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_8540717.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 { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8540717.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8540717.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" } 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 1 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: 1.18, per 1000 atoms: 0.35 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: 0.28 Conformation dependent library (CDL) restraints added in 107.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.94: 683 0.94 - 1.19: 987 1.19 - 1.44: 673 1.44 - 1.69: 784 1.69 - 1.94: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " ideal model delta sigma weight residual 1.326 1.116 0.210 1.10e-02 8.26e+03 3.65e+02 bond pdb=" N GLY A 100 " pdb=" CA GLY A 100 " ideal model delta sigma weight residual 1.450 1.657 -0.207 1.16e-02 7.43e+03 3.19e+02 bond pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta sigma weight residual 1.540 1.335 0.205 1.17e-02 7.31e+03 3.06e+02 bond pdb=" C GLU A 147 " pdb=" N LYS A 148 " ideal model delta sigma weight residual 1.332 1.113 0.219 1.26e-02 6.30e+03 3.01e+02 bond pdb=" CG HIS A 138 " pdb=" CD2 HIS A 138 " ideal model delta sigma weight residual 1.354 1.164 0.190 1.10e-02 8.26e+03 3.00e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 2885 4.09 - 8.18: 1796 8.18 - 12.26: 829 12.26 - 16.35: 224 16.35 - 20.44: 43 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N PRO A 54 " pdb=" CA PRO A 54 " pdb=" CB PRO A 54 " ideal model delta sigma weight residual 103.32 115.71 -12.39 8.40e-01 1.42e+00 2.18e+02 angle pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" O VAL A 177 " ideal model delta sigma weight residual 121.17 106.15 15.02 1.06e+00 8.90e-01 2.01e+02 angle pdb=" O AGLN A 80 " pdb=" C AGLN A 80 " pdb=" N ASN A 81 " ideal model delta sigma weight residual 122.12 107.19 14.93 1.06e+00 8.90e-01 1.99e+02 angle pdb=" CA ASP A 55 " pdb=" C ASP A 55 " pdb=" O ASP A 55 " ideal model delta sigma weight residual 119.97 136.10 -16.13 1.15e+00 7.56e-01 1.97e+02 angle pdb=" CA LYS A 32 " pdb=" C LYS A 32 " pdb=" O LYS A 32 " ideal model delta sigma weight residual 120.54 134.83 -14.29 1.04e+00 9.25e-01 1.89e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 1325 17.47 - 34.93: 97 34.93 - 52.40: 43 52.40 - 69.87: 14 69.87 - 87.33: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N PRO A 54 " pdb=" C PRO A 54 " pdb=" CA PRO A 54 " pdb=" CB PRO A 54 " ideal model delta harmonic sigma weight residual 115.10 132.99 -17.89 0 2.50e+00 1.60e-01 5.12e+01 dihedral pdb=" C CYS A 106 " pdb=" N CYS A 106 " pdb=" CA CYS A 106 " pdb=" CB CYS A 106 " ideal model delta harmonic sigma weight residual -122.60 -139.73 17.13 0 2.50e+00 1.60e-01 4.69e+01 dihedral pdb=" N ASP A 131 " pdb=" C ASP A 131 " pdb=" CA ASP A 131 " pdb=" CB ASP A 131 " ideal model delta harmonic sigma weight residual 122.80 106.22 16.58 0 2.50e+00 1.60e-01 4.40e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.183: 89 0.183 - 0.366: 76 0.366 - 0.549: 44 0.549 - 0.731: 25 0.731 - 0.914: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB THR A 154 " pdb=" CA THR A 154 " pdb=" OG1 THR A 154 " pdb=" CG2 THR A 154 " both_signs ideal model delta sigma weight residual False 2.55 1.64 0.91 2.00e-01 2.50e+01 2.09e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -1.74 -0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" CB VAL A 35 " pdb=" CA VAL A 35 " pdb=" CG1 VAL A 35 " pdb=" CG2 VAL A 35 " both_signs ideal model delta sigma weight residual False -2.63 -3.46 0.83 2.00e-01 2.50e+01 1.73e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.059 2.00e-02 2.50e+03 6.38e-02 1.22e+02 pdb=" CG BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.045 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.113 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.009 