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_2667343.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_2667343.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2667343.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 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.33, per 1000 atoms: 0.39 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: 0.33 Conformation dependent library (CDL) restraints added in 136.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 716 0.94 - 1.20: 972 1.20 - 1.46: 762 1.46 - 1.72: 690 1.72 - 1.98: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.235 1.027 0.208 1.02e-02 9.61e+03 4.16e+02 bond pdb=" C VAL A 44 " pdb=" O VAL A 44 " ideal model delta sigma weight residual 1.237 1.458 -0.221 1.10e-02 8.26e+03 4.03e+02 bond pdb=" CA CYS A 46 " pdb=" C CYS A 46 " ideal model delta sigma weight residual 1.528 1.279 0.250 1.38e-02 5.25e+03 3.27e+02 bond pdb=" C SER A 161 " pdb=" O SER A 161 " ideal model delta sigma weight residual 1.237 1.444 -0.207 1.17e-02 7.31e+03 3.14e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.148 0.173 1.00e-02 1.00e+04 2.99e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.14: 3450 5.14 - 10.28: 1734 10.28 - 15.42: 524 15.42 - 20.56: 62 20.56 - 25.70: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ASN A 135 " pdb=" CB ASN A 135 " pdb=" CG ASN A 135 " ideal model delta sigma weight residual 112.60 128.60 -16.00 1.00e+00 1.00e+00 2.56e+02 angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH2 ARG A 98 " ideal model delta sigma weight residual 119.20 132.41 -13.21 9.00e-01 1.23e+00 2.15e+02 angle pdb=" CA ILE A 105 " pdb=" C ILE A 105 " pdb=" O ILE A 105 " ideal model delta sigma weight residual 120.39 106.39 14.00 1.05e+00 9.07e-01 1.78e+02 angle pdb=" O ALA A 36 " pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 123.27 108.24 15.03 1.16e+00 7.43e-01 1.68e+02 angle pdb=" O ALA A 183 " pdb=" C ALA A 183 " pdb=" N PRO A 184 " ideal model delta sigma weight residual 121.32 136.11 -14.79 1.15e+00 7.56e-01 1.65e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.98: 1298 16.98 - 33.94: 130 33.94 - 50.91: 39 50.91 - 67.88: 10 67.88 - 84.85: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ILE A 21 " pdb=" C ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual 123.40 144.88 -21.48 0 2.50e+00 1.60e-01 7.38e+01 dihedral pdb=" C GLU A 116 " pdb=" N GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual -122.60 -141.39 18.79 0 2.50e+00 1.60e-01 5.65e+01 dihedral pdb=" N GLU A 116 " pdb=" C GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual 122.80 141.40 -18.60 0 2.50e+00 1.60e-01 5.54e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.204: 80 0.204 - 0.406: 74 0.406 - 0.608: 53 0.608 - 0.809: 30 0.809 - 1.011: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" C2 ADTT A 201 " pdb=" C1 ADTT A 201 " pdb=" C3 ADTT A 201 " pdb=" O2 ADTT A 201 " both_signs ideal model delta sigma weight residual False -2.43 -1.42 -1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" CA GLU A 116 " pdb=" N GLU A 116 " pdb=" C GLU A 116 " pdb=" CB GLU A 116 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.27e+01 chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.43 -0.92 2.00e-01 2.50e+01 2.13e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " -0.053 2.00e-02 2.50e+03 7.44e-02 1.24e+02 pdb=" CG HIS A 138 " -0.010 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.100 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " -0.078 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.128 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " 0.051 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.028 