Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6017437.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6017437.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6017437.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.14, per 1000 atoms: 0.34 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 134.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.89: 392 0.89 - 1.16: 1231 1.16 - 1.43: 698 1.43 - 1.70: 807 1.70 - 1.97: 25 Bond restraints: 3153 Sorted by residual: bond pdb=" N MET A 17 " pdb=" CA MET A 17 " ideal model delta sigma weight residual 1.459 1.669 -0.210 1.19e-02 7.06e+03 3.11e+02 bond pdb=" CA ALA A 36 " pdb=" C ALA A 36 " ideal model delta sigma weight residual 1.525 1.309 0.216 1.28e-02 6.10e+03 2.85e+02 bond pdb=" C LYS A 122 " pdb=" N VAL A 123 " ideal model delta sigma weight residual 1.332 1.134 0.198 1.20e-02 6.94e+03 2.73e+02 bond pdb=" CG HIS A 115 " pdb=" ND1 HIS A 115 " ideal model delta sigma weight residual 1.378 1.201 0.177 1.10e-02 8.26e+03 2.59e+02 bond pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 1.330 1.539 -0.209 1.30e-02 5.92e+03 2.58e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.41: 2948 4.41 - 8.82: 1933 8.82 - 13.22: 713 13.22 - 17.63: 166 17.63 - 22.03: 17 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 181 " pdb=" C VAL A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 121.87 104.73 17.14 9.70e-01 1.06e+00 3.12e+02 angle pdb=" CA LEU A 58 " pdb=" C LEU A 58 " pdb=" O LEU A 58 " ideal model delta sigma weight residual 120.92 137.20 -16.28 1.12e+00 7.97e-01 2.11e+02 angle pdb=" O GLY A 120 " pdb=" C GLY A 120 " pdb=" N SER A 121 " ideal model delta sigma weight residual 122.77 110.06 12.71 9.40e-01 1.13e+00 1.83e+02 angle pdb=" N PRO A 43 " pdb=" CA PRO A 43 " pdb=" CB PRO A 43 " ideal model delta sigma weight residual 103.32 114.67 -11.35 8.40e-01 1.42e+00 1.83e+02 angle pdb=" O LYS A 130 " pdb=" C LYS A 130 " pdb=" N ASP A 131 " ideal model delta sigma weight residual 122.07 109.18 12.89 1.03e+00 9.43e-01 1.57e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.29: 1310 17.29 - 34.58: 121 34.58 - 51.86: 32 51.86 - 69.15: 16 69.15 - 86.43: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C AGLU A 94 " pdb=" N AGLU A 94 " pdb=" CA AGLU A 94 " pdb=" CB AGLU A 94 " ideal model delta harmonic sigma weight residual -122.60 -142.08 19.48 0 2.50e+00 1.60e-01 6.07e+01 dihedral pdb=" C ALA A 86 " pdb=" N ALA A 86 " pdb=" CA ALA A 86 " pdb=" CB ALA A 86 " ideal model delta harmonic sigma weight residual -122.60 -141.23 18.63 0 2.50e+00 1.60e-01 5.55e+01 dihedral pdb=" N ALA A 14 " pdb=" C ALA A 14 " pdb=" CA ALA A 14 " pdb=" CB ALA A 14 " ideal model delta harmonic sigma weight residual 122.90 105.05 17.85 0 2.50e+00 1.60e-01 5.10e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.195: 102 0.195 - 0.390: 66 0.390 - 0.585: 44 0.585 - 0.779: 22 0.779 - 0.974: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.74 0.97 2.00e-01 2.50e+01 2.37e+01 chirality pdb=" CA BGLU A 94 " pdb=" N BGLU A 94 " pdb=" C BGLU A 94 " pdb=" CB BGLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 3.42 -0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.74 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.076 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG PHE A 119 " -0.087 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.062 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.078 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.107 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.072 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.022 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.049 2.00e-02 2.50e+03 5.91e-02 1.05e+02 pdb=" CG PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.138 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.035 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.089 