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.049 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.033 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.055 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.036 2.00e-02 2.50e+03 5.87e-02 1.03e+02 pdb=" CG PHE A 162 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.068 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.045 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.028 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.073 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.079 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.099 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.037 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 162 " 0.050 2.00e-02 2.50e+03 1.00e-01 1.00e+02 pdb=" C PHE A 162 " -0.173 2.00e-02 2.50e+03 pdb=" O PHE A 162 " 0.063 2.00e-02 2.50e+03 pdb=" N GLU A 163 " 0.060 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 641 2.26 - 2.84: 7707 2.84 - 3.43: 10608 3.43 - 4.01: 15403 4.01 - 4.60: 22229 Nonbonded interactions: 56588 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.671 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.797 2.100 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.799 2.450 nonbonded pdb="HH22 ARG A 5 " pdb=" O AGLU A 64 " model vdw 1.844 2.450 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.851 2.450 ... (remaining 56583 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_8540717_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= 0.2781 r_free= 0.1767 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.411963 | | target function (ml) not normalized (work): 71663.513763 | | target function (ml) not normalized (free): 3237.613052 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3187 0.2048 7.6308 5.0248| | 2: 3.63 - 2.88 1.00 2711 122 0.2636 0.1673 4.3178 4.3174| | 3: 2.88 - 2.52 1.00 2682 148 0.2561 0.1698 4.1737 4.1695| | 4: 2.52 - 2.29 1.00 2661 139 0.2547 0.1516 3.5042 3.5268| | 5: 2.29 - 2.13 1.00 2678 122 0.2630 0.1479 3.3686 3.3834| | 6: 2.13 - 2.00 1.00 2692 117 0.2735 0.1771 3.3087 3.3491| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.29 0.77 0.23 1266.50| | 2: 3.63 - 2.88 2711 122 0.83 23.52 1.32 0.23 1266.50| | 3: 2.88 - 2.52 2682 148 0.74 32.39 1.29 0.23 1266.50| | 4: 2.52 - 2.29 2661 139 0.94 10.41 1.30 0.26 121.33| | 5: 2.29 - 2.13 2678 122 0.93 12.48 1.32 0.26 121.33| | 6: 2.13 - 2.00 2692 117 0.91 15.24 1.33 0.26 121.33| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 121.33 max = 1266.50 mean = 700.29| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.89 mean = 18.56| |phase err.(test): min = 0.00 max = 89.53 mean = 18.74| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.227 1557 Z= 5.298 Angle : 5.387 17.599 2118 Z= 3.799 Chirality : 0.356 0.914 243 Planarity : 0.031 0.138 284 Dihedral : 14.041 87.333 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.54 % Allowed : 5.41 % Favored : 94.05 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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: -3.30 (0.45), residues: 224 helix: -3.52 (0.31), residues: 103 sheet: -1.85 (0.65), residues: 40 loop : 0.05 (0.59), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.020 ARG A 98 TYR 0.102 0.033 TYR A 139 PHE 0.077 0.036 PHE A 164 HIS 0.037 0.016 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= 0.2781 r_free= 0.1767 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.411963 | | target function (ml) not normalized (work): 71663.513763 | | target function (ml) not normalized (free): 3237.613052 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3574 percent. r_work = 0.2916 r_free = 0.1932 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2862 0.2916 0.1932 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2862 0.2916 0.1932 n_refl.: 17050 remove outliers: r(all,work,free)=0.2147 0.2161 0.1932 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2120 