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " -0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.122 9.50e-02 1.11e+02 8.35e-02 1.21e+02 pdb=" NE ARG A 5 " 0.072 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.075 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.109 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " -0.040 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " -0.072 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " 0.109 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.070 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.070 2.00e-02 2.50e+03 5.82e-02 1.02e+02 pdb=" CG PHE A 162 " 0.089 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.089 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.105 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.018 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.019 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " -0.012 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " 0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.047 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1255 2.35 - 2.91: 8223 2.91 - 3.47: 10470 3.47 - 4.04: 15282 4.04 - 4.60: 21441 Nonbonded interactions: 56671 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.786 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.798 2.450 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.821 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.839 2.100 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.862 2.450 x-y,-y,-z-4/3 ... (remaining 56666 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_2667343_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= 0.3624 r_free= 0.2061 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.466513 | | target function (ml) not normalized (work): 22019.911026 | | target function (ml) not normalized (free): 1152.729170 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2295 4.8549 4.9323| | 2: 3.78 - 3.00 1.00 2430 110 0.3398 0.1664 4.067 4.1122| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.89 0.83 0.13 6613.27| | 2: 3.78 - 3.00 2430 110 0.93 11.43 1.48 0.26 446.02| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 374.52 max = 12065.32 mean = 3573.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.42| |phase err.(test): min = 0.00 max = 89.97 mean = 33.45| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.250 1557 Z= 5.477 Angle : 5.405 17.557 2118 Z= 3.813 Chirality : 0.414 1.011 243 Planarity : 0.030 0.104 284 Dihedral : 13.616 84.852 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 36.22 % 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: -2.16 (0.48), residues: 224 helix: -2.44 (0.37), residues: 107 sheet: -0.79 (0.94), residues: 28 loop : 0.08 (0.59), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.022 ARG A 145 TYR 0.086 0.039 TYR A 141 PHE 0.092 0.051 PHE A 162 HIS 0.109 0.043 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= 0.3624 r_free= 0.2061 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.466513 | | target function (ml) not normalized (work): 22019.911026 | | target function (ml) not normalized (free): 1152.729170 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3584 0.3659 0.2169 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3584 0.3659 0.2169 n_refl.: 5182 remove outliers: r(all,work,free)=0.2532 0.2554 0.2169 n_refl.: 5178 overall B=-2.92 to atoms: r(all,work,free)=0.2421 0.2439 0.2120 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1576 0.1574 0.1624 n_refl.: 5178 remove outliers: r(all,work,free)=0.1574 0.1572 0.1624 n_refl.: 5177 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4028 444.990 408.366 0.666 1.059 0.398 