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.092 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.014 2.00e-02 2.50e+03 6.46e-02 9.40e+01 pdb=" CG HIS A 115 " 0.072 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " -0.035 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.094 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.009 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.115 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " 0.065 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 900 2.30 - 2.88: 8022 2.88 - 3.45: 10553 3.45 - 4.03: 15292 4.03 - 4.60: 21823 Nonbonded interactions: 56590 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.726 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.817 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.832 2.450 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.839 2.450 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.850 2.450 ... (remaining 56585 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 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 = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_6017437_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2795 r_free= 0.1815 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.392730 | | target function (ml) not normalized (work): 71351.109377 | | target function (ml) not normalized (free): 3262.792285 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3204 0.2126 7.485 5.0438| | 2: 3.63 - 2.88 1.00 2711 122 0.2651 0.1739 4.332 4.3478| | 3: 2.88 - 2.52 1.00 2682 148 0.2581 0.1665 4.1949 4.1839| | 4: 2.52 - 2.29 1.00 2661 139 0.2537 0.1539 3.5004 3.4966| | 5: 2.29 - 2.13 1.00 2678 122 0.2645 0.1503 3.3834 3.5199| | 6: 2.13 - 2.00 1.00 2692 117 0.2756 0.1892 3.299 3.3821| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 49.25 - 3.64 2819 159 0.88 17.76 0.77 0.23 1339.00| | 2: 3.63 - 2.88 2711 122 0.82 24.15 1.32 0.23 1339.00| | 3: 2.88 - 2.52 2682 148 0.73 33.19 1.29 0.23 1339.00| | 4: 2.52 - 2.29 2661 139 0.94 10.80 1.29 0.26 126.08| | 5: 2.29 - 2.13 2678 122 0.92 12.84 1.31 0.26 126.08| | 6: 2.13 - 2.00 2692 117 0.90 15.75 1.34 0.26 126.08| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 126.08 max = 1339.00 mean = 739.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.92 mean = 19.09| |phase err.(test): min = 0.00 max = 89.16 mean = 19.19| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.273 1557 Z= 5.355 Angle : 5.322 17.136 2118 Z= 3.696 Chirality : 0.367 0.974 243 Planarity : 0.032 0.088 284 Dihedral : 13.812 86.433 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 4.35 % Favored : 95.03 % Cbeta Deviations : 32.97 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.45), residues: 224 helix: -2.86 (0.34), residues: 106 sheet: -2.09 (0.75), residues: 28 loop : -0.04 (0.57), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.083 0.017 ARG A 48 TYR 0.064 0.030 TYR A 141 PHE 0.103 0.044 PHE A 119 HIS 0.073 0.031 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2795 r_free= 0.1815 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.392730 | | target function (ml) not normalized (work): 71351.109377 | | target function (ml) not normalized (free): 3262.792285 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3283 percent. r_work = 0.2927 r_free = 0.1986 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2874 0.2927 0.1986 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2874 0.2927 0.1986 n_refl.: 17050 remove outliers: r(all,work,free)=0.2164 0.2176 0.1986 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2137 0.2148 0.1967 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1625 0.1623 0.1658 n_refl.: 17045 remove outliers: r(all,work,free)=0.1624 0.1622 0.1658 n_refl.: 17044 ======================== 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 