Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7718462.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7718462.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7718462.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 = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.84, per 1000 atoms: 0.54 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: 0.45 Conformation dependent library (CDL) restraints added in 138.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.91: 489 0.91 - 1.18: 1179 1.18 - 1.45: 695 1.45 - 1.72: 774 1.72 - 1.99: 16 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ASP A 42 " pdb=" C ASP A 42 " ideal model delta sigma weight residual 1.528 1.310 0.218 1.11e-02 8.12e+03 3.86e+02 bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.590 -0.212 1.10e-02 8.26e+03 3.72e+02 bond pdb=" CA GLU A 176 " pdb=" C GLU A 176 " ideal model delta sigma weight residual 1.524 1.766 -0.242 1.26e-02 6.30e+03 3.69e+02 bond pdb=" C ALA A 114 " pdb=" O ALA A 114 " ideal model delta sigma weight residual 1.237 1.009 0.228 1.19e-02 7.06e+03 3.66e+02 bond pdb=" N BLEU A 153 " pdb=" CA BLEU A 153 " ideal model delta sigma weight residual 1.458 1.677 -0.219 1.19e-02 7.06e+03 3.37e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.70: 3153 4.70 - 9.40: 1878 9.40 - 14.10: 621 14.10 - 18.80: 117 18.80 - 23.50: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.06 106.41 16.65 9.50e-01 1.11e+00 3.07e+02 angle pdb=" O LEU A 7 " pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 123.27 140.11 -16.84 1.18e+00 7.18e-01 2.04e+02 angle pdb=" CA BASN A 76 " pdb=" C BASN A 76 " pdb=" O BASN A 76 " ideal model delta sigma weight residual 120.92 135.99 -15.07 1.12e+00 7.97e-01 1.81e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 114.75 127.20 -12.45 9.90e-01 1.02e+00 1.58e+02 angle pdb=" O GLU A 16 " pdb=" C GLU A 16 " pdb=" N MET A 17 " ideal model delta sigma weight residual 122.12 135.42 -13.30 1.06e+00 8.90e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 1320 17.76 - 35.53: 116 35.53 - 53.29: 30 53.29 - 71.06: 13 71.06 - 88.82: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ALA A 79 " pdb=" N ALA A 79 " pdb=" CA ALA A 79 " pdb=" CB ALA A 79 " ideal model delta harmonic sigma weight residual -122.60 -141.62 19.02 0 2.50e+00 1.60e-01 5.79e+01 dihedral pdb=" C THR A 110 " pdb=" N THR A 110 " pdb=" CA THR A 110 " pdb=" CB THR A 110 " ideal model delta harmonic sigma weight residual -122.00 -140.25 18.25 0 2.50e+00 1.60e-01 5.33e+01 dihedral pdb=" N LEU A 185 " pdb=" C LEU A 185 " pdb=" CA LEU A 185 " pdb=" CB LEU A 185 " ideal model delta harmonic sigma weight residual 122.80 139.99 -17.19 0 2.50e+00 1.60e-01 4.73e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.224: 107 0.224 - 0.447: 82 0.447 - 0.671: 34 0.671 - 0.894: 17 0.894 - 1.117: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.47 -1.12 2.00e-01 2.50e+01 3.12e+01 chirality pdb=" CB VAL A 69 " pdb=" CA VAL A 69 " pdb=" CG1 VAL A 69 " pdb=" CG2 VAL A 69 " both_signs ideal model delta sigma weight residual False -2.63 -1.55 -1.08 2.00e-01 2.50e+01 2.91e+01 chirality pdb=" CB VAL A 181 " pdb=" CA VAL A 181 " pdb=" CG1 VAL A 181 " pdb=" CG2 VAL A 181 " both_signs ideal model delta sigma weight residual False -2.63 -3.56 0.93 2.00e-01 2.50e+01 2.17e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.010 2.00e-02 2.50e+03 6.55e-02 1.29e+02 pdb=" CG PHE A 119 " -0.092 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.103 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.026 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.047 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.123 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.083 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.030 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.090 2.00e-02 2.50e+03 6.71e-02 