11.894-9.307 99.02 97 4 0.1874 714.376 695.533 0.949 1.057 0.382 9.237-7.194 100.00 213 7 0.2160 584.218 576.323 0.980 1.051 0.376 7.162-5.571 100.00 427 22 0.2358 438.385 424.248 0.942 1.040 0.297 5.546-4.326 100.00 867 58 0.1407 601.840 593.356 0.983 1.021 0.211 4.315-3.360 100.00 1859 96 0.1319 572.356 565.971 1.056 0.991 0.200 3.356-3.002 100.00 1373 60 0.1595 440.853 431.696 1.063 0.960 0.097 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.7536 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1572 r_free=0.1624 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1572 r_free=0.1624 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.468172 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.835974 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 0.1162 0.1793 0.0631 0.009 1.0 2.2 0.5 0.0 0 9.234 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 17.93 6.31 3.013 15.938 1.836 0.018 10.22 17.81 7.59 5.098 16.210 1.836 0.015 Individual atomic B min max mean iso aniso Overall: 1.98 111.38 17.48 5.39 1785 0 Protein: 1.98 110.98 14.78 5.38 1519 0 Water: 3.94 111.38 33.17 N/A 258 0 Other: 16.79 39.08 24.54 N/A 8 0 Chain A: 1.98 111.38 17.48 N/A 1785 0 Histogram: Values Number of atoms 1.98 - 12.92 899 12.92 - 23.86 496 23.86 - 34.80 193 34.80 - 45.74 108 45.74 - 56.68 54 56.68 - 67.62 17 67.62 - 78.56 8 78.56 - 89.50 6 89.50 - 100.44 1 100.44 - 111.38 3 =========================== Idealize ADP of riding H ========================== r_work=0.1022 r_free=0.1781 r_work=0.1017 r_free=0.1789 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1017 r_free = 0.1789 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1022 r_free = 0.1806 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1022 r_free= 0.1806 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014394 | | target function (ls_wunit_k1) not normalized (work): 70.888446 | | target function (ls_wunit_k1) not normalized (free): 10.585384 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1062 0.1022 0.1806 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2109 0.2108 0.2240 n_refl.: 5177 remove outliers: r(all,work,free)=0.2109 0.2108 0.2240 n_refl.: 5177 overall B=-1.04 to atoms: r(all,work,free)=0.2065 0.2062 0.2228 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1065 0.1025 0.1808 n_refl.: 5177 remove outliers: r(all,work,free)=0.1061 0.1021 0.1808 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 0.3284 326.636 303.776 0.650 1.002 0.360 11.894-9.307 99.02 97 4 0.1549 525.455 517.743 0.998 1.004 0.361 9.237-7.194 100.00 213 7 0.1701 429.718 429.336 1.037 1.004 0.341 7.162-5.571 100.00 427 22 0.1659 322.451 318.034 0.992 1.003 0.292 5.546-4.326 100.00 867 58 0.0913 442.679 439.607 1.002 1.002 0.197 4.315-3.360 100.00 1859 96 0.0776 420.993 421.125 1.048 1.000 0.194 3.356-3.002 100.00 1373 60 0.1002 324.266 322.729 1.016 0.998 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9557 b_overall=-3.6973 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1021 r_free=0.1808 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1023 r_free=0.1807 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1023 r_free=0.1807 | n_water=258 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.1053 r_free=0.1808 | n_water=248 | time (s): 20.460 (total time: 21.020) Filter (q & B) r_work=0.1054 r_free=0.1802 | n_water=244 | time (s): 1.930 (total time: 22.950) Compute maps r_work=0.1054 r_free=0.1802 | n_water=244 | time (s): 0.430 (total time: 23.380) Filter (map) r_work=0.1353 r_free=0.1877 | n_water=144 | time (s): 1.500 (total time: 24.880) Find peaks r_work=0.1353 r_free=0.1877 | n_water=144 | time (s): 0.550 (total time: 25.430) Add new water