Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4279219.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4279219.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_4279219.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 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 3 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.52, per 1000 atoms: 0.45 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 191.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 540 0.91 - 1.18: 1116 1.18 - 1.44: 680 1.44 - 1.70: 797 1.70 - 1.96: 20 Bond restraints: 3153 Sorted by residual: bond pdb=" CD2 HIS A 115 " pdb=" NE2 HIS A 115 " ideal model delta sigma weight residual 1.374 1.109 0.265 1.10e-02 8.26e+03 5.80e+02 bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.534 1.674 -0.140 6.80e-03 2.16e+04 4.22e+02 bond pdb=" C ILE A 91 " pdb=" O ILE A 91 " ideal model delta sigma weight residual 1.237 1.031 0.206 1.13e-02 7.83e+03 3.32e+02 bond pdb=" C MET A 17 " pdb=" O MET A 17 " ideal model delta sigma weight residual 1.236 1.037 0.200 1.15e-02 7.56e+03 3.02e+02 bond pdb=" CA GLY A 100 " pdb=" C GLY A 100 " ideal model delta sigma weight residual 1.518 1.351 0.167 1.00e-02 1.00e+04 2.77e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 3244 4.79 - 9.58: 1845 9.58 - 14.36: 584 14.36 - 19.15: 98 19.15 - 23.94: 6 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O BCYS A 53 " pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 121.23 133.71 -12.48 8.10e-01 1.52e+00 2.38e+02 angle pdb=" O ILE A 117 " pdb=" C ILE A 117 " pdb=" N GLY A 118 " ideal model delta sigma weight residual 123.03 107.07 15.96 1.11e+00 8.12e-01 2.07e+02 angle pdb=" CA BCYS A 53 " pdb=" C BCYS A 53 " pdb=" O BCYS A 53 " ideal model delta sigma weight residual 119.29 110.25 9.04 6.50e-01 2.37e+00 1.93e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.45 112.85 9.60 7.20e-01 1.93e+00 1.78e+02 angle pdb=" N GLY A 174 " pdb=" CA GLY A 174 " pdb=" C GLY A 174 " ideal model delta sigma weight residual 112.04 125.10 -13.06 1.02e+00 9.61e-01 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 1284 16.41 - 32.82: 133 32.82 - 49.22: 42 49.22 - 65.63: 18 65.63 - 82.04: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C VAL A 25 " pdb=" N VAL A 25 " pdb=" CA VAL A 25 " pdb=" CB VAL A 25 " ideal model delta harmonic sigma weight residual -122.00 -143.48 21.48 0 2.50e+00 1.60e-01 7.38e+01 dihedral pdb=" N CYS A 46 " pdb=" C CYS A 46 " pdb=" CA CYS A 46 " pdb=" CB CYS A 46 " ideal model delta harmonic sigma weight residual 122.80 140.35 -17.55 0 2.50e+00 1.60e-01 4.93e+01 dihedral pdb=" C CYS A 46 " pdb=" N CYS A 46 " pdb=" CA CYS A 46 " pdb=" CB CYS A 46 " ideal model delta harmonic sigma weight residual -122.60 -139.63 17.03 0 2.50e+00 1.60e-01 4.64e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.198: 89 0.198 - 0.396: 95 0.396 - 0.593: 35 0.593 - 0.791: 15 0.791 - 0.989: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 112 " pdb=" CB LEU A 112 " pdb=" CD1 LEU A 112 " pdb=" CD2 LEU A 112 " both_signs ideal model delta sigma weight residual False -2.59 -1.60 -0.99 2.00e-01 2.50e+01 2.44e+01 chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 3.41 -0.97 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 1.48 0.96 2.00e-01 2.50e+01 2.29e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.070 2.00e-02 2.50e+03 5.69e-02 9.72e+01 pdb=" CG PHE A 119 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.120 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.030 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.035 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.081 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.057 