Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3120282.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 { 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3120282.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3120282.pdb" } 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 2 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: 1.56, per 1000 atoms: 0.46 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: 0.57 Conformation dependent library (CDL) restraints added in 199.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.89: 397 0.89 - 1.14: 1208 1.14 - 1.39: 565 1.39 - 1.64: 914 1.64 - 1.90: 69 Bond restraints: 3153 Sorted by residual: bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.506 -0.185 1.00e-02 1.00e+04 3.42e+02 bond pdb=" N BLYS A 93 " pdb=" CA BLYS A 93 " ideal model delta sigma weight residual 1.459 1.670 -0.211 1.17e-02 7.31e+03 3.26e+02 bond pdb=" N AGLU A 94 " pdb=" CA AGLU A 94 " ideal model delta sigma weight residual 1.459 1.244 0.215 1.21e-02 6.83e+03 3.17e+02 bond pdb=" N TYR A 141 " pdb=" CA TYR A 141 " ideal model delta sigma weight residual 1.454 1.229 0.225 1.27e-02 6.20e+03 3.14e+02 bond pdb=" C ASN A 144 " pdb=" O ASN A 144 " ideal model delta sigma weight residual 1.234 1.031 0.203 1.22e-02 6.72e+03 2.76e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.77: 3188 4.77 - 9.53: 1877 9.53 - 14.30: 618 14.30 - 19.07: 88 19.07 - 23.83: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O VAL A 50 " pdb=" C VAL A 50 " pdb=" N VAL A 51 " ideal model delta sigma weight residual 122.67 140.42 -17.75 1.02e+00 9.61e-01 3.03e+02 angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH1 ARG A 98 " ideal model delta sigma weight residual 121.50 136.53 -15.03 1.00e+00 1.00e+00 2.26e+02 angle pdb=" O HIS A 126 " pdb=" C HIS A 126 " pdb=" N PRO A 127 " ideal model delta sigma weight residual 121.30 134.92 -13.62 1.03e+00 9.43e-01 1.75e+02 angle pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 120.55 134.31 -13.76 1.06e+00 8.90e-01 1.69e+02 angle pdb=" CA BGLU A 90 " pdb=" C BGLU A 90 " pdb=" O BGLU A 90 " ideal model delta sigma weight residual 120.55 134.06 -13.51 1.06e+00 8.90e-01 1.63e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 1296 17.29 - 34.58: 130 34.58 - 51.88: 43 51.88 - 69.17: 9 69.17 - 86.46: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ILE A 21 " pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual -122.00 -143.71 21.71 0 2.50e+00 1.60e-01 7.54e+01 dihedral pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CA ASP A 68 " pdb=" CB ASP A 68 " ideal model delta harmonic sigma weight residual 122.80 141.92 -19.12 0 2.50e+00 1.60e-01 5.85e+01 dihedral pdb=" C VAL A 186 " pdb=" N VAL A 186 " pdb=" CA VAL A 186 " pdb=" CB VAL A 186 " ideal model delta harmonic sigma weight residual -122.00 -140.17 18.17 0 2.50e+00 1.60e-01 5.28e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.222: 98 0.222 - 0.441: 79 0.441 - 0.660: 48 0.660 - 0.879: 16 0.879 - 1.099: 2 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.49 -1.10 2.00e-01 2.50e+01 3.02e+01 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 1.57 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CA LEU A 58 " pdb=" N LEU A 58 " pdb=" C LEU A 58 " pdb=" CB LEU A 58 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.86e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.023 2.00e-02 2.50e+03 6.81e-02 1.39e+02 pdb=" CG TYR A 139 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.064 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.056 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.135 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.056 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.068 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.064 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.011 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 27 " -0.145 