0.2133 0.1912 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1606 0.1607 0.1581 n_refl.: 17045 remove outliers: r(all,work,free)=0.1604 0.1605 0.1581 n_refl.: 17043 ======================== 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 98.94 88 5 0.3869 398.876 363.475 0.656 1.013 0.402 11.894-9.307 99.02 97 4 0.1833 633.509 616.134 0.931 1.014 0.389 9.237-7.194 100.00 213 7 0.2137 518.146 511.111 0.958 1.013 0.351 7.162-5.571 100.00 427 22 0.2312 388.869 376.777 0.927 1.012 0.284 5.546-4.326 100.00 867 58 0.1381 533.855 528.720 0.961 1.010 0.251 4.315-3.360 100.00 1859 96 0.1298 507.702 503.529 1.014 1.007 0.171 3.356-2.611 100.00 3867 181 0.1638 333.531 329.155 1.012 1.001 0.081 2.608-2.000 99.99 8818 434 0.1646 217.405 213.431 1.029 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4604 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1605 r_free=0.1581 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1605 r_free=0.1581 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.967548 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.837234 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 0.1352 0.1635 0.0283 0.008 1.0 1.0 0.5 0.0 0 10.984 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.35 2.83 3.013 18.449 0.837 0.023 12.76 16.54 3.78 3.608 18.728 0.837 0.020 Individual atomic B min max mean iso aniso Overall: 6.43 113.89 20.00 4.04 1785 0 Protein: 6.43 112.67 17.24 4.04 1519 0 Water: 8.80 113.89 36.05 N/A 258 0 Other: 22.05 37.25 26.53 N/A 8 0 Chain A: 6.43 113.89 20.00 N/A 1785 0 Histogram: Values Number of atoms 6.43 - 17.18 1096 17.18 - 27.93 334 27.93 - 38.67 182 38.67 - 49.42 101 49.42 - 60.16 46 60.16 - 70.91 13 70.91 - 81.65 5 81.65 - 92.40 4 92.40 - 103.14 1 103.14 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1654 r_work=0.1279 r_free=0.1661 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1279 r_free = 0.1661 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 = 0.1273 r_free = 0.1651 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.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1273 r_free= 0.1651 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019868 | | target function (ls_wunit_k1) not normalized (work): 322.579268 | | target function (ls_wunit_k1) not normalized (free): 27.011678 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1291 0.1273 0.1651 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1904 0.1903 0.1991 n_refl.: 17043 remove outliers: r(all,work,free)=0.1904 0.1903 0.1991 n_refl.: 17043 overall B=-0.39 to atoms: r(all,work,free)=0.1876 0.1874 0.1974 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1291 0.1273 0.1651 n_refl.: 17043 remove outliers: r(all,work,free)=0.1291 0.1273 0.1651 n_refl.: 17043 ======================== 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 96.88 88 5 0.3553 306.834 287.011 0.653 1.010 0.393 11.894-9.307 99.02 97 4 0.1694 487.325 476.877 0.916 1.010 0.380 9.237-7.194 100.00 213 7 0.1814 398.583 396.120 0.957 1.010 0.351 7.162-5.571 100.00 427 22 0.1818 299.137 294.827 0.932 1.009 0.298 5.546-4.326 100.00 867 58 0.1040 410.667 408.371 0.956 1.007 0.210 4.315-3.360 100.00 1859 96 0.0920 390.548 390.262 1.016 1.005 0.191 3.356-2.611 100.00 3867 181 0.1299 256.568 255.382 1.015 1.000 0.091 2.608-2.000 99.99 8818 434 0.1351 167.238 165.748 1.023 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.4021 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1651 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1651 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1651 | n_water=258 | time (s): 0.730 (total time: 0.730) Filter (dist) r_work=0.1279 r_free=0.1642 | n_water=253 | time (s): 20.220 (total time: 20.950) Filter (q & B) r_work=0.1279 r_free=0.1642 | n_water=251 | time (s): 1.420 (total time: 22.370) Compute maps r_work=0.1279 r_free=0.1642 | n_water=251 | time (s): 0.700 (total time: 23.070) Filter (map) r_work=0.1316 r_free=0.1632 | n_water=209 | time (s): 1.590 (total time: 24.660) Find peaks r_work=0.1316 r_free=0.1632 | n_water=209 | time (s): 0.420 (total time: 25.080) Add new water r_work=0.1547 r_free=0.1904 | n_water=364 | time (s): 1.540 (total time: 26.620) Refine new water occ: r_work=0.1339 r_free=0.1586 adp: r_work=0.1278 r_free=0.1584 occ: r_work=0.1284 r_free=0.1541 adp: r_work=0.1248 r_free=0.1555 occ: r_work=0.1249 r_free=0.1533 adp: r_work=0.1237 r_free=0.1544 ADP+occupancy (water only), MIN, final r_work=0.1237 r_free=0.1544 r_work=0.1237 r_free=0.1544 | n_water=364 | time (s): 9.780 (total time: 36.400) Filter (q & B) r_work=0.1240 r_free=0.1556 | n_water=356 | time (s): 1.970 (total time: 38.370) Filter (dist only) r_work=0.1241 r_free=0.1558 | n_water=355 | time (s): 27.960 (total time: 66.330) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.375281 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.934754 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 0.1613 0.0400 0.008 0.9 2.2 0.5 0.0 0 12.188 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 16.13 4.00 4.158 21.093 0.935 0.018 12.01 16.37 4.36 4.219 21.358 0.935 0.018 Individual atomic B min max mean iso aniso Overall: 6.89 107.28 21.36 4.26 1882 0 Protein: 6.89 107.28 17.79 4.25 1519 0 Water: 8.68 68.16 36.32 N/A 355 0 Other: 24.30 45.57 34.62 N/A 8 0 Chain A: 6.89 107.28 19.46 N/A 1736 0 Chain S: 17.72 66.89 43.92 N/A 146 0 Histogram: Values Number of atoms 6.89 - 16.93 1033 16.93 - 26.97 369 26.97 - 37.01 217 37.01 - 47.05 154 47.05 - 57.09 73 57.09 - 67.12 25 67.12 - 77.16 4 77.16 - 87.20 4 87.20 - 97.24 1 97.24 - 107.28 2 =========================== Idealize ADP of riding H ========================== r_work=0.1201 r_free=0.1637 r_work=0.1203 r_free=0.1639 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1203 r_free = 0.1639 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1201 r_free = 0.1630 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1201 r_free= 0.1630 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017187 | | target function (ls_wunit_k1) not normalized (work): 279.046103 | | target function (ls_wunit_k1) not normalized (free): 25.449925 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1222 0.1201 0.1630 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1820 0.1815 0.1978 n_refl.: 17043 remove outliers: r(all,work,free)=0.1820 0.1815 0.1978 n_refl.: 17043 overall B=-0.39 to atoms: r(all,work,free)=0.1792 0.1786 0.1959 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1215 0.1195 0.1619 n_refl.: 17043 remove outliers: r(all,work,free)=0.1213 0.1193 0.1619 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 0.3354 306.272 280.945 0.613 1.006 0.360 11.894-9.307 99.02 97 4 0.1549 487.325 482.689 0.913 1.006 0.360 9.237-7.194 100.00 213 7 0.1640 398.583 399.763 0.970 1.006 0.310 7.162-5.571 100.00 427 22 0.1546 299.137 296.421 0.938 1.005 0.271 5.546-4.326 100.00 867 58 0.0888 410.667 408.037 0.958 1.005 0.205 4.315-3.360 100.00 1859 96 0.0834 390.548 389.853 1.014 1.003 0.191 3.356-2.611 100.00 3867 181 0.1200 256.568 255.773 1.013 1.001 0.048 2.608-2.000 99.99 8818 434 0.1332 167.238 166.238 1.019 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.3960 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1193 r_free=0.1619 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.1193 r_free=0.1619 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1193 r_free=0.1619 | n_water=355 | time (s): 0.860 (total time: 0.860) Filter (dist) r_work=0.1193 r_free=0.1618 | n_water=354 | time (s): 27.430 (total time: 28.290) Filter (q & B) r_work=0.1193 r_free=0.1618 | n_water=354 | time (s): 0.890 (total time: 29.180) Compute maps r_work=0.1193 r_free=0.1618 | n_water=354 | time (s): 0.590 (total time: 29.770) Filter (map) r_work=0.1262 r_free=0.1622 | n_water=260 | time (s): 1.500 (total time: 31.270) Find peaks r_work=0.1262 r_free=0.1622 | n_water=260 | time (s): 0.450 (total time: 31.720) Add new water r_work=0.1441 r_free=0.1802 | n_water=409 | time (s): 1.460 (total time: 33.180) Refine new water occ: r_work=0.1240 r_free=0.1566 adp: r_work=0.1233 r_free=0.1578 occ: r_work=0.1215 r_free=0.1534 adp: r_work=0.1205 r_free=0.1545 occ: r_work=0.1198 r_free=0.1520 adp: r_work=0.1189 r_free=0.1526 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1526 r_work=0.1189 r_free=0.1526 | n_water=409 | time (s): 41.700 (total time: 74.880) Filter (q & B) r_work=0.1193 r_free=0.1531 | n_water=398 | time (s): 1.710 (total time: 76.590) Filter (dist only) r_work=0.1193 r_free=0.1531 | n_water=398 | time (s): 28.300 (total time: 104.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.910546 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.165687 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 0.1175 0.1530 0.0355 0.009 1.0 4.5 0.5 0.0 0 0.955 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.75 15.30 3.55 4.333 21.542 0.166 4.991 11.55 15.46 3.91 4.871 21.462 0.166 4.969 Individual atomic B min max mean iso aniso Overall: 6.48 105.56 20.88 4.65 1925 0 Protein: 6.48 105.56 17.02 4.65 1519 0 Water: 8.36 63.52 35.31 N/A 398 0 Other: 27.42 47.36 35.75 N/A 8 0 Chain A: 6.48 105.56 18.71 N/A 1731 0 Chain S: 15.58 63.52 40.26 N/A 194 0 Histogram: Values Number of atoms 6.48 - 16.39 1069 16.39 - 26.30 351 26.30 - 36.20 225 36.20 - 46.11 163 46.11 - 56.02 75 56.02 - 65.93 30 65.93 - 75.84 4 75.84 - 85.75 3 85.75 - 95.66 3 95.66 - 105.56 2 =========================== Idealize ADP of riding H ========================== r_work=0.1155 r_free=0.1546 r_work=0.1156 r_free=0.1549 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1156 r_free = 0.1549 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1145 r_free = 0.1527 target_work(ml) = 4.963 | | occupancies: max = 1.00 min = 0.25 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= 0.1145 r_free= 0.1527 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.962930 | | target function (ml) not normalized (work): 80568.212299 | | target function (ml) not normalized (free): 4181.092809 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1164 0.1145 0.1527 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1658 0.1649 0.1853 n_refl.: 17041 remove outliers: r(all,work,free)=0.1658 0.1649 0.1853 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1632 0.1623 0.1840 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1161 0.1142 0.1526 n_refl.: 17041 remove outliers: r(all,work,free)=0.1159 0.1141 0.1526 n_refl.: 17039 ======================== 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 92.71 84 5 0.3437 299.553 283.226 0.579 1.006 0.340 11.894-9.307 99.02 97 4 0.1757 487.325 481.184 0.914 1.007 0.340 9.237-7.194 100.00 213 7 0.1809 398.583 398.558 0.978 1.007 0.268 7.162-5.571 100.00 427 22 0.1643 299.137 293.923 0.938 1.006 0.248 5.546-4.326 100.00 867 58 0.0937 410.667 407.168 0.961 1.005 0.206 4.315-3.360 100.00 1859 96 0.0889 390.548 388.065 1.011 1.004 0.201 3.356-2.611 100.00 3867 181 0.1277 256.568 254.217 1.012 1.001 0.131 2.608-2.000 99.99 8818 434 0.1080 167.238 165.869 1.018 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-1.3311 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1141 r_free=0.1526 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1141 r_free=0.1526 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1141 r_free=0.1526 | n_water=398 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1141 r_free=0.1526 | n_water=398 | time (s): 31.560 (total time: 32.180) Filter (q & B) r_work=0.1141 r_free=0.1526 | n_water=398 | time (s): 1.200 (total time: 33.380) Compute maps r_work=0.1141 r_free=0.1526 | n_water=398 | time (s): 0.800 (total time: 34.180) Filter (map) r_work=0.1200 r_free=0.1571 | n_water=309 | time (s): 1.800 (total time: 35.980) Find peaks r_work=0.1200 r_free=0.1571 | n_water=309 | time (s): 0.410 (total