Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4813131.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=3 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_4813131.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4813131.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } 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: 2.14, per 1000 atoms: 0.63 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: 0.49 Conformation dependent library (CDL) restraints added in 228.2 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.63 - 0.89: 406 0.89 - 1.15: 1203 1.15 - 1.41: 628 1.41 - 1.67: 881 1.67 - 1.93: 35 Bond restraints: 3153 Sorted by residual: bond pdb=" C ALA A 11 " pdb=" N LYS A 12 " ideal model delta sigma weight residual 1.332 1.626 -0.295 1.35e-02 5.49e+03 4.76e+02 bond pdb=" CA ALA A 104 " pdb=" C ALA A 104 " ideal model delta sigma weight residual 1.520 1.294 0.227 1.22e-02 6.72e+03 3.46e+02 bond pdb=" N ALA A 39 " pdb=" CA ALA A 39 " ideal model delta sigma weight residual 1.456 1.214 0.242 1.32e-02 5.74e+03 3.36e+02 bond pdb=" N GLU A 163 " pdb=" CA GLU A 163 " ideal model delta sigma weight residual 1.459 1.671 -0.212 1.19e-02 7.06e+03 3.18e+02 bond pdb=" C ARG A 145 " pdb=" O ARG A 145 " ideal model delta sigma weight residual 1.237 1.441 -0.205 1.16e-02 7.43e+03 3.11e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.94: 3333 4.94 - 9.87: 1811 9.87 - 14.81: 548 14.81 - 19.74: 79 19.74 - 24.68: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA BLYS A 175 " pdb=" C BLYS A 175 " pdb=" O BLYS A 175 " ideal model delta sigma weight residual 120.55 136.26 -15.71 1.06e+00 8.90e-01 2.20e+02 angle pdb=" CA ATYR A 67 " pdb=" C ATYR A 67 " pdb=" O ATYR A 67 " ideal model delta sigma weight residual 120.71 135.51 -14.80 1.06e+00 8.90e-01 1.95e+02 angle pdb=" O BGLU A 94 " pdb=" C BGLU A 94 " pdb=" N GLN A 95 " ideal model delta sigma weight residual 122.15 106.38 15.77 1.14e+00 7.69e-01 1.91e+02 angle pdb=" CA MET A 133 " pdb=" C MET A 133 " pdb=" O MET A 133 " ideal model delta sigma weight residual 120.76 107.13 13.63 1.03e+00 9.43e-01 1.75e+02 angle pdb=" O GLU A 163 " pdb=" C GLU A 163 " pdb=" N PHE A 164 " ideal model delta sigma weight residual 122.07 109.11 12.96 1.03e+00 9.43e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 1308 17.33 - 34.66: 115 34.66 - 51.98: 40 51.98 - 69.31: 16 69.31 - 86.64: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C GLN A 180 " pdb=" N GLN A 180 " pdb=" CA GLN A 180 " pdb=" CB GLN A 180 " ideal model delta harmonic sigma weight residual -122.60 -138.25 15.65 0 2.50e+00 1.60e-01 3.92e+01 dihedral pdb=" C LEU A 113 " pdb=" N LEU A 113 " pdb=" CA LEU A 113 " pdb=" CB LEU A 113 " ideal model delta harmonic sigma weight residual -122.60 -138.20 15.60 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" N MET A 134 " pdb=" C MET A 134 " pdb=" CA MET A 134 " pdb=" CB MET A 134 " ideal model delta harmonic sigma weight residual 122.80 138.40 -15.60 0 2.50e+00 1.60e-01 3.90e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.215: 103 0.215 - 0.427: 77 0.427 - 0.640: 41 0.640 - 0.852: 19 0.852 - 1.065: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA VAL A 51 " pdb=" N VAL A 51 " pdb=" C VAL A 51 " pdb=" CB VAL A 51 " both_signs ideal model delta sigma weight residual False 2.44 3.51 -1.06 2.00e-01 2.50e+01 2.83e+01 chirality pdb=" CA VAL A 35 " pdb=" N VAL A 35 " pdb=" C VAL A 35 " pdb=" CB VAL A 35 " both_signs ideal model delta sigma weight residual False 2.44 3.41 -0.97 2.00e-01 2.50e+01 2.37e+01 chirality pdb=" CG LEU A 187 " pdb=" CB LEU A 187 " pdb=" CD1 LEU A 187 " pdb=" CD2 LEU A 187 " both_signs ideal model delta sigma weight residual False -2.59 -3.56 0.97 2.00e-01 2.50e+01 2.34e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 27 " -0.105 9.50e-02 1.11e+02 8.77e-02 1.47e+02 pdb=" NE