+01 " C15 BCL B 6 " - " C16 BCL B 6 " 1.540 1.460 0.080 2.50e+03 1.60e+01 " N PRO A 188 " - " CD PRO A 188 " 1.473 1.418 0.055 5.10e+03 1.56e+01 ... (remaining 6429 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 9 2.17 - 2.85: 1981 2.85 - 3.53: 8408 3.53 - 4.22: 16251 4.22 - 4.90: 27426 Nonbonded interactions sorted by model distance: atom i - atom j model vdw sym.op. j " OG SER A 24 " - " C GLY C 23 " 1.486 3.270 " OG SER A 24 " - " N SER C 24 " 1.747 3.120 " OH TYR A 330 " - " OE1 GLN C 333 " 1.870 3.040 x-1/4,-z-1/4,y+1/4 " C ASN A 121 " - " N LEU A 122 " 1.941 3.350 x+1,y+1,z+1 " OG SER A 24 " - " O GLY C 23 " 1.956 3.040 ... (remaining 54070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.73: 1959 22.73 - 45.46: 198 45.46 - 68.20: 68 68.20 - 90.93: 27 90.93 - 113.66: 1 Dihedral angle restraints sorted by residual: " CA ALA C 327 " " C ALA C 327 " " N PRO C 328 " " CA PRO C 328 " ideal model delta periodicty weight residual 180.00 -66.34 -113.66 1 4.00e-02 5.17e+02 " C2B BCL D 7 " " C3B BCL D 7 " " CAB BCL D 7 " " OBB BCL D 7 " ideal model delta periodicty weight residual 0.00 147.16 32.84 2 4.00e-02 4.31e+01 " C2B BCL B 7 " " C3B BCL B 7 " " CAB BCL B 7 " " OBB BCL B 7 " ideal model delta periodicty weight residual 0.00 147.20 32.80 2 4.00e-02 4.30e+01 ... (remaining 2250 not shown) ==================== Fixing bad ADP in input model (if any) =================== ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 4 Type Number sf(0) Gaussians S 14 15.96 2 O 1076 7.97 2 N 1007 6.97 2 C 4158 5.97 2 sf(0) = scattering factor at diffraction angle 0. ====================== Modifying start model if requested ===================== atom_attributes_list is modified in-place to define missing element types when possible. ==================== Fixing bad ADP in input model (if any) =================== ================== Extract refinement strategy and selections ================= individual_sites = True rigid_body = False individual_adp = True group_adp = False tls = False individual_occupancies = False group_occupancies = False group_anomalous = False size = 6255 n_use = 6255 n_use_u_iso = 6255 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 n_anisotropic_flag = 0 total number of scatterers = 6255 ==================== Process input NCS or/and find new NCS ==================== NCS groups found in parameter file: 0 Automatic NCS search: Chains in this PDB file: ['A', 'C'] GROUPS BASED ON QUICK COMPARISON: [] Looking for invariant domains for ...: ['A', 'C'] [[[9, 366]], [[9, 366]]] Updated/new NCS groups: refinement.ncs.restraint_group { reference = chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 ) selection = chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 ) } ----------Building NCS restraints---------- NCS restraint group 1: NCS operator 1: Reference selection: "chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )" Other selection: "chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )" Number of atom pairs: 2603 Rotation={{-0.999509, -0.0190423, 0.0248896}, {0.0243783, 0.0266261, 0.999348}, {-0.0196926, 0.999464, -0.0261488}} Translation={{38.5072}, {-44.0643}, {42.3394}} Histogram of differences: 0.001760 - 0.701888: 2552 0.701888 - 1.402017: 14 1.402017 - 2.102145: 22 2.102145 - 2.802274: 6 2.802274 - 3.502402: 4 3.502402 - 4.202531: 5 RMS difference with respect to the reference: 0.312576 =================== Write initial parameters into .eff file =================== ============================ 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 = "/usr/users/dale/structure/fmo-ct/tronrud_2007/AutoBuild_run_3_/TEMP0/LIG_EDITED_EDITED_edit_model.pdb" } xray_data { file_name = "AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz" labels = "FP,SIGFP" high_resolution = 2.2 r_free_flags { file_name = "AutoBuild_run_3_/TEMP0/exptl_fobs_phases_freeR_flags.mtz" label = "FreeR_flag" test_flag_value = 0 } } monomers { file_name = "/usr/users/dale/geometry/chromophores/bcl_tnt.cif" } } output { prefix = "AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3" serial = 1 write_eff_file = False write_geo_file = False write_def_file = False export_final_f_model = *mtz cns write_maps = False } main { ordered_solvent = True ncs = True use_experimental_phases = False random_seed = 516344 } ncs { special_position_warnings_only = True restraint_group { reference = "chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )" selection = "chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )" } } ordered_solvent { low_resolution = 3 } mask { ignore_zero_occupancy_atoms = False } } #phil __OFF__ ============================= ml refinement start ============================= ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.3243 r_free= 0.3131 ksol= 0.00 Bsol= 0.00 scale= 1.698 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.40 A | | x-ray target function (ml) for work reflections: 7.754289 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 75.6707 - 5.1788 0.97 3272 159 0.4168 0.3905 8.6988 8.5536| | 2: 5.1788 - 4.1106 0.98 3112 155 0.2200 0.2341 8.4215 8.4968| | 3: 4.1106 - 3.5910 0.97 3000 188 0.2279 0.2321 8.1284 8.1202| | 4: 3.5910 - 3.2627 0.97 2977 168 0.2388 0.2465 7.9459 8.0053| | 5: 3.2627 - 3.0288 0.95 2930 152 0.2747 0.2878 7.8061 7.8021| | 6: 3.0288 - 2.8502 0.93 2844 159 0.2741 0.2804 7.6418 7.6974| | 7: 2.8502 - 2.7075 0.93 2860 139 0.2757 0.3123 7.5349 7.6274| | 8: 2.7075 - 2.5896 0.89 2705 156 0.2878 0.3340 7.453 7.4977| | 9: 2.5896 - 2.4899 0.89 2715 135 0.2982 0.3356 7.3586 7.5621| | 10: 2.4899 - 2.4040 0.81 2488 115 0.3089 0.3543 7.3181 7.3706| | 11: 2.4040 - 2.3288 0.72 2176 109 0.3142 0.3613 7.3041 7.3373| | 12: 2.3288 - 2.2623 0.67 2018 110 0.3096 0.3293 7.3086 7.3357| | 13: 2.2623 - 2.2027 0.58 1742 104 0.3370 0.3823 7.3303 7.508| | 14: 2.2027 - 2.1490 0.46 1395 76 0.3749 0.3710 7.4161 7.4587| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 75.6707 - 5.1788 3272 159 0.64 39.15 1.16 1.12 4689001.73| | 2: 5.1788 - 4.1106 3112 155 0.79 26.44 2.03 1.66 3059064.97| | 3: 4.1106 - 3.5910 3000 188 0.82 24.63 2.13 1.94 1936112.07| | 4: 3.5910 - 3.2627 2977 168 0.81 25.88 2.18 2.02 1377840.11| | 5: 3.2627 - 3.0288 2930 152 0.78 28.52 2.16 2.01 1065329.57| | 6: 3.0288 - 2.8502 2844 159 0.76 30.45 2.06 1.97 856549.95| | 7: 2.8502 - 2.7075 2860 139 0.77 30.05 2.04 1.88 690049.30| | 8: 2.7075 - 2.5896 2705 156 0.75 31.56 1.99 1.78 594991.98| | 9: 2.5896 - 2.4899 2715 135 0.72 34.01 1.90 1.74 528160.82| | 10: 2.4899 - 2.4040 2488 115 0.71 35.26 1.94 1.68 488836.19| | 11: 2.4040 - 2.3288 2176 109 0.72 34.25 1.95 1.68 443633.67| | 12: 2.3288 - 2.2623 2018 110 0.73 33.21 1.92 1.64 434086.87| | 13: 2.2623 - 2.2027 1742 104 0.67 39.14 2.01 1.62 524747.84| | 14: 2.2027 - 2.1490 1395 76 0.56 47.31 2.05 1.54 720558.54| |alpha: min = 1.12 max = 2.02 mean = 1.74| |beta: min = 434086.87 max = 4689001.73 mean = 1388851.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.74| |phase err.(work): min = 0.00 max = 89.94 mean = 31.97| |phase err.(test): min = 0.00 max = 89.63 mean = 32.13| |-----------------------------------------------------------------------------| ============================== Outliers rejection ============================= basic_wilson_outliers = 0 extreme_wilson_outliers = 2 beamstop_shadow_outliers = 6 total = 8 ====================== Target weights (before refinement) ===================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 12.037420 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 96.336 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.231372 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 93.656 (deg) | |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- |-Geometry statistics: start--------------------------------------------------| | Histogram of deviations from ideal values for | | Bonds | Angles | Nonbonded contacts | | 0.000 - 0.009: 4797 | 0.000 - 2.504: 7924 | 1.486 - 1.828: 2 | | 0.009 - 0.019: 1097 | 2.504 - 5.009: 655 | 1.828 - 2.169: 7 | | 0.019 - 0.028: 284 | 5.009 - 7.513: 145 | 2.169 - 2.511: 30 | | 0.028 - 0.038: 144 | 7.513 - 10.018: 40 | 2.511 - 2.852: 1951 | | 0.038 - 0.047: 61 | 10.018 - 12.522: 8 | 2.852 - 3.193: 3550 | | 0.047 - 0.057: 31 | 12.522 - 15.026: 4 | 3.193 - 3.535: 4858 | | 0.057 - 0.066: 13 | 15.026 - 17.531: 2 | 3.535 - 3.876: 8239 | | 0.066 - 0.076: 3 | 17.531 - 20.035: 0 | 3.876 - 4.217: 8012 | | 0.076 - 0.085: 2 | 20.035 - 22.539: 0 | 4.217 - 4.559: 11917 | | 0.085 - 0.095: 2 | 22.539 - 25.044: 1 | 4.559 - 4.900: 15509 | |-----------------------------------------------------------------------------| |-Geometry statistics: start--------------------------------------------------| | Type | Count | Deviation from ideal | Targets | Target (sum) | | | | rmsd max min | | | | bond | 6434 | 0.012 0.095 0.000 | 0.323 | | | angle | 8779 | 1.693 25.044 0.000 | 0.420 | | | chirality | 905 | 0.089 0.406 0.000 | 0.199 | 0.156 | | planarity | 977 | 0.007 0.154 0.000 | 0.242 | | | dihedral | 2253 | 17.723 113.659 0.001 | 1.614 | | | nonbonded | 6434 | 4.142 4.900 1.486 | 0.255 | | |-----------------------------------------------------------------------------| |-ADP statistics (Wilson B = 25.121)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 6255 0 7.67 118.66 27.52 None None None | | all(noH): 6255 0 7.67 118.66 27.52 None None None | | Sol. : 0 0 None None None None None None | | Mac. : 6255 0 7.67 118.66 27.52 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: 7.670 - 18.769: 1649 | 5: 63.165 - 74.264: 119 | | 1: 18.769 - 29.868: 2973 | 6: 74.264 - 85.363: 80 | | 2: 29.868 - 40.967: 840 | 7: 85.363 - 96.462: 50 | | 3: 40.967 - 52.066: 296 | 8: 96.462 - 107.561: 28 | | 4: 52.066 - 63.165: 198 | 9: 107.561 - 118.660: 22 | | =>continue=> | |-----------------------------------------------------------------------------| |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.3243 r_free= 0.3131 ksol= 0.00 Bsol= 0.00 scale= 1.698 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.40 A | | x-ray target function (ml) for work reflections: 7.754289 | |-----------------------------------------------------------------------------| ====================== bulk solvent modeling and scaling ====================== |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.2582 r_free= 0.2742 ksol= 0.35 Bsol= 50.00 scale= 2.164 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (2.32,2.32,2.32,0.00,0.00,-0.00); trace/3= 2.32 | | | | maximum likelihood estimate for coordinate error: 0.39 A | | x-ray target function (ml) for work reflections: 7.690252 | |-----------------------------------------------------------------------------| ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 10.750300 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 96.207 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.205411 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 94.015 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.2582 final r-factor (work) = 0.2348 | | start r-factor (free) = 0.2742 final r-factor (free) = 0.2713 | |-----------------------------------------------------------------------------| | T_start = wxc * wxc_scale * Exray + wc * Echem | | 42.5209 = 10.75 * 0.50 * 7.7632 + 1.00 * 0.7926 | | | | T_final = wxc * wxc_scale * Exray + wc * Echem | | 41.1803 = 10.75 * 0.50 * 7.6326 + 1.00 * 0.1541 | |-----------------------------------------------------------------------------| | number of iterations = 25 | number of function evaluations = 26 | |-----------------------------------------------------------------------------| ================================ ADP refinement =============================== ----------Individual ADP refinement---------- |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.2348 final r-factor (work) = 0.2216 | | start r-factor (free) = 0.2713 final r-factor (free) = 0.2676 | |-----------------------------------------------------------------------------| | T_start = wxu * wxu_scale * Exray + wu * Eadp | | 1.5745 = 0.21 * 1.00 * 7.6326 + 1.00 * 0.0067 | | | | T_final = wxu * wxu_scale * Exray + wu * Eadp | | 1.5631 = 0.21 * 1.00 * 7.5874 + 1.00 * 0.0045 | |-----------------------------------------------------------------------------| | number of iterations = 23 | number of function evaluations = 24 | |-----------------------------------------------------------------------------| |-ADP statistics (Wilson B = 25.121)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 6255 0 0.00 117.10 26.33 None None None | | all(noH): 6255 0 0.00 117.10 26.33 None None None | | Sol. : 0 0 None None None None None None | | Mac. : 6255 0 0.00 117.10 26.33 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: 0.000 - 11.710: 203 | 5: 58.550 - 70.260: 136 | | 1: 11.710 - 23.420: 3284 | 6: 70.260 - 81.969: 72 | | 2: 23.420 - 35.130: 1811 | 7: 81.969 - 93.679: 42 | | 3: 35.130 - 46.840: 395 | 8: 93.679 - 105.389: 25 | | 4: 46.840 - 58.550: 266 | 9: 105.389 - 117.099: 21 | | =>continue=> | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.2216 r_free= 0.2676 ksol= 0.35 Bsol= 50.00 scale= 2.155 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (2.32,2.32,2.32,0.00,0.00,-0.00); trace/3= 