32.574-12.150 100.00 89 5 0.4042 394.969 363.306 0.652 1.013 0.399 11.894-9.307 99.02 97 4 0.1851 633.937 618.380 0.926 1.013 0.390 9.237-7.194 100.00 213 7 0.2171 518.496 509.705 0.959 1.013 0.350 7.162-5.571 100.00 427 22 0.2350 389.132 375.988 0.917 1.012 0.283 5.546-4.326 100.00 867 58 0.1406 534.216 527.988 0.957 1.010 0.215 4.315-3.360 100.00 1859 96 0.1309 508.044 503.793 1.020 1.006 0.201 3.356-2.611 100.00 3867 181 0.1678 333.756 328.771 1.014 1.000 0.029 2.608-2.000 99.99 8818 434 0.1644 217.552 213.524 1.030 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4678 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1622 r_free=0.1658 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1632 r_free=0.1663 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.774344 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.960999 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1351 0.1634 0.0283 0.008 1.0 1.3 0.5 0.0 0 10.887 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.34 2.83 3.013 18.448 0.961 0.023 12.76 16.53 3.77 3.634 18.698 0.961 0.020 Individual atomic B min max mean iso aniso Overall: 6.29 113.89 19.95 4.14 1785 0 Protein: 6.29 113.20 17.17 4.14 1519 0 Water: 8.74 113.89 36.15 N/A 258 0 Other: 21.36 37.34 26.29 N/A 8 0 Chain A: 6.29 113.89 19.95 N/A 1785 0 Histogram: Values Number of atoms 6.29 - 17.05 1094 17.05 - 27.81 334 27.81 - 38.57 183 38.57 - 49.33 97 49.33 - 60.09 50 60.09 - 70.85 13 70.85 - 81.61 6 81.61 - 92.37 4 92.37 - 103.13 1 103.13 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1653 r_work=0.1279 r_free=0.1659 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1659 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1275 r_free = 0.1654 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1275 r_free= 0.1654 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020019 | | target function (ls_wunit_k1) not normalized (work): 325.045070 | | target function (ls_wunit_k1) not normalized (free): 27.149862 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1654 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1907 0.1906 0.1977 n_refl.: 17044 remove outliers: r(all,work,free)=0.1907 0.1906 0.1977 n_refl.: 17044 overall B=-0.37 to atoms: r(all,work,free)=0.1880 0.1879 0.1962 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1290 0.1273 0.1648 n_refl.: 17044 remove outliers: r(all,work,free)=0.1289 0.1271 0.1648 n_refl.: 17042 ======================== 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 32.574-12.150 95.83 87 5 0.3536 303.791 279.365 0.624 1.007 0.369 11.894-9.307 99.02 97 4 0.1696 488.600 477.139 0.914 1.007 0.368 9.237-7.194 100.00 213 7 0.1800 399.626 396.797 0.958 1.007 0.351 7.162-5.571 100.00 427 22 0.1842 299.919 294.471 0.930 1.007 0.301 5.546-4.326 100.00 867 58 0.1043 411.741 409.204 0.955 1.006 0.206 4.315-3.360 100.00 1859 96 0.0924 391.570 390.990 1.015 1.004 0.201 3.356-2.611 100.00 3867 181 0.1298 257.239 255.890 1.011 1.001 0.091 2.608-2.000 99.99 8818 434 0.1344 167.676 166.344 1.016 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3124 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1271 r_free=0.1648 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1273 r_free=0.1647 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1647 | n_water=258 | time (s): 0.870 (total time: 0.870) Filter (dist) r_work=0.1281 r_free=0.1635 | n_water=252 | time (s): 20.070 (total time: 20.940) Filter (q & B) r_work=0.1281 r_free=0.1633 | n_water=250 | time (s): 1.690 (total time: 22.630) Compute maps r_work=0.1281 r_free=0.1633 | n_water=250 | time (s): 0.800 (total time: 23.430) Filter (map) r_work=0.1322 r_free=0.1611 | n_water=210 | time (s): 2.000 (total time: 25.430) Find peaks r_work=0.1322 r_free=0.1611 | n_water=210 | time (s): 0.450 (total time: 25.880) Add new water r_work=0.1545 r_free=0.1853 | n_water=372 | time (s): 1.410 (total time: 27.290) Refine new water occ: r_work=0.1337 r_free=0.1572 adp: r_work=0.1276 r_free=0.1558 occ: r_work=0.1281 r_free=0.1539 adp: r_work=0.1247 r_free=0.1543 occ: r_work=0.1247 r_free=0.1538 adp: r_work=0.1236 r_free=0.1538 ADP+occupancy (water only), MIN, final r_work=0.1236 r_free=0.1538 r_work=0.1236 r_free=0.1538 | n_water=372 | time (s): 14.500 (total time: 41.790) Filter (q & B) r_work=0.1241 r_free=0.1549 | n_water=357 | time (s): 1.820 (total time: 43.610) Filter (dist only) r_work=0.1241 r_free=0.1550 | n_water=356 | time (s): 27.930 (total time: 71.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.854603 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.989421 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1213 0.1606 0.0393 0.008 0.9 1.9 0.5 0.0 0 12.927 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 16.06 3.93 4.198 21.061 0.989 0.018 11.99 16.24 4.25 4.283 21.379 0.989 0.018 Individual atomic B min max mean iso aniso Overall: 6.93 107.83 21.47 4.39 1883 0 Protein: 6.93 107.83 17.87 4.37 1519 0 Water: 8.34 65.80 36.48 N/A 356 0 Other: 25.25 47.75 37.31 N/A 8 0 Chain A: 6.93 107.83 19.58 N/A 1737 0 Chain S: 17.26 63.72 43.97 N/A 146 0 Histogram: Values Number of atoms 6.93 - 17.02 1032 17.02 - 27.11 373 27.11 - 37.20 208 37.20 - 47.29 156 47.29 - 57.38 84 57.38 - 67.47 17 67.47 - 77.56 6 77.56 - 87.65 4 87.65 - 97.74 1 97.74 - 107.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1624 r_work=0.1201 r_free=0.1627 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1201 r_free = 0.1627 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1195 r_free = 0.1623 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1195 r_free= 0.1623 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017080 | | target function (ls_wunit_k1) not normalized (work): 277.290031 | | target function (ls_wunit_k1) not normalized (free): 25.169793 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1216 0.1195 0.1623 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1763 0.1753 0.1998 n_refl.: 17042 remove outliers: r(all,work,free)=0.1763 0.1753 0.1998 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1738 0.1727 0.1981 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1211 0.1190 0.1617 n_refl.: 17042 remove outliers: r(all,work,free)=0.1210 0.1189 0.1617 n_refl.: 17041 ======================== 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 32.574-12.150 94.79 86 5 0.3181 300.625 286.137 0.604 1.006 0.350 11.894-9.307 99.02 97 4 0.1517 488.600 487.490 0.912 1.006 0.337 9.237-7.194 100.00 213 7 0.1669 399.626 401.087 0.973 1.006 0.310 7.162-5.571 100.00 427 22 0.1535 299.919 295.750 0.934 1.006 0.261 5.546-4.326 100.00 867 58 0.0869 411.741 409.332 0.958 1.005 0.211 4.315-3.360 100.00 1859 96 0.0826 391.570 390.846 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1201 257.239 256.481 1.012 1.000 0.058 2.608-2.000 99.99 8818 434 0.1333 167.676 166.554 1.018 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3526 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1617 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN B Total number of N/Q/H flips: 1 r_work=0.1189 r_free=0.1619 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1619 | n_water=356 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1189 r_free=0.1621 | n_water=355 | time (s): 26.520 (total time: 27.130) Filter (q & B) r_work=0.1189 r_free=0.1621 | n_water=355 | time (s): 0.760 (total time: 27.890) Compute maps r_work=0.1189 r_free=0.1621 | n_water=355 | time (s): 0.590 (total time: 28.480) Filter (map) r_work=0.1262 r_free=0.1622 | n_water=257 | time (s): 1.730 (total time: 30.210) Find peaks r_work=0.1262 r_free=0.1622 | n_water=257 | time (s): 0.500 (total time: 30.710) Add new water r_work=0.1467 r_free=0.1764 | n_water=418 | time (s): 1.900 (total time: 32.610) Refine new water occ: r_work=0.1251 r_free=0.1550 adp: r_work=0.1243 r_free=0.1548 occ: r_work=0.1221 r_free=0.1521 adp: r_work=0.1211 r_free=0.1515 occ: r_work=0.1202 r_free=0.1515 adp: r_work=0.1193 r_free=0.1506 ADP+occupancy (water only), MIN, final r_work=0.1193 r_free=0.1506 r_work=0.1193 r_free=0.1506 | n_water=418 | time (s): 44.390 (total time: 77.000) Filter (q & B) r_work=0.1195 r_free=0.1515 | n_water=408 | time (s): 1.740 (total time: 78.740) Filter (dist only) r_work=0.1194 r_free=0.1518 | n_water=407 | time (s): 34.150 (total time: 112.