ARG A 27 " 0.057 2.00e-02 2.50e+03 pdb=" CZ ARG A 27 " 0.091 2.00e-02 2.50e+03 pdb=" NH1 ARG A 27 " 0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG A 27 " -0.131 2.00e-02 2.50e+03 pdb="HH11 ARG A 27 " -0.096 2.00e-02 2.50e+03 pdb="HH12 ARG A 27 " -0.009 2.00e-02 2.50e+03 pdb="HH21 ARG A 27 " -0.069 2.00e-02 2.50e+03 pdb="HH22 ARG A 27 " 0.115 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.073 2.00e-02 2.50e+03 6.18e-02 1.15e+02 pdb=" CG PHE A 164 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.062 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.069 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.092 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.078 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.082 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.042 2.00e-02 2.50e+03 5.78e-02 1.00e+02 pdb=" CG TYR A 139 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.127 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.058 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.045 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.040 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.033 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.044 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.062 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.034 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 869 2.29 - 2.87: 7884 2.87 - 3.44: 10567 3.44 - 4.02: 15298 4.02 - 4.60: 22023 Nonbonded interactions: 56641 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.710 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.805 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.834 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.870 2.100 nonbonded pdb=" O GLY A 75 " pdb=" H ALA A 79 " model vdw 1.895 2.450 ... (remaining 56636 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 1 N 265 6.97 1 C 957 5.97 2 H 1596 1.00 1 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_4813131_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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3627 r_free= 0.2044 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.466510 | | target function (ml) not normalized (work): 22019.892894 | | target function (ml) not normalized (free): 1152.694204 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3814 0.2223 4.8555 4.9039| | 2: 3.78 - 3.00 1.00 2430 110 0.3399 0.1741 4.0663 4.1486| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2500 142 0.50 48.87 0.83 0.13 6614.39| | 2: 3.78 - 3.00 2430 110 0.94 11.06 1.48 0.26 442.84| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 371.34 max = 12071.44 mean = 3572.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.23| |phase err.(test): min = 0.00 max = 89.99 mean = 33.31| |-----------------------------------------------------------------------------| ----------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 : 0.080 0.295 1557 Z= 5.317 Angle : 5.198 18.421 2118 Z= 3.650 Chirality : 0.370 1.065 243 Planarity : 0.032 0.132 284 Dihedral : 14.016 86.638 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 2.48 % Favored : 96.27 % Cbeta Deviations : 28.65 % 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: -2.38 (0.47), residues: 224 helix: -1.87 (0.39), residues: 109 sheet: -1.46 (0.77), residues: 38 loop : -0.76 (0.62), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.125 0.030 ARG A 28 TYR 0.076 0.029 TYR A 139 PHE 0.121 0.037 PHE A 164 HIS 0.088 0.036 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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3627 r_free= 0.2044 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.466510 | | target function (ml) not normalized (work): 22019.892894 | | target function (ml) not normalized (free): 1152.694204 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3583 