time: 36.390) Add new water r_work=0.1359 r_free=0.1728 | n_water=454 | time (s): 1.400 (total time: 37.790) Refine new water occ: r_work=0.1186 r_free=0.1534 adp: r_work=0.1178 r_free=0.1540 occ: r_work=0.1159 r_free=0.1512 adp: r_work=0.1149 r_free=0.1515 occ: r_work=0.1139 r_free=0.1500 adp: r_work=0.1130 r_free=0.1501 ADP+occupancy (water only), MIN, final r_work=0.1130 r_free=0.1501 r_work=0.1130 r_free=0.1501 | n_water=454 | time (s): 38.170 (total time: 75.960) Filter (q & B) r_work=0.1134 r_free=0.1509 | n_water=441 | time (s): 1.550 (total time: 77.510) Filter (dist only) r_work=0.1137 r_free=0.1507 | n_water=439 | time (s): 36.210 (total time: 113.720) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.015186 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.150746 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 0.1121 0.1540 0.0419 0.010 1.0 4.2 0.5 0.0 0 1.008 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.21 15.40 4.19 4.478 21.158 0.151 4.952 11.12 15.36 4.24 4.633 21.147 0.151 4.946 Individual atomic B min max mean iso aniso Overall: 5.88 102.92 21.02 4.73 1966 0 Protein: 5.88 102.92 16.59 4.73 1519 0 Water: 8.41 65.30 36.10 N/A 439 0 Other: 26.74 46.56 34.98 N/A 8 0 Chain A: 5.88 102.92 18.22 N/A 1730 0 Chain S: 17.09 65.30 41.52 N/A 236 0 Histogram: Values Number of atoms 5.88 - 15.59 1038 15.59 - 25.29 363 25.29 - 34.99 223 34.99 - 44.70 202 44.70 - 54.40 88 54.40 - 64.11 37 64.11 - 73.81 6 73.81 - 83.51 4 83.51 - 93.22 3 93.22 - 102.92 2 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1536 r_work=0.1111 r_free=0.1534 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1534 target_work(ml) = 4.945 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1102 r_free = 0.1531 target_work(ml) = 4.940 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1102 r_free= 0.1531 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.939835 | | target function (ml) not normalized (work): 80183.401204 | | target function (ml) not normalized (free): 4173.637544 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1123 0.1102 0.1531 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1591 0.1578 0.1851 n_refl.: 17039 remove outliers: r(all,work,free)=0.1591 0.1578 0.1851 n_refl.: 17039 overall B=-0.32 to atoms: r(all,work,free)=0.1571 0.1558 0.1841 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1121 0.1100 0.1528 n_refl.: 17039 remove outliers: r(all,work,free)=0.1121 0.1100 0.1528 n_refl.: 17039 ======================== 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 92.71 84 5 0.3532 299.553 276.218 0.562 1.000 0.330 11.894-9.307 99.02 97 4 0.1805 487.325 479.893 0.921 1.001 0.324 9.237-7.194 100.00 213 7 0.1629 398.583 399.155 0.994 1.002 0.231 7.162-5.571 100.00 427 22 0.1486 299.137 294.392 0.941 1.002 0.223 5.546-4.326 100.00 867 58 0.0905 410.667 406.770 0.966 1.002 0.201 4.315-3.360 100.00 1859 96 0.0868 390.548 387.969 1.010 1.002 0.201 3.356-2.611 100.00 3867 181 0.1241 256.568 254.399 1.006 1.001 0.101 2.608-2.000 99.99 8818 434 0.1038 167.238 166.430 1.006 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1074 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1100 r_free=0.1528 After: r_work=0.1102 r_free=0.1528 ================================== NQH flips ================================== r_work=0.1102 r_free=0.1528 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1102 r_free=0.1528 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1102 r_free=0.1528 | n_water=439 | time (s): 0.950 (total time: 0.950) Filter (dist) r_work=0.1102 r_free=0.1528 | n_water=439 | time (s): 33.700 (total time: 34.650) Filter (q & B) r_work=0.1102 r_free=0.1528 | n_water=438 | time (s): 1.520 (total time: 36.170) Compute maps r_work=0.1102 r_free=0.1528 | n_water=438 | time (s): 0.730 (total time: 36.900) Filter (map) r_work=0.1180 r_free=0.1560 | n_water=336 | time (s): 1.980 (total time: 38.880) Find peaks r_work=0.1180 