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_3657390.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_3657390.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3657390.pdb" 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" 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" } 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: 1.25, per 1000 atoms: 0.37 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: 0.32 Conformation dependent library (CDL) restraints added in 181.7 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 550 0.92 - 1.17: 1109 1.17 - 1.43: 658 1.43 - 1.68: 799 1.68 - 1.94: 37 Bond restraints: 3153 Sorted by residual: bond pdb=" C ASP A 131 " pdb=" N BLYS A 132 " ideal model delta sigma weight residual 1.334 1.581 -0.247 1.27e-02 6.20e+03 3.77e+02 bond pdb=" CA VAL A 169 " pdb=" C VAL A 169 " ideal model delta sigma weight residual 1.524 1.766 -0.242 1.30e-02 5.92e+03 3.48e+02 bond pdb=" CA LEU A 7 " pdb=" C LEU A 7 " ideal model delta sigma weight residual 1.524 1.295 0.229 1.23e-02 6.61e+03 3.47e+02 bond pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 1.237 1.024 0.213 1.17e-02 7.31e+03 3.31e+02 bond pdb=" C VAL A 70 " pdb=" O VAL A 70 " ideal model delta sigma weight residual 1.237 1.049 0.187 1.07e-02 8.73e+03 3.06e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 3194 4.61 - 9.21: 1808 9.21 - 13.82: 668 13.82 - 18.43: 100 18.43 - 23.04: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 169 " pdb=" C VAL A 169 " pdb=" N GLU A 170 " ideal model delta sigma weight residual 121.83 139.60 -17.77 1.03e+00 9.43e-01 2.98e+02 angle pdb=" ND1 HIS A 138 " pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " ideal model delta sigma weight residual 106.10 120.74 -14.64 1.00e+00 1.00e+00 2.14e+02 angle pdb=" CA ASP A 131 " pdb=" C ASP A 131 " pdb=" O ASP A 131 " ideal model delta sigma weight residual 120.90 135.17 -14.27 1.07e+00 8.73e-01 1.78e+02 angle pdb=" CA VAL A 181 " pdb=" C VAL A 181 " pdb=" O VAL A 181 " ideal model delta sigma weight residual 120.85 134.81 -13.96 1.06e+00 8.90e-01 1.73e+02 angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.45 120.38 -9.93 7.80e-01 1.64e+00 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.79: 1286 15.79 - 31.58: 132 31.58 - 47.37: 39 47.37 - 63.16: 22 63.16 - 78.95: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N SER A 142 " pdb=" C SER A 142 " pdb=" CA SER A 142 " pdb=" CB SER A 142 " ideal model delta harmonic sigma weight residual 122.80 105.75 17.05 0 2.50e+00 1.60e-01 4.65e+01 dihedral pdb=" C LYS A 62 " pdb=" N LYS A 62 " pdb=" CA LYS A 62 " pdb=" CB LYS A 62 " ideal model delta harmonic sigma weight residual -122.60 -139.10 16.50 0 2.50e+00 1.60e-01 4.36e+01 dihedral pdb=" N APRO A 66 " pdb=" C APRO A 66 " pdb=" CA APRO A 66 " pdb=" CB APRO A 66 " ideal model delta harmonic sigma weight residual 115.10 98.77 16.33 0 2.50e+00 1.60e-01 4.27e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.228: 103 0.228 - 0.451: 84 0.451 - 0.674: 37 0.674 - 0.897: 14 0.897 - 1.120: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB ILE A 105 " pdb=" CA ILE A 105 " pdb=" CG1 ILE A 105 " pdb=" CG2 ILE A 105 " both_signs ideal model delta sigma weight residual False 2.64 1.52 1.12 2.00e-01 2.50e+01 3.14e+01 chirality pdb=" CA ASN A 144 " pdb=" N ASN A 144 " pdb=" C ASN A 144 " pdb=" CB ASN A 144 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CG LEU A 7 " pdb=" CB LEU A 7 " pdb=" CD1 LEU A 7 " pdb=" CD2 LEU A 7 " both_signs ideal model delta sigma weight residual False -2.59 -3.58 0.99 2.00e-01 2.50e+01 2.46e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " 0.003 2.00e-02 2.50e+03 6.40e-02 1.23e+02 pdb=" CG PHE A 162 " -0.128 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.080 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.032 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.105 