0.3661 0.2147 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3583 0.3661 0.2147 n_refl.: 5182 remove outliers: r(all,work,free)=0.2528 0.2552 0.2147 n_refl.: 5178 overall B=-2.44 to atoms: r(all,work,free)=0.2432 0.2453 0.2113 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1563 0.1560 0.1621 n_refl.: 5178 remove outliers: r(all,work,free)=0.1559 0.1556 0.1621 n_refl.: 5176 ======================== 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 0.3859 449.368 406.284 0.620 1.093 0.398 11.894-9.307 99.02 97 4 0.1902 713.857 694.634 0.888 1.088 0.382 9.237-7.194 100.00 213 7 0.2185 583.793 573.473 0.919 1.078 0.353 7.162-5.571 100.00 427 22 0.2302 438.066 423.365 0.888 1.061 0.345 5.546-4.326 100.00 867 58 0.1389 601.402 594.780 0.938 1.033 0.220 4.315-3.360 100.00 1859 96 0.1312 571.940 565.702 1.025 0.986 0.199 3.356-3.002 100.00 1373 60 0.1574 440.532 433.712 1.060 0.939 0.077 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-4.2268 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1556 r_free=0.1621 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1556 r_free=0.1621 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.653646 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.590624 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1157 0.1791 0.0634 0.010 1.0 2.2 0.5 0.0 0 9.827 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 17.91 6.34 3.013 16.422 1.591 0.018 10.27 17.99 7.72 4.459 16.548 1.591 0.015 Individual atomic B min max mean iso aniso Overall: 2.74 112.07 17.69 4.93 1785 0 Protein: 2.74 112.07 14.98 4.92 1519 0 Water: 4.43 111.86 33.42 N/A 258 0 Other: 16.84 37.10 23.74 N/A 8 0 Chain A: 2.74 112.07 17.69 N/A 1785 0 Histogram: Values Number of atoms 2.74 - 13.67 947 13.67 - 24.60 465 24.60 - 35.54 183 35.54 - 46.47 106 46.47 - 57.40 55 57.40 - 68.33 13 68.33 - 79.27 7 79.27 - 90.20 5 90.20 - 101.13 1 101.13 - 112.07 3 =========================== Idealize ADP of riding H ========================== r_work=0.1027 r_free=0.1799 r_work=0.1020 r_free=0.1801 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1020 r_free = 0.1801 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1011 r_free = 0.1784 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1011 r_free= 0.1784 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013860 | | target function (ls_wunit_k1) not normalized (work): 68.248375 | | target function (ls_wunit_k1) not normalized (free): 10.355684 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1051 0.1011 0.1784 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2115 0.2114 0.2238 n_refl.: 5176 remove outliers: r(all,work,free)=0.2115 0.2114 0.2238 n_refl.: 5176 overall B=-1.06 to atoms: r(all,work,free)=0.2069 0.2067 0.2226 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1049 0.1010 0.1778 n_refl.: 5176 remove outliers: r(all,work,free)=0.1049 0.1010 0.1778 n_refl.: 5176 ======================== 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 0.3325 317.950 302.114 0.652 1.050 0.381 11.894-9.307 99.02 97 4 0.1483 505.089 496.481 0.952 1.048 0.361 9.237-7.194 100.00 213 7 0.1639 413.063 412.753 0.988 1.042 0.326 7.162-5.571 100.00 427 22 0.1617 309.953 306.459 0.958 1.033 0.312 5.546-4.326 100.00 867 58 0.0918 425.522 422.833 0.987 1.017 0.202 4.315-3.360 100.00 1859 96 0.0762 404.676 404.431 1.056 0.991 0.194 3.356-3.002 100.00 1373 60 0.1001 311.698 310.178 1.058 0.965 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.7942 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1010 r_free=0.1778 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1010 r_free=0.1778 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1010 r_free=0.1778 | n_water=258 | time (s): 0.500 (total time: 0.500) Filter (dist) r_work=0.1041 r_free=0.1788 | n_water=248 | time (s): 19.500 (total time: 20.000) Filter (q & B) r_work=0.1041 r_free=0.1785 | n_water=245 | time (s): 1.460 (total time: 21.460) Compute maps r_work=0.1041 r_free=0.1785 | n_water=245 | time (s): 0.520 (total time: 21.980) Filter (map) r_work=0.1363 r_free=0.1823 | n_water=142 | time (s): 1.640 (total time: 23.620) Find peaks r_work=0.1363 r_free=0.1823 | n_water=142 | time (s): 0.400 (total time: 24.020) Add new water r_work=0.1723 r_free=0.2073 | n_water=227 | time (s): 1.410 (total time: 25.430) Refine new water occ: r_work=0.1163 r_free=0.1649 adp: r_work=0.1143 r_free=0.1668 occ: r_work=0.1138 r_free=0.1637 adp: r_work=0.1129 r_free=0.1654 occ: r_work=0.1127 r_free=0.1638 adp: r_work=0.1124 r_free=0.1650 ADP+occupancy (water only), MIN, final r_work=0.1124 r_free=0.1650 r_work=0.1124 r_free=0.1650 | n_water=227 | time (s): 3.090 (total time: 28.520) Filter (q & B) r_work=0.1124 r_free=0.1650 | n_water=227 | time (s): 0.860 (total time: 29.380) Filter (dist only) r_work=0.1129 r_free=0.1645 | n_water=225 | time (s): 16.510 (total time: 45.890) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.489328 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.797506 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.1014 0.1749 0.0735 0.010 1.0 3.5 0.5 0.6 0 11.745 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.14 17.49 7.35 4.464 16.916 2.798 0.014 9.41 17.51 8.10 5.450 17.233 2.798 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 109.84 16.55 6.48 1752 0 Protein: 0.00 109.84 15.01 6.48 1519 0 Water: 0.00 63.09 26.73 N/A 225 0 Other: 12.55 34.10 21.69 N/A 8 0 Chain A: 0.00 109.84 15.74 N/A 1667 0 Chain S: 4.01 58.43 32.45 N/A 85 0 Histogram: Values Number of atoms 0.00 - 10.98 708 10.98 - 21.97 654 21.97 - 32.95 206 32.95 - 43.94 107 43.94 - 54.92 40 54.92 - 65.91 27 65.91 - 76.89 4 76.89 - 87.88 3 87.88 - 98.86 1 98.86 - 109.84 2 =========================== Idealize ADP of riding H ========================== r_work=0.0941 r_free=0.1751 r_work=0.0937 r_free=0.1750 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0937 r_free = 0.1750 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0936 r_free = 0.1760 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0936 r_free= 0.1760 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012033 | | target function (ls_wunit_k1) not normalized (work): 59.248586 | | target function (ls_wunit_k1) not normalized (free): 10.020298 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0977 0.0936 0.1760 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2137 0.2145 0.2136 n_refl.: 5176 remove outliers: r(all,work,free)=0.2137 0.2145 0.2136 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2137 0.2145 0.2136 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0979 0.0938 0.1762 n_refl.: 5176 remove outliers: r(all,work,free)=0.0977 0.0935 0.1762 n_refl.: 5175 ======================== 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 0.3266 315.272 301.411 0.663 1.026 0.370 11.894-9.307 99.02 97 4 0.1489 505.089 498.308 0.965 1.027 0.340 9.237-7.194 100.00 213 7 0.1487 413.063 413.912 1.007 1.025 0.330 7.162-5.571 100.00 427 22 0.1410 309.953 307.558 0.980 1.019 0.300 5.546-4.326 100.00 867 58 0.0794 425.522 422.831 1.004 1.010 0.214 4.315-3.360 100.00 1859 96 0.0723 404.676 404.599 1.065 0.995 0.200 3.356-3.002 100.00 1373 60 0.0955 311.698 310.733 1.058 0.980 0.068 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.4847 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0935 r_free=0.1762 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0936 r_free=0.1765 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0936 r_free=0.1765 | n_water=225 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0959 r_free=0.1760 | n_water=220 | time (s): 19.450 (total time: 19.960) Filter (q & B) r_work=0.1037 r_free=0.1766 | n_water=217 | time (s): 1.430 (total time: 21.390) Compute maps r_work=0.1037 r_free=0.1766 | n_water=217 | time (s): 0.450 (total time: 21.840) Filter (map) r_work=0.1270 r_free=0.1896 | n_water=155 | time (s): 1.370 (total time: 23.210) Find peaks r_work=0.1270 r_free=0.1896 | n_water=155 | time (s): 0.490 (total time: 23.700) Add new water r_work=0.1609 r_free=0.2222 | n_water=230 | time (s): 1.670 (total time: 25.370) Refine new water occ: r_work=0.1063 r_free=0.1803 adp: r_work=0.1057 r_free=0.1814 occ: r_work=0.1047 r_free=0.1799 adp: r_work=0.1046 r_free=0.1803 occ: r_work=0.1036 r_free=0.1792 adp: r_work=0.1035 r_free=0.1795 ADP+occupancy (water only), MIN, final r_work=0.1035 r_free=0.1795 r_work=0.1035 r_free=0.1795 | n_water=230 | time (s): 12.980 (total time: 38.350) Filter (q & B) r_work=0.1035 r_free=0.1795 | n_water=230 | time (s): 0.930 (total time: 39.280) Filter (dist only) r_work=0.1034 r_free=0.1792 | n_water=229 | time (s): 16.910 (total time: 56.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.099051 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.210216 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0938 0.1777 0.0839 0.011 1.1 4.2 0.5 0.6 0 0.550 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.38 17.77 8.39 5.411 17.831 0.210 5.117 8.95 17.98 9.03 7.126 17.790 0.210 5.025 Individual atomic B min max mean iso aniso Overall: 0.00 110.25 16.36 8.73 1756 0 Protein: 0.00 110.25 15.02 8.73 1519 0 Water: 0.00 63.60 25.01 N/A 229 0 Other: 10.79 36.63 22.02 N/A 8 0 Chain A: 0.00 110.25 15.70 N/A 1654 0 Chain S: 0.00 63.60 27.02 N/A 102 0 Histogram: Values Number of atoms 0.00 - 11.03 711 11.03 - 22.05 653 22.05 - 33.08 212 33.08 - 44.10 114 44.10 - 55.13 33 55.13 - 66.15 15 66.15 - 77.18 13 77.18 - 88.20 0 88.20 - 99.23 4 99.23 - 110.25 1 =========================== Idealize ADP of riding H ========================== r_work=0.0895 r_free=0.1798 r_work=0.0901 r_free=0.1809 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0901 r_free = 0.1809 target_work(ml) = 5.029 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0891 r_free = 0.1797 target_work(ml) = 5.023 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0891 r_free= 0.1797 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.022905 | | target function (ml) not normalized (work): 24727.763578 | | target function (ml) not normalized (free): 1789.735532 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0937 0.0891 0.1797 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2132 0.2143 0.2117 n_refl.: 5175 remove outliers: r(all,work,free)=0.2132 0.2143 0.2117 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2132 0.2143 0.2117 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0934 0.0889 0.1800 n_refl.: 5175 remove outliers: r(all,work,free)=0.0932 0.0887 0.1800 n_refl.: 5174 ======================== 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 0.3609 317.369 284.442 0.590 0.994 0.334 11.894-9.307 99.02 97 4 0.1854 505.089 489.871 0.954 0.998 0.330 9.237-7.194 100.00 213 7 0.1859 413.063 411.764 1.013 1.000 0.310 7.162-5.571 100.00 427 22 0.1857 309.953 302.880 0.979 1.001 0.290 5.546-4.326 100.00 867 58 0.0914 425.522 420.431 1.004 1.002 0.220 4.315-3.360 100.00 1859 96 0.0587 404.676 404.402 1.065 1.002 0.220 3.356-3.002 100.00 1373 60 0.0603 311.698 310.761 1.047 1.002 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.8686 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0887 r_free=0.1800 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=0.0888 r_free=0.1797 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0888 r_free=0.1797 | n_water=229 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.0900 r_free=0.1797 | n_water=226 | time (s): 18.560 (total time: 19.170) Filter (q & B) r_work=0.0937 r_free=0.1816 | n_water=225 | time (s): 1.510 (total time: 20.680) Compute maps