9.50e-02 1.11e+02 7.50e-02 7.62e+01 pdb=" NE ARG A 27 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG A 27 " 0.126 2.00e-02 2.50e+03 pdb=" NH1 ARG A 27 " 0.037 2.00e-02 2.50e+03 pdb=" NH2 ARG A 27 " 0.048 2.00e-02 2.50e+03 pdb="HH11 ARG A 27 " -0.030 2.00e-02 2.50e+03 pdb="HH12 ARG A 27 " -0.032 2.00e-02 2.50e+03 pdb="HH21 ARG A 27 " -0.016 2.00e-02 2.50e+03 pdb="HH22 ARG A 27 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.010 2.00e-02 2.50e+03 4.87e-02 7.12e+01 pdb=" CG PHE A 162 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.071 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.075 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.066 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.055 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.016 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.036 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.051 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1409 2.37 - 2.93: 8343 2.93 - 3.48: 10434 3.48 - 4.04: 15114 4.04 - 4.60: 21323 Nonbonded interactions: 56623 Sorted by model distance: nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.811 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.828 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.846 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.858 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.868 2.100 ... (remaining 56618 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_3120282_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= 0.2794 r_free= 0.1816 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.396016 | | target function (ml) not normalized (work): 71404.490702 | | target function (ml) not normalized (free): 3263.137199 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3197 0.2182 7.5289 5.0425| | 2: 3.63 - 2.88 1.00 2711 122 0.2647 0.1702 4.3316 4.3102| | 3: 2.88 - 2.52 1.00 2682 148 0.2566 0.1648 4.1855 4.1906| | 4: 2.52 - 2.29 1.00 2661 139 0.2556 0.1508 3.4951 3.5472| | 5: 2.29 - 2.13 1.00 2678 122 0.2676 0.1490 3.3723 3.4508| | 6: 2.13 - 2.00 1.00 2692 117 0.2739 0.1862 3.2988 3.4296| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.59 0.77 0.23 1315.06| | 2: 3.63 - 2.88 2711 122 0.83 23.88 1.31 0.23 1315.06| | 3: 2.88 - 2.52 2682 148 0.73 33.03 1.29 0.23 1315.06| | 4: 2.52 - 2.29 2661 139 0.94 10.94 1.30 0.26 129.22| | 5: 2.29 - 2.13 2678 122 0.92 13.23 1.32 0.26 129.22| | 6: 2.13 - 2.00 2692 117 0.90 15.86 1.33 0.26 129.22| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 129.22 max = 1315.06 mean = 728.74| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.99 mean = 19.09| |phase err.(test): min = 0.00 max = 89.08 mean = 19.50| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.291 1557 Z= 5.341 Angle : 5.232 17.755 2118 Z= 3.705 Chirality : 0.382 1.099 243 Planarity : 0.029 0.073 284 Dihedral : 13.950 86.460 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 0.62 % Allowed : 4.97 % Favored : 94.41 % Cbeta Deviations : 31.89 % 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: -2.51 (0.47), residues: 224 helix: -2.60 (0.37), residues: 108 sheet: -0.34 (0.88), residues: 28 loop : -0.50 (0.57), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.112 0.034 ARG A 48 TYR 0.100 0.043 TYR A 139 PHE 0.073 0.033 PHE A 162 HIS 0.060 0.029 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2794 r_free= 0.1816 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.396016 | | target function (ml) not normalized (work): 71404.490702 | | target function (ml) not normalized (free): 3263.137199 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3401 percent. r_work = 0.2928 r_free = 0.1974 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2875 0.2928 0.1974 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2875 0.2928 0.1974 n_refl.: 17050 remove outliers: r(all,work,free)=0.2170 0.2183 0.1974 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2142 