Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_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=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 { 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" 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_7718462.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7718462.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.16, per 1000 atoms: 0.34 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 118.4 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.48 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 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_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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3622 r_free= 0.2090 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.472729 | | target function (ml) not normalized (work): 22050.555622 | | target function (ml) not normalized (free): 1158.090029 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3805 0.2315 4.8481 4.9315| | 2: 3.78 - 3.00 1.00 2430 110 0.3399 0.1709 4.0866 4.162| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.82 0.83 0.13 6610.48| | 2: 3.78 - 3.00 2430 110 0.94 11.44 1.48 0.26 455.43| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 389.37 max = 12076.50 mean = 3576.65| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.39| |phase err.(test): min = 0.00 max = 89.96 mean = 33.44| |-----------------------------------------------------------------------------| ----------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: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3622 r_free= 0.2090 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.472729 | | target function (ml) not normalized (work): 22050.555622 | | target function (ml) not normalized (free): 1158.090029 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3580 0.3655 0.2159 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3580 0.3655 0.2159 n_refl.: 5182 remove outliers: r(all,work,free)=0.2529 0.2552 0.2159 n_refl.: 5178 overall B=-2.75 to atoms: r(all,work,free)=0.2424 0.2444 0.2113 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1575 0.1570 0.1665 n_refl.: 5178 remove outliers: r(all,work,free)=0.1573 0.1568 0.1665 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 0.3982 445.332 408.455 0.684 1.010 0.409 11.894-9.307 99.02 97 4 0.1847 714.925 689.374 0.959 1.012 0.401 9.237-7.194 100.00 213 7 0.2145 584.667 573.261 0.980 1.011 0.358 7.162-5.571 100.00 427 22 0.2286 438.722 423.208 0.941 1.009 0.298 5.546-4.326 100.00 867 58 0.1392 602.302 592.985 0.972 1.005 0.258 4.315-3.360 100.00 1859 96 0.1325 572.796 566.985 1.021 0.999 0.179 3.356-3.002 100.00 1373 60 0.1618 441.192 437.178 1.015 0.992 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.7931 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1568 r_free=0.1665 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=0.1568 r_free=0.1665 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.468319 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.828177 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 0.1164 0.1825 0.0661 0.010 1.0 2.2 0.5 0.0 0 9.734 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 18.25 6.61 3.013 16.110 1.828 0.018 10.25 18.05 7.79 4.866 16.342 1.828 0.015 Individual atomic B min max mean iso aniso Overall: 2.08 111.55 17.58 5.28 1785 0 Protein: 2.08 111.04 14.85 5.28 1519 0 Water: 4.12 111.55 33.43 N/A 258 0 Other: 17.27 37.08 24.68 N/A 8 0 