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.036 2.00e-02 2.50e+03 5.37e-02 8.66e+01 pdb=" CG BTYR A 67 " 0.056 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.044 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.037 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.040 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.078 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.054 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.066 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.092 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.045 9.50e-02 1.11e+02 6.26e-02 8.32e+01 pdb=" NE ARG A 5 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " -0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.051 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.093 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.108 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " 0.021 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " 0.084 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.36: 1297 2.36 - 2.92: 8286 2.92 - 3.48: 10469 3.48 - 4.04: 15144 4.04 - 4.60: 21483 Nonbonded interactions: 56679 Sorted by model distance: nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.794 2.450 nonbonded pdb="HH12 ARG A 5 " pdb=" O BGLU A 64 " model vdw 1.829 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.833 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.833 2.100 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.850 2.450 ... (remaining 56674 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_4279219_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= 0.3626 r_free= 0.2004 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464862 | | target function (ml) not normalized (work): 22011.771350 | | target function (ml) not normalized (free): 1154.249947 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3810 0.2206 4.8485 4.9128| | 2: 3.78 - 3.00 1.00 2430 110 0.3402 0.1661 4.0702 4.1512| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.72 0.83 0.13 6597.77| | 2: 3.78 - 3.00 2430 110 0.93 11.42 1.48 0.26 447.81| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 381.31 max = 12060.86 mean = 3566.45| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.33| |phase err.(test): min = 0.00 max = 89.98 mean = 33.28| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.265 1557 Z= 5.480 Angle : 5.250 16.235 2118 Z= 3.755 Chirality : 0.363 0.989 243 Planarity : 0.033 0.112 284 Dihedral : 13.970 82.037 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 29.19 % 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: -2.70 (0.47), residues: 224 helix: -2.63 (0.39), residues: 102 sheet: -0.96 (0.92), residues: 28 loop : -0.76 (0.53), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.048 0.013 ARG A 27 TYR 0.078 0.033 TYR A 141 PHE 0.088 0.037 PHE A 162 HIS 0.088 0.049 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3626 r_free= 0.2004 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464862 | | target function (ml) not normalized (work): 22011.771350 | | target function (ml) not normalized (free): 1154.249947 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3581 0.3660 0.2117 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3581 0.3660 0.2117 n_refl.: 5182 remove outliers: r(all,work,free)=0.2526 0.2551 0.2117 n_refl.: 5178 overall B=-2.81 to atoms: r(all,work,free)=0.2418 0.2440 0.2070 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1568 0.1567 0.1582 n_refl.: 5178 remove outliers: r(all,work,free)=0.1564 0.1562 0.1582 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 0.3863 449.662 408.704 0.657 1.080 0.404 11.894-9.307 99.02 97 4 0.1870 714.323 692.420 0.928 1.075 0.387 9.237-7.194 100.00 