r_free=0.1560 | n_water=336 | time (s): 0.460 (total time: 39.340) Add new water r_work=0.1295 r_free=0.1690 | n_water=478 | time (s): 1.420 (total time: 40.760) Refine new water occ: r_work=0.1139 r_free=0.1523 adp: r_work=0.1132 r_free=0.1527 occ: r_work=0.1118 r_free=0.1503 adp: r_work=0.1111 r_free=0.1504 occ: r_work=0.1104 r_free=0.1491 adp: r_work=0.1097 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1097 r_free=0.1489 r_work=0.1097 r_free=0.1489 | n_water=478 | time (s): 44.630 (total time: 85.390) Filter (q & B) r_work=0.1102 r_free=0.1492 | n_water=468 | time (s): 1.970 (total time: 87.360) Filter (dist only) r_work=0.1102 r_free=0.1492 | n_water=467 | time (s): 38.500 (total time: 125.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.873604 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.181060 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 0.1125 0.1512 0.0387 0.010 1.1 6.7 0.5 0.0 0 0.937 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.25 15.12 3.87 4.482 20.872 0.181 4.949 11.12 15.07 3.95 4.587 21.004 0.181 4.941 Individual atomic B min max mean iso aniso Overall: 5.55 101.48 21.16 5.02 1994 0 Protein: 5.55 101.48 16.34 5.00 1519 0 Water: 8.08 64.73 36.61 N/A 467 0 Other: 26.65 45.51 35.27 N/A 8 0 Chain A: 5.55 101.48 17.97 N/A 1730 0 Chain S: 19.41 64.73 42.09 N/A 264 0 Histogram: Values Number of atoms 5.55 - 15.15 1027 15.15 - 24.74 371 24.74 - 34.33 213 34.33 - 43.93 191 43.93 - 53.52 141 53.52 - 63.11 29 63.11 - 72.70 13 72.70 - 82.30 1 82.30 - 91.89 5 91.89 - 101.48 3 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1507 r_work=0.1112 r_free=0.1508 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1112 r_free = 0.1508 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1514 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17039 (all), 4.74 % free)------------| | | | r_work= 0.1103 r_free= 0.1514 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.936339 | | target function (ml) not normalized (work): 80126.651218 | | target function (ml) not normalized (free): 4169.543665 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2809 159 0.1092 0.1393 5.443 5.6703| | 2: 3.63 - 2.88 1.00 2711 122 0.1103 0.1479 5.2239 5.373| | 3: 2.88 - 2.52 1.00 2681 148 0.1362 0.1692 5.138 5.2049| | 4: 2.52 - 2.29 1.00 2661 139 0.0923 0.1536 4.6247 4.9424| | 5: 2.29 - 2.13 1.00 2678 122 0.0975 0.1464 4.5831 4.8748| | 6: 2.13 - 2.00 1.00 2692 117 0.1126 0.1761 4.5765 4.7898| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2809 159 0.94 9.14 1.00 0.96 6487.79| | 2: 3.63 - 2.88 2711 122 0.92 13.04 1.01 0.96 6487.79| | 3: 2.88 - 2.52 2681 148 0.87 19.15 0.99 0.96 6487.79| | 4: 2.52 - 2.29 2661 139 0.93 12.17 1.00 0.97 2129.23| | 5: 2.29 - 2.13 2678 122 0.91 14.27 1.00 0.97 2129.23| | 6: 2.13 - 2.00 2692 117 0.89 16.91 0.99 0.97 2129.23| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2129.23 max = 6487.79 mean = 4331.33| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.94 mean = 14.08| |phase err.(test): min = 0.00 max = 87.91 mean = 13.70| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1123 0.1103 0.1514 n_refl.: 17039 re-set all scales: r(all,work,free)=0.1557 0.1545 0.1818 n_refl.: 17039 remove outliers: r(all,work,free)=0.1557 0.1545 0.1818 n_refl.: 17039 overall B=-0.24 to atoms: r(all,work,free)=0.1544 0.1531 0.1810 n_refl.: 17039 bulk-solvent and scaling: r(all,work,free)=0.1124 0.1104 0.1511 n_refl.: 17039 remove outliers: r(all,work,free)=0.1124 0.1104 0.1511 n_refl.: 17039 ======================== 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 92.71 84 5 0.3455 299.553 277.083 0.554 1.004 0.330 11.894-9.307 99.02 97 4 0.1699 487.325 482.705 0.922 1.005 0.317 9.237-7.194 100.00 213 7 0.1652 398.583 400.774 0.991 1.005 0.228 7.162-5.571 100.00 427 22 0.1576 299.137 293.507 0.934 1.005 0.205 5.546-4.326 100.00 867 58 0.0926 410.667 407.936 0.961 1.004 0.181 4.315-3.360 100.00 1859 96 0.0858 390.548 