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.922417 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.164228 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1168 0.1554 0.0385 0.009 1.0 2.6 0.5 0.0 0 0.961 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.68 15.54 3.85 4.415 21.721 0.164 4.994 11.45 15.60 4.15 5.014 21.602 0.164 4.971 Individual atomic B min max mean iso aniso Overall: 6.09 105.14 21.01 4.81 1934 0 Protein: 6.09 105.14 17.07 4.80 1519 0 Water: 8.64 64.68 35.46 N/A 407 0 Other: 26.96 46.67 35.24 N/A 8 0 Chain A: 6.09 105.14 18.80 N/A 1733 0 Chain S: 14.43 64.68 40.11 N/A 201 0 Histogram: Values Number of atoms 6.09 - 15.99 1044 15.99 - 25.90 367 25.90 - 35.80 216 35.80 - 45.71 181 45.71 - 55.62 83 55.62 - 65.52 29 65.52 - 75.43 5 75.43 - 85.33 5 85.33 - 95.24 2 95.24 - 105.14 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1560 r_work=0.1146 r_free=0.1561 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1146 r_free = 0.1561 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1138 r_free = 0.1570 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1138 r_free= 0.1570 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.971092 | | target function (ml) not normalized (work): 80700.712180 | | target function (ml) not normalized (free): 4197.981333 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1159 0.1138 0.1570 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1676 0.1666 0.1913 n_refl.: 17041 remove outliers: r(all,work,free)=0.1676 0.1666 0.1913 n_refl.: 17041 overall B=-0.47 to atoms: r(all,work,free)=0.1644 0.1633 0.1898 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1136 0.1572 n_refl.: 17041 remove outliers: r(all,work,free)=0.1156 0.1136 0.1572 n_refl.: 17040 ======================== 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 32.574-12.150 93.75 85 5 0.3419 297.056 281.472 0.571 1.006 0.350 11.894-9.307 99.02 97 4 0.1765 488.600 483.358 0.910 1.007 0.350 9.237-7.194 100.00 213 7 0.1771 399.626 399.462 0.978 1.007 0.291 7.162-5.571 100.00 427 22 0.1553 299.919 294.191 0.943 1.006 0.235 5.546-4.326 100.00 867 58 0.0932 411.741 407.744 0.962 1.005 0.211 4.315-3.360 100.00 1859 96 0.0890 391.570 389.548 1.012 1.004 0.202 3.356-2.611 100.00 3867 181 0.1251 257.239 255.380 1.011 1.001 0.142 2.608-2.000 99.99 8818 434 0.1095 167.676 166.243 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.1777 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1136 r_free=0.1572 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1137 r_free=0.1568 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1568 | n_water=407 | time (s): 0.740 (total time: 0.740) Filter (dist) r_work=0.1137 r_free=0.1569 | n_water=406 | time (s): 33.480 (total time: 34.220) Filter (q & B) r_work=0.1137 r_free=0.1569 | n_water=406 | time (s): 1.040 (total time: 35.260) Compute maps r_work=0.1137 r_free=0.1569 | n_water=406 | time (s): 0.730 (total time: 35.990) Filter (map) r_work=0.1195 r_free=0.1583 | n_water=315 | time (s): 1.600 (total time: 37.590) Find peaks r_work=0.1195 r_free=0.1583 | n_water=315 | time (s): 0.470 (total time: 38.060) Add new water r_work=0.1342 r_free=0.1696 | n_water=463 | time (s): 1.730 (total time: 39.790) Refine new water occ: r_work=0.1174 r_free=0.1538 adp: r_work=0.1165 r_free=0.1545 occ: r_work=0.1149 r_free=0.1516 adp: r_work=0.1139 r_free=0.1523 occ: r_work=0.1133 r_free=0.1506 adp: r_work=0.1124 r_free=0.1508 ADP+occupancy (water only), MIN, final r_work=0.1124 r_free=0.1508 r_work=0.1124 r_free=0.1508 | n_water=463 | time (s): 39.670 (total time: 79.460) Filter (q & B) r_work=0.1130 r_free=0.1513 | n_water=451 | time (s): 1.900 (total time: 81.360) Filter (dist only) r_work=0.1130 r_free=0.1511 | n_water=450 | time (s): 36.730 (total time: 118.