Chain A: 2.08 111.55 17.58 N/A 1785 0 Histogram: Values Number of atoms 2.08 - 13.03 897 13.03 - 23.97 505 23.97 - 34.92 190 34.92 - 45.87 104 45.87 - 56.82 56 56.82 - 67.76 16 67.76 - 78.71 8 78.71 - 89.66 5 89.66 - 100.60 1 100.60 - 111.55 3 =========================== Idealize ADP of riding H ========================== r_work=0.1025 r_free=0.1805 r_work=0.1020 r_free=0.1809 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1020 r_free = 0.1809 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 = 0.1811 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.18 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= 0.1811 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.014351 | | target function (ls_wunit_k1) not normalized (work): 70.678129 | | target function (ls_wunit_k1) not normalized (free): 10.721863 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1062 0.1022 0.1811 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2129 0.2130 0.2214 n_refl.: 5177 remove outliers: r(all,work,free)=0.2129 0.2130 0.2214 n_refl.: 5177 overall B=-1.00 to atoms: r(all,work,free)=0.2086 0.2085 0.2202 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1060 0.1021 0.1795 n_refl.: 5177 remove outliers: r(all,work,free)=0.1058 0.1019 0.1795 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3446 315.412 297.170 0.637 1.007 0.365 11.894-9.307 99.02 97 4 0.1550 510.714 502.670 0.954 1.008 0.361 9.237-7.194 100.00 213 7 0.1687 417.662 416.605 0.993 1.008 0.331 7.162-5.571 100.00 427 22 0.1650 313.405 309.566 0.952 1.006 0.292 5.546-4.326 100.00 867 58 0.0922 430.260 426.992 0.970 1.004 0.222 4.315-3.360 100.00 1859 96 0.0765 409.182 409.165 1.018 0.999 0.183 3.356-3.002 100.00 1373 60 0.0998 315.169 313.829 1.000 0.995 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.4769 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1019 r_free=0.1795 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1019 r_free=0.1795 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1019 r_free=0.1795 | n_water=258 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.1045 r_free=0.1806 | n_water=248 | time (s): 20.290 (total time: 20.870) Filter (q & B) r_work=0.1045 r_free=0.1807 | n_water=245 | time (s): 1.290 (total time: 22.160) Compute maps r_work=0.1045 r_free=0.1807 | n_water=245 | time (s): 0.530 (total time: 22.690) Filter (map) r_work=0.1330 r_free=0.1897 | n_water=149 | time (s): 1.880 (total time: 24.570) Find peaks r_work=0.1330 r_free=0.1897 | n_water=149 | time (s): 0.600 (total time: 25.170) Add new water r_work=0.1694 r_free=0.2164 | n_water=240 | time (s): 1.660 (total time: 26.830) Refine new water occ: r_work=0.1151 r_free=0.1676 adp: r_work=0.1121 r_free=0.1685 occ: r_work=0.1117 r_free=0.1657 adp: r_work=0.1104 r_free=0.1670 occ: r_work=0.1104 r_free=0.1644 adp: r_work=0.1100 r_free=0.1652 ADP+occupancy (water only), MIN, final r_work=0.1100 r_free=0.1652 r_work=0.1100 r_free=0.1652 | n_water=240 | time (s): 3.360 (total time: 30.190) Filter (q & B) r_work=0.1100 r_free=0.1652 | n_water=240 | time (s): 1.100 (total time: 31.290) Filter (dist only) r_work=0.1104 r_free=0.1651 | n_water=237 | time (s): 18.160 (total time: 49.450) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.285898 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.581821 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 0.1007 0.1763 0.0755 0.009 1.0 4.2 0.5 0.0 0 11.143 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.07 17.63 7.55 4.662 16.961 