r_work=0.1699 r_free=0.2150 | n_water=232 | time (s): 1.930 (total time: 27.360) Refine new water occ: r_work=0.1159 r_free=0.1695 adp: r_work=0.1134 r_free=0.1693 occ: r_work=0.1134 r_free=0.1679 adp: r_work=0.1120 r_free=0.1679 occ: r_work=0.1119 r_free=0.1667 adp: r_work=0.1119 r_free=0.1667 ADP+occupancy (water only), MIN, final r_work=0.1119 r_free=0.1667 r_work=0.1119 r_free=0.1667 | n_water=232 | time (s): 4.260 (total time: 31.620) Filter (q & B) r_work=0.1119 r_free=0.1667 | n_water=232 | time (s): 0.910 (total time: 32.530) Filter (dist only) r_work=0.1124 r_free=0.1669 | n_water=230 | time (s): 17.140 (total time: 49.670) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.447092 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.723152 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 0.1020 0.1736 0.0716 0.009 1.0 4.2 0.5 0.6 0 11.224 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.20 17.36 7.16 4.730 16.701 2.723 0.014 9.55 17.50 7.95 5.548 17.085 2.723 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 108.84 16.38 6.52 1757 0 Protein: 0.00 108.84 14.90 6.50 1519 0 Water: 0.00 62.62 25.91 N/A 230 0 Other: 10.75 37.57 23.66 N/A 8 0 Chain A: 0.00 108.84 15.62 N/A 1669 0 Chain S: 5.25 62.30 30.84 N/A 88 0 Histogram: Values Number of atoms 0.00 - 10.88 699 10.88 - 21.77 661 21.77 - 32.65 213 32.65 - 43.54 117 43.54 - 54.42 33 54.42 - 65.30 23 65.30 - 76.19 4 76.19 - 87.07 2 87.07 - 97.96 3 97.96 - 108.84 2 =========================== Idealize ADP of riding H ========================== r_work=0.0955 r_free=0.1750 r_work=0.0953 r_free=0.1750 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0953 r_free = 0.1750 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0951 r_free = 0.1732 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0951 r_free= 0.1732 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.012279 | | target function (ls_wunit_k1) not normalized (work): 60.450573 | | target function (ls_wunit_k1) not normalized (free): 9.214124 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0990 0.0951 0.1732 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2064 0.2065 0.2149 n_refl.: 5175 remove outliers: r(all,work,free)=0.2064 0.2065 0.2149 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2064 0.2065 0.2149 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0988 0.0949 0.1728 n_refl.: 5175 remove outliers: r(all,work,free)=0.0988 0.0949 0.1728 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 0.3282 326.636 310.963 0.641 1.004 0.340 11.894-9.307 99.02 97 4 0.1552 525.455 520.058 0.987 1.007 0.339 9.237-7.194 100.00 213 7 0.1477 429.718 430.093 1.034 1.007 0.330 7.162-5.571 100.00 427 22 0.1455 322.451 320.215 0.999 1.006 0.280 5.546-4.326 100.00 867 58 0.0801 442.679 440.262 1.011 1.003 0.220 4.315-3.360 100.00 1859 96 0.0730 420.993 421.083 1.062 0.999 0.200 3.356-3.002 100.00 1373 60 0.0976 324.266 322.839 1.036 0.995 0.100 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.4268 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0949 r_free=0.1728 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0951 r_free=0.1735 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0951 r_free=0.1735 | n_water=230 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.0979 r_free=0.1753 | n_water=224 | time (s): 17.050 (total time: 17.690) Filter (q & B) r_work=0.1054 r_free=0.1775 | n_water=221 | time (s): 1.430 (total time: 19.120) Compute maps r_work=0.1054 r_free=0.1775 | n_water=221 | time (s): 0.470 (total time: 19.590) Filter (map) r_work=0.1302 r_free=0.1821 | n_water=149 | time (s): 1.860 (total time: 21.450) Find peaks r_work=0.1302 r_free=0.1821 | n_water=149 | time (s): 