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.101 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.028 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.024 2.00e-02 2.50e+03 5.86e-02 1.03e+02 pdb=" CG ATYR A 67 " 0.047 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.038 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.007 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.136 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 26 " -0.047 2.00e-02 2.50e+03 9.91e-02 9.82e+01 pdb=" N ARG A 27 " 0.170 2.00e-02 2.50e+03 pdb=" CA ARG A 27 " -0.044 2.00e-02 2.50e+03 pdb=" H ARG A 27 " -0.080 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1028 2.32 - 2.89: 8144 2.89 - 3.46: 10513 3.46 - 4.03: 15152 4.03 - 4.60: 21723 Nonbonded interactions: 56560 Sorted by model distance: nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.754 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.791 2.450 nonbonded pdb=" O LEU A 7 " pdb=" H VAL A 71 " model vdw 1.806 2.450 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.830 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.831 2.450 ... (remaining 56555 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_3657390_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= 0.2789 r_free= 0.1817 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.409411 | | target function (ml) not normalized (work): 71622.059730 | | target function (ml) not normalized (free): 3273.982611 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3205 0.2090 7.5448 5.028| | 2: 3.63 - 2.88 1.00 2711 122 0.2621 0.1689 4.3229 4.3373| | 3: 2.88 - 2.52 1.00 2682 148 0.2586 0.1734 4.1811 4.192| | 4: 2.52 - 2.29 1.00 2661 139 0.2515 0.1611 3.5048 3.6165| | 5: 2.29 - 2.13 1.00 2678 122 0.2677 0.1511 3.4018 3.4576| | 6: 2.13 - 2.00 1.00 2692 117 0.2745 0.1915 3.3372 3.4226| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.54 0.77 0.23 1303.21| | 2: 3.63 - 2.88 2711 122 0.83 23.77 1.31 0.23 1303.21| | 3: 2.88 - 2.52 2682 148 0.73 32.98 1.29 0.23 1303.21| | 4: 2.52 - 2.29 2661 139 0.93 11.65 1.29 0.26 141.50| | 5: 2.29 - 2.13 2678 122 0.92 13.93 1.32 0.26 141.50| | 6: 2.13 - 2.00 2692 117 0.90 16.69 1.33 0.26 141.50| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 141.50 max = 1303.21 mean = 728.83| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 90.00 mean = 19.43| |phase err.(test): min = 0.00 max = 89.81 mean = 19.63| |-----------------------------------------------------------------------------| ----------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 : 0.086 0.247 1557 Z= 5.709 Angle : 5.210 17.773 2118 Z= 3.742 Chirality : 0.378 1.120 243 Planarity : 0.031 0.091 284 Dihedral : 13.578 78.948 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 4.35 % Favored : 94.41 % Cbeta Deviations : 29.73 % 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: -2.50 (0.48), residues: 224 helix: -2.32 (0.41), residues: 109 sheet: -0.85 (0.73), residues: 38 loop : -0.63 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.065 0.019 ARG A 27 TYR 0.091 0.041 TYR A 141 PHE 0.106 0.048 PHE A 162 HIS 0.043 0.022 HIS A 138 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= 0.2789 r_free= 0.1817 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.409411 | | target function (ml) not normalized (work): 71622.059730 | | target function (ml) not normalized (free): 3273.982611 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3364 percent. r_work = 0.2922 r_free = 0.2007 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2869 0.2922 0.2007 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2869 0.2922 0.2007 n_refl.: 17050 remove outliers: r(all,work,free)=0.2156 0.2166 0.2007 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2129 0.2139 0.1988 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1615 0.1610 0.1707 