2.582 0.014 9.43 17.81 8.38 5.576 17.639 2.582 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.23 17.41 6.60 1764 0 Protein: 1.25 106.23 15.70 6.58 1519 0 Water: 0.00 62.90 27.94 N/A 237 0 Other: 18.42 43.82 31.12 N/A 8 0 Chain A: 0.00 106.23 16.47 N/A 1674 0 Chain S: 4.79 59.65 34.89 N/A 90 0 Histogram: Values Number of atoms 0.00 - 10.62 595 10.62 - 21.25 719 21.25 - 31.87 234 31.87 - 42.49 119 42.49 - 53.12 53 53.12 - 63.74 27 63.74 - 74.36 9 74.36 - 84.99 3 84.99 - 95.61 3 95.61 - 106.23 2 =========================== Idealize ADP of riding H ========================== r_work=0.0943 r_free=0.1781 r_work=0.0940 r_free=0.1786 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0940 r_free = 0.1786 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0937 r_free = 0.1765 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0937 r_free= 0.1765 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011827 | | target function (ls_wunit_k1) not normalized (work): 58.235216 | | target function (ls_wunit_k1) not normalized (free): 9.968017 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0980 0.0937 0.1765 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2173 0.2177 0.2228 n_refl.: 5176 remove outliers: r(all,work,free)=0.2173 0.2177 0.2228 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2173 0.2177 0.2228 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0979 0.0937 0.1763 n_refl.: 5176 remove outliers: r(all,work,free)=0.0978 0.0935 0.1763 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 0.3038 317.473 298.405 0.673 1.008 0.360 11.894-9.307 99.02 97 4 0.1423 510.714 506.531 0.986 1.009 0.340 9.237-7.194 100.00 213 7 0.1441 417.662 417.520 1.025 1.008 0.331 7.162-5.571 100.00 427 22 0.1387 313.405 311.603 1.000 1.007 0.290 5.546-4.326 100.00 867 58 0.0790 430.260 427.940 1.016 1.004 0.240 4.315-3.360 100.00 1859 96 0.0737 409.182 409.282 1.068 0.999 0.190 3.356-3.002 100.00 1373 60 0.0969 315.169 314.072 1.052 0.995 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.9085 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0935 r_free=0.1763 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0935 r_free=0.1763 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0935 r_free=0.1763 | n_water=237 | time (s): 0.670 (total time: 0.670) Filter (dist) r_work=0.0947 r_free=0.1750 | n_water=234 | time (s): 20.340 (total time: 21.010) Filter (q & B) r_work=0.1004 r_free=0.1809 | n_water=232 | time (s): 1.900 (total time: 22.910) Compute maps r_work=0.1004 r_free=0.1809 | n_water=232 | time (s): 0.480 (total time: 23.390) Filter (map) r_work=0.1266 r_free=0.1916 | n_water=154 | time (s): 1.870 (total time: 25.260) Find peaks r_work=0.1266 r_free=0.1916 | n_water=154 | time (s): 0.610 (total time: 25.870) Add new water r_work=0.1654 r_free=0.2258 | n_water=239 | time (s): 1.850 (total time: 27.720) Refine new water occ: r_work=0.1057 r_free=0.1744 adp: r_work=0.1054 r_free=0.1750 occ: r_work=0.1041 r_free=0.1726 adp: r_work=0.1041 r_free=0.1733 occ: r_work=0.1030 r_free=0.1711 adp: r_work=0.1030 r_free=0.1718 ADP+occupancy (water only), MIN, final r_work=0.1030 r_free=0.1718 r_work=0.1030 r_free=0.1718 | n_water=239 | time (s): 10.620 (total time: 38.340) Filter (q & B) r_work=0.1030 r_free=0.1718 | n_water=239 | time (s): 0.900 (total time: 39.240) Filter (dist only) r_work=0.1035 r_free=0.1725 | n_water=238 | time (s): 17.060 (total time: 56.