0.590 (total time: 22.040) Add new water r_work=0.1668 r_free=0.2145 | n_water=237 | time (s): 1.670 (total time: 23.710) Refine new water occ: r_work=0.1063 r_free=0.1729 adp: r_work=0.1057 r_free=0.1730 occ: r_work=0.1047 r_free=0.1719 adp: r_work=0.1047 r_free=0.1721 occ: r_work=0.1039 r_free=0.1712 adp: r_work=0.1038 r_free=0.1713 ADP+occupancy (water only), MIN, final r_work=0.1038 r_free=0.1713 r_work=0.1038 r_free=0.1713 | n_water=237 | time (s): 11.210 (total time: 34.920) Filter (q & B) r_work=0.1039 r_free=0.1716 | n_water=235 | time (s): 1.690 (total time: 36.610) Filter (dist only) r_work=0.1039 r_free=0.1716 | n_water=235 | time (s): 17.920 (total time: 54.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.065620 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.237086 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 0.0947 0.1796 0.0849 0.010 1.0 5.4 0.5 0.6 0 0.533 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.47 17.96 8.49 5.429 17.619 0.237 5.170 9.06 18.45 9.39 7.290 17.662 0.237 5.074 Individual atomic B min max mean iso aniso Overall: 0.00 109.01 16.30 9.01 1762 0 Protein: 0.00 109.01 15.11 9.00 1519 0 Water: 0.00 60.27 23.71 N/A 235 0 Other: 6.33 39.26 24.08 N/A 8 0 Chain A: 0.00 109.01 15.72 N/A 1654 0 Chain S: 0.00 60.27 25.05 N/A 108 0 Histogram: Values Number of atoms 0.00 - 10.90 689 10.90 - 21.80 662 21.80 - 32.70 229 32.70 - 43.60 111 43.60 - 54.51 38 54.51 - 65.41 18 65.41 - 76.31 7 76.31 - 87.21 3 87.21 - 98.11 4 98.11 - 109.01 1 =========================== Idealize ADP of riding H ========================== r_work=0.0906 r_free=0.1845 r_work=0.0912 r_free=0.1856 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0912 r_free = 0.1856 target_work(ml) = 5.078 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0902 r_free = 0.1839 target_work(ml) = 5.071 | | occupancies: max = 1.00 min = 0.21 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= 0.0902 r_free= 0.1839 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 5.070685 | | target function (ml) not normalized (work): 24962.984275 | | target function (ml) not normalized (free): 1830.324709 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0949 0.0902 0.1839 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2070 0.2072 0.2211 n_refl.: 5175 remove outliers: r(all,work,free)=0.2070 0.2072 0.2211 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2070 0.2072 0.2211 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0944 0.0898 0.1827 n_refl.: 5175 remove outliers: r(all,work,free)=0.0944 0.0898 0.1827 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 0.3677 326.636 302.632 0.597 0.992 0.329 11.894-9.307 99.02 97 4 0.1873 525.455 508.114 0.944 0.996 0.328 9.237-7.194 100.00 213 7 0.1873 429.718 423.133 1.007 0.998 0.322 7.162-5.571 100.00 427 22 0.1885 322.451 312.618 0.983 0.999 0.280 5.546-4.326 100.00 867 58 0.0911 442.679 437.979 0.996 1.001 0.220 4.315-3.360 100.00 1859 96 0.0600 420.993 420.398 1.053 1.002 0.210 3.356-3.002 100.00 1373 60 0.0616 324.266 324.062 1.029 1.004 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.2532 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0898 r_free=0.1827 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0898 r_free=0.1827 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0898 r_free=0.1827 | n_water=235 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.0916 r_free=0.1832 | n_water=229 | time (s): 17.150 (total time: 17.670) Filter (q & B) r_work=0.0986 r_free=0.1884 | n_water=227 | time (s): 1.320 (total time: 18.990) Compute maps r_work=0.0986 r_free=0.1884 | n_water=227 | time (s): 0.500 (total time: 19.490) Filter (map) r_work=0.1235 r_free=0.1890 | n_water=160 | time (s): 1.780 (total time: 21.270) Find peaks r_work=0.1235 r_free=0.1890 | n_water=160 | time (s): 0.590 (total time: 21.860) Add new water r_work=0.1547 r_free=0.2169 | n_water=240 | time (s): 1.830 (total time: 23.690) Refine new water occ: r_work=0.1006 r_free=0.1850 adp: r_work=0.0998 r_free=0.1855 occ: r_work=0.0991 r_free=0.1837 adp: r_work=0.0990 r_free=0.1845 occ: r_work=0.0984 r_free=0.1827 adp: r_work=0.0982 r_free=0.1833 ADP+occupancy (water only), MIN, final r_work=0.0982 r_free=0.1833 r_work=0.0982 r_free=0.1833 | n_water=240 | time (s): 9.620 (total time: 33.310) Filter (q & B) r_work=0.0983 r_free=0.1846 | n_water=236 | time (s): 1.880 (total time: 35.190) Filter (dist only) r_work=0.0994 r_free=0.1843 | n_water=233 | time (s): 18.220 (total time: 53.410) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.033844 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.215415 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 0.0905 0.1889 0.0984 0.011 1.1 4.8 0.5 0.0 0 0.517 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.05 18.89 9.84 7.015 17.908 0.215 5.038 8.85 18.97 10.11 8.150 18.032 0.215 4.974 Individual atomic B min max mean iso aniso Overall: 0.00 109.16 16.66 10.62 1760 0 Protein: 0.00 109.16 15.51 10.61 1519 0 Water: 0.00 62.83 23.82 N/A 233 0 Other: 8.47 44.17 25.67 N/A 8 0 Chain A: 0.00 109.16 16.05 N/A 1646 0 Chain S: 0.00 62.83 25.43 N/A 114 0 Histogram: Values Number of atoms 0.00 - 10.92 685 10.92 - 21.83 640 21.83 - 32.75 258 32.75 - 43.67 102 43.67 - 54.58 41 54.58 - 65.50 13 65.50 - 76.41 13 76.41 - 87.33 3 87.33 - 98.25 4 98.25 - 109.16 1 =========================== Idealize ADP of riding H ========================== r_work=0.0885 r_free=0.1897 r_work=0.0890 r_free=0.1899 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0890 r_free = 0.1899 target_work(ml) = 4.979 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0880 r_free = 0.1885 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0880 r_free= 0.1885 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.970001 | | target function (ml) not normalized (work): 24467.312821 | | target function (ml) not normalized (free): 2176.623725 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0930 0.0880 0.1885 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2109 0.2111 0.2235 n_refl.: 5175 remove outliers: r(all,work,free)=0.2109 0.2111 0.2235 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2109 0.2111 0.2235 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0929 0.0879 0.1880 n_refl.: 5175 remove outliers: r(all,work,free)=0.0929 0.0879 0.1880 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 0.3786 326.636 298.552 0.581 0.986 0.318 11.894-9.307 99.02 97 4 0.1951 525.455 506.760 0.948 0.992 0.317 9.237-7.194 100.00 213 7 0.2065 429.718 422.038 1.007 0.996 0.308 7.162-5.571 100.00 427 22 0.2041 322.451 310.460 0.990 0.997 0.270 5.546-4.326 100.00 867 58 0.0978 442.679 436.381 1.016 1.000 0.230 4.315-3.360 100.00 1859 96 0.0557 420.993 420.876 1.080 1.003 0.220 3.356-3.002 100.00 1373 60 0.0451 324.266 324.289 1.055 1.005 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.4796 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0879 r_free=0.1880 After: r_work=0.0882 r_free=0.1879 ================================== NQH flips ================================== r_work=0.0882 r_free=0.1879 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0882 r_free=0.1879 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0882 r_free=0.1879 | n_water=233 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.0904 r_free=0.1890 | n_water=227 | time (s): 19.730 (total time: 20.410) Filter (q & B) r_work=0.1020 