n_refl.: 17045 remove outliers: r(all,work,free)=0.1614 0.1609 0.1707 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 0.3975 394.672 364.470 0.653 1.009 0.397 11.894-9.307 99.02 97 4 0.1864 633.460 615.061 0.932 1.011 0.380 9.237-7.194 100.00 213 7 0.2167 518.106 508.924 0.961 1.011 0.351 7.162-5.571 100.00 427 22 0.2300 388.839 375.981 0.918 1.010 0.284 5.546-4.326 100.00 867 58 0.1389 533.814 528.066 0.960 1.009 0.220 4.315-3.360 100.00 1859 96 0.1287 507.662 503.918 1.018 1.005 0.201 3.356-2.611 100.00 3867 181 0.1642 333.505 329.029 1.014 1.000 0.044 2.608-2.000 99.99 8818 434 0.1656 217.388 213.308 1.028 0.990 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4440 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1609 r_free=0.1707 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1610 r_free=0.1707 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.791185 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.857923 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 0.1641 0.0290 0.009 1.0 1.0 0.5 0.0 0 11.896 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.41 2.90 3.012 18.455 0.858 0.023 12.77 16.62 3.85 3.592 18.709 0.858 0.020 Individual atomic B min max mean iso aniso Overall: 6.32 113.89 19.96 4.05 1785 0 Protein: 6.32 113.35 17.21 4.05 1519 0 Water: 8.71 113.89 36.01 N/A 258 0 Other: 22.00 36.18 26.25 N/A 8 0 Chain A: 6.32 113.89 19.96 N/A 1785 0 Histogram: Values Number of atoms 6.32 - 17.08 1097 17.08 - 27.84 329 27.84 - 38.59 187 38.59 - 49.35 96 49.35 - 60.11 49 60.11 - 70.87 13 70.87 - 81.62 6 81.62 - 92.38 4 92.38 - 103.14 1 103.14 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1277 r_free=0.1662 r_work=0.1280 r_free=0.1669 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1669 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 = 0.1660 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 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= 0.1660 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019985 | | target function (ls_wunit_k1) not normalized (work): 324.502739 | | target function (ls_wunit_k1) not normalized (free): 27.341442 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1660 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1911 0.1910 0.1994 n_refl.: 17044 remove outliers: r(all,work,free)=0.1911 0.1910 0.1994 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1883 0.1881 0.1978 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1654 n_refl.: 17044 remove outliers: r(all,work,free)=0.1292 0.1273 0.1654 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 0.3509 303.453 279.633 0.625 1.009 0.368 11.894-9.307 99.02 97 4 0.1664 488.056 477.723 0.919 1.010 0.367 9.237-7.194 100.00 213 7 0.1813 399.181 396.700 0.959 1.010 0.351 7.162-5.571 100.00 427 22 0.1824 299.586 295.114 0.930 1.009 0.301 5.546-4.326 100.00 867 58 0.1039 411.283 409.027 0.958 1.007 0.210 4.315-3.360 100.00 1859 96 0.0931 391.134 390.815 1.018 1.005 0.191 3.356-2.611 100.00 3867 181 0.1298 256.953 255.662 1.015 1.000 0.111 2.608-2.000 99.99 8818 434 0.1350 167.489 165.992 1.024 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4057 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1654 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1275 r_free=0.1657 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1657 | n_water=258 | time (s): 0.810 (total time: 0.810) Filter (dist) r_work=0.1279 r_free=0.1648 | n_water=254 | time (s): 19.970 (total time: 20.780) Filter (q & B) r_work=0.1279 r_free=0.1648 | n_water=252 | time (s): 1.640 (total time: 22.420) Compute maps r_work=0.1279 r_free=0.1648 | n_water=252 | time (s): 0.630 (total time: 23.050) Filter (map) r_work=0.1310 r_free=0.1636 | n_water=213 | time (s): 1.430 (total time: 24.480) Find peaks r_work=0.1310 r_free=0.1636 | n_water=213 | time (s): 0.430 (total time: 24.910) Add