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.947350 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.170886 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1119 0.1560 0.0441 0.009 1.0 7.4 0.5 0.0 0 0.974 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.19 15.60 4.41 4.581 21.146 0.171 4.961 11.08 15.51 4.42 4.762 21.140 0.171 4.952 Individual atomic B min max mean iso aniso Overall: 5.49 103.63 21.00 4.90 1977 0 Protein: 5.49 103.63 16.50 4.88 1519 0 Water: 8.24 66.07 36.02 N/A 450 0 Other: 21.49 42.32 29.91 N/A 8 0 Chain A: 5.49 103.63 18.12 N/A 1731 0 Chain S: 16.20 66.07 41.21 N/A 246 0 Histogram: Values Number of atoms 5.49 - 15.31 1029 15.31 - 25.12 379 25.12 - 34.93 224 34.93 - 44.75 190 44.75 - 54.56 100 54.56 - 64.38 40 64.38 - 74.19 7 74.19 - 84.00 4 84.00 - 93.82 2 93.82 - 103.63 2 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1551 r_work=0.1108 r_free=0.1551 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1551 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1574 target_work(ml) = 4.950 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1574 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.949653 | | target function (ml) not normalized (work): 80347.717671 | | target function (ml) not normalized (free): 4195.554328 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1124 0.1102 0.1574 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1592 0.1575 0.1931 n_refl.: 17040 remove outliers: r(all,work,free)=0.1592 0.1575 0.1931 n_refl.: 17040 overall B=-0.29 to atoms: r(all,work,free)=0.1574 0.1557 0.1921 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1123 0.1100 0.1575 n_refl.: 17040 remove outliers: r(all,work,free)=0.1123 0.1100 0.1575 n_refl.: 17040 ======================== 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 32.574-12.150 93.75 85 5 0.3551 297.056 276.109 0.552 0.999 0.330 11.894-9.307 99.02 97 4 0.1815 488.600 480.549 0.917 1.001 0.330 9.237-7.194 100.00 213 7 0.1663 399.626 399.488 0.986 1.001 0.260 7.162-5.571 100.00 427 22 0.1490 299.919 294.311 0.948 1.002 0.222 5.546-4.326 100.00 867 58 0.0923 411.741 407.476 0.966 1.002 0.200 4.315-3.360 100.00 1859 96 0.0859 391.570 388.959 1.008 1.002 0.188 3.356-2.611 100.00 3867 181 0.1237 257.239 255.123 1.005 1.001 0.151 2.608-2.000 99.99 8818 434 0.1039 167.676 166.813 1.000 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9922 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1100 r_free=0.1575 After: r_work=0.1102 r_free=0.1573 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1573 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1102 r_free=0.1573 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1573 | n_water=450 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1102 r_free=0.1573 | n_water=450 | time (s): 38.260 (total time: 38.900) Filter (q & B) r_work=0.1103 r_free=0.1574 | n_water=448 | time (s): 2.070 (total time: 40.970) Compute maps r_work=0.1103 r_free=0.1574 | n_water=448 | time (s): 0.820 (total time: 41.790) Filter (map) r_work=0.1182 r_free=0.1575 | n_water=331 | time (s): 1.820 (total time: 43.610) Find peaks r_work=0.1182 r_free=0.1575 | n_water=331 | time (s): 0.460 (total time: 44.070) Add new water r_work=0.1310 r_free=0.1684 | n_water=466 | time (s): 1.370 (total time: 45.440) Refine new water occ: r_work=0.1152 r_free=0.1547 adp: r_work=0.1144 r_free=0.1545 occ: r_work=0.1128 r_free=0.1533 adp: r_work=0.1119 r_free=0.1531 occ: r_work=0.1111 r_free=0.1524 adp: r_work=0.1103 r_free=0.1524 ADP+occupancy (water only), MIN, final r_work=0.1103 r_free=0.1524 r_work=0.1103 r_free=0.1524 | n_water=466 | time (s): 26.810 (total time: 72.250) Filter (q & B) r_work=0.1107 r_free=0.1533 | n_water=454 | time (s): 1.630 (total time: 73.880) Filter (dist only) r_work=0.1111 r_free=0.1532 | n_water=452 | time (s): 37.480 (total time: 111.