r_work=0.0937 r_free=0.1816 | n_water=225 | time (s): 0.450 (total time: 21.130) Filter (map) r_work=0.1219 r_free=0.1863 | n_water=157 | time (s): 1.270 (total time: 22.400) Find peaks r_work=0.1219 r_free=0.1863 | n_water=157 | time (s): 0.470 (total time: 22.870) Add new water r_work=0.1542 r_free=0.2172 | n_water=238 | time (s): 1.550 (total time: 24.420) Refine new water occ: r_work=0.1007 r_free=0.1773 adp: r_work=0.1002 r_free=0.1787 occ: r_work=0.0992 r_free=0.1761 adp: r_work=0.0992 r_free=0.1776 occ: r_work=0.0982 r_free=0.1747 adp: r_work=0.0983 r_free=0.1763 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1763 r_work=0.0983 r_free=0.1763 | n_water=238 | time (s): 12.390 (total time: 36.810) Filter (q & B) r_work=0.0982 r_free=0.1764 | n_water=237 | time (s): 1.860 (total time: 38.670) Filter (dist only) r_work=0.0993 r_free=0.1767 | n_water=236 | time (s): 18.240 (total time: 56.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.079207 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.261319 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0912 0.1828 0.0916 0.011 1.1 4.5 0.5 0.6 0 0.540 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.12 18.28 9.16 6.822 17.889 0.261 5.003 8.90 18.67 9.77 8.143 18.008 0.261 4.934 Individual atomic B min max mean iso aniso Overall: 0.00 113.04 16.75 10.64 1763 0 Protein: 0.00 113.04 15.45 10.64 1519 0 Water: 0.00 57.15 24.95 N/A 236 0 Other: 12.77 36.97 21.86 N/A 8 0 Chain A: 0.00 113.04 16.04 N/A 1641 0 Chain S: 0.00 57.15 26.31 N/A 122 0 Histogram: Values Number of atoms 0.00 - 11.30 722 11.30 - 22.61 630 22.61 - 33.91 228 33.91 - 45.21 112 45.21 - 56.52 40 56.52 - 67.82 15 67.82 - 79.12 11 79.12 - 90.43 0 90.43 - 101.73 4 101.73 - 113.04 1 =========================== Idealize ADP of riding H ========================== r_work=0.0890 r_free=0.1867 r_work=0.0894 r_free=0.1870 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0894 r_free = 0.1870 target_work(ml) = 4.939 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0880 r_free = 0.1849 target_work(ml) = 4.930 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0880 r_free= 0.1849 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.930214 | | target function (ml) not normalized (work): 24266.511897 | | target function (ml) not normalized (free): 2041.883083 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0929 0.0880 0.1849 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2077 0.2081 0.2145 n_refl.: 5174 remove outliers: r(all,work,free)=0.2077 0.2081 0.2145 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2077 0.2081 0.2145 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0927 0.0879 0.1846 n_refl.: 5174 remove outliers: r(all,work,free)=0.0927 0.0879 0.1846 n_refl.: 5174 ======================== 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 0.3795 317.369 288.179 0.590 0.985 0.324 11.894-9.307 99.02 97 4 0.1860 505.089 486.675 0.944 0.991 0.320 9.237-7.194 100.00 213 7 0.2127 413.063 405.966 1.011 0.994 0.310 7.162-5.571 100.00 427 22 0.2045 309.953 300.746 0.993 0.996 0.290 5.546-4.326 100.00 867 58 0.0977 425.522 419.882 1.019 0.998 0.220 4.315-3.360 100.00 1859 96 0.0555 404.676 404.526 1.087 1.001 0.220 3.356-3.002 100.00 1373 60 0.0449 311.698 311.439 1.067 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.8077 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0879 r_free=0.1846 After: r_work=0.0881 r_free=0.1845 ================================== NQH flips ================================== r_work=0.0881 r_free=0.1845 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=0.0881 r_free=0.1847 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0881 r_free=0.1847 | n_water=236 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.0894 r_free=0.1849 | n_water=231 | time (s): 19.010 (total time: 19.710) Filter (q & B) r_work=0.0966 r_free=0.1891 | n_water=229 | time (s): 1.760 (total time: 21.470) Compute maps r_work=0.0966 r_free=0.1891 | n_water=229 | time (s): 0.670 (total time: 22.140) Filter (map) r_work=0.1269 r_free=0.1918 | n_water=153 | time (s): 1.920 (total time: 24.060) Find peaks r_work=0.1269 r_free=0.1918 | n_water=153 | time (s): 0.420 (total time: 24.480) Add new water r_work=0.1577 r_free=0.2115 | n_water=233 | time (s): 1.620 (total time: 26.100) Refine new water occ: r_work=0.1007 r_free=0.1803 adp: r_work=0.0998 r_free=0.1815 occ: r_work=0.0993 r_free=0.1798 adp: r_work=0.0991 r_free=0.1807 occ: r_work=0.0986 r_free=0.1793 adp: r_work=0.0983 r_free=0.1802 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1802 r_work=0.0983 r_free=0.1802 | n_water=233 | time (s): 14.910 (total time: 41.010) Filter (q & B) r_work=0.0983 r_free=0.1805 | n_water=230 | time (s): 1.810 (total time: 42.820) Filter (dist only) r_work=0.0986 r_free=0.1802 | n_water=229 | time (s): 17.460 (total time: 60.280) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.939010 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.247118 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 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 0.0925 0.1812 0.0887 0.010 1.2 8.0 0.5 0.6 0 0.470 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.25 18.12 8.87 8.096 18.260 0.247 4.991 9.03 18.03 9.00 9.017 18.337 0.247 4.935 Individual atomic B min max mean iso aniso Overall: 0.00 115.36 16.91 11.90 1756 0 Protein: 0.00 115.36 15.79 11.89 1519 0 Water: 0.00 58.27 24.20 N/A 229 0 Other: 10.00 41.43 20.94 N/A 8 0 Chain A: 0.00 115.36 16.29 N/A 1633 0 Chain S: 0.00 56.29 25.07 N/A 123 0 Histogram: Values Number of atoms 0.00 - 11.54 723 11.54 - 23.07 632 23.07 - 34.61 228 34.61 - 46.15 105 46.15 - 57.68 40 57.68 - 69.22 13 69.22 - 80.75 9 80.75 - 92.29 3 92.29 - 103.83 2 103.83 - 115.36 1 =========================== Idealize ADP of riding H ========================== r_work=0.0903 r_free=0.1803 r_work=0.0907 r_free=0.1804 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0907 r_free = 0.1804 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0897 r_free = 0.1790 target_work(ml) = 4.933 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0897 r_free= 0.1790 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 4.932759 | | target function (ml) not normalized (work): 24279.037906 | | target function (ml) not normalized (free): 1939.702684 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1275 0.1812 5.5021 6.1356| | 2: 3.78 - 3.00 1.00 2430 110 0.0436 0.1752 4.3489 9.7131| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.79 2492 142 0.91 12.23 1.00 0.94 12388.84| | 2: 3.78 - 3.00 2430 110 0.99 2.00 1.00 0.95 902.53| |alpha: min = 0.93 max = 0.96 mean = 0.94| |beta: min = 584.65 max = 20764.53 mean = 6718.03| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.48 mean = 7.18| |phase err.(test): min = 0.00 max = 88.19 mean = 7.48| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0941 0.0897 0.1790 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2129 0.2132 0.2191 n_refl.: 5174 remove outliers: r(all,work,free)=0.2129 0.2132 0.2191 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2129 0.2132 0.2191 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0948 0.0904 0.1788 n_refl.: 5174 remove outliers: r(all,work,free)=0.0948 0.0904 0.1788 n_refl.: 5174 ======================== 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 0.3787 317.369 278.501 0.614 0.982 0.327 11.894-9.307 99.02 97 4 0.1869 505.089 492.995 1.006 0.990 0.324 9.237-7.194 100.00 213 7 0.2173 413.063 405.143 1.061 0.994 0.294 7.162-5.571 100.00 427 22 0.2083 309.953 300.871 1.034 0.996 0.280 5.546-4.326 100.00 867 58 0.1041 425.522 418.569 1.064 0.998 0.207 4.315-3.360 100.00 1859 96 0.0586 404.676 405.246 