1.01e+02 pdb=" CG HIS A 138 " -0.066 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.016 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " -0.084 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.083 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.112 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.024 2.00e-02 2.50e+03 6.36e-02 9.10e+01 pdb=" CG HIS A 126 " -0.111 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.039 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " 0.103 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " -0.001 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.35: 1226 2.35 - 2.91: 8308 2.91 - 3.47: 10369 3.47 - 4.04: 15199 4.04 - 4.60: 21558 Nonbonded interactions: 56660 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.784 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.791 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.816 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O GLU A 147 " pdb=" H BTHR A 154 " model vdw 1.827 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.832 2.100 ... (remaining 56655 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_7718462_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2788 r_free= 0.1836 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.395344 | | target function (ml) not normalized (work): 71393.579700 | | target function (ml) not normalized (free): 3271.072507 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3200 0.2215 7.4632 5.0394| | 2: 3.63 - 2.88 1.00 2711 122 0.2651 0.1745 4.3381 4.3391| | 3: 2.88 - 2.52 1.00 2682 148 0.2542 0.1660 4.1919 4.1974| | 4: 2.52 - 2.29 1.00 2661 139 0.2547 0.1497 3.51 3.5719| | 5: 2.29 - 2.13 1.00 2678 122 0.2668 0.1460 3.3954 3.4725| | 6: 2.13 - 2.00 1.00 2692 117 0.2727 0.1913 3.3131 3.411| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.64 2819 159 0.88 17.78 0.77 0.23 1335.61| | 2: 3.63 - 2.88 2711 122 0.83 24.03 1.32 0.23 1335.61| | 3: 2.88 - 2.52 2682 148 0.73 33.16 1.28 0.23 1335.61| | 4: 2.52 - 2.29 2661 139 0.93 11.28 1.29 0.26 135.05| | 5: 2.29 - 2.13 2678 122 0.92 13.33 1.32 0.26 135.05| | 6: 2.13 - 2.00 2692 117 0.90 16.26 1.33 0.26 135.05| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 135.05 max = 1335.61 mean = 742.02| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.97 mean = 19.31| |phase err.(test): min = 0.00 max = 89.08 mean = 19.68| |-----------------------------------------------------------------------------| ----------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 0.258 1557 Z= 5.613 Angle : 5.190 17.692 2118 Z= 3.674 Chirality : 0.371 1.117 243 Planarity : 0.029 0.127 284 Dihedral : 13.817 88.820 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 28.65 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.49), residues: 224 helix: -2.06 (0.41), residues: 102 sheet: -1.01 (0.66), residues: 40 loop : 0.38 (0.65), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.052 0.012 ARG A 98 TYR 0.073 0.030 TYR A 141 PHE 0.097 0.045 PHE A 162 HIS 0.061 0.030 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2788 r_free= 0.1836 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.395344 | | target function (ml) not normalized (work): 71393.579700 | | target function (ml) not normalized (free): 3271.072507 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.2971 percent. r_work = 0.2918 r_free = 0.1996 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2918 0.1996 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2918 0.1996 n_refl.: 17050 remove outliers: r(all,work,free)=0.2157 0.2168 0.1996 n_refl.: 17045 overall B=-0.40 to atoms: r(all,work,free)=0.2131 0.2141 0.1978 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1617 0.1614 0.1680 n_refl.: 17045 remove outliers: r(all,work,free)=0.1616 0.1613 0.1680 n_refl.: 17044 ======================== 