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.209442 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.213494 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 0.0927 0.1825 0.0898 0.012 1.1 4.8 0.5 0.6 0 0.605 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.27 18.25 8.98 5.532 18.614 0.213 5.111 8.88 18.19 9.32 7.294 18.620 0.213 5.017 Individual atomic B min max mean iso aniso Overall: 0.00 105.68 17.12 8.97 1765 0 Protein: 0.00 105.68 15.78 8.96 1519 0 Water: 0.00 57.90 25.17 N/A 238 0 Other: 18.73 43.97 32.34 N/A 8 0 Chain A: 0.00 105.68 16.53 N/A 1661 0 Chain S: 0.00 54.55 26.61 N/A 104 0 Histogram: Values Number of atoms 0.00 - 10.57 620 10.57 - 21.14 685 21.14 - 31.70 249 31.70 - 42.27 126 42.27 - 52.84 47 52.84 - 63.41 18 63.41 - 73.97 10 73.97 - 84.54 5 84.54 - 95.11 4 95.11 - 105.68 1 =========================== Idealize ADP of riding H ========================== r_work=0.0888 r_free=0.1819 r_work=0.0892 r_free=0.1825 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0892 r_free = 0.1825 target_work(ml) = 5.021 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0881 r_free = 0.1808 target_work(ml) = 5.013 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0881 r_free= 0.1808 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.013131 | | target function (ml) not normalized (work): 24679.644362 | | target function (ml) not normalized (free): 1827.684108 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0929 0.0881 0.1808 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2076 0.2084 0.2059 n_refl.: 5175 remove outliers: r(all,work,free)=0.2076 0.2084 0.2059 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2076 0.2084 0.2059 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0919 0.0872 0.1798 n_refl.: 5175 remove outliers: r(all,work,free)=0.0919 0.0872 0.1798 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 0.3649 317.473 294.526 0.602 0.993 0.330 11.894-9.307 99.02 97 4 0.1841 510.714 495.591 0.951 0.996 0.325 9.237-7.194 100.00 213 7 0.1871 417.662 409.484 1.007 0.998 0.320 7.162-5.571 100.00 427 22 0.1760 313.405 304.761 0.980 0.999 0.290 5.546-4.326 100.00 867 58 0.0909 430.260 425.194 1.009 1.001 0.248 4.315-3.360 100.00 1859 96 0.0580 409.182 408.966 1.066 1.003 0.200 3.356-3.002 100.00 1373 60 0.0586 315.169 314.918 1.050 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.0580 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0872 r_free=0.1798 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0872 r_free=0.1803 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0872 r_free=0.1803 | n_water=238 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.0878 r_free=0.1821 | n_water=236 | time (s): 19.260 (total time: 19.840) Filter (q & B) r_work=0.0976 r_free=0.1887 | n_water=233 | time (s): 1.610 (total time: 21.450) Compute maps r_work=0.0976 r_free=0.1887 | n_water=233 | time (s): 0.670 (total time: 22.120) Filter (map) r_work=0.1243 r_free=0.1918 | n_water=159 | time (s): 1.920 (total time: 24.040) Find peaks r_work=0.1243 r_free=0.1918 | n_water=159 | time (s): 0.480 (total time: 24.520) Add new water r_work=0.1576 r_free=0.2195 | n_water=238 | time (s): 1.350 (total time: 25.870) Refine new water r_work=0.1576 r_free=0.2195 | n_water=238 | time (s): 0.070 (total time: 25.940) Filter (q & B) r_work=0.1243 r_free=0.1918 | n_water=159 | time (s): 1.230 (total time: 27.170) Filter (dist only) r_work=0.1263 r_free=0.1905 | n_water=154 | time (s): 11.510 (total time: 38.