387.840 1.003 1.003 0.167 3.356-2.611 100.00 3867 181 0.1248 256.568 254.142 1.001 1.000 0.063 2.608-2.000 99.99 8818 434 0.1038 167.238 165.895 0.995 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8167 ================= 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 : 0.2781 0.1767 0.082 5.387 8.8 119.3 19.9 258 0.000 1_bss: 0.1605 0.1581 0.082 5.387 8.4 118.9 19.5 258 0.000 1_settarget: 0.1605 0.1581 0.082 5.387 8.4 118.9 19.5 258 0.000 1_nqh: 0.1605 0.1581 0.082 5.387 8.4 118.9 19.5 258 0.000 1_weight: 0.1605 0.1581 0.082 5.387 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1352 0.1635 0.008 0.959 8.4 118.9 19.5 258 0.153 1_adp: 0.1276 0.1654 0.008 0.959 6.4 113.9 20.0 258 0.153 1_regHadp: 0.1279 0.1661 0.008 0.959 6.4 113.9 20.0 258 0.153 1_occ: 0.1273 0.1651 0.008 0.959 6.4 113.9 20.0 258 0.153 2_bss: 0.1273 0.1651 0.008 0.959 6.0 113.5 19.6 258 0.153 2_settarget: 0.1273 0.1651 0.008 0.959 6.0 113.5 19.6 258 0.153 2_updatecdl: 0.1273 0.1651 0.008 0.975 6.0 113.5 19.6 258 0.153 2_nqh: 0.1273 0.1651 0.008 0.975 6.0 113.5 19.6 258 0.153 2_sol: 0.1241 0.1558 0.008 0.975 6.0 112.3 20.9 355 n/a 2_weight: 0.1241 0.1558 0.008 0.975 6.0 112.3 20.9 355 n/a 2_xyzrec: 0.1213 0.1613 0.008 0.921 6.0 112.3 20.9 355 n/a 2_adp: 0.1201 0.1637 0.008 0.921 6.9 107.3 21.4 355 n/a 2_regHadp: 0.1203 0.1639 0.008 0.921 6.9 107.3 21.4 355 n/a 2_occ: 0.1201 0.1630 0.008 0.921 6.9 107.3 21.4 355 n/a 3_bss: 0.1193 0.1619 0.008 0.921 6.5 106.9 21.0 355 n/a 3_settarget: 0.1193 0.1619 0.008 0.921 6.5 106.9 21.0 355 n/a 3_updatecdl: 0.1193 0.1619 0.008 0.922 6.5 106.9 21.0 355 n/a 3_nqh: 0.1193 0.1619 0.008 0.922 6.5 106.9 21.0 355 n/a 3_sol: 0.1193 0.1531 0.008 0.922 6.5 106.9 21.0 398 n/a 3_weight: 0.1193 0.1531 0.008 0.922 6.5 106.9 21.0 398 n/a 3_xyzrec: 0.1175 0.1530 0.009 0.970 6.5 106.9 21.0 398 n/a 3_adp: 0.1155 0.1546 0.009 0.970 6.5 105.6 20.9 398 n/a 3_regHadp: 0.1156 0.1549 0.009 0.970 6.5 105.6 20.9 398 n/a 3_occ: 0.1145 0.1527 0.009 0.970 6.5 105.6 20.9 398 n/a 4_bss: 0.1141 0.1526 0.009 0.970 6.1 105.2 20.5 398 n/a 4_settarget: 0.1141 0.1526 0.009 0.970 6.1 105.2 20.5 398 n/a 4_updatecdl: 0.1141 0.1526 0.009 0.970 6.1 105.2 20.5 398 n/a 4_nqh: 0.1141 0.1526 0.009 0.970 6.1 105.2 20.5 398 n/a 4_sol: 0.1137 0.1507 0.009 0.970 6.1 105.2 21.0 439 n/a 4_weight: 0.1137 0.1507 0.009 0.970 6.1 105.2 21.0 439 n/a 4_xyzrec: 0.1121 0.1540 0.010 0.985 6.1 105.2 21.0 439 n/a 4_adp: 0.1112 0.1536 0.010 0.985 5.9 102.9 21.0 439 n/a 4_regHadp: 0.1111 0.1534 0.010 0.985 5.9 102.9 21.0 439 n/a 4_occ: 0.1102 0.1531 0.010 0.985 5.9 102.9 21.0 439 n/a 5_bss: 0.1100 0.1528 0.010 0.985 5.6 102.6 20.7 439 n/a 5_settarget: 0.1100 0.1528 0.010 0.985 5.6 102.6 20.7 439 n/a 5_updatecdl: 0.1100 0.1528 0.010 0.986 5.6 102.6 20.7 439 n/a 5_setrh: 0.1102 0.1528 0.010 0.986 5.6 102.6 20.7 439 n/a 5_nqh: 0.1102 0.1528 0.010 0.986 5.6 102.6 20.7 439 n/a 5_sol: 0.1102 0.1492 0.010 0.986 5.6 102.6 20.9 467 n/a 5_weight: 0.1102 0.1492 0.010 0.986 5.6 102.6 20.9 467 n/a 5_xyzrec: 0.1125 0.1512 0.010 1.064 5.6 102.6 20.9 467 n/a 5_adp: 0.1112 0.1507 0.010 1.064 5.6 101.5 21.2 467 n/a 5_regHadp: 0.1112 0.1508 0.010 1.064 5.6 101.5 21.2 467 n/a 5_occ: 0.1103 0.1514 0.010 1.064 5.6 101.5 21.2 467 n/a end: 0.1104 0.1511 0.010 1.064 5.3 101.2 20.9 467 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8540717_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_8540717_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6400 Refinement macro-cycles (run) : 932.6900 Write final files (write_after_run_outputs) : 21.0900 Total : 957.4200 Total CPU time: 16.32 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:20 PST -0800 (1735494080.67 s) Start R-work = 0.1605, R-free = 0.1581 Final R-work = 0.1104, R-free = 0.1511 =============================================================================== Job complete usr+sys time: 999.90 seconds wall clock time: 17 minutes 3.12 seconds (1023.12 seconds total)