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_2514713.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_2514713.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2514713.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 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.59, per 1000 atoms: 0.47 Number of scatterers: 3381 At special positions: 0 Unit cell: (75.227, 75.227, 75.227, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 O1- 2 9.00 O 551 8.00 N 265 7.00 C 957 6.00 H 1596 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 122.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.67 - 0.92: 565 0.92 - 1.17: 1086 1.17 - 1.42: 642 1.42 - 1.67: 817 1.67 - 1.92: 43 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 40 " pdb=" CA GLY A 40 " ideal model delta sigma weight residual 1.444 1.695 -0.251 1.38e-02 5.25e+03 3.31e+02 bond pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.337 1.529 -0.193 1.11e-02 8.12e+03 3.01e+02 bond pdb=" N ASP A 49 " pdb=" CA ASP A 49 " ideal model delta sigma weight residual 1.459 1.235 0.224 1.32e-02 5.74e+03 2.88e+02 bond pdb=" C THR A 125 " pdb=" O THR A 125 " ideal model delta sigma weight residual 1.233 1.043 0.190 1.17e-02 7.31e+03 2.65e+02 bond pdb=" N ALA A 178 " pdb=" CA ALA A 178 " ideal model delta sigma weight residual 1.459 1.652 -0.193 1.21e-02 6.83e+03 2.53e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 3049 4.68 - 9.35: 1933 9.35 - 14.03: 681 14.03 - 18.71: 104 18.71 - 23.38: 10 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ALA A 179 " pdb=" C ALA A 179 " pdb=" O ALA A 179 " ideal model delta sigma weight residual 120.55 138.65 -18.10 1.06e+00 8.90e-01 2.92e+02 angle pdb=" O ALA A 111 " pdb=" C ALA A 111 " pdb=" N LEU A 112 " ideal model delta sigma weight residual 122.12 136.63 -14.51 1.06e+00 8.90e-01 1.87e+02 angle pdb=" O ALA A 61 " pdb=" C ALA A 61 " pdb=" N LYS A 62 " ideal model delta sigma weight residual 122.33 140.46 -18.13 1.34e+00 5.57e-01 1.83e+02 angle pdb=" CA ALA A 179 " pdb=" C ALA A 179 " pdb=" N GLN A 180 " ideal model delta sigma weight residual 117.30 102.08 15.22 1.16e+00 7.43e-01 1.72e+02 angle pdb=" CA ALA A 178 " pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 120.55 106.79 13.76 1.06e+00 8.90e-01 1.68e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 1275 16.43 - 32.87: 150 32.87 - 49.30: 40 49.30 - 65.73: 13 65.73 - 82.16: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ARG A 156 " pdb=" N ARG A 156 " pdb=" CA ARG A 156 " pdb=" CB ARG A 156 " ideal model delta harmonic sigma weight residual -122.60 -144.90 22.30 0 2.50e+00 1.60e-01 7.96e+01 dihedral pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CA ARG A 156 " pdb=" CB ARG A 156 " ideal model delta harmonic sigma weight residual 122.80 144.57 -21.77 0 2.50e+00 1.60e-01 7.58e+01 dihedral pdb=" N ARG A 27 " pdb=" C ARG A 27 " pdb=" CA ARG A 27 " pdb=" CB ARG A 27 " ideal model delta harmonic sigma weight residual 122.80 143.34 -20.54 0 2.50e+00 1.60e-01 6.75e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.251: 103 0.251 - 0.500: 86 0.500 - 0.750: 42 0.750 - 0.999: 9 0.999 - 1.248: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 178 " pdb=" N ALA A 178 " pdb=" C ALA A 178 " pdb=" CB ALA A 178 " both_signs ideal model delta sigma weight residual False 2.48 3.73 -1.25 2.00e-01 2.50e+01 3.90e+01 chirality pdb=" CA ARG A 156 " pdb=" N ARG A 156 " pdb=" C ARG A 156 " pdb=" CB ARG A 156 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.19 2.00e-01 2.50e+01 3.53e+01 chirality pdb=" CA BGLU A 94 " pdb=" N BGLU A 94 " pdb=" C BGLU A 94 " pdb=" CB BGLU A 94 " both_signs ideal model delta sigma weight residual False 2.51 3.51 -1.00 2.00e-01 2.50e+01 2.50e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.095 2.00e-02 2.50e+03 6.85e-02 1.41e+02 pdb=" CG PHE A 119 " -0.147 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.092 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.042 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.072 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.001 2.00e-02 2.50e+03 5.66e-02 9.60e+01 pdb=" CG BTYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.023 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.073 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.114 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.080 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.062 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.068 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.004 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.044 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.071 2.00e-02 2.50e+03 5.58e-02 9.33e+01 pdb=" CG PHE A 162 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " 0.082 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " -0.052 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " 0.105 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " -0.035 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.049 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " 0.012 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " -0.063 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.28: 782 2.28 - 2.86: 7820 2.86 - 3.44: 10665 3.44 - 4.02: 15303 4.02 - 4.60: 22068 Nonbonded interactions: 56638 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.700 2.100 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.806 2.100 nonbonded pdb=" O VAL A 8 " pdb=" H ALA A 36 " model vdw 1.822 2.450 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.833 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.839 2.100 ... (remaining 56633 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_2514713_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= 0.3619 r_free= 0.1996 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468075 | | target function (ml) not normalized (work): 22027.612186 | | target function (ml) not normalized (free): 1151.797488 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3796 0.2168 4.8506 4.9122| | 2: 3.78 - 3.00 1.00 2430 110 0.3403 0.1704 4.0745 4.1297| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.64 0.83 0.13 6588.19| | 2: 3.78 - 3.00 2430 110 0.93 11.52 1.48 0.26 450.08| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 384.51 max = 12042.48 mean = 3562.71| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.97 mean = 30.35| |phase err.