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.372029 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.304178 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 0.1117 0.1988 0.0871 0.012 1.1 6.1 0.5 0.0 0 0.686 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.17 19.88 8.71 7.022 18.504 0.304 5.329 10.53 20.09 9.56 8.443 18.552 0.304 5.242 Individual atomic B min max mean iso aniso Overall: 0.00 104.99 16.79 10.53 1681 0 Protein: 0.00 104.99 15.95 10.52 1519 0 Water: 0.31 56.35 24.27 N/A 154 0 Other: 21.37 47.94 32.29 N/A 8 0 Chain A: 0.00 104.99 16.61 N/A 1646 0 Chain S: 7.52 56.35 25.34 N/A 35 0 Histogram: Values Number of atoms 0.00 - 10.50 595 10.50 - 21.00 638 21.00 - 31.50 253 31.50 - 42.00 109 42.00 - 52.50 48 52.50 - 62.99 15 62.99 - 73.49 12 73.49 - 83.99 5 83.99 - 94.49 4 94.49 - 104.99 2 =========================== Idealize ADP of riding H ========================== r_work=0.1053 r_free=0.2009 r_work=0.1059 r_free=0.2014 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1059 r_free = 0.2014 target_work(ml) = 5.246 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1058 r_free = 0.2016 target_work(ml) = 5.245 | | occupancies: max = 1.00 min = 0.18 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= 0.1058 r_free= 0.2016 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 5.244634 | | target function (ml) not normalized (work): 25819.332968 | | target function (ml) not normalized (free): 1697.597108 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1107 0.1058 0.2016 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2360 0.2361 0.2455 n_refl.: 5175 remove outliers: r(all,work,free)=0.2360 0.2361 0.2455 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2360 0.2361 0.2455 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1095 0.1044 0.2018 n_refl.: 5175 remove outliers: r(all,work,free)=0.1095 0.1044 0.2018 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 0.3712 317.473 294.653 0.639 0.998 0.340 11.894-9.307 99.02 97 4 0.1719 510.714 496.856 0.986 1.002 0.370 9.237-7.194 100.00 213 7 0.1942 417.662 410.177 1.016 1.004 0.370 7.162-5.571 100.00 427 22 0.1869 313.405 308.064 0.981 1.004 0.310 5.546-4.326 100.00 867 58 0.1088 430.260 424.648 1.001 1.003 0.280 4.315-3.360 100.00 1859 96 0.0758 409.182 407.174 1.083 1.000 0.230 3.356-3.002 100.00 1373 60 0.0823 315.169 313.283 1.085 0.998 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9038 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1044 r_free=0.2018 After: r_work=0.1047 r_free=0.2018 ================================== NQH flips ================================== r_work=0.1047 r_free=0.2018 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN Total number of N/Q/H flips: 1 r_work=0.1053 r_free=0.2021 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1053 r_free=0.2021 | n_water=154 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.1069 r_free=0.2012 | n_water=149 | time (s): 12.570 (total time: 13.090) Filter (q & B) r_work=0.1092 r_free=0.1992 | n_water=148 | time (s): 1.780 (total time: 14.870) Compute maps r_work=0.1092 r_free=0.1992 | n_water=148 | time (s): 0.570 (total time: 15.440) Filter (map) r_work=0.1153 r_free=0.1961 | n_water=133 | time (s): 1.430 (total time: 16.870) Find peaks r_work=0.1153 r_free=0.1961 | n_water=133 | time (s): 0.410 (total time: 17.280) Add new water r_work=0.1440 r_free=0.2181 | n_water=190 | time (s): 1.420 (total time: 18.700) Refine new water occ: r_work=0.1133 r_free=0.2016 adp: r_work=0.1132 r_free=0.2033 occ: r_work=0.1117 r_free=0.2016 adp: r_work=0.1119 r_free=0.2027 occ: r_work=0.1103 r_free=0.2010 adp: r_work=0.1105 r_free=0.2021 ADP+occupancy (water only), MIN, final r_work=0.1105 r_free=0.2021 r_work=0.1105 r_free=0.2021 | n_water=190 | time (s): 10.800 (total time: 29.500) Filter (q & B) r_work=0.1105 r_free=0.2023 | n_water=189 | time (s): 1.490 (total time: 30.990) Filter (dist only) r_work=0.1114 r_free=0.2022 | n_water=185 | time (s): 13.850 (total time: 44.