0.2154 0.1958 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1621 0.1620 0.1639 n_refl.: 17045 remove outliers: r(all,work,free)=0.1619 0.1618 0.1639 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 0.3881 399.309 361.370 0.647 1.024 0.403 11.894-9.307 99.02 97 4 0.1846 634.197 615.176 0.923 1.024 0.390 9.237-7.194 100.00 213 7 0.2199 518.710 509.481 0.952 1.023 0.355 7.162-5.571 100.00 427 22 0.2416 389.292 373.098 0.910 1.021 0.287 5.546-4.326 100.00 867 58 0.1422 534.436 528.485 0.951 1.017 0.224 4.315-3.360 100.00 1859 96 0.1320 508.253 503.598 1.010 1.011 0.201 3.356-2.611 100.00 3867 181 0.1662 333.894 329.501 1.014 1.000 0.019 2.608-2.000 99.99 8818 434 0.1630 217.641 213.626 1.042 0.980 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4804 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1618 r_free=0.1639 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=0.1622 r_free=0.1647 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.419897 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.893059 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 0.1640 0.0289 0.009 1.0 1.3 0.5 0.0 0 11.210 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.51 16.40 2.89 3.013 18.443 0.893 0.022 12.74 16.67 3.92 3.638 18.738 0.893 0.020 Individual atomic B min max mean iso aniso Overall: 6.19 113.88 20.03 4.08 1785 0 Protein: 6.19 112.74 17.26 4.08 1519 0 Water: 8.91 113.88 36.16 N/A 258 0 Other: 21.68 37.67 26.58 N/A 8 0 Chain A: 6.19 113.88 20.03 N/A 1785 0 Histogram: Values Number of atoms 6.19 - 16.96 1084 16.96 - 27.73 338 27.73 - 38.50 187 38.50 - 49.27 102 49.27 - 60.04 46 60.04 - 70.81 14 70.81 - 81.58 6 81.58 - 92.34 4 92.34 - 103.11 1 103.11 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1274 r_free=0.1667 r_work=0.1277 r_free=0.1672 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1277 r_free = 0.1672 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 = 0.1270 r_free = 0.1665 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.16 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= 0.1270 r_free= 0.1665 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019738 | | target function (ls_wunit_k1) not normalized (work): 320.469206 | | target function (ls_wunit_k1) not normalized (free): 27.575760 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1289 0.1270 0.1665 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1909 0.1907 0.1995 n_refl.: 17043 remove outliers: r(all,work,free)=0.1909 0.1907 0.1995 n_refl.: 17043 overall B=-0.40 to atoms: r(all,work,free)=0.1879 0.1877 0.1977 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1291 0.1272 0.1657 n_refl.: 17043 remove outliers: r(all,work,free)=0.1290 0.1271 0.1657 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 0.3562 304.061 283.436 0.641 1.010 0.380 11.894-9.307 99.02 97 4 0.1691 487.023 476.267 0.916 1.010 0.367 9.237-7.194 100.00 213 7 0.1809 398.336 396.320 0.959 1.010 0.341 7.162-5.571 100.00 427 22 0.1809 298.951 294.202 0.932 1.009 0.301 5.546-4.326 100.00 867 58 0.1038 410.412 408.288 0.957 1.008 0.205 4.315-3.360 100.00 1859 96 0.0922 390.306 389.890 1.017 1.005 0.191 3.356-2.611 100.00 3867 181 0.1296 256.409 255.188 1.016 1.000 0.081 2.608-2.000 99.99 8818 434 0.1351 167.135 165.623 1.026 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4389 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1271 r_free=0.1657 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=0.1274 r_free=0.1661 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1661 | n_water=258 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1282 r_free=0.1649 | n_water=253 | time (s): 22.050 (total time: 22.770) Filter (q & B) r_work=0.1281 r_free=0.1647 | n_water=251 | time (s): 1.570 (total time: 24.340) Compute maps r_work=0.1281 r_free=0.1647 | n_water=251 | time (s): 0.640 (total time: 24.980) Filter (map) r_work=0.1320 