2.32 | | | | maximum likelihood estimate for coordinate error: 0.37 A | | x-ray target function (ml) for work reflections: 7.578854 | |-----------------------------------------------------------------------------| ================== ordered solvent: location/analysis/update ================== Start model: number = 0 b_iso_min = None (limit = 1.00) b_iso_max = None (limit = 50.00) b_iso_mean = None occupancy_min = None (limit = 0.10) occupancy_max = None (limit = 1.20) dist_sol_mol_min = None (limit = 1.80) dist_sol_mol_max = None (limit = 6.00) Peak search: maximum allowed number of peaks: 6250 number of peaks from mFobs-DFmodel map: 449 number of peaks from 2mFobs-DFmodel map: 2500 number of peaks after clustering: 392 Filter by distance & map next to the model: mapped sites are within: 0.520 - 5.987 number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 291 from: 392 mapped sites are within: 1.816 - 5.987 Peak filtering (peak - peak close contact elimination): peaks rejected: 0 total number of peaks selected: 291 Final model: number = 291 b_iso_min = 26.33 (limit = 1.00) b_iso_max = 26.33 (limit = 50.00) b_iso_mean = 26.33 occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 1.82 (limit = 1.80) dist_sol_mol_max = 5.99 (limit = 6.00) ====================== bulk solvent modeling and scaling ====================== |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.2037 r_free= 0.2379 ksol= 0.34 Bsol= 50.00 scale= 2.123 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (2.43,2.43,2.43,0.00,0.00,-0.00); trace/3= 2.43 | | | | maximum likelihood estimate for coordinate error: 0.32 A | | x-ray target function (ml) for work reflections: 7.486761 | |-----------------------------------------------------------------------------| ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 6.888030 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 121.803 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.171233 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 117.753 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.2037 final r-factor (work) = 0.1944 | | start r-factor (free) = 0.2379 final r-factor (free) = 0.2423 | |-----------------------------------------------------------------------------| | T_start = wxc * wxc_scale * Exray + wc * Echem | | 26.1593 = 6.89 * 0.50 * 7.5465 + 1.00 * 0.1690 | | | | T_final = wxc * wxc_scale * Exray + wc * Echem | | 25.8504 = 6.89 * 0.50 * 7.4673 + 1.00 * 0.1330 | |-----------------------------------------------------------------------------| | number of iterations = 25 | number of function evaluations = 27 | |-----------------------------------------------------------------------------| ================================ ADP refinement =============================== ----------Individual ADP refinement---------- |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.1944 final r-factor (work) = 0.1882 | | start r-factor (free) = 0.2423 final r-factor (free) = 0.2396 | |-----------------------------------------------------------------------------| | T_start = wxu * wxu_scale * Exray + wu * Eadp | | 1.2834 = 0.17 * 1.00 * 7.4673 + 1.00 * 0.0047 | | | | T_final = wxu * wxu_scale * Exray + wu * Eadp | | 1.2813 = 0.17 * 1.00 * 7.4563 + 1.00 * 0.0045 | |-----------------------------------------------------------------------------| | number of iterations = 18 | number of function evaluations = 19 | |-----------------------------------------------------------------------------| |-ADP statistics (Wilson B = 25.121)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 6546 0 2.33 119.19 25.98 None None None | | all(noH): 6546 0 2.33 119.19 25.98 None None None | | Sol. : 291 0 3.23 59.44 29.93 None None None | | Mac. : 6255 0 2.33 119.19 25.79 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: 2.330 - 14.016: 627 | 5: 60.762 - 72.449: 124 | | 1: 14.016 - 25.703: 3737 | 6: 72.449 - 84.135: 75 | | 2: 25.703 - 37.389: 1297 | 7: 84.135 - 95.822: 35 | | 3: 37.389 - 49.076: 396 | 8: 95.822 - 107.508: 18 | | 4: 49.076 - 60.762: 219 | 9: 107.508 - 119.195: 18 | | =>continue=> | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.1882 r_free= 0.2396 ksol= 0.34 Bsol= 50.00 scale= 2.114 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (2.43,2.43,2.43,0.00,0.00,-0.00); trace/3= 2.43 | | | | maximum likelihood estimate for coordinate error: 0.33 A | | x-ray target