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.149824 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.267289 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 0.1071 0.2008 0.0938 0.011 1.2 8.0 0.5 1.2 0 0.575 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.71 20.08 9.38 8.045 18.793 0.267 5.222 10.42 20.64 10.23 9.045 18.846 0.267 5.163 Individual atomic B min max mean iso aniso Overall: 0.00 103.81 17.30 11.73 1712 0 Protein: 0.00 103.81 16.18 11.72 1519 0 Water: 1.05 57.11 25.78 N/A 185 0 Other: 17.12 49.46 32.66 N/A 8 0 Chain A: 0.00 103.81 16.69 N/A 1633 0 Chain S: 4.07 57.11 29.78 N/A 79 0 Histogram: Values Number of atoms 0.00 - 10.38 591 10.38 - 20.76 620 20.76 - 31.14 284 31.14 - 41.52 120 41.52 - 51.90 54 51.90 - 62.28 16 62.28 - 72.67 13 72.67 - 83.05 7 83.05 - 93.43 4 93.43 - 103.81 3 =========================== Idealize ADP of riding H ========================== r_work=0.1042 r_free=0.2064 r_work=0.1046 r_free=0.2074 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1046 r_free = 0.2074 target_work(ml) = 5.167 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1016 r_free = 0.2033 target_work(ml) = 5.148 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.1016 r_free= 0.2033 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 5.148354 | | target function (ml) not normalized (work): 25345.347414 | | target function (ml) not normalized (free): 1759.823838 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1326 0.2074 5.5683 6.2066| | 2: 3.78 - 3.00 1.00 2430 110 0.0637 0.1964 4.7175 7.9862| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.64 1.00 0.95 12872.67| | 2: 3.78 - 3.00 2430 110 0.98 3.69 1.01 0.98 1736.40| |alpha: min = 0.94 max = 0.98 mean = 0.97| |beta: min = 1249.97 max = 20474.78 mean = 7375.79| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.85 mean = 8.22| |phase err.(test): min = 0.00 max = 87.89 mean = 8.81| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1068 0.1016 0.2033 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2322 0.2320 0.2441 n_refl.: 5175 remove outliers: r(all,work,free)=0.2322 0.2320 0.2441 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2322 0.2320 0.2441 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1061 0.1010 0.2020 n_refl.: 5175 remove outliers: r(all,work,free)=0.1061 0.1010 0.2020 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 0.3874 317.473 288.423 0.635 0.988 0.320 11.894-9.307 99.02 97 4 0.1841 510.714 498.196 1.021 0.994 0.320 9.237-7.194 100.00 213 7 0.2171 417.662 407.712 1.076 0.997 0.310 7.162-5.571 100.00 427 22 0.2060 313.405 306.077 1.042 0.998 0.300 5.546-4.326 100.00 867 58 0.1097 430.260 424.225 1.072 1.000 0.280 4.315-3.360 100.00 1859 96 0.0701 409.182 408.190 1.164 1.002 0.240 3.356-3.002 100.00 1373 60 0.0640 315.169 314.359 1.168 1.004 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-9.6177 ================= 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 : 0.3622 0.2090 0.084 5.190 8.8 119.3 19.9 258 0.000 1_bss: 0.1568 0.1665 0.084 5.190 6.1 116.5 17.1 258 0.000 1_settarget: 0.1568 