r_free=0.1637 | n_water=208 | time (s): 2.160 (total time: 27.140) Find peaks r_work=0.1320 r_free=0.1637 | n_water=208 | time (s): 0.660 (total time: 27.800) Add new water r_work=0.1546 r_free=0.1864 | n_water=369 | time (s): 1.640 (total time: 29.440) Refine new water occ: r_work=0.1335 r_free=0.1642 adp: r_work=0.1276 r_free=0.1613 occ: r_work=0.1280 r_free=0.1596 adp: r_work=0.1247 r_free=0.1589 occ: r_work=0.1249 r_free=0.1592 adp: r_work=0.1236 r_free=0.1590 ADP+occupancy (water only), MIN, final r_work=0.1236 r_free=0.1590 r_work=0.1236 r_free=0.1590 | n_water=369 | time (s): 14.160 (total time: 43.600) Filter (q & B) r_work=0.1236 r_free=0.1596 | n_water=363 | time (s): 1.490 (total time: 45.090) Filter (dist only) r_work=0.1237 r_free=0.1597 | n_water=362 | time (s): 29.040 (total time: 74.130) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.544900 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.975073 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 0.1205 0.1621 0.0416 0.008 0.9 2.6 0.5 0.0 0 12.272 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.05 16.21 4.16 4.177 21.083 0.975 0.018 11.92 16.51 4.59 4.143 21.328 0.975 0.018 Individual atomic B min max mean iso aniso Overall: 6.58 107.34 21.31 4.15 1889 0 Protein: 6.58 107.34 17.74 4.14 1519 0 Water: 8.54 65.76 36.00 N/A 362 0 Other: 24.57 44.95 33.44 N/A 8 0 Chain A: 6.58 107.34 19.40 N/A 1735 0 Chain S: 16.87 63.89 42.78 N/A 154 0 Histogram: Values Number of atoms 6.58 - 16.65 1010 16.65 - 26.73 386 26.73 - 36.81 235 36.81 - 46.88 158 46.88 - 56.96 67 56.96 - 67.04 23 67.04 - 77.11 3 77.11 - 87.19 5 87.19 - 97.27 0 97.27 - 107.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.1192 r_free=0.1651 r_work=0.1193 r_free=0.1653 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1193 r_free = 0.1653 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1191 r_free = 0.1653 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.17 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= 0.1191 r_free= 0.1653 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.016903 | | target function (ls_wunit_k1) not normalized (work): 274.413547 | | target function (ls_wunit_k1) not normalized (free): 26.284192 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1213 0.1191 0.1653 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1813 0.1805 0.2002 n_refl.: 17042 remove outliers: r(all,work,free)=0.1813 0.1805 0.2002 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1786 0.1778 0.1984 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1185 0.1643 n_refl.: 17042 remove outliers: r(all,work,free)=0.1206 0.1184 0.1643 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 0.3321 306.083 278.417 0.602 1.006 0.360 11.894-9.307 99.02 97 4 0.1429 487.023 485.289 0.918 1.006 0.350 9.237-7.194 100.00 213 7 0.1634 398.336 399.125 0.974 1.006 0.310 7.162-5.571 100.00 427 22 0.1535 298.951 295.813 0.936 1.006 0.261 5.546-4.326 100.00 867 58 0.0870 410.412 407.735 0.958 1.005 0.206 4.315-3.360 100.00 1859 96 0.0828 390.306 389.676 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1185 256.409 255.571 1.011 1.001 0.111 2.608-2.000 99.99 8818 434 0.1331 167.135 166.084 1.018 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3644 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1184 r_free=0.1643 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1184 r_free=0.1643 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1184 r_free=0.1643 | n_water=362 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1185 r_free=0.1647 | n_water=359 | time (s): 27.660 (total time: 28.300) Filter (q & B) r_work=0.1185 r_free=0.1648 | n_water=358 | time (s): 1.510 (total time: 29.810) Compute maps r_work=0.1185 r_free=0.1648 | n_water=358 | time (s): 0.590 (total time: 30.400) Filter (map) r_work=0.1245 r_free=0.1646 | n_water=265 | time (s): 1.910 (total time: 32.310) Find peaks r_work=0.1245 