new water r_work=0.1537 r_free=0.1903 | n_water=372 | time (s): 1.750 (total time: 26.660) Refine new water occ: r_work=0.1335 r_free=0.1601 adp: r_work=0.1274 r_free=0.1592 occ: r_work=0.1283 r_free=0.1576 adp: r_work=0.1247 r_free=0.1570 occ: r_work=0.1248 r_free=0.1567 adp: r_work=0.1236 r_free=0.1560 ADP+occupancy (water only), MIN, final r_work=0.1236 r_free=0.1560 r_work=0.1236 r_free=0.1560 | n_water=372 | time (s): 10.090 (total time: 36.750) Filter (q & B) r_work=0.1239 r_free=0.1568 | n_water=365 | time (s): 1.750 (total time: 38.500) Filter (dist only) r_work=0.1239 r_free=0.1573 | n_water=364 | time (s): 27.870 (total time: 66.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.834720 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.986155 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 0.1210 0.1612 0.0402 0.008 0.9 2.2 0.5 0.0 0 11.917 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 16.12 4.02 4.157 21.110 0.986 0.018 11.96 16.31 4.35 4.208 21.390 0.986 0.018 Individual atomic B min max mean iso aniso Overall: 6.48 107.95 21.47 4.30 1891 0 Protein: 6.48 107.95 17.76 4.29 1519 0 Water: 8.85 67.13 36.64 N/A 364 0 Other: 25.23 44.94 35.36 N/A 8 0 Chain A: 6.48 107.95 19.52 N/A 1740 0 Chain S: 18.16 67.13 43.89 N/A 151 0 Histogram: Values Number of atoms 6.48 - 16.62 1013 16.62 - 26.77 387 26.77 - 36.92 224 36.92 - 47.07 147 47.07 - 57.21 81 57.21 - 67.36 28 67.36 - 77.51 4 77.51 - 87.66 5 87.66 - 97.80 0 97.80 - 107.95 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1631 r_work=0.1199 r_free=0.1632 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1199 r_free = 0.1632 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1196 r_free = 0.1634 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 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= 0.1196 r_free= 0.1634 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017017 | | target function (ls_wunit_k1) not normalized (work): 276.268201 | | target function (ls_wunit_k1) not normalized (free): 25.461249 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1217 0.1196 0.1634 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1758 0.1751 0.1952 n_refl.: 17042 remove outliers: r(all,work,free)=0.1758 0.1751 0.1952 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1734 0.1726 0.1936 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1189 0.1628 n_refl.: 17042 remove outliers: r(all,work,free)=0.1210 0.1189 0.1628 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 0.3248 303.453 284.295 0.594 1.005 0.340 11.894-9.307 99.02 97 4 0.1491 488.056 483.913 0.912 1.006 0.340 9.237-7.194 100.00 213 7 0.1677 399.181 400.245 0.976 1.006 0.285 7.162-5.571 100.00 427 22 0.1503 299.586 295.817 0.933 1.005 0.262 5.546-4.326 100.00 867 58 0.0871 411.283 409.148 0.960 1.005 0.215 4.315-3.360 100.00 1859 96 0.0831 391.134 390.302 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1201 256.953 256.239 1.012 1.001 0.131 2.608-2.000 99.99 8818 434 0.1331 167.489 166.494 1.017 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3596 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1628 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1189 r_free=0.1628 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1189 r_free=0.1628 | n_water=364 | time (s): 0.820 (total time: 0.820) Filter (dist) r_work=0.1188 r_free=0.1632 | n_water=362 | time (s): 29.250 (total time: 30.070) Filter (q & B) r_work=0.1188 r_free=0.1632 | n_water=362 | time (s): 1.050 (total time: 31.120) Compute maps r_work=0.1188 r_free=0.1632 | n_water=362 | time (s): 0.630 (total time: 31.750) Filter (map) r_work=0.1256 r_free=0.1655 | n_water=267 | time (s): 2.020 (total time: 33.770) Find peaks r_work=0.1256 r_free=0.1655 | n_water=267 | time (s): 0.660 (total time: 34.430) Add new water r_work=0.1437 r_free=0.1812 | n_water=417 | time (s): 