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.851131 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.184317 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1133 0.1521 0.0388 0.009 1.0 6.1 0.5 0.0 0 0.926 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.33 15.21 3.88 4.580 20.743 0.184 4.955 11.19 15.02 3.82 4.669 20.827 0.184 4.943 Individual atomic B min max mean iso aniso Overall: 5.17 103.02 20.85 5.03 1979 0 Protein: 5.17 103.02 16.21 5.02 1519 0 Water: 8.36 66.83 36.33 N/A 452 0 Other: 19.61 38.78 26.52 N/A 8 0 Chain A: 5.17 103.02 17.81 N/A 1730 0 Chain S: 15.71 66.83 41.93 N/A 249 0 Histogram: Values Number of atoms 5.17 - 14.95 1022 14.95 - 24.74 397 24.74 - 34.52 198 34.52 - 44.31 193 44.31 - 54.09 116 54.09 - 63.88 34 63.88 - 73.66 11 73.66 - 83.45 3 83.45 - 93.23 2 93.23 - 103.02 3 =========================== Idealize ADP of riding H ========================== r_work=0.1119 r_free=0.1502 r_work=0.1119 r_free=0.1501 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1119 r_free = 0.1501 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1113 r_free = 0.1510 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1113 r_free= 0.1510 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.942653 | | target function (ml) not normalized (work): 80234.090154 | | target function (ml) not normalized (free): 4171.521149 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1124 0.1373 5.4603 5.6665| | 2: 3.63 - 2.88 1.00 2711 122 0.1101 0.1581 5.2402 5.3891| | 3: 2.88 - 2.52 1.00 2681 148 0.1374 0.1698 5.1483 5.2203| | 4: 2.52 - 2.29 1.00 2661 139 0.0943 0.1508 4.6283 4.9687| | 5: 2.29 - 2.13 1.00 2678 122 0.0964 0.1431 4.5796 4.8553| | 6: 2.13 - 2.00 1.00 2692 117 0.1107 0.1649 4.5697 4.7648| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 32.57 - 3.64 2810 159 0.94 9.34 1.00 0.95 6679.55| | 2: 3.63 - 2.88 2711 122 0.92 13.21 1.01 0.95 6679.55| | 3: 2.88 - 2.52 2681 148 0.87 19.41 0.99 0.95 6679.55| | 4: 2.52 - 2.29 2661 139 0.93 12.09 1.01 0.98 2106.75| | 5: 2.29 - 2.13 2678 122 0.92 14.02 1.00 0.98 2106.75| | 6: 2.13 - 2.00 2692 117 0.90 16.71 0.99 0.98 2106.75| |alpha: min = 0.95 max = 0.98 mean = 0.97| |beta: min = 2106.75 max = 6679.55 mean = 4417.23| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.80 mean = 14.09| |phase err.(test): min = 0.00 max = 86.60 mean = 13.87| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1132 0.1113 0.1510 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1583 0.1571 0.1827 n_refl.: 17040 remove outliers: r(all,work,free)=0.1583 0.1571 0.1827 n_refl.: 17040 overall B=-0.23 to atoms: r(all,work,free)=0.1569 0.1558 0.1818 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1133 0.1114 0.1512 n_refl.: 17040 remove outliers: r(all,work,free)=0.1133 0.1114 0.1512 n_refl.: 17040 ======================== 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 32.574-12.150 93.75 85 5 0.3591 297.056 275.747 0.552 1.003 0.330 11.894-9.307 99.02 97 4 0.1792 488.600 478.803 0.914 1.005 0.304 9.237-7.194 100.00 213 7 0.1686 399.626 400.592 0.988 1.005 0.242 7.162-5.571 100.00 427 22 0.1551 299.919 294.650 0.938 1.005 0.213 5.546-4.326 100.00 867 58 0.0955 411.741 408.280 0.961 1.004 0.195 4.315-3.360 100.00 1859 96 0.0882 391.570 389.071 1.003 1.003 0.184 3.356-2.611 100.00 3867 181 0.1256 257.239 254.799 0.999 1.001 0.151 2.608-2.000 99.99 