function (ml) for work reflections: 7.449879 | |-----------------------------------------------------------------------------| ================== ordered solvent: location/analysis/update ================== Start model: number = 291 b_iso_min = 3.23 (limit = 1.00) b_iso_max = 59.44 (limit = 50.00) b_iso_mean = 29.93 occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 2.06 (limit = 1.80) dist_sol_mol_max = 5.96 (limit = 6.00) Peak search: maximum allowed number of peaks: 6250 number of peaks from mFobs-DFmodel map: 420 number of peaks from 2mFobs-DFmodel map: 2405 number of peaks after clustering: 300 Filter by distance & map next to the model: mapped sites are within: 0.214 - 5.940 number of sites selected in [dist_min= 1.80, dist_max= 6.00]: 118 from: 300 mapped sites are within: 1.802 - 5.940 Peak filtering (peak - peak close contact elimination): peaks rejected: 0 total number of peaks selected: 118 Final model: number = 398 b_iso_min = 3.23 (limit = 1.00) b_iso_max = 49.81 (limit = 50.00) b_iso_mean = 28.22 occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 1.80 (limit = 1.80) dist_sol_mol_max = 5.96 (limit = 6.00) ====================== bulk solvent modeling and scaling ====================== |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.1875 r_free= 0.2312 ksol= 0.33 Bsol= 50.00 scale= 2.126 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (3.18,3.18,3.18,0.00,0.00,-0.00); trace/3= 3.18 | | | | maximum likelihood estimate for coordinate error: 0.31 A | | x-ray target function (ml) for work reflections: 7.433926 | |-----------------------------------------------------------------------------| ========================== Target weights: x-ray data ========================= |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.792070 wxc_scale = 0.500 wc = 1.000 | | angle between x-ray and geometry gradient vectors: 137.678 (deg) | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxc = 0.173077 wxc_scale = 1.000 wc = 1.000 | | angle between Xray and ADP gradient vectors: 129.742 (deg) | |-----------------------------------------------------------------------------| ================================ xyz refinement =============================== |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.1875 final r-factor (work) = 0.1857 | | start r-factor (free) = 0.2312 final r-factor (free) = 0.2341 | |-----------------------------------------------------------------------------| | T_start = wxc * wxc_scale * Exray + wc * Echem | | 18.0062 = 4.79 * 0.50 * 7.4550 + 1.00 * 0.1437 | | | | T_final = wxc * wxc_scale * Exray + wc * Echem | | 17.9146 = 4.79 * 0.50 * 7.4304 + 1.00 * 0.1110 | |-----------------------------------------------------------------------------| | number of iterations = 25 | number of function evaluations = 27 | |-----------------------------------------------------------------------------| ================================ ADP refinement =============================== ----------Individual ADP refinement---------- |-LBFGS minimization----------------------------------------------------------| | start r-factor (work) = 0.1857 final r-factor (work) = 0.1818 | | start r-factor (free) = 0.2341 final r-factor (free) = 0.2331 | |-----------------------------------------------------------------------------| | T_start = wxu * wxu_scale * Exray + wu * Eadp | | 1.2906 = 0.17 * 1.00 * 7.4304 + 1.00 * 0.0046 | | | | T_final = wxu * wxu_scale * Exray + wu * Eadp | | 1.2897 = 0.17 * 1.00 * 7.4228 + 1.00 * 0.0050 | |-----------------------------------------------------------------------------| | number of iterations = 9 | number of function evaluations = 9 | |-----------------------------------------------------------------------------| |-ADP statistics (Wilson B = 25.121)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 6653 0 0.00 118.91 25.71 None None None | | all(noH): 6653 0 0.00 118.91 25.71 None None None | | Sol. : 398 0 0.00 55.54 31.76 None None None | | Mac. : 6255 0 2.01 118.91 25.32 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: 0.000 - 11.891: 364 | 5: 59.455 - 71.345: 131 | | 1: 11.891 - 23.782: 3643 | 6: 71.345 - 83.236: 75 | | 2: 23.782 - 35.673: 1625 | 7: 83.236 - 95.127: 43 | | 3: 35.673 - 47.564: 492 | 8: 95.127 - 107.018: 20 | | 4: 47.564 - 59.455: 243 | 9: 107.018 - 118.909: 17 | | =>continue=> | |-----------------------------------------------------------------------------| ======================= ordered