1.600 (total time: 36.030) Refine new water occ: r_work=0.1239 r_free=0.1572 adp: r_work=0.1230 r_free=0.1575 occ: r_work=0.1214 r_free=0.1546 adp: r_work=0.1203 r_free=0.1549 occ: r_work=0.1197 r_free=0.1535 adp: r_work=0.1187 r_free=0.1538 ADP+occupancy (water only), MIN, final r_work=0.1187 r_free=0.1538 r_work=0.1187 r_free=0.1538 | n_water=417 | time (s): 33.900 (total time: 69.930) Filter (q & B) r_work=0.1191 r_free=0.1546 | n_water=406 | time (s): 1.880 (total time: 71.810) Filter (dist only) r_work=0.1191 r_free=0.1546 | n_water=406 | time (s): 32.400 (total time: 104.210) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.856239 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.175105 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 0.1167 0.1544 0.0377 0.009 1.0 4.2 0.5 0.0 0 0.928 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.67 15.44 3.77 4.361 21.613 0.175 4.995 11.45 15.54 4.10 4.978 21.524 0.175 4.973 Individual atomic B min max mean iso aniso Overall: 6.02 105.48 20.97 4.82 1933 0 Protein: 6.02 105.48 17.00 4.81 1519 0 Water: 8.56 63.51 35.53 N/A 406 0 Other: 27.60 47.80 35.94 N/A 8 0 Chain A: 6.02 105.48 18.81 N/A 1736 0 Chain S: 12.49 63.51 40.05 N/A 197 0 Histogram: Values Number of atoms 6.02 - 15.97 1049 15.97 - 25.91 359 25.91 - 35.86 224 35.86 - 45.81 175 45.81 - 55.75 85 55.75 - 65.70 28 65.70 - 75.64 5 75.64 - 85.59 3 85.59 - 95.54 3 95.54 - 105.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.1145 r_free=0.1554 r_work=0.1145 r_free=0.1555 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1145 r_free = 0.1555 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1136 r_free = 0.1543 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1136 r_free= 0.1543 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.966833 | | target function (ml) not normalized (work): 80636.537678 | | target function (ml) not normalized (free): 4185.191503 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1156 0.1136 0.1543 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1668 0.1662 0.1828 n_refl.: 17042 remove outliers: r(all,work,free)=0.1668 0.1662 0.1828 n_refl.: 17042 overall B=-0.46 to atoms: r(all,work,free)=0.1637 0.1630 0.1814 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1155 0.1135 0.1544 n_refl.: 17042 remove outliers: r(all,work,free)=0.1155 0.1135 0.1544 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 0.3639 303.453 281.911 0.570 1.006 0.340 11.894-9.307 99.02 97 4 0.1719 488.056 482.130 0.909 1.007 0.340 9.237-7.194 100.00 213 7 0.1815 399.181 400.010 0.987 1.007 0.260 7.162-5.571 100.00 427 22 0.1596 299.586 294.202 0.937 1.007 0.241 5.546-4.326 100.00 867 58 0.0932 411.283 407.697 0.964 1.006 0.221 4.315-3.360 100.00 1859 96 0.0865 391.134 388.956 1.011 1.004 0.212 3.356-2.611 100.00 3867 181 0.1259 256.953 254.917 1.011 1.001 0.142 2.608-2.000 99.99 8818 434 0.1091 167.489 166.105 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1655 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1135 r_free=0.1544 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1135 r_free=0.1544 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1135 r_free=0.1544 | n_water=406 | time (s): 0.770 (total time: 0.770) Filter (dist) r_work=0.1135 r_free=0.1544 | n_water=406 | time (s): 31.370 (total time: 32.140) Filter (q & B) r_work=0.1136 r_free=0.1545 | n_water=404 | time (s): 2.210 (total time: 34.350) Compute maps r_work=0.1136 r_free=0.1545 | n_water=404 | time (s): 0.760 (total time: 35.110) Filter (map) r_work=0.1197 r_free=0.1562 | n_water=318 | time (s): 1.850 (total time: 36.960) Find peaks r_work=0.1197 r_free=0.1562 | n_water=318 | time (s): 0.620 (total time: 37.580) Add new water r_work=0.1339 r_free=0.1680 | n_water=456 | time (s): 2.200 (total time: 39.780) Refine new water occ: r_work=0.1171 r_free=0.1503 adp: r_work=0.1161 r_free=0.1503 occ: r_work=0.1146 r_free=0.1488 adp: r_work=0.1137 r_free=0.1485 occ: r_work=0.1129 r_free=0.1482 adp: r_work=0.1123 r_free=0.1476 ADP+occupancy (water only), MIN, final r_work=0.1123 r_free=0.1476 r_work=0.1123 r_free=0.1476 | n_water=456 | time (s): 21.480 (total time: 61.260) Filter (q & B) r_work=0.1126 r_free=0.1493 | n_water=444 | time (s): 2.290 (total time: 63.550) Filter (dist only) r_work=0.1126 r_free=0.1493 | n_water=444 | time (s): 35.300 (total time: 98.