8818 434 0.1036 167.676 166.354 0.992 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7819 ================= 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) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.2795 0.1815 0.081 5.322 8.8 119.3 19.9 258 0.000 1_bss: 0.1622 0.1658 0.081 5.322 8.4 118.9 19.5 258 0.000 1_settarget: 0.1622 0.1658 0.081 5.322 8.4 118.9 19.5 258 0.000 1_nqh: 0.1632 0.1663 0.081 5.322 8.4 118.9 19.5 258 0.007 1_weight: 0.1632 0.1663 0.081 5.322 8.4 118.9 19.5 258 0.007 1_xyzrec: 0.1351 0.1634 0.008 0.951 8.4 118.9 19.5 258 0.153 1_adp: 0.1276 0.1653 0.008 0.951 6.3 113.9 19.9 258 0.153 1_regHadp: 0.1279 0.1659 0.008 0.951 6.3 113.9 19.9 258 0.153 1_occ: 0.1275 0.1654 0.008 0.951 6.3 113.9 19.9 258 0.153 2_bss: 0.1271 0.1648 0.008 0.951 5.9 113.5 19.6 258 0.153 2_settarget: 0.1271 0.1648 0.008 0.951 5.9 113.5 19.6 258 0.153 2_updatecdl: 0.1271 0.1648 0.008 0.975 5.9 113.5 19.6 258 0.153 2_nqh: 0.1273 0.1647 0.008 0.975 5.9 113.5 19.6 258 0.150 2_sol: 0.1241 0.1550 0.008 0.975 5.9 112.8 20.9 356 n/a 2_weight: 0.1241 0.1550 0.008 0.975 5.9 112.8 20.9 356 n/a 2_xyzrec: 0.1213 0.1606 0.008 0.939 5.9 112.8 20.9 356 n/a 2_adp: 0.1199 0.1624 0.008 0.939 6.9 107.8 21.5 356 n/a 2_regHadp: 0.1201 0.1627 0.008 0.939 6.9 107.8 21.5 356 n/a 2_occ: 0.1195 0.1623 0.008 0.939 6.9 107.8 21.5 356 n/a 3_bss: 0.1189 0.1617 0.008 0.939 6.5 107.4 21.1 356 n/a 3_settarget: 0.1189 0.1617 0.008 0.939 6.5 107.4 21.1 356 n/a 3_updatecdl: 0.1189 0.1617 0.008 0.942 6.5 107.4 21.1 356 n/a 3_nqh: 0.1189 0.1619 0.008 0.942 6.5 107.4 21.1 356 n/a 3_sol: 0.1194 0.1518 0.008 0.942 6.5 107.4 21.2 407 n/a 3_weight: 0.1194 0.1518 0.008 0.942 6.5 107.4 21.2 407 n/a 3_xyzrec: 0.1168 0.1554 0.009 0.982 6.5 107.4 21.2 407 n/a 3_adp: 0.1145 0.1560 0.009 0.982 6.1 105.1 21.0 407 n/a 3_regHadp: 0.1146 0.1561 0.009 0.982 6.1 105.1 21.0 407 n/a 3_occ: 0.1138 0.1570 0.009 0.982 6.1 105.1 21.0 407 n/a 4_bss: 0.1136 0.1572 0.009 0.982 5.6 104.7 20.5 407 n/a 4_settarget: 0.1136 0.1572 0.009 0.982 5.6 104.7 20.5 407 n/a 4_updatecdl: 0.1136 0.1572 0.009 0.980 5.6 104.7 20.5 407 n/a 4_nqh: 0.1137 0.1568 0.009 0.980 5.6 104.7 20.5 407 n/a 4_sol: 0.1130 0.1511 0.009 0.980 5.6 104.7 21.0 450 n/a 4_weight: 0.1130 0.1511 0.009 0.980 5.6 104.7 21.0 450 n/a 4_xyzrec: 0.1119 0.1560 0.009 0.978 5.6 104.7 21.0 450 n/a 4_adp: 0.1108 0.1551 0.009 0.978 5.5 103.6 21.0 450 n/a 4_regHadp: 0.1108 0.1551 0.009 0.978 5.5 103.6 21.0 450 n/a 4_occ: 0.1102 0.1574 0.009 0.978 5.5 103.6 21.0 450 n/a 5_bss: 0.1100 0.1575 0.009 0.978 5.2 103.3 20.7 450 n/a 5_settarget: 0.1100 0.1575 0.009 0.978 5.2 103.3 20.7 450 n/a 5_updatecdl: 0.1100 0.1575 0.009 0.981 5.2 103.3 20.7 450 n/a 5_setrh: 0.1102 0.1573 0.009 0.981 5.2 103.3 20.7 450 n/a 5_nqh: 0.1102 0.1573 0.009 0.981 5.2 103.3 20.7 450 n/a 5_sol: 0.1111 0.1532 0.009 0.981 5.2 103.3 20.7 452 n/a 5_weight: 0.1111 0.1532 0.009 0.981 5.2 103.3 20.7 452 n/a 5_xyzrec: 0.1133 0.1521 0.009 1.032 5.2 103.3 20.7 452 n/a 5_adp: 0.1119 0.1502 0.009 1.032 5.2 103.0 20.8 452 n/a 5_regHadp: 0.1119 0.1501 0.009 1.032 5.2 103.0 20.8 452 n/a 5_occ: 0.1113 0.1510 0.009 1.032 5.2 103.0 20.8 452 n/a end: 0.1114 0.1512 0.009 1.032 4.9 102.8 20.6 452 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6017437_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_6017437_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6500 Refinement macro-cycles (run) : 947.2500 Write final files (write_after_run_outputs) : 19.2900 Total : 970.1900 Total CPU time: 16.52 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:30 PST -0800 (1735494091.00 s) Start R-work = 0.1622, R-free = 0.1658 Final R-work = 0.1114, R-free = 0.1512 =============================================================================== Job complete usr+sys time: 1011.67 seconds wall clock time: 17 minutes 13.28 seconds (1033.28 seconds total)