1.149 1.001 0.173 3.356-3.002 100.00 1373 60 0.0425 311.698 310.246 1.128 1.003 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.4378 ================= 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 : 0.3627 0.2044 0.080 5.198 8.8 119.3 19.9 258 0.000 1_bss: 0.1556 0.1621 0.080 5.198 6.4 116.9 17.4 258 0.000 1_settarget: 0.1556 0.1621 0.080 5.198 6.4 116.9 17.4 258 0.000 1_nqh: 0.1556 0.1621 0.080 5.198 6.4 116.9 17.4 258 0.000 1_weight: 0.1556 0.1621 0.080 5.198 6.4 116.9 17.4 258 0.000 1_xyzrec: 0.1157 0.1791 0.010 0.991 6.4 116.9 17.4 258 0.203 1_adp: 0.1027 0.1799 0.010 0.991 2.7 112.1 17.7 258 0.203 1_regHadp: 0.1020 0.1801 0.010 0.991 2.7 112.1 17.7 258 0.203 1_occ: 0.1011 0.1784 0.010 0.991 2.7 112.1 17.7 258 0.203 2_bss: 0.1010 0.1778 0.010 0.991 1.7 111.0 16.6 258 0.203 2_settarget: 0.1010 0.1778 0.010 0.991 1.7 111.0 16.6 258 0.203 2_updatecdl: 0.1010 0.1778 0.010 1.021 1.7 111.0 16.6 258 0.203 2_nqh: 0.1010 0.1778 0.010 1.021 1.7 111.0 16.6 258 0.203 2_sol: 0.1129 0.1645 0.010 1.021 1.0 111.0 15.9 225 n/a 2_weight: 0.1129 0.1645 0.010 1.021 1.0 111.0 15.9 225 n/a 2_xyzrec: 0.1014 0.1749 0.010 0.991 1.0 111.0 15.9 225 n/a 2_adp: 0.0941 0.1751 0.010 0.991 0.0 109.8 16.5 225 n/a 2_regHadp: 0.0937 0.1750 0.010 0.991 0.0 109.8 16.5 225 n/a 2_occ: 0.0936 0.1760 0.010 0.991 0.0 109.8 16.5 225 n/a 3_bss: 0.0935 0.1762 0.010 0.991 0.0 109.8 16.5 225 n/a 3_settarget: 0.0935 0.1762 0.010 0.991 0.0 109.8 16.5 225 n/a 3_updatecdl: 0.0935 0.1762 0.010 0.998 0.0 109.8 16.5 225 n/a 3_nqh: 0.0936 0.1765 0.010 0.998 0.0 109.8 16.5 225 n/a 3_sol: 0.1034 0.1792 0.010 0.998 0.0 109.8 16.4 229 n/a 3_weight: 0.1034 0.1792 0.010 0.998 0.0 109.8 16.4 229 n/a 3_xyzrec: 0.0938 0.1777 0.011 1.055 0.0 109.8 16.4 229 n/a 3_adp: 0.0895 0.1798 0.011 1.055 0.0 110.3 16.4 229 n/a 3_regHadp: 0.0901 0.1809 0.011 1.055 0.0 110.3 16.4 229 n/a 3_occ: 0.0891 0.1797 0.011 1.055 0.0 110.3 16.4 229 n/a 4_bss: 0.0887 0.1800 0.011 1.055 0.0 110.3 16.4 229 n/a 4_settarget: 0.0887 0.1800 0.011 1.055 0.0 110.3 16.4 229 n/a 4_updatecdl: 0.0887 0.1800 0.011 1.056 0.0 110.3 16.4 229 n/a 4_nqh: 0.0888 0.1797 0.011 1.056 0.0 110.3 16.4 229 n/a 4_sol: 0.0993 0.1767 0.011 1.056 0.0 110.3 16.5 236 n/a 4_weight: 0.0993 0.1767 0.011 1.056 0.0 110.3 16.5 236 n/a 4_xyzrec: 0.0912 0.1828 0.011 1.059 0.0 110.3 16.5 236 n/a 4_adp: 0.0890 0.1867 0.011 1.059 0.0 113.0 16.7 236 n/a 4_regHadp: 0.0894 0.1870 0.011 1.059 0.0 113.0 16.7 236 n/a 4_occ: 0.0880 0.1849 0.011 1.059 0.0 113.0 16.7 236 n/a 5_bss: 0.0879 0.1846 0.011 1.059 0.0 113.0 16.7 236 n/a 5_settarget: 0.0879 0.1846 0.011 1.059 0.0 113.0 16.7 236 n/a 5_updatecdl: 0.0879 0.1846 0.011 1.072 0.0 113.0 16.7 236 n/a 5_setrh: 0.0881 0.1845 0.011 1.072 0.0 113.0 16.7 236 n/a 5_nqh: 0.0881 0.1847 0.011 1.072 0.0 113.0 16.7 236 n/a 5_sol: 0.0986 0.1802 0.011 1.072 0.0 113.0 16.8 229 n/a 5_weight: 0.0986 0.1802 0.011 1.072 0.0 113.0 16.8 229 n/a 5_xyzrec: 0.0925 0.1812 0.010 1.151 0.0 113.0 16.8 229 n/a 5_adp: 0.0903 0.1803 0.010 1.151 0.0 115.4 16.9 229 n/a 5_regHadp: 0.0907 0.1804 0.010 1.151 0.0 115.4 16.9 229 n/a 5_occ: 0.0897 0.1790 0.010 1.151 0.0 115.4 16.9 229 n/a end: 0.0904 0.1788 0.010 1.151 0.0 115.4 16.9 229 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4813131_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4813131_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.3800 Refinement macro-cycles (run) : 493.2100 Write final files (write_after_run_outputs) : 9.2300 Total : 505.8200 Total CPU time: 8.83 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:11 PST -0800 (1735492751.18 s) Start R-work = 0.1556, R-free = 0.1621 Final R-work = 0.0904, R-free = 0.1788 =============================================================================== Job complete usr+sys time: 537.42 seconds wall clock time: 9 minutes 19.52 seconds (559.52 seconds total)