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.952799 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.181528 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 0.1110 0.1515 0.0404 0.010 1.0 5.1 0.5 0.0 0 0.976 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.10 15.15 4.04 4.570 21.033 0.182 4.951 10.99 15.23 4.24 4.744 21.040 0.182 4.945 Individual atomic B min max mean iso aniso Overall: 5.67 103.75 20.91 5.00 1971 0 Protein: 5.67 103.75 16.45 4.99 1519 0 Water: 8.40 65.12 35.90 N/A 444 0 Other: 27.06 48.51 35.23 N/A 8 0 Chain A: 5.67 103.75 18.20 N/A 1736 0 Chain S: 17.37 65.12 40.88 N/A 235 0 Histogram: Values Number of atoms 5.67 - 15.48 1054 15.48 - 25.29 362 25.29 - 35.09 210 35.09 - 44.90 197 44.90 - 54.71 108 54.71 - 64.52 24 64.52 - 74.33 7 74.33 - 84.13 4 84.13 - 93.94 3 93.94 - 103.75 2 =========================== Idealize ADP of riding H ========================== r_work=0.1099 r_free=0.1523 r_work=0.1099 r_free=0.1523 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1099 r_free = 0.1523 target_work(ml) = 4.945 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1093 r_free = 0.1519 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1093 r_free= 0.1519 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.940194 | | target function (ml) not normalized (work): 80204.047829 | | target function (ml) not normalized (free): 4170.434450 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1113 0.1093 0.1519 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1581 0.1572 0.1791 n_refl.: 17042 remove outliers: r(all,work,free)=0.1581 0.1572 0.1791 n_refl.: 17042 overall B=-0.26 to atoms: r(all,work,free)=0.1564 0.1556 0.1784 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1112 0.1091 0.1514 n_refl.: 17042 remove outliers: r(all,work,free)=0.1112 0.1091 0.1514 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 0.3771 303.453 281.330 0.563 1.001 0.340 11.894-9.307 99.02 97 4 0.1740 488.056 481.224 0.917 1.002 0.340 9.237-7.194 100.00 213 7 0.1729 399.181 400.919 0.990 1.003 0.250 7.162-5.571 100.00 427 22 0.1509 299.586 293.795 0.940 1.003 0.230 5.546-4.326 100.00 867 58 0.0888 411.283 407.995 0.966 1.003 0.211 4.315-3.360 100.00 1859 96 0.0824 391.134 388.963 1.006 1.002 0.201 3.356-2.611 100.00 3867 181 0.1214 256.953 254.821 1.001 1.002 0.131 2.608-2.000 99.99 8818 434 0.1047 167.489 166.265 0.995 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.9107 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1091 r_free=0.1514 After: r_work=0.1094 r_free=0.1513 ================================== NQH flips ================================== r_work=0.1094 r_free=0.1513 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1094 r_free=0.1513 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1094 r_free=0.1513 | n_water=444 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1097 r_free=0.1517 | n_water=442 | time (s): 37.350 (total time: 38.030) Filter (q & B) r_work=0.1097 r_free=0.1514 | n_water=439 | time (s): 1.970 (total time: 40.000) Compute maps r_work=0.1097 r_free=0.1514 | n_water=439 | time (s): 0.690 (total time: 40.690) Filter (map) r_work=0.1175 r_free=0.1558 | n_water=343 | time (s): 1.690 (total time: 42.380) Find peaks r_work=0.1175 r_free=0.1558 | n_water=343 | time (s): 0.440 (total time: 42.820) Add new water r_work=0.1294 r_free=0.1624 | n_water=474 | time (s): 