213 7 0.2129 584.175 575.155 0.955 1.067 0.384 7.162-5.571 100.00 427 22 0.2344 438.352 423.485 0.928 1.052 0.299 5.546-4.326 100.00 867 58 0.1393 601.795 595.688 0.979 1.028 0.268 4.315-3.360 100.00 1859 96 0.1315 572.314 565.661 1.057 0.988 0.200 3.356-3.002 100.00 1373 60 0.1595 440.820 433.298 1.073 0.948 0.064 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.5989 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1562 r_free=0.1582 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1566 r_free=0.1589 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.376735 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.982396 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 0.1167 0.1806 0.0639 0.010 1.0 3.2 0.5 0.0 0 9.688 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.67 18.06 6.39 3.013 16.045 1.982 0.018 10.26 17.96 7.70 4.966 16.237 1.982 0.015 Individual atomic B min max mean iso aniso Overall: 2.09 111.56 17.44 5.33 1785 0 Protein: 2.09 111.56 14.74 5.32 1519 0 Water: 4.05 111.48 33.08 N/A 258 0 Other: 16.15 38.22 24.17 N/A 8 0 Chain A: 2.09 111.56 17.44 N/A 1785 0 Histogram: Values Number of atoms 2.09 - 13.04 907 13.04 - 23.98 492 23.98 - 34.93 188 34.93 - 45.88 110 45.88 - 56.83 55 56.83 - 67.77 16 67.77 - 78.72 8 78.72 - 89.67 5 89.67 - 100.62 1 100.62 - 111.56 3 =========================== Idealize ADP of riding H ========================== r_work=0.1026 r_free=0.1796 r_work=0.1021 r_free=0.1805 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1021 r_free = 0.1805 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 = 0.1013 r_free = 0.1808 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= 0.1013 r_free= 0.1808 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013939 | | target function (ls_wunit_k1) not normalized (work): 68.637157 | | target function (ls_wunit_k1) not normalized (free): 10.719297 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1053 0.1013 0.1808 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2102 0.2102 0.2225 n_refl.: 5176 remove outliers: r(all,work,free)=0.2102 0.2102 0.2225 n_refl.: 5176 overall B=-0.94 to atoms: r(all,work,free)=0.2062 0.2060 0.2214 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1052 0.1012 0.1797 n_refl.: 5176 remove outliers: r(all,work,free)=0.1052 0.1012 0.1797 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 0.3335 329.390 311.939 0.663 1.031 0.385 11.894-9.307 99.02 97 4 0.1505 523.262 515.800 0.964 1.031 0.368 9.237-7.194 100.00 213 7 0.1688 427.924 427.357 0.999 1.028 0.331 7.162-5.571 100.00 427 22 0.1633 321.105 317.249 0.963 1.021 0.292 5.546-4.326 100.00 867 58 0.0906 440.832 437.837 0.990 1.011 0.232 4.315-3.360 100.00 1859 96 0.0762 419.236 419.251 1.046 0.995 0.193 3.356-3.002 100.00 1373 60 0.1002 322.913 321.397 1.030 0.978 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3739 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1012 r_free=0.1797 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1012 r_free=0.1797 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1012 r_free=0.1797 | n_water=258 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.1037 r_free=0.1798 | n_water=249 | time (s): 20.290 (total time: 20.820) Filter (q & B) r_work=0.1036 r_free=0.1795 | n_water=246 | time (s): 1.980 (total time: 22.800) Compute maps r_work=0.1036 r_free=0.1795 | n_water=246 | time (s): 0.600 (total time: 23.400) Filter (map) r_work=0.1342 r_free=0.1886 | n_water=145 | time (s): 1.800 (total time: 25.200) Find peaks r_work=0.1342 r_free=0.1886 | n_water=145 | time (s): 0.620 (total time: 25.820) Add new water r_work=0.1719 r_free=0.2178 | n_water=236 | time (s): 1.550 (total time: 27.370) Refine new water occ: r_work=0.1155 r_free=0.1694 adp: r_work=0.1133 r_free=0.1693 occ: r_work=0.1129 r_free=0.1672 adp: r_work=0.1118 r_free=0.1675 occ: r_work=0.1116 r_free=0.1663 adp: r_work=0.1113 r_free=0.1661 ADP+occupancy (water only), MIN, final r_work=0.1113 r_free=0.1661 r_work=0.1113 r_free=0.1661 | n_water=236 | time (s): 4.490 (total time: 31.860) Filter (q & B) r_work=0.1113 r_free=0.1661 | n_water=236 | time (s): 0.840 (total time: 32.700) Filter (dist only) r_work=0.1118 r_free=0.1652 | n_water=233 | time (s): 17.750 (total time: 50.