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 0.4027 395.166 365.164 0.661 1.012 0.409 11.894-9.307 99.02 97 4 0.1855 634.254 616.337 0.933 1.013 0.400 9.237-7.194 100.00 213 7 0.2142 518.756 512.006 0.956 1.012 0.350 7.162-5.571 100.00 427 22 0.2278 389.327 378.062 0.923 1.011 0.288 5.546-4.326 100.00 867 58 0.1400 534.483 529.271 0.960 1.009 0.241 4.315-3.360 100.00 1859 96 0.1300 508.299 503.836 1.015 1.006 0.181 3.356-2.611 100.00 3867 181 0.1661 333.923 329.822 1.013 1.000 0.071 2.608-2.000 99.99 8818 434 0.1646 217.661 213.839 1.028 0.989 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4176 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1613 r_free=0.1680 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1613 r_free=0.1680 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.883883 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.906991 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1350 0.1629 0.0279 0.009 1.0 1.0 0.5 0.0 0 11.942 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.50 16.29 2.79 3.013 18.462 0.907 0.023 12.78 16.48 3.70 3.577 18.673 0.907 0.021 Individual atomic B min max mean iso aniso Overall: 6.03 113.90 19.89 4.09 1785 0 Protein: 6.03 113.15 17.11 4.10 1519 0 Water: 8.22 113.90 36.06 N/A 258 0 Other: 21.67 36.45 26.11 N/A 8 0 Chain A: 6.03 113.90 19.89 N/A 1785 0 Histogram: Values Number of atoms 6.03 - 16.82 1085 16.82 - 27.61 338 27.61 - 38.39 189 38.39 - 49.18 94 49.18 - 59.97 52 59.97 - 70.75 12 70.75 - 81.54 7 81.54 - 92.33 4 92.33 - 103.12 1 103.12 - 113.90 3 =========================== Idealize ADP of riding H ========================== r_work=0.1278 r_free=0.1648 r_work=0.1281 r_free=0.1654 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1281 r_free = 0.1654 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1278 r_free = 0.1650 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1278 r_free= 0.1650 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020124 | | target function (ls_wunit_k1) not normalized (work): 326.753183 | | target function (ls_wunit_k1) not normalized (free): 27.308271 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1295 0.1278 0.1650 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1907 0.1906 0.1971 n_refl.: 17044 remove outliers: r(all,work,free)=0.1907 0.1906 0.1971 n_refl.: 17044 overall B=-0.51 to atoms: r(all,work,free)=0.1870 0.1869 0.1952 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1275 0.1642 n_refl.: 17044 remove outliers: r(all,work,free)=0.1291 0.1273 0.1642 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3542 303.698 279.002 0.626 1.006 0.369 11.894-9.307 99.02 97 4 0.1700 488.451 477.284 0.921 1.007 0.368 9.237-7.194 100.00 213 7 0.1836 399.503 395.831 0.961 1.007 0.351 7.162-5.571 100.00 427 22 0.1847 299.828 294.190 0.932 1.006 0.301 5.546-4.326 100.00 867 58 0.1053 411.615 408.935 0.958 1.005 0.210 4.315-3.360 100.00 1859 96 0.0934 391.450 390.997 1.015 1.004 0.192 3.356-2.611 100.00 3867 181 0.1294 257.161 255.802 1.010 1.001 0.081 2.608-2.000 99.99 8818 434 0.1344 167.625 166.332 1.011 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9583 b_overall=-1.1446 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1273 r_free=0.1642 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1273 r_free=0.1642 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1273 r_free=0.1642 | n_water=258 | time (s): 0.830 (total time: 0.830) Filter (dist) r_work=0.1282 r_free=0.1630 | n_water=253 | time (s): 19.350 (total time: 20.180) Filter (q & B) r_work=0.1282 r_free=0.1631 | n_water=251 | time (s): 1.590 (total time: 21.770) Compute maps r_work=0.1282 r_free=0.1631 | n_water=251 | time (s): 0.730 (total time: 22.500) Filter (map) r_work=0.1322 r_free=0.1613 | n_water=210 | time (s): 2.190 (total time: 24.690) Find peaks r_work=0.1322 r_free=0.1613 | n_water=210 | time (s): 0.520 (total time: 25.210) Add new water r_work=0.1539 r_free=0.1853 | n_water=370 | time (s): 1.740 (total time: 26.950) Refine new water occ: r_work=0.1331 r_free=0.1588 adp: r_work=0.1272 r_free=0.1589 occ: r_work=0.1278 r_free=0.1555 adp: r_work=0.1244 r_free=0.1561 occ: r_work=0.1246 r_free=0.1549 adp: r_work=0.1233 r_free=0.1553 ADP+occupancy (water only), MIN, final r_work=0.1233 r_free=0.1553 r_work=0.1233 r_free=0.1553 | n_water=370 | time (s): 16.060 (total time: 43.010) Filter (q & B) r_work=0.1234 r_free=0.1560 | n_water=362 | time (s): 1.480 (total time: 44.490) Filter (dist only) r_work=0.1235 r_free=0.1562 | n_water=361 | time (s): 27.730 (total time: 72.220) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 25.385376 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.993562 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1208 0.1586 0.0379 0.009 0.9 2.6 0.5 0.0 0 12.693 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.08 15.86 3.79 4.171 20.840 0.994 0.018 11.93 16.20 4.26 4.215 21.187 0.994 0.017 Individual atomic B min max mean iso aniso Overall: 6.41 107.64 21.29 4.33 1888 0 Protein: 6.41 107.64 17.66 4.32 1519 0 Water: 8.63 65.68 36.25 N/A 361 0 Other: 25.19 46.04 35.38 N/A 8 0 Chain A: 6.41 107.64 19.40 N/A 1737 0 Chain S: 18.93 65.38 43.10 N/A 151 0 Histogram: Values Number of atoms 6.41 - 16.53 1018 16.53 - 26.65 380 26.65 - 36.78 228 36.78 - 46.90 149 46.90 - 57.02 76 57.02 - 67.15 27 67.15 - 77.27 3 77.27 - 87.39 4 87.39 - 97.52 1 97.52 - 107.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.1193 r_free=0.1620 r_work=0.1195 r_free=0.1620 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1195 r_free = 0.1620 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1627 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1193 r_free= 0.1627 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016910 | | target function (ls_wunit_k1) not normalized (work): 274.528915 | | target function (ls_wunit_k1) not normalized (free): 25.245196 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1193 0.1627 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1754 0.1747 0.1936 n_refl.: 17042 remove outliers: r(all,work,free)=0.1754 0.1747 0.1936 n_refl.: 17042 overall B=-0.42 to atoms: r(all,work,free)=0.1728 0.1720 0.1920 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1210 0.1189 0.1624 n_refl.: 17042 remove outliers: r(all,work,free)=0.1210 0.1189 0.1624 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3376 303.698 283.071 0.606 1.007 0.350 11.894-9.307 99.02 97 4 0.1531 488.451 486.071 0.919 1.007 0.350 9.237-7.194 100.00 213 7 0.1635 399.503 400.360 0.978 1.007 0.311 7.162-5.571 100.00 427 22 0.1497 299.828 297.026 0.932 1.007 0.261 5.546-4.326 100.00 867 58 0.0877 411.615 409.064 0.959 1.006 0.216 4.315-3.360 100.00 1859 96 0.0829 391.450 390.646 1.015 1.004 0.212 3.356-2.611 100.00 3867 181 0.1194 257.161 256.461 1.010 1.001 0.101 2.608-2.000 99.99 8818 434 0.1335 167.625 166.566 1.012 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1644 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1189 r_free=0.1624 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=0.1190 r_free=0.1625 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1190 r_free=0.1625 | n_water=361 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1189 r_free=0.1634 | n_water=359 | time (s): 30.490 (total time: 31.100) Filter (q & B) r_work=0.1189 r_free=0.1634 | n_water=359 | time (s): 1.190 (total time: 32.290) Compute maps r_work=0.1189 r_free=0.1634 | n_water=359 | time (s): 0.830 (total time: 33.120) Filter (map) r_work=0.1258 r_free=0.1625 | n_water=263 | time (s): 1.910 (total time: 35.030) Find peaks r_work=0.1258 r_free=0.1625 | n_water=263 | time (s): 0.500 (total time: 35.530) Add new water r_work=0.1437 r_free=0.1791 | n_water=413 | time (s): 1.670 (total time: 37.200) Refine new water occ: r_work=0.1244 r_free=0.1583 adp: r_work=0.1235 r_free=0.1583 occ: r_work=0.1218 r_free=0.1554 adp: r_work=0.1207 r_free=0.1551 occ: r_work=0.1201 r_free=0.1539 adp: r_work=0.1190 r_free=0.1536 ADP+occupancy (water only), MIN, final r_work=0.1190 r_free=0.1536 r_work=0.1190 r_free=0.1536 | n_water=413 | time (s): 42.670 (total time: 79.870) Filter (q & B) r_work=0.1192 r_free=0.1541 | n_water=401 | time (s): 1.460 (total time: 81.330) Filter (dist only) r_work=0.1192 r_free=0.1541 | n_water=401 | time (s): 33.230 (total time: 114.