1.450 (total time: 44.270) Refine new water occ: r_work=0.1136 r_free=0.1477 adp: r_work=0.1129 r_free=0.1476 occ: r_work=0.1116 r_free=0.1463 adp: r_work=0.1108 r_free=0.1462 occ: r_work=0.1102 r_free=0.1452 adp: r_work=0.1095 r_free=0.1454 ADP+occupancy (water only), MIN, final r_work=0.1095 r_free=0.1454 r_work=0.1095 r_free=0.1454 | n_water=474 | time (s): 31.220 (total time: 75.490) Filter (q & B) r_work=0.1098 r_free=0.1467 | n_water=463 | time (s): 1.810 (total time: 77.300) Filter (dist only) r_work=0.1100 r_free=0.1463 | n_water=461 | time (s): 37.900 (total time: 115.200) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.961214 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.158278 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 0.1122 0.1514 0.0392 0.010 1.1 4.5 0.5 0.0 0 0.981 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.22 15.14 3.92 4.628 20.808 0.158 4.949 11.13 15.08 3.95 4.644 20.897 0.158 4.942 Individual atomic B min max mean iso aniso Overall: 5.53 102.96 21.01 5.05 1988 0 Protein: 5.53 102.96 16.27 5.04 1519 0 Water: 8.23 64.90 36.39 N/A 461 0 Other: 26.58 47.18 35.00 N/A 8 0 Chain A: 5.53 102.96 17.96 N/A 1734 0 Chain S: 15.88 64.90 41.88 N/A 254 0 Histogram: Values Number of atoms 5.53 - 15.28 1047 15.28 - 25.02 369 25.02 - 34.76 213 34.76 - 44.50 190 44.50 - 54.25 119 54.25 - 63.99 34 63.99 - 73.73 7 73.73 - 83.47 3 83.47 - 93.21 2 93.21 - 102.96 4 =========================== Idealize ADP of riding H ========================== r_work=0.1113 r_free=0.1508 r_work=0.1114 r_free=0.1509 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1114 r_free = 0.1509 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1105 r_free = 0.1505 target_work(ml) = 4.937 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1105 r_free= 0.1505 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.936711 | | target function (ml) not normalized (work): 80147.497228 | | target function (ml) not normalized (free): 4159.955544 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2812 159 0.1106 0.1350 5.4513 5.6165| | 2: 3.63 - 2.88 1.00 2711 122 0.1072 0.1472 5.201 5.3435| | 3: 2.88 - 2.52 1.00 2681 148 0.1352 0.1691 5.1164 5.18| | 4: 2.52 - 2.29 1.00 2661 139 0.0962 0.1534 4.6418 4.9615| | 5: 2.29 - 2.13 1.00 2678 122 0.0983 0.1508 4.5932 4.8953| | 6: 2.13 - 2.00 1.00 2692 117 0.1128 0.1785 4.5873 4.7993| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2812 159 0.95 8.73 1.00 0.96 6075.85| | 2: 3.63 - 2.88 2711 122 0.93 12.54 1.01 0.96 6075.85| | 3: 2.88 - 2.52 2681 148 0.88 18.45 0.99 0.96 6075.85| | 4: 2.52 - 2.29 2661 139 0.93 12.22 1.01 0.99 2164.51| | 5: 2.29 - 2.13 2678 122 0.91 14.32 1.01 0.99 2164.51| | 6: 2.13 - 2.00 2692 117 0.89 16.93 0.99 0.99 2164.51| |alpha: min = 0.96 max = 0.99 mean = 0.97| |beta: min = 2164.51 max = 6075.85 mean = 4141.02| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.84 mean = 13.82| |phase err.(test): min = 0.00 max = 89.77 mean = 13.50| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1105 0.1505 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1586 0.1576 0.1810 n_refl.: 17042 remove outliers: r(all,work,free)=0.1586 0.1576 0.1810 n_refl.: 17042 overall B=-0.24 to atoms: r(all,work,free)=0.1571 0.1561 0.1801 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1124 0.1105 0.1504 n_refl.: 17042 remove outliers: r(all,work,free)=0.1123 0.1104 0.1504 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 0.3626 299.962 283.131 0.555 1.004 0.340 11.894-9.307 99.02 97 4 0.1724 488.056 480.389 0.914 1.005 0.334 9.237-7.194 100.00 213 7 0.1735 399.181 401.600 0.990 1.005 0.230 7.162-5.571 100.00 427 22 0.1553 299.586 293.781 0.935 1.005 0.230 5.546-4.326 100.00 867 58 0.0915 411.283 408.151 0.962 1.004 0.201 4.315-3.360 100.00 1859 96 0.0849 391.134 389.305 1.005 1.003 0.201 3.356-2.611 100.00 3867 181 0.1230 256.953 254.652 