r_free=0.1646 | n_water=265 | time (s): 0.500 (total time: 32.810) Add new water r_work=0.1433 r_free=0.1840 | n_water=408 | time (s): 1.440 (total time: 34.250) Refine new water occ: r_work=0.1251 r_free=0.1599 adp: r_work=0.1241 r_free=0.1608 occ: r_work=0.1226 r_free=0.1567 adp: r_work=0.1213 r_free=0.1574 occ: r_work=0.1207 r_free=0.1536 adp: r_work=0.1195 r_free=0.1544 ADP+occupancy (water only), MIN, final r_work=0.1195 r_free=0.1544 r_work=0.1195 r_free=0.1544 | n_water=408 | time (s): 32.930 (total time: 67.180) Filter (q & B) r_work=0.1198 r_free=0.1550 | n_water=401 | time (s): 1.640 (total time: 68.820) Filter (dist only) r_work=0.1198 r_free=0.1550 | n_water=401 | time (s): 29.810 (total time: 98.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.845079 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.145057 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 0.1180 0.1539 0.0359 0.009 1.0 5.1 0.5 0.0 0 0.923 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.80 15.39 3.59 4.272 21.497 0.145 4.996 11.57 15.42 3.85 4.823 21.391 0.145 4.971 Individual atomic B min max mean iso aniso Overall: 6.43 105.06 20.80 4.51 1928 0 Protein: 6.43 105.06 16.95 4.51 1519 0 Water: 8.14 66.66 35.17 N/A 401 0 Other: 25.86 43.74 33.04 N/A 8 0 Chain A: 6.43 105.06 18.63 N/A 1732 0 Chain S: 12.90 66.66 40.06 N/A 196 0 Histogram: Values Number of atoms 6.43 - 16.29 1066 16.29 - 26.15 349 26.15 - 36.02 233 36.02 - 45.88 161 45.88 - 55.74 77 55.74 - 65.61 29 65.61 - 75.47 5 75.47 - 85.33 4 85.33 - 95.20 2 95.20 - 105.06 2 =========================== Idealize ADP of riding H ========================== r_work=0.1157 r_free=0.1542 r_work=0.1158 r_free=0.1542 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1158 r_free = 0.1542 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1150 r_free = 0.1526 target_work(ml) = 4.962 | | 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.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1150 r_free= 0.1526 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.961771 | | target function (ml) not normalized (work): 80549.385709 | | target function (ml) not normalized (free): 4179.825207 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1168 0.1150 0.1526 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1668 0.1660 0.1852 n_refl.: 17041 remove outliers: r(all,work,free)=0.1668 0.1660 0.1852 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1643 0.1634 0.1837 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1167 0.1148 0.1528 n_refl.: 17041 remove outliers: r(all,work,free)=0.1167 0.1148 0.1528 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 0.3459 306.083 284.197 0.584 1.007 0.350 11.894-9.307 99.02 97 4 0.1687 487.023 481.335 0.910 1.007 0.342 9.237-7.194 100.00 213 7 0.1756 398.336 399.485 0.983 1.007 0.259 7.162-5.571 100.00 427 22 0.1627 298.951 293.595 0.939 1.006 0.220 5.546-4.326 100.00 867 58 0.0951 410.412 406.624 0.963 1.005 0.211 4.315-3.360 100.00 1859 96 0.0900 390.306 388.162 1.011 1.003 0.211 3.356-2.611 100.00 3867 181 0.1286 256.409 254.180 1.010 1.001 0.121 2.608-2.000 99.99 8818 434 0.1089 167.135 165.723 1.017 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3293 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1148 r_free=0.1528 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1148 r_free=0.1528 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1148 r_free=0.1528 | n_water=401 | time (s): 0.900 (total time: 0.900) Filter (dist) r_work=0.1151 r_free=0.1527 | n_water=400 | time (s): 31.690 (total time: 32.590) Filter (q & B) r_work=0.1152 r_free=0.1528 | n_water=399 | time (s): 1.440 (total time: 34.030) Compute maps r_work=0.1152 r_free=0.1528 | n_water=399 | time (s): 0.590 (total time: 34.620) Filter (map) r_work=0.1202 r_free=0.1591 | n_water=316 | time (s): 1.680 (total time: 36.300) Find peaks r_work=0.1202 r_free=0.1591 | n_water=316 | time (s): 0.430 (total time: 36.730) Add new water r_work=0.1353 r_free=0.1718 | n_water=461 | time (s): 1.420 (total time: 38.150) Refine new water occ: r_work=0.1185 r_free=0.1506 adp: r_work=0.1175 r_free=0.1519 occ: r_work=0.1159 r_free=0.1489 adp: r_work=0.1149 r_free=0.1500 occ: r_work=0.1141 r_free=0.1482 adp: r_work=0.1132 r_free=0.1489 ADP+occupancy (water only), MIN, final r_work=0.1132 r_free=0.1489 r_work=0.1132 r_free=0.1489 | n_water=461 | time (s): 33.930 (total time: 72.080) Filter (q & B) r_work=0.1136 r_free=0.1502 | n_water=450 | time (s): 1.580 (total time: 73.660) Filter (dist only) r_work=0.1136 r_free=0.1502 | n_water=450 | time (s): 34.170 (total time: 107.830) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.939612 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.160123 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 0.1117 0.1536 0.0419 0.010 1.0 6.7 0.5 0.0 0 0.970 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 15.36 4.19 4.388 21.122 0.160 4.951 11.06 15.34 4.29 4.575 21.148 0.160 4.944 Individual atomic B min max mean iso aniso Overall: 5.95 102.95 21.12 4.80 1977 0 Protein: 5.95 102.95 16.54 4.79 1519 0 Water: 8.06 61.36 36.35 N/A 450 0 Other: 25.29 43.73 32.79 N/A 8 0 Chain A: 5.95 102.95 18.17 N/A 1730 0 Chain S: 17.51 61.36 41.78 N/A 247 0 Histogram: Values Number of atoms 5.95 - 15.65 1041 15.65 - 25.35 370 25.35 - 35.05 211 35.05 - 44.75 203 44.75 - 54.45 103 54.45 - 64.15 37 64.15 - 73.85 5 73.85 - 83.55 2 83.55 - 93.25 3 93.25 - 102.95 2 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1534 r_work=0.1106 r_free=0.1535 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1535 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1099 r_free = 0.1546 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1099 r_free= 0.1546 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.941482 | | target function (ml) not normalized (work): 80220.020194 | | target function (ml) not normalized (free): 4176.448720 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1121 0.1099 0.1546 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1573 0.1559 0.1858 n_refl.: 17041 remove outliers: r(all,work,free)=0.1573 0.1559 0.1858 n_refl.: 17041 overall B=-0.29 to atoms: r(all,work,free)=0.1555 0.1540 0.1847 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1119 0.1098 0.1539 n_refl.: 17041 remove outliers: r(all,work,free)=0.1118 0.1097 0.1539 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3567 302.596 282.392 0.561 1.002 0.340 11.894-9.307 99.02 97 4 0.1743 487.023 483.514 0.916 1.003 0.332 9.237-7.194 100.00 213 7 0.1706 398.336 399.012 0.988 1.004 0.230 7.162-5.571 100.00 427 22 0.1532 298.951 293.747 0.942 1.003 0.210 5.546-4.326 100.00 867 58 0.0903 410.412 407.062 0.966 1.003 0.211 4.315-3.360 100.00 1859 96 0.0859 390.306 388.008 1.008 1.002 0.191 3.356-2.611 100.00 3867 181 0.1229 256.409 254.327 1.004 1.001 0.121 2.608-2.000 99.99 8818 434 0.1035 167.135 165.984 1.003 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-1.0060 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1097 r_free=0.1539 After: r_work=0.1099 r_free=0.1538 ================================== NQH flips ================================== r_work=0.1099 r_free=0.1538 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1099 r_free=0.1538 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1099 r_free=0.1538 | n_water=450 | time (s): 0.920 (total time: 0.920) Filter (dist) r_work=0.1101 r_free=0.1537 | n_water=449 | time (s): 36.660 (total time: 37.580) Filter (q & B) r_work=0.1101 r_free=0.1539 | n_water=447 | time (s): 1.740 (total time: 39.320) Compute maps r_work=0.1101 r_free=0.1539 | n_water=447 | time (s): 0.720 (total time: 40.040) Filter (map) r_work=0.1185 r_free=0.1556 | n_water=341 | time (s): 2.080 (total time: 42.120) Find peaks r_work=0.1185 r_free=0.1556 | n_water=341 | time (s): 0.530 (total