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.558214 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.875554 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 0.0997 0.1815 0.0818 0.009 1.0 3.2 0.5 0.6 0 11.779 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.97 18.15 8.18 4.692 16.907 2.876 0.013 9.31 18.14 8.82 5.446 17.301 2.876 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.72 16.72 6.46 1760 0 Protein: 0.00 108.72 15.06 6.45 1519 0 Water: 0.00 62.82 27.36 N/A 233 0 Other: 11.09 35.16 22.80 N/A 8 0 Chain A: 0.00 108.72 15.82 N/A 1669 0 Chain S: 4.02 60.16 33.22 N/A 91 0 Histogram: Values Number of atoms 0.00 - 10.87 668 10.87 - 21.74 684 21.74 - 32.62 214 32.62 - 43.49 112 43.49 - 54.36 40 54.36 - 65.23 30 65.23 - 76.10 5 76.10 - 86.97 3 86.97 - 97.85 2 97.85 - 108.72 2 =========================== Idealize ADP of riding H ========================== r_work=0.0931 r_free=0.1814 r_work=0.0930 r_free=0.1810 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0930 r_free = 0.1810 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0924 r_free = 0.1808 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 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= 0.0924 r_free= 0.1808 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011716 | | target function (ls_wunit_k1) not normalized (work): 57.691883 | | target function (ls_wunit_k1) not normalized (free): 10.106051 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0968 0.0924 0.1808 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2121 0.2122 0.2226 n_refl.: 5176 remove outliers: r(all,work,free)=0.2121 0.2122 0.2226 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2121 0.2122 0.2226 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0972 0.0928 0.1814 n_refl.: 5176 remove outliers: r(all,work,free)=0.0970 0.0926 0.1814 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 0.3262 326.615 313.597 0.663 1.021 0.364 11.894-9.307 99.02 97 4 0.1462 523.262 518.768 0.967 1.021 0.340 9.237-7.194 100.00 213 7 0.1455 427.924 430.187 1.007 1.020 0.304 7.162-5.571 100.00 427 22 0.1389 321.105 319.281 0.982 1.015 0.290 5.546-4.326 100.00 867 58 0.0786 440.832 438.524 1.004 1.008 0.240 4.315-3.360 100.00 1859 96 0.0710 419.236 418.916 1.057 0.996 0.190 3.356-3.002 100.00 1373 60 0.0960 322.913 322.201 1.041 0.984 0.076 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.0756 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0926 r_free=0.1814 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0931 r_free=0.1811 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0931 r_free=0.1811 | n_water=233 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.0940 r_free=0.1797 | n_water=231 | time (s): 18.150 (total time: 18.690) Filter (q & B) r_work=0.1025 r_free=0.1790 | n_water=228 | time (s): 1.570 (total time: 20.260) Compute maps r_work=0.1025 r_free=0.1790 | n_water=228 | time (s): 0.510 (total time: 20.770) Filter (map) r_work=0.1279 r_free=0.1887 | n_water=153 | time (s): 1.360 (total time: 22.130) Find peaks r_work=0.1279 r_free=0.1887 | n_water=153 | time (s): 0.400 (total time: 22.530) Add new water r_work=0.1670 r_free=0.2335 | n_water=242 | time (s): 