1.000 1.001 0.131 2.608-2.000 99.99 8818 434 0.1051 167.489 166.166 0.994 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.8220 ================= 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 : 0.2789 0.1817 0.086 5.210 8.8 119.3 19.9 258 0.000 1_bss: 0.1609 0.1707 0.086 5.210 8.4 118.9 19.5 258 0.000 1_settarget: 0.1609 0.1707 0.086 5.210 8.4 118.9 19.5 258 0.000 1_nqh: 0.1610 0.1707 0.086 5.210 8.4 118.9 19.5 258 0.003 1_weight: 0.1610 0.1707 0.086 5.210 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1351 0.1641 0.009 0.980 8.4 118.9 19.5 258 0.144 1_adp: 0.1277 0.1662 0.009 0.980 6.3 113.9 20.0 258 0.144 1_regHadp: 0.1280 0.1669 0.009 0.980 6.3 113.9 20.0 258 0.144 1_occ: 0.1275 0.1660 0.009 0.980 6.3 113.9 20.0 258 0.144 2_bss: 0.1273 0.1654 0.009 0.980 5.9 113.5 19.6 258 0.144 2_settarget: 0.1273 0.1654 0.009 0.980 5.9 113.5 19.6 258 0.144 2_updatecdl: 0.1273 0.1654 0.009 0.997 5.9 113.5 19.6 258 0.144 2_nqh: 0.1275 0.1657 0.009 0.997 5.9 113.5 19.6 258 0.141 2_sol: 0.1239 0.1573 0.009 0.997 5.9 113.0 21.0 364 n/a 2_weight: 0.1239 0.1573 0.009 0.997 5.9 113.0 21.0 364 n/a 2_xyzrec: 0.1210 0.1612 0.008 0.930 5.9 113.0 21.0 364 n/a 2_adp: 0.1196 0.1631 0.008 0.930 6.5 108.0 21.5 364 n/a 2_regHadp: 0.1199 0.1632 0.008 0.930 6.5 108.0 21.5 364 n/a 2_occ: 0.1196 0.1634 0.008 0.930 6.5 108.0 21.5 364 n/a 3_bss: 0.1189 0.1628 0.008 0.930 6.1 107.6 21.1 364 n/a 3_settarget: 0.1189 0.1628 0.008 0.930 6.1 107.6 21.1 364 n/a 3_updatecdl: 0.1189 0.1628 0.008 0.928 6.1 107.6 21.1 364 n/a 3_nqh: 0.1189 0.1628 0.008 0.928 6.1 107.6 21.1 364 n/a 3_sol: 0.1191 0.1546 0.008 0.928 6.1 107.6 21.1 406 n/a 3_weight: 0.1191 0.1546 0.008 0.928 6.1 107.6 21.1 406 n/a 3_xyzrec: 0.1167 0.1544 0.009 0.954 6.1 107.6 21.1 406 n/a 3_adp: 0.1145 0.1554 0.009 0.954 6.0 105.5 21.0 406 n/a 3_regHadp: 0.1145 0.1555 0.009 0.954 6.0 105.5 21.0 406 n/a 3_occ: 0.1136 0.1543 0.009 0.954 6.0 105.5 21.0 406 n/a 4_bss: 0.1135 0.1544 0.009 0.954 5.6 105.0 20.5 406 n/a 4_settarget: 0.1135 0.1544 0.009 0.954 5.6 105.0 20.5 406 n/a 4_updatecdl: 0.1135 0.1544 0.009 0.957 5.6 105.0 20.5 406 n/a 4_nqh: 0.1135 0.1544 0.009 0.957 5.6 105.0 20.5 406 n/a 4_sol: 0.1126 0.1493 0.009 0.957 5.6 105.0 20.9 444 n/a 4_weight: 0.1126 0.1493 0.009 0.957 5.6 105.0 20.9 444 n/a 4_xyzrec: 0.1110 0.1515 0.010 0.978 5.6 105.0 20.9 444 n/a 4_adp: 0.1099 0.1523 0.010 0.978 5.7 103.7 20.9 444 n/a 4_regHadp: 0.1099 0.1523 0.010 0.978 5.7 103.7 20.9 444 n/a 4_occ: 0.1093 0.1519 0.010 0.978 5.7 103.7 20.9 444 n/a 5_bss: 0.1091 0.1514 0.010 0.978 5.4 103.5 20.6 444 n/a 5_settarget: 0.1091 0.1514 0.010 0.978 5.4 103.5 20.6 444 n/a 5_updatecdl: 0.1091 0.1514 0.010 0.978 5.4 103.5 20.6 444 n/a 5_setrh: 0.1094 0.1513 0.010 0.978 5.4 103.5 20.6 444 n/a 5_nqh: 0.1094 0.1513 0.010 0.978 5.4 103.5 20.6 444 n/a 5_sol: 0.1100 0.1463 0.010 0.978 5.4 103.5 20.9 461 n/a 5_weight: 0.1100 0.1463 0.010 0.978 5.4 103.5 20.9 461 n/a 5_xyzrec: 0.1122 0.1514 0.010 1.058 5.4 103.5 20.9 461 n/a 5_adp: 0.1113 0.1508 0.010 1.058 5.5 103.0 21.0 461 n/a 5_regHadp: 0.1114 0.1509 0.010 1.058 5.5 103.0 21.0 461 n/a 5_occ: 0.1105 0.1505 0.010 1.058 5.5 103.0 21.0 461 n/a end: 0.1104 0.1504 0.010 1.058 5.3 102.7 20.8 461 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3657390_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3657390_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.2200 Refinement macro-cycles (run) : 921.4700 Write final files (write_after_run_outputs) : 20.5500 Total : 945.2400 Total CPU time: 16.13 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:09 PST -0800 (1735494069.15 s) Start R-work = 0.1609, R-free = 0.1707 Final R-work = 0.1104, R-free = 0.1504 =============================================================================== Job complete usr+sys time: 989.79 seconds wall clock time: 16 minutes 53.00 seconds (1013.00 seconds total)