r_free=0.1920 | n_water=224 | time (s): 1.820 (total time: 22.230) Compute maps r_work=0.1020 r_free=0.1920 | n_water=224 | time (s): 0.530 (total time: 22.760) Filter (map) r_work=0.1281 r_free=0.1906 | n_water=154 | time (s): 1.840 (total time: 24.600) Find peaks r_work=0.1281 r_free=0.1906 | n_water=154 | time (s): 0.590 (total time: 25.190) Add new water r_work=0.1605 r_free=0.2188 | n_water=233 | time (s): 1.370 (total time: 26.560) Refine new water r_work=0.1605 r_free=0.2188 | n_water=233 | time (s): 0.050 (total time: 26.610) Filter (q & B) r_work=0.1281 r_free=0.1906 | n_water=154 | time (s): 1.430 (total time: 28.040) Filter (dist only) r_work=0.1295 r_free=0.1938 | n_water=147 | time (s): 12.220 (total time: 40.260) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.347040 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.284822 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 0.1197 0.1938 0.0742 0.011 1.2 6.7 0.5 0.6 0 0.674 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.97 19.38 7.42 8.088 18.043 0.285 5.414 11.25 19.63 8.39 8.981 18.119 0.285 5.323 Individual atomic B min max mean iso aniso Overall: 0.00 109.10 16.33 11.36 1674 0 Protein: 0.00 109.10 15.66 11.34 1519 0 Water: 0.00 57.92 22.78 N/A 147 0 Other: 9.18 48.93 26.21 N/A 8 0 Chain A: 0.00 109.10 16.16 N/A 1636 0 Chain S: 0.00 57.92 23.99 N/A 38 0 Histogram: Values Number of atoms 0.00 - 10.91 685 10.91 - 21.82 573 21.82 - 32.73 248 32.73 - 43.64 97 43.64 - 54.55 37 54.55 - 65.46 10 65.46 - 76.37 15 76.37 - 87.28 3 87.28 - 98.19 4 98.19 - 109.10 2 =========================== Idealize ADP of riding H ========================== r_work=0.1125 r_free=0.1963 r_work=0.1130 r_free=0.1965 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1130 r_free = 0.1965 target_work(ml) = 5.328 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1124 r_free = 0.1960 target_work(ml) = 5.325 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1124 r_free= 0.1960 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 5.324548 | | target function (ml) not normalized (work): 26212.749723 | | target function (ml) not normalized (free): 1712.624432 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1386 0.1872 5.669 6.0995| | 2: 3.78 - 3.00 1.00 2430 110 0.0804 0.2109 4.9712 7.6954| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 2493 142 0.91 13.21 0.99 0.98 14201.44| | 2: 3.78 - 3.00 2430 110 0.97 5.44 1.01 1.00 2798.17| |alpha: min = 0.97 max = 1.01 mean = 0.99| |beta: min = 2118.28 max = 21358.44 mean = 8572.77| |figures of merit: min = 0.01 max = 1.00 mean = 0.94| |phase err.(work): min = 0.00 max = 89.23 mean = 9.37| |phase err.(test): min = 0.00 max = 86.01 mean = 9.17| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1168 0.1124 0.1960 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2439 0.2444 0.2471 n_refl.: 5175 remove outliers: r(all,work,free)=0.2439 0.2444 0.2471 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2439 0.2444 0.2471 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1147 0.1102 0.1986 n_refl.: 5175 remove outliers: r(all,work,free)=0.1147 0.1102 0.1986 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 0.3690 326.636 302.376 0.704 0.994 0.368 11.894-9.307 99.02 97 4 0.1653 525.455 511.939 0.987 0.999 0.362 9.237-7.194 100.00 213 7 0.2008 429.718 422.376 1.000 1.001 0.357 7.162-5.571 100.00 427 22 0.2052 322.451 312.386 0.974 1.001 0.320 5.546-4.326 100.00 867 58 0.1182 442.679 436.117 0.990 1.002 0.268 4.315-3.360 100.00 1859 96 0.0823 420.993 418.895 1.077 1.001 0.247 3.356-3.002 100.00 1373 60 0.0818 324.266 322.428 1.071 1.000 0.092 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.4803 ================= 