time: 42.650) Add new water r_work=0.1307 r_free=0.1672 | n_water=480 | time (s): 1.970 (total time: 44.620) Refine new water occ: r_work=0.1143 r_free=0.1501 adp: r_work=0.1137 r_free=0.1512 occ: r_work=0.1121 r_free=0.1486 adp: r_work=0.1112 r_free=0.1497 occ: r_work=0.1106 r_free=0.1479 adp: r_work=0.1099 r_free=0.1487 ADP+occupancy (water only), MIN, final r_work=0.1099 r_free=0.1487 r_work=0.1099 r_free=0.1487 | n_water=480 | time (s): 37.820 (total time: 82.440) Filter (q & B) r_work=0.1103 r_free=0.1499 | n_water=469 | time (s): 1.650 (total time: 84.090) Filter (dist only) r_work=0.1103 r_free=0.1499 | n_water=469 | time (s): 34.220 (total time: 118.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.941240 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.164898 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 0.1116 0.1536 0.0420 0.010 1.1 4.2 0.5 0.0 0 0.971 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.36 4.20 4.510 20.900 0.165 4.942 11.06 15.31 4.25 4.625 20.978 0.165 4.934 Individual atomic B min max mean iso aniso Overall: 5.83 100.46 21.13 5.01 1996 0 Protein: 5.83 100.46 16.27 4.99 1519 0 Water: 7.94 66.07 36.67 N/A 469 0 Other: 26.58 46.86 34.49 N/A 8 0 Chain A: 5.83 100.46 17.88 N/A 1730 0 Chain S: 18.40 66.07 42.30 N/A 266 0 Histogram: Values Number of atoms 5.83 - 15.29 1046 15.29 - 24.76 357 24.76 - 34.22 215 34.22 - 43.68 196 43.68 - 53.14 117 53.14 - 62.61 48 62.61 - 72.07 8 72.07 - 81.53 2 81.53 - 91.00 4 91.00 - 100.46 3 =========================== Idealize ADP of riding H ========================== r_work=0.1106 r_free=0.1531 r_work=0.1106 r_free=0.1530 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1530 target_work(ml) = 4.933 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1098 r_free = 0.1519 target_work(ml) = 4.926 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1098 r_free= 0.1519 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.925773 | | target function (ml) not normalized (work): 79960.067473 | | target function (ml) not normalized (free): 4157.998401 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1104 0.1445 5.4445 5.6777| | 2: 3.63 - 2.88 1.00 2711 122 0.1082 0.1460 5.2147 5.3384| | 3: 2.88 - 2.52 1.00 2681 148 0.1348 0.1661 5.128 5.1847| | 4: 2.52 - 2.29 1.00 2661 139 0.0924 0.1567 4.6108 4.9444| | 5: 2.29 - 2.13 1.00 2678 122 0.0954 0.1433 4.5656 4.8506| | 6: 2.13 - 2.00 1.00 2692 117 0.1124 0.1707 4.5617 4.7655| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.95 9.06 1.00 0.96 6340.69| | 2: 3.63 - 2.88 2711 122 0.92 12.73 1.01 0.96 6340.69| | 3: 2.88 - 2.52 2681 148 0.88 18.86 0.99 0.96 6340.69| | 4: 2.52 - 2.29 2661 139 0.93 11.83 1.01 0.97 2036.57| | 5: 2.29 - 2.13 2678 122 0.92 13.81 1.00 0.97 2036.57| | 6: 2.13 - 2.00 2692 117 0.90 16.51 0.99 0.97 2036.57| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2036.57 max = 6340.69 mean = 4211.30| |figures of merit: min = 0.00 max = 1.00 mean = 0.92| |phase err.(work): min = 0.00 max = 89.92 mean = 13.76| |phase err.(test): min = 0.00 max = 89.59 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1118 0.1098 0.1519 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1557 0.1544 0.1821 n_refl.: 17040 remove outliers: r(all,work,free)=0.1557 0.1544 0.1821 n_refl.: 17040 overall B=-0.24 to atoms: r(all,work,free)=0.1543 0.1530 0.1813 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1118 0.1098 0.1515 n_refl.: 17040 remove outliers: r(all,work,free)=0.1118 0.1098 0.1515 n_refl.: 17040 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 93.75 85 5 0.3631 302.596 278.381 0.544 1.001 0.324 11.894-9.307 99.02 97 4 0.1730 487.023 480.070 0.917 1.002 0.320 9.237-7.194 100.00 213 7 0.1716 398.336 399.832 0.989 1.003 0.240 7.162-5.571 100.00 427 22 0.1552 298.951 292.427 0.941 1.003 0.210 5.546-4.326 100.00 867 58 0.0906 410.412 407.167 0.965 1.003 0.190 4.315-3.360 100.00 1859 96 0.0860 390.306 388.604 