solvent: final clean up ======================= Start model: number = 398 b_iso_min = 0.00 (limit = 1.00) b_iso_max = 55.54 (limit = 50.00) b_iso_mean = 31.76 occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 2.05 (limit = 1.80) dist_sol_mol_max = 5.96 (limit = 6.00) Final model: number = 388 b_iso_min = 3.51 (limit = 1.00) b_iso_max = 49.97 (limit = 50.00) b_iso_mean = 31.36 occupancy_min = 1.00 (limit = 0.10) occupancy_max = 1.00 (limit = 1.20) dist_sol_mol_min = 2.05 (limit = 1.80) dist_sol_mol_max = 5.96 (limit = 6.00) ----------X-ray data---------- |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.1831 r_free= 0.2329 ksol= 0.33 Bsol= 50.00 scale= 2.114 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (3.18,3.18,3.18,0.00,0.00,-0.00); trace/3= 3.18 | | | | maximum likelihood estimate for coordinate error: 0.32 A | | x-ray target function (ml) for work reflections: 7.422958 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 75.6707 - 5.1788 0.97 3272 159 0.2130 0.2552 8.1276 8.228| | 2: 5.1788 - 4.1106 0.98 3112 155 0.1356 0.1644 7.8761 8.0672| | 3: 4.1106 - 3.5910 0.97 3000 188 0.1468 0.1750 7.7387 7.8215| | 4: 3.5910 - 3.2627 0.97 2977 168 0.1558 0.1979 7.5865 7.8088| | 5: 3.2627 - 3.0288 0.95 2930 152 0.1709 0.2266 7.4557 7.5858| | 6: 3.0288 - 2.8502 0.93 2844 159 0.1755 0.2362 7.2991 7.4461| | 7: 2.8502 - 2.7075 0.93 2860 139 0.1762 0.2620 7.2285 7.4876| | 8: 2.7075 - 2.5896 0.89 2705 156 0.1910 0.2717 7.1596 7.3038| | 9: 2.5896 - 2.4899 0.89 2715 135 0.2060 0.2556 7.0999 7.3902| | 10: 2.4899 - 2.4040 0.81 2488 115 0.2115 0.3023 7.0774 7.2784| | 11: 2.4040 - 2.3288 0.72 2176 109 0.2299 0.3153 7.0902 7.1912| | 12: 2.3288 - 2.2623 0.67 2018 110 0.2312 0.2806 7.1132 7.2823| | 13: 2.2623 - 2.2027 0.58 1742 104 0.2705 0.3734 7.181 7.532| | 14: 2.2027 - 2.1490 0.46 1395 76 0.3164 0.3752 7.339 7.432| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 75.6707 - 5.1788 3272 159 0.84 21.52 2.03 1.91 1706271.76| | 2: 5.1788 - 4.1106 3112 155 0.92 13.72 2.19 2.12 1119490.86| | 3: 4.1106 - 3.5910 3000 188 0.90 16.33 2.16 2.10 948218.23| | 4: 3.5910 - 3.2627 2977 168 0.88 18.25 2.15 2.06 723060.91| | 5: 3.2627 - 3.0288 2930 152 0.86 20.64 2.12 2.04 602696.08| | 6: 3.0288 - 2.8502 2844 159 0.85 21.95 2.09 2.03 469088.14| | 7: 2.8502 - 2.7075 2860 139 0.84 22.75 2.07 2.01 423879.11| | 8: 2.7075 - 2.5896 2705 156 0.83 23.91 2.02 1.89 364459.47| | 9: 2.5896 - 2.4899 2715 135 0.80 26.95 1.96 1.80 333699.76| | 10: 2.4899 - 2.4040 2488 115 0.80 26.92 1.99 1.83 318772.98| | 11: 2.4040 - 2.3288 2176 109 0.80 27.04 2.01 1.79 305463.63| | 12: 2.3288 - 2.2623 2018 110 0.81 26.41 2.04 1.78 298736.36| | 13: 2.2623 - 2.2027 1742 104 0.76 30.75 2.14 1.86 366985.74| | 14: 2.2027 - 2.1490 1395 76 0.63 41.90 2.25 1.80 624233.56| |alpha: min = 1.78 max = 2.12 mean = 1.95| |beta: min = 298736.36 max = 1706271.76 mean = 657914.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 90.00 mean = 23.00| |phase err.(test): min = 0.00 max = 89.39 mean = 23.30| |-----------------------------------------------------------------------------| ====================== bulk solvent modeling and scaling ====================== |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.1826 r_free= 0.2324 ksol= 0.34 Bsol= 65.65 scale= 2.111 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.32 A | | x-ray target function (ml) for work reflections: 7.421608 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.15 - 75.62 A; n_refl. = 38159)------------------------------| | | | r_work= 0.1826 r_free= 0.2324 ksol= 0.34 Bsol= 65.65 scale= 2.111 | | | | overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):| | (0.00,0.00,0.00,0.00,0.00,-0.00); trace/3= 0.00 | | | | maximum likelihood estimate for coordinate error: 0.32 A | | x-ray target function (ml) for work reflections: 7.421608 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 75.6707 - 5.1788 0.97 3272 159 0.2125 0.2562 8.1276 8.23| | 2: 5.1788 - 4.1106 0.98 3112 155 0.1356 0.1646 7.8765 8.0679| | 3: 4.1106 - 3.5910 0.97 3000 188 0.1471 0.1753 7.7395 7.8223| | 4: 3.5910 - 3.2627 0.97 2977 168 0.1557 0.1975 7.5862 7.8097| | 5: 3.2627 - 3.0288 0.95 2930 152 0.1700 0.2270 7.4544 7.5859| | 6: 3.0288 - 2.8502 0.93 2844 159 0.1744 0.2359 7.2964 7.4451| | 7: 2.8502 - 2.7075 0.93 2860 139 0.1754 0.2619 7.227 7.4839| | 8: 2.7075 - 2.5896 0.89 2705 156 0.1902 0.2712 7.1561 7.3014| | 9: 2.5896 - 2.4899 0.89 2715 135 0.2054 0.2548 7.0962 7.3838| | 10: 2.4899 - 2.4040 0.81 2488 115 0.2109 0.3026 7.0744 7.2786| | 11: 2.4040 - 2.3288 0.72 2176 109 0.2295 0.3132 7.088 7.1878| | 12: 2.3288 - 2.2623 0.67 2018 110 0.2309 0.2813 7.112 7.2824| | 13: 2.2623 - 2.2027 0.58 1742 104 0.2704 0.3724 7.1801 7.5313| | 14: 2.2027 - 2.1490 0.46 1395 76 0.3163 0.3749 7.3386 7.432| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 75.6707 - 5.1788 3272 159 0.83 21.68 2.02 1.90 1729678.56| | 2: 5.1788 - 4.1106 3112 155 0.92 13.76 2.19 2.11 1122862.76| | 3: 4.1106 - 3.5910 3000 188 0.90 16.38 2.16 2.10 950321.91| | 4: 3.5910 - 3.2627 2977 168 0.88 18.29 2.16 2.07 725331.21| | 5: 3.2627 - 3.0288 2930 152 0.86 20.71 2.13 2.04 606450.12| | 6: 3.0288 - 2.8502 2844 159 0.85 22.01 2.10 2.04 469766.50| | 7: 2.8502 - 2.7075 2860 139 0.84 22.78 2.08 2.02 424394.38| | 8: 2.7075 - 2.5896 2705 156 0.83 23.83 2.03 1.89 361907.39| | 9: 2.5896 - 2.4899 2715 135 0.80 26.81 1.97 1.81 330530.78| | 10: 2.4899 - 2.4040 2488 115 0.80 26.80 1.99 1.84 316100.00| | 11: 2.4040 - 2.3288 2176 109 0.80 26.93 2.01 1.80 303267.90| | 12: 2.3288 - 2.2623 2018 110 0.81 26.36 2.05 1.79 297871.94| | 13: 2.2623 - 2.2027 1742 104 0.76 30.68 2.15 1.87 365788.30| | 14: 2.2027 - 2.1490 1395 76 0.63 41.83 2.25 1.81 622797.66| |alpha: min = 1.79 max = 2.11 mean = 1.95| |beta: min = 297871.94 max = 1729678.56 mean = 660171.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.91 mean = 23.00| |phase err.(test): min = 0.00 max = 89.92 mean = 23.31| |-----------------------------------------------------------------------------| |-ADP statistics (Wilson B = 25.121)------------------------------------------| | Atom | Number of | Isotropic or equivalent| Anisotropy lmin/max | | type |iso aniso | min max mean | min max mean | | - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - - | | all : 6643 0 5.23 122.12 28.89 None None None | | all(noH): 6643 0 5.23 122.12 28.89 None None None | | Sol. : 388 0 6.73 53.19 34.57 None None None | | Mac. : 6255 0 5.23 122.12 28.54 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: 5.229 - 16.918: 693 | 5: 63.676 - 75.366: 120 | | 1: 16.918 - 28.608: 3694 | 6: 75.366 - 87.055: 73 | | 2: 28.608 - 40.297: 1313 | 7: 87.055 - 98.744: 43 | | 3: 40.297 - 51.987: 450 | 8: 98.744 - 110.434: 19 | | 4: 51.987 - 63.676: 221 | 9: 110.434 - 122.123: 17 | | =>continue=> | |-----------------------------------------------------------------------------| ================= 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) 1_wat: ordered solvent update (add / remove) ------------------------------------------------------------------------ R-factors, x-ray target values and norm of gradient of x-ray target stage r-work r-free xray_target_w xray_target_t 0 : 0.3243 0.3131 7.754289e+00 7.797944e+00 1_bss: 0.2582 0.2742 7.690252e+00 7.754360e+00 1_xyz: 0.2348 0.2713 7.623999e+00 7.734510e+00 1_adp: 0.2216 0.2676 7.578854e+00 7.714267e+00 2_bss: 0.2037 0.2379 7.486761e+00 7.615026e+00 2_xyz: 0.1944 0.2423 7.473436e+00 7.629683e+00 2_adp: 0.1882 0.2396 7.449879e+00 7.620893e+00 3_bss: 0.1875 0.2312 7.433926e+00 7.596287e+00 3_xyz: 0.1857 0.2341 7.435421e+00 7.607941e+00 3_adp: 0.1818 0.2331 7.418785e+00 7.599553e+00 3_bss: 0.1826 0.2324 7.421608e+00 7.597030e+00 ------------------------------------------------------------------------ stage k_sol b_sol b11 b22 b33 b12 b13 b23 0 : 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1_bss: 0.347 50.000 2.318 2.318 2.318 0.000 0.000 -0.000 1_xyz: 0.347 50.000 2.318 2.318 2.318 0.000 0.000 -0.000 1_adp: 0.347 50.000 2.318 2.318 2.318 0.000 0.000 -0.000 2_bss: 0.337 50.000 2.425 2.425 2.425 0.000 0.000 -0.000 2_xyz: 0.337 50.000 2.425 2.425 2.425 0.000 0.000 -0.000 2_adp: 0.337 50.000 2.425 2.425 2.425 0.000 0.000 -0.000 3_bss: 0.335 50.000 3.181 3.181 3.181 0.000 0.000 -0.000 3_xyz: 0.335 50.000 3.181 3.181 3.181 0.000 0.000 -0.000 3_adp: 0.335 50.000 3.181 3.181 3.181 0.000 0.000 -0.000 3_bss: 0.337 65.653 0.000 0.000 0.000 0.000 0.000 -0.000 ------------------------------------------------------------------------ stage <pher> fom alpha beta 0 : 31.982 0.7396 1.7443 1387840.945 1_bss: 29.194 0.7699 1.9599 974799.679 1_xyz: 28.118 0.7819 1.9866 928279.367 1_adp: 27.348 0.7902 1.9633 892955.282 2_bss: 24.199 0.8225 1.9720 689127.593 2_xyz: 