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.909586 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.152468 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1166 0.1557 0.0391 0.009 1.0 3.5 0.5 0.0 0 0.955 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.66 15.57 3.91 4.366 21.422 0.152 5.000 11.46 15.68 4.23 4.879 21.307 0.152 4.978 Individual atomic B min max mean iso aniso Overall: 6.39 105.07 20.72 4.64 1928 0 Protein: 6.39 105.07 16.85 4.63 1519 0 Water: 8.34 60.66 35.06 N/A 401 0 Other: 27.86 47.29 36.29 N/A 8 0 Chain A: 6.39 105.07 18.63 N/A 1735 0 Chain S: 13.84 60.66 39.48 N/A 193 0 Histogram: Values Number of atoms 6.39 - 16.26 1083 16.26 - 26.13 335 26.13 - 35.99 227 35.99 - 45.86 170 45.86 - 55.73 77 55.73 - 65.60 23 65.60 - 75.46 6 75.46 - 85.33 2 85.33 - 95.20 3 95.20 - 105.07 2 =========================== Idealize ADP of riding H ========================== r_work=0.1146 r_free=0.1568 r_work=0.1146 r_free=0.1571 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1146 r_free = 0.1571 target_work(ml) = 4.979 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1137 r_free = 0.1570 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1137 r_free= 0.1570 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.971974 | | target function (ml) not normalized (work): 80719.991541 | | target function (ml) not normalized (free): 4198.761147 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1158 0.1137 0.1570 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1665 0.1657 0.1861 n_refl.: 17042 remove outliers: r(all,work,free)=0.1665 0.1657 0.1861 n_refl.: 17042 overall B=-0.34 to atoms: r(all,work,free)=0.1642 0.1634 0.1851 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1157 0.1137 0.1570 n_refl.: 17042 remove outliers: r(all,work,free)=0.1157 0.1137 0.1570 n_refl.: 17042 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3641 303.698 278.384 0.572 1.007 0.340 11.894-9.307 99.02 97 4 0.1749 488.451 482.913 0.914 1.008 0.330 9.237-7.194 100.00 213 7 0.1718 399.503 399.678 0.985 1.008 0.300 7.162-5.571 100.00 427 22 0.1542 299.828 295.035 0.941 1.007 0.241 5.546-4.326 100.00 867 58 0.0928 411.615 408.596 0.963 1.006 0.221 4.315-3.360 100.00 1859 96 0.0880 391.450 388.881 1.012 1.004 0.211 3.356-2.611 100.00 3867 181 0.1258 257.161 255.011 1.011 1.001 0.141 2.608-2.000 99.99 8818 434 0.1098 167.625 166.155 1.013 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1699 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1137 r_free=0.1570 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1137 r_free=0.1570 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1137 r_free=0.1570 | n_water=401 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.1137 r_free=0.1574 | n_water=400 | time (s): 34.830 (total time: 35.530) Filter (q & B) r_work=0.1138 r_free=0.1575 | n_water=399 | time (s): 1.710 (total time: 37.240) Compute maps r_work=0.1138 r_free=0.1575 | n_water=399 | time (s): 0.570 (total time: 37.810) Filter (map) r_work=0.1194 r_free=0.1571 | n_water=317 | time (s): 1.590 (total time: 39.400) Find peaks r_work=0.1194 r_free=0.1571 | n_water=317 | time (s): 0.480 (total time: 39.880) Add new water r_work=0.1340 r_free=0.1704 | n_water=466 | time (s): 1.920 (total time: 41.800) Refine new water