1.006 1.002 0.181 3.356-2.611 100.00 3867 181 0.1233 256.409 254.251 1.000 1.001 0.101 2.608-2.000 99.99 8818 434 0.1031 167.135 165.860 0.992 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8319 ================= 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 : 0.2794 0.1816 0.081 5.232 8.8 119.3 19.9 258 0.000 1_bss: 0.1618 0.1639 0.081 5.232 8.4 118.9 19.5 258 0.000 1_settarget: 0.1618 0.1639 0.081 5.232 8.4 118.9 19.5 258 0.000 1_nqh: 0.1622 0.1647 0.081 5.232 8.4 118.9 19.5 258 0.003 1_weight: 0.1622 0.1647 0.081 5.232 8.4 118.9 19.5 258 0.003 1_xyzrec: 0.1351 0.1640 0.009 0.961 8.4 118.9 19.5 258 0.157 1_adp: 0.1274 0.1667 0.009 0.961 6.2 113.9 20.0 258 0.157 1_regHadp: 0.1277 0.1672 0.009 0.961 6.2 113.9 20.0 258 0.157 1_occ: 0.1270 0.1665 0.009 0.961 6.2 113.9 20.0 258 0.157 2_bss: 0.1271 0.1657 0.009 0.961 5.8 113.5 19.6 258 0.157 2_settarget: 0.1271 0.1657 0.009 0.961 5.8 113.5 19.6 258 0.157 2_updatecdl: 0.1271 0.1657 0.009 0.971 5.8 113.5 19.6 258 0.157 2_nqh: 0.1274 0.1661 0.009 0.971 5.8 113.5 19.6 258 0.154 2_sol: 0.1237 0.1597 0.009 0.971 5.8 112.3 20.9 362 n/a 2_weight: 0.1237 0.1597 0.009 0.971 5.8 112.3 20.9 362 n/a 2_xyzrec: 0.1205 0.1621 0.008 0.927 5.8 112.3 20.9 362 n/a 2_adp: 0.1192 0.1651 0.008 0.927 6.6 107.3 21.3 362 n/a 2_regHadp: 0.1193 0.1653 0.008 0.927 6.6 107.3 21.3 362 n/a 2_occ: 0.1191 0.1653 0.008 0.927 6.6 107.3 21.3 362 n/a 3_bss: 0.1184 0.1643 0.008 0.927 6.2 107.0 20.9 362 n/a 3_settarget: 0.1184 0.1643 0.008 0.927 6.2 107.0 20.9 362 n/a 3_updatecdl: 0.1184 0.1643 0.008 0.927 6.2 107.0 20.9 362 n/a 3_nqh: 0.1184 0.1643 0.008 0.927 6.2 107.0 20.9 362 n/a 3_sol: 0.1198 0.1550 0.008 0.927 6.2 107.0 21.0 401 n/a 3_weight: 0.1198 0.1550 0.008 0.927 6.2 107.0 21.0 401 n/a 3_xyzrec: 0.1180 0.1539 0.009 0.955 6.2 107.0 21.0 401 n/a 3_adp: 0.1157 0.1542 0.009 0.955 6.4 105.1 20.8 401 n/a 3_regHadp: 0.1158 0.1542 0.009 0.955 6.4 105.1 20.8 401 n/a 3_occ: 0.1150 0.1526 0.009 0.955 6.4 105.1 20.8 401 n/a 4_bss: 0.1148 0.1528 0.009 0.955 6.1 104.7 20.4 401 n/a 4_settarget: 0.1148 0.1528 0.009 0.955 6.1 104.7 20.4 401 n/a 4_updatecdl: 0.1148 0.1528 0.009 0.953 6.1 104.7 20.4 401 n/a 4_nqh: 0.1148 0.1528 0.009 0.953 6.1 104.7 20.4 401 n/a 4_sol: 0.1136 0.1502 0.009 0.953 6.1 104.7 21.1 450 n/a 4_weight: 0.1136 0.1502 0.009 0.953 6.1 104.7 21.1 450 n/a 4_xyzrec: 0.1117 0.1536 0.010 0.978 6.1 104.7 21.1 450 n/a 4_adp: 0.1106 0.1534 0.010 0.978 6.0 102.9 21.1 450 n/a 4_regHadp: 0.1106 0.1535 0.010 0.978 6.0 102.9 21.1 450 n/a 4_occ: 0.1099 0.1546 0.010 0.978 6.0 102.9 21.1 450 n/a 5_bss: 0.1097 0.1539 0.010 0.978 5.7 102.7 20.8 450 n/a 5_settarget: 0.1097 0.1539 0.010 0.978 5.7 102.7 20.8 450 n/a 5_updatecdl: 0.1097 0.1539 0.010 0.980 5.7 102.7 20.8 450 n/a 5_setrh: 0.1099 0.1538 0.010 0.980 5.7 102.7 20.8 450 n/a 5_nqh: 0.1099 0.1538 0.010 0.980 5.7 102.7 20.8 450 n/a 5_sol: 0.1103 0.1499 0.010 0.980 5.7 102.7 21.0 469 n/a 5_weight: 0.1103 0.1499 0.010 0.980 5.7 102.7 21.0 469 n/a 5_xyzrec: 0.1116 0.1536 0.010 1.068 5.7 102.7 21.0 469 n/a 5_adp: 0.1106 0.1531 0.010 1.068 5.8 100.5 21.1 469 n/a 5_regHadp: 0.1106 0.1530 0.010 1.068 5.8 100.5 21.1 469 n/a 5_occ: 0.1098 0.1519 0.010 1.068 5.8 100.5 21.1 469 n/a end: 0.1098 0.1515 0.010 1.068 5.6 100.2 20.9 469 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3120282_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3120282_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9800 Refinement macro-cycles (run) : 916.7300 Write final files (write_after_run_outputs) : 20.3900 Total : 941.1000 Total CPU time: 16.06 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:05 PST -0800 (1735494065.73 s) Start R-work = 0.1618, R-free = 0.1639 Final R-work = 0.1098, R-free = 0.1515 =============================================================================== Job complete usr+sys time: 987.37 seconds wall clock time: 16 minutes 51.02 seconds (1011.02 seconds total)