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 : 0.3624 0.2061 0.084 5.405 8.8 119.3 19.9 258 0.000 1_bss: 0.1572 0.1624 0.084 5.405 5.9 116.4 17.0 258 0.000 1_settarget: 0.1572 0.1624 0.084 5.405 5.9 116.4 17.0 258 0.000 1_nqh: 0.1572 0.1624 0.084 5.405 5.9 116.4 17.0 258 0.000 1_weight: 0.1572 0.1624 0.084 5.405 5.9 116.4 17.0 258 0.000 1_xyzrec: 0.1162 0.1793 0.009 0.964 5.9 116.4 17.0 258 0.211 1_adp: 0.1022 0.1781 0.009 0.964 2.0 111.4 17.5 258 0.211 1_regHadp: 0.1017 0.1789 0.009 0.964 2.0 111.4 17.5 258 0.211 1_occ: 0.1022 0.1806 0.009 0.964 2.0 111.4 17.5 258 0.211 2_bss: 0.1021 0.1808 0.009 0.964 0.9 110.3 16.4 258 0.211 2_settarget: 0.1021 0.1808 0.009 0.964 0.9 110.3 16.4 258 0.211 2_updatecdl: 0.1021 0.1808 0.009 0.982 0.9 110.3 16.4 258 0.211 2_nqh: 0.1023 0.1807 0.009 0.982 0.9 110.3 16.4 258 0.214 2_sol: 0.1124 0.1669 0.009 0.982 0.9 109.9 15.6 230 n/a 2_weight: 0.1124 0.1669 0.009 0.982 0.9 109.9 15.6 230 n/a 2_xyzrec: 0.1020 0.1736 0.009 0.966 0.9 109.9 15.6 230 n/a 2_adp: 0.0955 0.1750 0.009 0.966 0.0 108.8 16.4 230 n/a 2_regHadp: 0.0953 0.1750 0.009 0.966 0.0 108.8 16.4 230 n/a 2_occ: 0.0951 0.1732 0.009 0.966 0.0 108.8 16.4 230 n/a 3_bss: 0.0949 0.1728 0.009 0.966 0.0 108.8 16.4 230 n/a 3_settarget: 0.0949 0.1728 0.009 0.966 0.0 108.8 16.4 230 n/a 3_updatecdl: 0.0949 0.1728 0.009 0.974 0.0 108.8 16.4 230 n/a 3_nqh: 0.0951 0.1735 0.009 0.974 0.0 108.8 16.4 230 n/a 3_sol: 0.1039 0.1716 0.009 0.974 0.0 108.8 16.2 235 n/a 3_weight: 0.1039 0.1716 0.009 0.974 0.0 108.8 16.2 235 n/a 3_xyzrec: 0.0947 0.1796 0.010 1.036 0.0 108.8 16.2 235 n/a 3_adp: 0.0906 0.1845 0.010 1.036 0.0 109.0 16.3 235 n/a 3_regHadp: 0.0912 0.1856 0.010 1.036 0.0 109.0 16.3 235 n/a 3_occ: 0.0902 0.1839 0.010 1.036 0.0 109.0 16.3 235 n/a 4_bss: 0.0898 0.1827 0.010 1.036 0.0 109.0 16.3 235 n/a 4_settarget: 0.0898 0.1827 0.010 1.036 0.0 109.0 16.3 235 n/a 4_updatecdl: 0.0898 0.1827 0.010 1.050 0.0 109.0 16.3 235 n/a 4_nqh: 0.0898 0.1827 0.010 1.050 0.0 109.0 16.3 235 n/a 4_sol: 0.0994 0.1843 0.010 1.050 0.0 109.0 16.4 233 n/a 4_weight: 0.0994 0.1843 0.010 1.050 0.0 109.0 16.4 233 n/a 4_xyzrec: 0.0905 0.1889 0.011 1.069 0.0 109.0 16.4 233 n/a 4_adp: 0.0885 0.1897 0.011 1.069 0.0 109.2 16.7 233 n/a 4_regHadp: 0.0890 0.1899 0.011 1.069 0.0 109.2 16.7 233 n/a 4_occ: 0.0880 0.1885 0.011 1.069 0.0 109.2 16.7 233 n/a 5_bss: 0.0879 0.1880 0.011 1.069 0.0 109.2 16.7 233 n/a 5_settarget: 0.0879 0.1880 0.011 1.069 0.0 109.2 16.7 233 n/a 5_updatecdl: 0.0879 0.1880 0.011 1.080 0.0 109.2 16.7 233 n/a 5_setrh: 0.0882 0.1879 0.011 1.080 0.0 109.2 16.7 233 n/a 5_nqh: 0.0882 0.1879 0.011 1.080 0.0 109.2 16.7 233 n/a 5_sol: 0.1295 0.1938 0.011 1.080 0.0 109.2 16.2 147 n/a 5_weight: 0.1295 0.1938 0.011 1.080 0.0 109.2 16.2 147 n/a 5_xyzrec: 0.1197 0.1938 0.011 1.236 0.0 109.2 16.2 147 n/a 5_adp: 0.1125 0.1963 0.011 1.236 0.0 109.1 16.3 147 n/a 5_regHadp: 0.1130 0.1965 0.011 1.236 0.0 109.1 16.3 147 n/a 5_occ: 0.1124 0.1960 0.011 1.236 0.0 109.1 16.3 147 n/a end: 0.1102 0.1986 0.011 1.236 0.0 109.1 16.3 147 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2667343_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2667343_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0100 Refinement macro-cycles (run) : 459.6600 Write final files (write_after_run_outputs) : 12.3900 Total : 475.0600 Total CPU time: 8.27 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:37 PST -0800 (1735492717.89 s) Start R-work = 0.1572, R-free = 0.1624 Final R-work = 0.1102, R-free = 0.1986 =============================================================================== Job complete usr+sys time: 505.72 seconds wall clock time: 8 minutes 48.30 seconds (528.30 seconds total)