1.380 (total time: 23.910) Refine new water occ: r_work=0.1075 r_free=0.1815 adp: r_work=0.1065 r_free=0.1832 occ: r_work=0.1052 r_free=0.1808 adp: r_work=0.1052 r_free=0.1818 occ: r_work=0.1040 r_free=0.1793 adp: r_work=0.1040 r_free=0.1803 ADP+occupancy (water only), MIN, final r_work=0.1040 r_free=0.1803 r_work=0.1040 r_free=0.1803 | n_water=242 | time (s): 13.620 (total time: 37.530) Filter (q & B) r_work=0.1041 r_free=0.1801 | n_water=241 | time (s): 1.780 (total time: 39.310) Filter (dist only) r_work=0.1047 r_free=0.1805 | n_water=240 | time (s): 18.210 (total time: 57.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.122820 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.231403 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 0.0941 0.1838 0.0896 0.011 1.1 2.9 0.5 0.0 0 0.561 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.41 18.38 8.96 5.398 17.911 0.231 5.152 8.98 18.65 9.67 7.281 17.903 0.231 5.053 Individual atomic B min max mean iso aniso Overall: 0.00 108.39 16.56 8.95 1767 0 Protein: 0.00 108.39 15.15 8.93 1519 0 Water: 0.00 57.82 25.18 N/A 240 0 Other: 15.55 40.43 25.53 N/A 8 0 Chain A: 0.00 108.39 15.88 N/A 1655 0 Chain S: 0.00 55.75 26.52 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.84 662 10.84 - 21.68 683 21.68 - 32.52 229 32.52 - 43.36 117 43.36 - 54.20 44 54.20 - 65.04 15 65.04 - 75.87 10 75.87 - 86.71 2 86.71 - 97.55 4 97.55 - 108.39 1 =========================== Idealize ADP of riding H ========================== r_work=0.0898 r_free=0.1865 r_work=0.0904 r_free=0.1873 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0904 r_free = 0.1873 target_work(ml) = 5.057 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0893 r_free = 0.1851 target_work(ml) = 5.049 | | occupancies: max = 1.00 min = 0.20 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= 0.0893 r_free= 0.1851 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.049087 | | target function (ml) not normalized (work): 24856.655092 | | target function (ml) not normalized (free): 1804.523618 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0941 0.0893 0.1851 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2109 0.2117 0.2129 n_refl.: 5175 remove outliers: r(all,work,free)=0.2109 0.2117 0.2129 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2109 0.2117 0.2129 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0933 0.0886 0.1841 n_refl.: 5175 remove outliers: r(all,work,free)=0.0931 0.0883 0.1841 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 0.3528 328.788 298.461 0.591 0.993 0.326 11.894-9.307 99.02 97 4 0.1838 523.262 511.500 0.944 0.998 0.305 9.237-7.194 100.00 213 7 0.1924 427.924 423.660 0.997 1.000 0.290 7.162-5.571 100.00 427 22 0.1840 321.105 311.810 0.975 1.000 0.280 5.546-4.326 100.00 867 58 0.0913 440.832 436.069 1.010 1.001 0.240 4.315-3.360 100.00 1859 96 0.0584 419.236 418.470 1.061 1.001 0.200 3.356-3.002 100.00 1373 60 0.0595 322.913 322.330 1.039 1.001 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.5971 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0883 r_free=0.1841 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0883 r_free=0.1841 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0883 r_free=0.1841 | n_water=240 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.0886 r_free=0.1847 | n_water=239 | time (s): 20.890 (total time: 21.410) Filter (q & B) r_work=0.0969 r_free=0.1891 | n_water=236 | time (s): 1.530 (total time: 22.940) Compute maps r_work=0.0969 r_free=0.1891 | n_water=236 | time (s): 0.680 (total time: 23.620) Filter (map) r_work=0.1239 r_free=0.2018 | n_water=162 | time (s): 1.970 (total time: 25.590) Find peaks r_work=0.1239 r_free=0.2018 | n_water=162 | time (s): 0.500 (total time: 26.090) Add new water r_work=0.1526 r_free=0.2306 | n_water=234 | time (s): 1.430 (total time: 27.520) Refine new water occ: r_work=0.1007 r_free=0.1827 adp: r_work=0.1002 r_free=0.1835 occ: r_work=0.0993 r_free=0.1814 adp: r_work=0.0993 r_free=0.1823 occ: r_work=0.0985 r_free=0.1803 adp: r_work=0.0984 r_free=0.1812 ADP+occupancy (water only), MIN, final r_work=0.0984 r_free=0.1812 r_work=0.0984 r_free=0.1812 | n_water=234 | time (s): 11.840 (total time: 39.360) Filter (q & B) r_work=0.0984 r_free=0.1811 | n_water=233 | time (s): 1.460 (total time: 40.820) Filter (dist only) r_work=0.0994 r_free=0.1822 | n_water=230 | time (s): 18.180 (total time: 59.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.026082 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.247938 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 0.0900 0.1861 0.0961 0.011 1.0 4.5 0.5 0.0 0 0.513 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.00 18.61 9.61 6.971 18.032 0.248 5.031 8.78 18.97 10.19 8.136 18.159 0.248 4.967 Individual atomic B min max mean iso aniso Overall: 0.00 107.77 16.83 10.61 1757 0 Protein: 0.00 107.77 15.58 10.59 1519 0 Water: 0.00 60.96 24.75 N/A 230 0 Other: 13.23 46.85 26.58 N/A 8 0 Chain A: 0.00 107.77 16.19 N/A 1642 0 Chain S: 0.00 60.96 25.92 N/A 115 0 Histogram: Values Number of atoms 0.00 - 10.78 634 10.78 - 21.56 677 21.56 - 32.33 249 32.33 - 43.11 115 43.11 - 53.89 47 53.89 - 64.66 13 64.66 - 75.44 14 75.44 - 86.22 3 86.22 - 97.00 3 97.00 - 107.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.0878 r_free=0.1897 r_work=0.0883 r_free=0.1907 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0883 r_free = 0.1907 target_work(ml) = 4.973 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0870 r_free = 0.1865 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.17 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= 0.0870 r_free= 0.1865 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.964337 | | target function (ml) not normalized (work): 24434.467323 | | target function (ml) not normalized (free): 2078.182679 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0920 0.0870 0.1865 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2082 0.2078 0.2238 n_refl.: 5174 remove outliers: r(all,work,free)=0.2082 0.2078 0.2238 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2082 0.2078 0.2238 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0920 0.0869 0.1876 n_refl.: 5174 remove outliers: r(all,work,free)=0.0920 0.0869 0.1876 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 0.3753 328.788 299.844 0.599 0.987 0.322 11.894-9.307 99.02 97 4 0.1828 523.262 508.707 0.947 0.993 0.303 9.237-7.194 100.00 213 7 0.2089 427.924 420.839 0.995 0.996 0.290 7.162-5.571 100.00 427 22 0.2007 321.105 310.913 0.985 0.998 0.290 5.546-4.326 100.00 867 58 0.0976 440.832 435.407 1.017 0.999 0.223 4.315-3.360 100.00 1859 96 0.0546 419.236 418.922 1.079 1.001 0.206 3.356-3.002 100.00 1373 60 0.0452 322.913 322.385 1.058 1.003 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.4142 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0869 r_free=0.1876 After: r_work=0.0872 r_free=0.1873 ================================== NQH flips ================================== r_work=0.0872 r_free=0.1873 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=0.0872 r_free=0.1875 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0872 r_free=0.1875 | n_water=230 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.0881 r_free=0.1891 | n_water=227 | time (s): 18.690 (total time: 19.180) Filter (q & B) r_work=0.0961 r_free=0.1943 | n_water=224 | time (s): 2.010 (total time: 21.190) Compute maps r_work=0.0961 r_free=0.1943 | n_water=224 | time (s): 0.580 (total time: 21.770) Filter (map) r_work=0.1245 r_free=0.2040 | n_water=160 | time (s): 1.520 (total time: 23.290) Find peaks r_work=0.1245 r_free=0.2040 | n_water=160 | time (s): 0.400 (total time: 23.690) Add new water r_work=0.1511 r_free=0.2326 | n_water=225 | time (s): 1.260 (total time: 24.950) Refine new water occ: r_work=0.0993 r_free=0.1899 adp: r_work=0.0985 r_free=0.1897 occ: r_work=0.0977 r_free=0.1881 adp: r_work=0.0976 r_free=0.1886 occ: r_work=0.0968 r_free=0.1869 adp: r_work=0.0967 r_free=0.1874 ADP+occupancy (water only), MIN, final r_work=0.0967 r_free=0.1874 r_work=0.0967 r_free=0.1874 | n_water=225 | time (s): 10.420 (total time: 35.370) Filter (q & B) r_work=0.0967 r_free=0.1874 | n_water=225 | time (s): 0.720 (total time: 36.090) Filter (dist only) r_work=0.0967 r_free=0.1874 | n_water=225 | time (s): 17.460 (total time: 53.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.043563 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.218599 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 0.1896 0.0984 0.011 1.1 5.8 0.5 0.0 0 0.522 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.12 18.96 9.84 8.078 18.429 0.219 5.003 8.94 19.20 10.25 8.907 18.544 0.219 4.953 Individual atomic B min max mean iso aniso Overall: 0.00 107.55 17.12 11.80 1752 0 Protein: 0.00 107.55 15.95 11.77 1519 0 Water: 0.00 64.24 24.67 N/A 225 0 Other: 8.74 44.74 27.14 N/A 8 0 Chain A: 0.00 107.55 16.49 N/A 1636 0 Chain S: 0.00 64.24 25.99 N/A 116 0 Histogram: Values Number of atoms 0.00 - 10.76 636 10.76 - 21.51 644 21.51 - 32.27 267 32.27 - 43.02 114 43.02 - 53.78 51 53.78 - 64.53 18 64.53 - 75.29 9 75.29 - 86.04 9 86.04 - 96.80 1 96.80 - 107.55 3 =========================== Idealize ADP of riding H ========================== r_work=0.0894 r_free=0.1920 r_work=0.0898 r_free=0.1924 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0898 r_free = 0.1924 target_work(ml) = 4.958 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0891 r_free = 0.1916 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0891 r_free= 0.1916 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.953852 | | target function (ml) not normalized (work): 24382.861282 | | target function (ml) not normalized (free): 2095.853985 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1268 0.1991 5.5345 6.3696| | 2: 3.78 - 3.00 1.00 2430 110 0.0430 0.1789 4.3584 10.831| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.22 1.00 0.97 13172.98| | 2: 3.78 - 3.00 2430 110 0.99 1.91 1.00 0.99 930.80| |alpha: min = 0.96 max = 1.00 mean = 0.98| |beta: min = 596.61 max = 22015.63 mean = 7129.00| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.96 mean = 7.13| |phase err.(test): min = 0.00 max = 83.17 mean = 6.88| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0943 0.0891 0.1916 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2133 0.2130 0.2284 n_refl.: 5174 remove outliers: r(all,work,free)=0.2133 0.2130 0.2284 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2133 0.2130 0.2284 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0943 0.0891 0.1916 n_refl.: 5174 remove outliers: r(all,work,free)=0.0943 0.0891 0.1916 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 0.3918 328.788 298.848 0.621 0.985 0.320 11.894-9.307 99.02 97 4 0.1868 523.262 508.307 1.001 0.993 0.310 9.237-7.194 100.00 213 7 0.2178 427.924 419.332 1.041 0.997 0.295 7.162-5.571 100.00 427 22 0.2056 321.105 311.266 1.025 0.998 0.290 5.546-4.326 100.00 867 58 0.1035 440.832 434.673 1.071 1.000 0.219 4.315-3.360 100.00 1859 96 0.0565 419.236 418.923 1.145 1.001 0.200 3.356-3.002 100.00 1373 60 0.0413 322.913 322.402 1.126 1.002 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.3386 ================= 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 : 0.3626 0.2004 0.082 5.250 8.8 119.3 19.9 258 0.000 1_bss: 0.1562 0.1582 0.082 5.250 6.0 116.5 17.1 258 0.000 1_settarget: 0.1562 0.1582 0.082 5.250 6.0 116.5 17.1 258 0.000 1_nqh: 0.1566 0.1589 0.082 5.250 6.0 116.5 17.1 258 0.006 1_weight: 0.1566 0.1589 0.082 5.250 6.0 116.5 17.1 258 0.006 1_xyzrec: 0.1167 0.1806 0.010 0.989 6.0 116.5 17.1 258 0.210 1_adp: 0.1026 0.1796 0.010 0.989 2.1 111.6 17.4 258 0.210 1_regHadp: 0.1021 0.1805 0.010 0.989 2.1 111.6 17.4 258 0.210 1_occ: 0.1013 0.1808 0.010 0.989 2.1 111.6 17.4 258 0.210 2_bss: 0.1012 0.1797 0.010 0.989 1.1 110.6 16.5 258 0.210 2_settarget: 0.1012 0.1797 0.010 0.989 1.1 110.6 16.5 258 0.210 2_updatecdl: 0.1012 0.1797 0.010 1.006 1.1 110.6 16.5 258 0.210 2_nqh: 0.1012 0.1797 0.010 1.006 1.1 110.6 16.5 258 0.210 2_sol: 0.1118 0.1652 0.010 1.006 1.0 110.6 16.0 233 n/a 2_weight: 0.1118 0.1652 0.010 1.006 1.0 110.6 16.0 233 n/a 2_xyzrec: 0.0997 0.1815 0.009 0.978 1.0 110.6 16.0 233 n/a 2_adp: 0.0931 0.1814 0.009 0.978 0.0 108.7 16.7 233 n/a 2_regHadp: 0.0930 0.1810 0.009 0.978 0.0 108.7 16.7 233 n/a 2_occ: 0.0924 0.1808 0.009 0.978 0.0 108.7 16.7 233 n/a 3_bss: 0.0926 0.1814 0.009 0.978 0.0 108.7 16.7 233 n/a 3_settarget: 0.0926 0.1814 0.009 0.978 0.0 108.7 16.7 233 n/a 3_updatecdl: 0.0926 0.1814 0.009 0.978 0.0 108.7 16.7 233 n/a 3_nqh: 0.0931 0.1811 0.009 0.978 0.0 108.7 16.7 233 n/a 3_sol: 0.1047 0.1805 0.009 0.978 0.0 108.7 16.6 240 n/a 3_weight: 0.1047 0.1805 0.009 0.978 0.0 108.7 16.6 240 n/a 3_xyzrec: 0.0941 0.1838 0.011 1.058 0.0 108.7 16.6 240 n/a 3_adp: 0.0898 0.1865 0.011 1.058 0.0 108.4 16.6 240 n/a 3_regHadp: 0.0904 0.1873 0.011 1.058 0.0 108.4 16.6 240 n/a 3_occ: 0.0893 0.1851 0.011 1.058 0.0 108.4 16.6 240 n/a 4_bss: 0.0883 0.1841 0.011 1.058 0.0 108.4 16.6 240 n/a 4_settarget: 0.0883 0.1841 0.011 1.058 0.0 108.4 16.6 240 n/a 4_updatecdl: 0.0883 0.1841 0.011 1.073 0.0 108.4 16.6 240 n/a 4_nqh: 0.0883 0.1841 0.011 1.073 0.0 108.4 16.6 240 n/a 4_sol: 0.0994 0.1822 0.011 1.073 0.0 108.4 16.6 230 n/a 4_weight: 0.0994 0.1822 0.011 1.073 0.0 108.4 16.6 230 n/a 4_xyzrec: 0.0900 0.1861 0.011 1.041 0.0 108.4 16.6 230 n/a 4_adp: 0.0878 0.1897 0.011 1.041 0.0 107.8 16.8 230 n/a 4_regHadp: 0.0883 0.1907 0.011 1.041 0.0 107.8 16.8 230 n/a 4_occ: 0.0870 0.1865 0.011 1.041 0.0 107.8 16.8 230 n/a 5_bss: 0.0869 0.1876 0.011 1.041 0.0 107.8 16.8 230 n/a 5_settarget: 0.0869 0.1876 0.011 1.041 0.0 107.8 16.8 230 n/a 5_updatecdl: 0.0869 0.1876 0.011 1.050 0.0 107.8 16.8 230 n/a 5_setrh: 0.0872 0.1873 0.011 1.050 0.0 107.8 16.8 230 n/a 5_nqh: 0.0872 0.1875 0.011 1.050 0.0 107.8 16.8 230 n/a 5_sol: 0.0967 0.1874 0.011 1.050 0.0 107.8 16.9 225 n/a 5_weight: 0.0967 0.1874 0.011 1.050 0.0 107.8 16.9 225 n/a 5_xyzrec: 0.0912 0.1896 0.011 1.148 0.0 107.8 16.9 225 n/a 5_adp: 0.0894 0.1920 0.011 1.148 0.0 107.6 17.1 225 n/a 5_regHadp: 0.0898 0.1924 0.011 1.148 0.0 107.6 17.1 225 n/a 5_occ: 0.0891 0.1916 0.011 1.148 0.0 107.6 17.1 225 n/a end: 0.0891 0.1916 0.011 1.148 0.0 107.6 17.1 225 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4279219_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_4279219_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.0300 Refinement macro-cycles (run) : 501.0700 Write final files (write_after_run_outputs) : 9.4200 Total : 514.5200 Total CPU time: 8.92 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:17 PST -0800 (1735492757.11 s) Start R-work = 0.1562, R-free = 0.1582 Final R-work = 0.0891, R-free = 0.1916 =============================================================================== Job complete usr+sys time: 542.91 seconds wall clock time: 9 minutes 25.46 seconds (565.46 seconds total)