0.1665 0.084 5.190 6.1 116.5 17.1 258 0.000 1_nqh: 0.1568 0.1665 0.084 5.190 6.1 116.5 17.1 258 0.000 1_weight: 0.1568 0.1665 0.084 5.190 6.1 116.5 17.1 258 0.000 1_xyzrec: 0.1164 0.1825 0.010 0.985 6.1 116.5 17.1 258 0.198 1_adp: 0.1025 0.1805 0.010 0.985 2.1 111.5 17.6 258 0.198 1_regHadp: 0.1020 0.1809 0.010 0.985 2.1 111.5 17.6 258 0.198 1_occ: 0.1022 0.1811 0.010 0.985 2.1 111.5 17.6 258 0.198 2_bss: 0.1019 0.1795 0.010 0.985 1.1 110.6 16.6 258 0.198 2_settarget: 0.1019 0.1795 0.010 0.985 1.1 110.6 16.6 258 0.198 2_updatecdl: 0.1019 0.1795 0.010 1.012 1.1 110.6 16.6 258 0.198 2_nqh: 0.1019 0.1795 0.010 1.012 1.1 110.6 16.6 258 0.198 2_sol: 0.1104 0.1651 0.010 1.012 1.0 110.0 16.1 237 n/a 2_weight: 0.1104 0.1651 0.010 1.012 1.0 110.0 16.1 237 n/a 2_xyzrec: 0.1007 0.1763 0.009 0.979 1.0 110.0 16.1 237 n/a 2_adp: 0.0943 0.1781 0.009 0.979 0.0 106.2 17.4 237 n/a 2_regHadp: 0.0940 0.1786 0.009 0.979 0.0 106.2 17.4 237 n/a 2_occ: 0.0937 0.1765 0.009 0.979 0.0 106.2 17.4 237 n/a 3_bss: 0.0935 0.1763 0.009 0.979 0.0 106.2 17.4 237 n/a 3_settarget: 0.0935 0.1763 0.009 0.979 0.0 106.2 17.4 237 n/a 3_updatecdl: 0.0935 0.1763 0.009 0.983 0.0 106.2 17.4 237 n/a 3_nqh: 0.0935 0.1763 0.009 0.983 0.0 106.2 17.4 237 n/a 3_sol: 0.1035 0.1725 0.009 0.983 1.0 106.2 17.1 238 n/a 3_weight: 0.1035 0.1725 0.009 0.983 1.0 106.2 17.1 238 n/a 3_xyzrec: 0.0927 0.1825 0.012 1.105 1.0 106.2 17.1 238 n/a 3_adp: 0.0888 0.1819 0.012 1.105 0.0 105.7 17.1 238 n/a 3_regHadp: 0.0892 0.1825 0.012 1.105 0.0 105.7 17.1 238 n/a 3_occ: 0.0881 0.1808 0.012 1.105 0.0 105.7 17.1 238 n/a 4_bss: 0.0872 0.1798 0.012 1.105 0.0 105.7 17.1 238 n/a 4_settarget: 0.0872 0.1798 0.012 1.105 0.0 105.7 17.1 238 n/a 4_updatecdl: 0.0872 0.1798 0.012 1.116 0.0 105.7 17.1 238 n/a 4_nqh: 0.0872 0.1803 0.012 1.116 0.0 105.7 17.1 238 n/a 4_sol: 0.1263 0.1905 0.012 1.116 0.0 105.7 16.7 154 n/a 4_weight: 0.1263 0.1905 0.012 1.116 0.0 105.7 16.7 154 n/a 4_xyzrec: 0.1117 0.1988 0.012 1.087 0.0 105.7 16.7 154 n/a 4_adp: 0.1053 0.2009 0.012 1.087 0.0 105.0 16.8 154 n/a 4_regHadp: 0.1059 0.2014 0.012 1.087 0.0 105.0 16.8 154 n/a 4_occ: 0.1058 0.2016 0.012 1.087 0.0 105.0 16.8 154 n/a 5_bss: 0.1044 0.2018 0.012 1.087 0.0 105.0 16.8 154 n/a 5_settarget: 0.1044 0.2018 0.012 1.087 0.0 105.0 16.8 154 n/a 5_updatecdl: 0.1044 0.2018 0.012 1.096 0.0 105.0 16.8 154 n/a 5_setrh: 0.1047 0.2018 0.012 1.096 0.0 105.0 16.8 154 n/a 5_nqh: 0.1053 0.2021 0.012 1.096 0.0 105.0 16.8 154 n/a 5_sol: 0.1114 0.2022 0.012 1.096 0.0 105.0 17.2 185 n/a 5_weight: 0.1114 0.2022 0.012 1.096 0.0 105.0 17.2 185 n/a 5_xyzrec: 0.1071 0.2008 0.011 1.185 0.0 105.0 17.2 185 n/a 5_adp: 0.1042 0.2064 0.011 1.185 0.0 103.8 17.3 185 n/a 5_regHadp: 0.1046 0.2074 0.011 1.185 0.0 103.8 17.3 185 n/a 5_occ: 0.1016 0.2033 0.011 1.185 0.0 103.8 17.3 185 n/a end: 0.1010 0.2020 0.011 1.185 0.0 103.8 17.3 185 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7718462_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7718462_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9400 Refinement macro-cycles (run) : 459.0600 Write final files (write_after_run_outputs) : 12.4300 Total : 475.4300 Total CPU time: 8.27 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:38 PST -0800 (1735492718.23 s) Start R-work = 0.1568, R-free = 0.1665 Final R-work = 0.1010, R-free = 0.2020 =============================================================================== Job complete usr+sys time: 506.33 seconds wall clock time: 8 minutes 48.91 seconds (528.91 seconds total)