24.569 0.8186 1.9572 710017.017 2_adp: 23.913 0.8260 1.9393 697946.465 3_bss: 23.043 0.8347 1.9776 647848.901 3_xyz: 23.264 0.8326 1.9689 664228.536 3_adp: 22.951 0.8359 1.9502 655975.202 3_bss: 23.013 0.8352 1.9517 659994.149 ------------------------------------------------------------------------ stage angl bond chir dihe plan repu geom_target 0 : 1.693 0.012 0.089 17.723 0.007 4.142 1.5608e-01 1_bss: 1.693 0.012 0.089 17.723 0.007 4.142 1.5608e-01 1_xyz: 1.635 0.010 0.087 18.407 0.008 4.141 1.4451e-01 1_adp: 1.635 0.010 0.087 18.407 0.008 4.141 1.4451e-01 2_bss: 1.635 0.010 0.087 18.407 0.008 4.135 1.6105e-01 2_xyz: 1.421 0.009 0.083 18.369 0.007 4.141 1.2821e-01 2_adp: 1.421 0.009 0.083 18.369 0.007 4.141 1.2821e-01 3_bss: 1.421 0.009 0.083 18.369 0.007 4.136 1.3974e-01 3_xyz: 1.283 0.007 0.075 17.946 0.007 4.138 1.0907e-01 3_adp: 1.283 0.007 0.075 17.946 0.007 4.138 1.0907e-01 3_bss: 1.283 0.007 0.075 17.946 0.007 4.138 1.0822e-01 ------------------------------------------------------------------------ Maximal deviations: stage angl bond chir dihe plan repu |grad| 0 : 25.044 0.095 0.406113.659 0.154 1.486 1.5120e-01 1_bss: 25.044 0.095 0.406113.659 0.154 1.486 1.5120e-01 1_xyz: 25.658 0.089 0.312115.970 0.157 1.921 6.5351e-02 1_adp: 25.658 0.089 0.312115.970 0.157 1.921 6.5351e-02 2_bss: 25.658 0.089 0.312115.970 0.157 1.816 6.3368e-02 2_xyz: 23.516 0.082 0.391119.400 0.155 1.926 4.8056e-02 2_adp: 23.516 0.082 0.391119.400 0.155 1.926 4.8056e-02 3_bss: 23.516 0.082 0.391119.400 0.155 1.802 4.8972e-02 3_xyz: 23.841 0.048 0.338113.663 0.152 1.976 3.4188e-02 3_adp: 23.841 0.048 0.338113.663 0.152 1.976 3.4188e-02 3_bss: 23.841 0.048 0.338113.663 0.152 1.976 3.4255e-02 ------------------------------------------------------------------------ |-----overall-----|---macromolecule----|------solvent-------| stage b_max b_min b_ave b_max b_min b_ave b_max b_min b_ave 0 : 118.66 7.67 27.52 117.10 0.00 26.33 26.33 26.33 26.33 1_bss: 118.66 7.67 27.52 117.10 0.00 26.33 26.33 26.33 26.33 1_xyz: 118.66 7.67 27.52 119.19 2.33 25.79 59.44 3.23 29.93 1_adp: 117.10 0.00 26.33 119.19 2.33 25.79 49.81 3.23 28.22 2_bss: 117.10 0.00 26.33 119.19 2.33 25.79 49.81 3.23 28.22 2_xyz: 117.10 0.00 26.33 118.91 2.01 25.32 55.54 0.00 31.76 2_adp: 119.19 2.33 25.98 122.12 5.23 28.54 53.19 6.73 34.57 ------------------------------------------------------------------------ stage Deviation of refined model from start model max min mean 0 : 0.000 0.000 0.000 1_bss: 0.000 0.000 0.000 1_xyz: 2.308 0.002 0.111 1_adp: 2.308 0.002 0.111 2_bss: 2.308 0.002 0.111 2_xyz: 2.461 0.002 0.117 2_adp: 2.461 0.002 0.117 3_bss: 2.461 0.002 0.117 3_xyz: 2.748 0.003 0.122 3_adp: 2.748 0.003 0.122 3_bss: 2.748 0.003 0.122 ------------------------------------------------------------------------ stage number of ordered solvent 0 : 0 1_bss: 0 1_xyz: 0 1_adp: 0 2_bss: 291 2_xyz: 291 2_adp: 291 3_bss: 398 3_xyz: 398 3_adp: 398 3_bss: 388 ------------------------------------------------------------------------ ===================== NCS restraints at end of refinement ===================== NCS restraint group 1: NCS operator 1: Reference selection: "chain A and (resseq 9:118 or resseq 128:207 or resseq 215:366 )" Other selection: "chain C and (resseq 9:118 or resseq 128:207 or resseq 215:366 )" Number of atom pairs: 2603 Rotation={{-0.999497, -0.0191321, 0.0252909}, {0.0247831, 0.0263321, 0.999346}, {-0.0197855, 0.99947, -0.0258447}} Translation={{38.4881}, {-44.0747}, {42.34}} Histogram of differences: 0.002570 - 0.054938: 2350 0.054938 - 0.107305: 233 0.107305 - 0.159673: 16 0.159673 - 0.212040: 2 0.212040 - 0.264408: 1 0.264408 - 0.316775: 1 RMS difference with respect to the reference: 0.037521 Writing refined structure to PDB file: AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3.pdb n_use = 6643 n_use_u_iso = 6643 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 6643 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 n_anisotropic_flag = 0 total number of scatterers = 6643 Writing map coefficients to MTZ file: /usr/users/dale/structure/fmo-ct/tronrud_2007/AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3_001_map_coeffs.mtz Writing refined fmodel to MTZ file: /usr/users/dale/structure/fmo-ct/tronrud_2007/AutoBuild_run_3_/TEMP0/Build_composite_refined_side_3_001_f_model.mtz # Date 2007/12/14 11:38:03 Final R(work) = 0.1826, R(free) = 0.2324