occ: r_work=0.1172 r_free=0.1514 adp: r_work=0.1162 r_free=0.1520 occ: r_work=0.1151 r_free=0.1492 adp: r_work=0.1140 r_free=0.1495 occ: r_work=0.1136 r_free=0.1484 adp: r_work=0.1127 r_free=0.1484 ADP+occupancy (water only), MIN, final r_work=0.1127 r_free=0.1484 r_work=0.1127 r_free=0.1484 | n_water=466 | time (s): 27.540 (total time: 69.340) Filter (q & B) r_work=0.1130 r_free=0.1498 | n_water=457 | time (s): 2.250 (total time: 71.590) Filter (dist only) r_work=0.1130 r_free=0.1498 | n_water=457 | time (s): 33.410 (total time: 105.000) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.927572 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.167697 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1116 0.1564 0.0448 0.010 1.0 5.4 0.5 0.0 0 0.964 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.16 15.64 4.48 4.457 21.040 0.168 4.962 11.05 15.71 4.66 4.619 21.075 0.168 4.957 Individual atomic B min max mean iso aniso Overall: 5.66 103.76 21.02 4.81 1984 0 Protein: 5.66 103.76 16.46 4.80 1519 0 Water: 8.42 62.73 35.93 N/A 457 0 Other: 26.92 47.46 35.02 N/A 8 0 Chain A: 5.66 103.76 18.17 N/A 1734 0 Chain S: 16.19 62.73 40.74 N/A 250 0 Histogram: Values Number of atoms 5.66 - 15.47 1050 15.47 - 25.28 365 25.28 - 35.09 218 35.09 - 44.90 200 44.90 - 54.71 109 54.71 - 64.52 29 64.52 - 74.33 6 74.33 - 84.14 2 84.14 - 93.95 3 93.95 - 103.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.1105 r_free=0.1571 r_work=0.1105 r_free=0.1571 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1105 r_free = 0.1571 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1096 r_free = 0.1578 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1096 r_free= 0.1578 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.953620 | | target function (ml) not normalized (work): 80422.014184 | | target function (ml) not normalized (free): 4194.902297 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1119 0.1096 0.1578 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1580 0.1568 0.1858 n_refl.: 17042 remove outliers: r(all,work,free)=0.1580 0.1568 0.1858 n_refl.: 17042 overall B=-0.26 to atoms: r(all,work,free)=0.1565 0.1552 0.1851 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1117 0.1094 0.1571 n_refl.: 17042 remove outliers: r(all,work,free)=0.1116 0.1093 0.1571 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3685 300.204 280.204 0.563 1.001 0.340 11.894-9.307 99.02 97 4 0.1734 488.451 481.526 0.921 1.002 0.330 9.237-7.194 100.00 213 7 0.1679 399.503 399.954 0.989 1.003 0.270 7.162-5.571 100.00 427 22 0.1451 299.828 295.132 0.944 1.003 0.230 5.546-4.326 100.00 867 58 0.0901 411.615 408.289 0.966 1.003 0.201 4.315-3.360 100.00 1859 96 0.0841 391.450 389.256 1.006 1.002 0.201 3.356-2.611 100.00 3867 181 0.1214 257.161 254.989 1.000 1.001 0.141 2.608-2.000 99.99 8818 434 0.1050 167.625 166.346 0.994 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.8878 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1093 r_free=0.1571 After: r_work=0.1095 r_free=0.1570 ================================== NQH flips ================================== r_work=0.1095 r_free=0.1570 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1095 r_free=0.1570 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1095 r_free=0.1570 | n_water=457 | time (s): 0.650 (total time: 0.650) Filter (dist) r_work=0.1103 r_free=0.1571 | n_water=453 | time (s): 37.130 (total time: 37.780) Filter (q & B) r_work=0.1103 r_free=0.1571 | n_water=452 | time (s): 2.040 (total time: 39.820) Compute maps r_work=0.1103 r_free=0.1571 | n_water=452 | time (s): 0.860 (total time: 40.680) Filter (map) r_work=0.1192 r_free=0.1580 | n_water=332 | time (s): 2.110 (total time: 42.790) Find peaks r_work=0.1192 r_free=0.1580 | n_water=332 | time (s): 0.560 (total time: 43.350) Add new water r_work=0.1311 r_free=0.1684 | n_water=469 | time (s): 1.770 (total time: 45.120) Refine new water occ: r_work=0.1142 r_free=0.1565 adp: r_work=0.1135 r_free=0.1562 occ: r_work=0.1122 r_free=0.1545 adp: r_work=0.1113 r_free=0.1541 occ: r_work=0.1107 r_free=0.1537 adp: r_work=0.1100 r_free=0.1531 ADP+occupancy (water only), MIN, final r_work=0.1100 r_free=0.1531 r_work=0.1100 r_free=0.1531 | n_water=469 | time (s): 20.610 (total time: 65.730) Filter (q & B) r_work=0.1103 r_free=0.1547 | n_water=458 | time (s): 2.170 (total time: 67.900) Filter (dist only) r_work=0.1103 r_free=0.1547 | n_water=458 | time (s): 35.410 (total time: 103.310) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.005019 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.166059 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1120 0.1557 0.0437 0.010 1.1 3.8 0.5 0.0 0 1.003 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.20 15.57 4.37 4.521 20.759 0.166 4.958 11.08 15.47 4.38 4.602 20.822 0.166 4.950 Individual atomic B min max mean iso aniso Overall: 5.29 101.48 20.87 4.89 1985 0 Protein: 5.29 101.48 16.17 4.87 1519 0 Water: 8.54 64.44 36.21 N/A 458 0 Other: 26.60 45.87 34.74 N/A 8 0 Chain A: 5.29 101.48 17.80 N/A 1730 0 Chain S: 16.97 64.44 41.71 N/A 255 0 Histogram: Values Number of atoms 5.29 - 14.91 1037 14.91 - 24.53 367 24.53 - 34.15 211 34.15 - 43.77 191 43.77 - 53.39 128 53.39 - 63.00 34 63.00 - 72.62 8 72.62 - 82.24 3 82.24 - 91.86 3 91.86 - 101.48 3 =========================== Idealize ADP of riding H ========================== r_work=0.1108 r_free=0.1547 r_work=0.1108 r_free=0.1546 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1108 r_free = 0.1546 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1103 r_free = 0.1551 target_work(ml) = 4.946 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1103 r_free= 0.1551 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.946087 | | target function (ml) not normalized (work): 80294.783667 | | target function (ml) not normalized (free): 4179.898535 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1121 0.1406 5.4613 5.658| | 2: 3.63 - 2.88 1.00 2711 122 0.1088 0.1574 5.2207 5.362| | 3: 2.88 - 2.52 1.00 2681 148 0.1318 0.1690 5.1217 5.1984| | 4: 2.52 - 2.29 1.00 2661 139 0.0938 0.1636 4.6458 5.0273| | 5: 2.29 - 2.13 1.00 2678 122 0.0963 0.1522 4.6012 4.9101| | 6: 2.13 - 2.00 1.00 2692 117 0.1133 0.1715 4.5965 4.7771| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2811 159 0.94 9.11 1.00 0.96 6408.85| | 2: 3.63 - 2.88 2711 122 0.92 12.86 1.01 0.96 6408.85| | 3: 2.88 - 2.52 2681 148 0.87 19.04 0.99 0.96 6408.85| | 4: 2.52 - 2.29 2661 139 0.92 12.54 1.01 0.98 2258.57| | 5: 2.29 - 2.13 2678 122 0.91 14.65 1.00 0.98 2258.57| | 6: 2.13 - 2.00 2692 117 0.89 17.44 0.99 0.98 2258.57| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2258.57 max = 6408.85 mean = 4355.70| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.84 mean = 14.23| |phase err.(test): min = 0.00 max = 85.01 mean = 13.73| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1125 0.1103 0.1551 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1573 0.1559 0.1866 n_refl.: 17041 remove outliers: r(all,work,free)=0.1573 0.1559 0.1866 n_refl.: 17041 overall B=-0.22 to atoms: r(all,work,free)=0.1560 0.1546 0.1859 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1124 0.1102 0.1552 n_refl.: 17041 remove outliers: r(all,work,free)=0.1124 0.1102 0.1552 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3666 300.204 279.384 0.550 1.004 0.324 11.894-9.307 99.02 97 4 0.1714 488.451 481.725 0.923 1.005 0.320 9.237-7.194 100.00 213 7 0.1747 399.503 399.326 0.983 1.005 0.240 7.162-5.571 100.00 427 22 0.1518 299.828 294.465 0.938 1.005 0.220 5.546-4.326 100.00 867 58 0.0925 411.615 408.472 0.963 1.004 0.200 4.315-3.360 100.00 1859 96 0.0877 391.450 389.028 1.004 1.003 0.201 3.356-2.611 100.00 3867 181 0.1223 257.161 254.859 0.999 1.000 0.131 2.608-2.000 99.99 8818 434 0.1036 167.625 166.332 0.992 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.7654 ================= 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 : 0.2788 0.1836 0.084 5.190 8.8 119.3 19.9 258 0.000 1_bss: 0.1613 0.1680 0.084 5.190 8.4 118.9 19.5 258 0.000 1_settarget: 0.1613 0.1680 0.084 5.190 8.4 118.9 19.5 258 0.000 1_nqh: 0.1613 0.1680 0.084 5.190 8.4 118.9 19.5 258 0.000 1_weight: 0.1613 0.1680 0.084 5.190 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1350 0.1629 0.009 0.981 8.4 118.9 19.5 258 0.139 1_adp: 0.1278 0.1648 0.009 0.981 6.0 113.9 19.9 258 0.139 1_regHadp: 0.1281 0.1654 0.009 0.981 6.0 113.9 19.9 258 0.139 1_occ: 0.1278 0.1650 0.009 0.981 6.0 113.9 19.9 258 0.139 2_bss: 0.1273 0.1642 0.009 0.981 5.5 113.4 19.4 258 0.139 2_settarget: 0.1273 0.1642 0.009 0.981 5.5 113.4 19.4 258 0.139 2_updatecdl: 0.1273 0.1642 0.009 0.996 5.5 113.4 19.4 258 0.139 2_nqh: 0.1273 0.1642 0.009 0.996 5.5 113.4 19.4 258 0.139 2_sol: 0.1235 0.1562 0.009 0.996 5.5 112.6 20.7 361 n/a 2_weight: 0.1235 0.1562 0.009 0.996 5.5 112.6 20.7 361 n/a 2_xyzrec: 0.1208 0.1586 0.009 0.938 5.5 112.6 20.7 361 n/a 2_adp: 0.1193 0.1620 0.009 0.938 6.4 107.6 21.3 361 n/a 2_regHadp: 0.1195 0.1620 0.009 0.938 6.4 107.6 21.3 361 n/a 2_occ: 0.1193 0.1627 0.009 0.938 6.4 107.6 21.3 361 n/a 3_bss: 0.1189 0.1624 0.009 0.938 6.0 107.2 20.9 361 n/a 3_settarget: 0.1189 0.1624 0.009 0.938 6.0 107.2 20.9 361 n/a 3_updatecdl: 0.1189 0.1624 0.009 0.942 6.0 107.2 20.9 361 n/a 3_nqh: 0.1190 0.1625 0.009 0.942 6.0 107.2 20.9 361 n/a 3_sol: 0.1192 0.1541 0.009 0.942 6.0 107.2 20.9 401 n/a 3_weight: 0.1192 0.1541 0.009 0.942 6.0 107.2 20.9 401 n/a 3_xyzrec: 0.1166 0.1557 0.009 0.975 6.0 107.2 20.9 401 n/a 3_adp: 0.1146 0.1568 0.009 0.975 6.4 105.1 20.7 401 n/a 3_regHadp: 0.1146 0.1571 0.009 0.975 6.4 105.1 20.7 401 n/a 3_occ: 0.1137 0.1570 0.009 0.975 6.4 105.1 20.7 401 n/a 4_bss: 0.1137 0.1570 0.009 0.975 6.1 104.7 20.4 401 n/a 4_settarget: 0.1137 0.1570 0.009 0.975 6.1 104.7 20.4 401 n/a 4_updatecdl: 0.1137 0.1570 0.009 0.973 6.1 104.7 20.4 401 n/a 4_nqh: 0.1137 0.1570 0.009 0.973 6.1 104.7 20.4 401 n/a 4_sol: 0.1130 0.1498 0.009 0.973 6.1 104.7 21.0 457 n/a 4_weight: 0.1130 0.1498 0.009 0.973 6.1 104.7 21.0 457 n/a 4_xyzrec: 0.1116 0.1564 0.010 0.979 6.1 104.7 21.0 457 n/a 4_adp: 0.1105 0.1571 0.010 0.979 5.7 103.8 21.0 457 n/a 4_regHadp: 0.1105 0.1571 0.010 0.979 5.7 103.8 21.0 457 n/a 4_occ: 0.1096 0.1578 0.010 0.979 5.7 103.8 21.0 457 n/a 5_bss: 0.1093 0.1571 0.010 0.979 5.4 103.5 20.8 457 n/a 5_settarget: 0.1093 0.1571 0.010 0.979 5.4 103.5 20.8 457 n/a 5_updatecdl: 0.1093 0.1571 0.010 0.980 5.4 103.5 20.8 457 n/a 5_setrh: 0.1095 0.1570 0.010 0.980 5.4 103.5 20.8 457 n/a 5_nqh: 0.1095 0.1570 0.010 0.980 5.4 103.5 20.8 457 n/a 5_sol: 0.1103 0.1547 0.010 0.980 5.4 103.5 20.8 458 n/a 5_weight: 0.1103 0.1547 0.010 0.980 5.4 103.5 20.8 458 n/a 5_xyzrec: 0.1120 0.1557 0.010 1.138 5.4 103.5 20.8 458 n/a 5_adp: 0.1108 0.1547 0.010 1.138 5.3 101.5 20.9 458 n/a 5_regHadp: 0.1108 0.1546 0.010 1.138 5.3 101.5 20.9 458 n/a 5_occ: 0.1103 0.1551 0.010 1.138 5.3 101.5 20.9 458 n/a end: 0.1102 0.1552 0.010 1.138 5.1 101.3 20.6 458 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7718462_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7718462_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6600 Refinement macro-cycles (run) : 940.4600 Write final files (write_after_run_outputs) : 19.1100 Total : 963.2300 Total CPU time: 16.41 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:26 PST -0800 (1735494086.50 s) Start R-work = 0.1613, R-free = 0.1680 Final R-work = 0.1102, R-free = 0.1552 =============================================================================== Job complete usr+sys time: 1004.54 seconds wall clock time: 17 minutes 7.80 seconds (1027.80 seconds total)