(test): min = 0.00 max = 89.97 mean = 33.13| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.251 1557 Z= 5.405 Angle : 5.461 18.127 2118 Z= 3.839 Chirality : 0.407 1.248 243 Planarity : 0.033 0.095 284 Dihedral : 13.777 82.164 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.16 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 37.84 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.46), residues: 224 helix: -2.69 (0.38), residues: 109 sheet: -1.93 (0.70), residues: 30 loop : -0.19 (0.57), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.029 ARG A 5 TYR 0.078 0.038 TYR A 139 PHE 0.145 0.050 PHE A 119 HIS 0.079 0.041 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3619 r_free= 0.1996 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468075 | | target function (ml) not normalized (work): 22027.612186 | | target function (ml) not normalized (free): 1151.797488 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3573 0.3650 0.2112 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3573 0.3650 0.2112 n_refl.: 5182 remove outliers: r(all,work,free)=0.2521 0.2546 0.2112 n_refl.: 5178 overall B=-2.94 to atoms: r(all,work,free)=0.2406 0.2427 0.2062 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1561 0.1560 0.1595 n_refl.: 5178 remove outliers: r(all,work,free)=0.1557 0.1555 0.1595 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3902 449.783 409.492 0.664 1.068 0.397 11.894-9.307 99.02 97 4 0.1872 714.516 697.139 0.943 1.064 0.372 9.237-7.194 100.00 213 7 0.2188 584.332 575.633 0.966 1.057 0.352 7.162-5.571 100.00 427 22 0.2334 438.470 423.350 0.938 1.045 0.291 5.546-4.326 100.00 867 58 0.1362 601.958 594.800 0.982 1.024 0.248 4.315-3.360 100.00 1859 96 0.1308 572.468 566.077 1.059 0.990 0.190 3.356-3.002 100.00 1373 60 0.1590 440.939 432.319 1.068 0.955 0.097 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9555 b_overall=-3.7645 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1555 r_free=0.1595 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=0.1556 r_free=0.1591 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.550937 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.043863 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1162 0.1781 0.0618 0.010 1.0 3.2 0.5 0.0 0 9.775 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 17.81 6.18 3.013 15.917 2.044 0.018 10.18 17.78 7.59 4.930 16.105 2.044 0.014 Individual atomic B min max mean iso aniso Overall: 1.75 111.37 17.30 5.34 1785 0 Protein: 1.75 111.37 14.58 5.33 1519 0 Water: 3.92 111.36 33.13 N/A 258 0 Other: 16.14 35.24 23.44 N/A 8 0 Chain A: 1.75 111.37 17.30 N/A 1785 0 Histogram: Values Number of atoms 1.75 - 12.71 893 12.71 - 23.68 501 23.68 - 34.64 194 34.64 - 45.60 109 45.60 - 56.56 54 56.56 - 67.52 17 67.52 - 78.48 8 78.48 - 89.45 5 89.45 - 100.41 1 100.41 - 111.37 3 =========================== Idealize ADP of riding H ========================== r_work=0.1018 r_free=0.1778 r_work=0.1013 r_free=0.1783 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1013 r_free = 0.1783 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1007 r_free = 0.1778 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1007 r_free= 0.1778 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.013828 | | target function (ls_wunit_k1) not normalized (work): 68.089059 | | target function (ls_wunit_k1) not normalized (free): 10.327894 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1047 0.1007 0.1778 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2079 0.2075 0.2254 n_refl.: 5176 remove outliers: r(all,work,free)=0.2079 0.2075 0.2254 n_refl.: 5176 overall B=-0.94 to atoms: r(all,work,free)=0.2040 0.2035 0.2241 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1051 0.1011 0.1782 n_refl.: 5176 remove outliers: r(all,work,free)=0.1051 0.1011 0.1782 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 0.3305 331.689 323.134 0.704 1.000 0.381 11.894-9.307 99.02 97 4 0.1516 526.914 519.267 0.989 1.002 0.361 9.237-7.194 100.00 213 7 0.1627 430.911 431.714 1.026 1.002 0.316 7.162-5.571 100.00 427 22 0.1605 323.346 320.330 0.984 1.002 0.302 5.546-4.326 100.00 867 58 0.0908 443.909 439.875 0.996 1.001 0.232 4.315-3.360 100.00 1859 96 0.0770 422.162 422.217 1.042 1.000 0.193 3.356-3.002 100.00 1373 60 0.1004 325.167 323.490 1.007 0.999 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3763 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1011 r_free=0.1782 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1011 r_free=0.1782 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1011 r_free=0.1782 | n_water=258 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.1043 r_free=0.1770 | n_water=246 | time (s): 21.060 (total time: 21.550) Filter (q & B) r_work=0.1043 r_free=0.1772 | n_water=243 | time (s): 1.280 (total time: 22.830) Compute maps r_work=0.1043 r_free=0.1772 | n_water=243 | time (s): 0.580 (total time: 23.410) Filter (map) r_work=0.1361 r_free=0.1806 | n_water=141 | time (s): 1.590 (total time: 25.000) Find peaks r_work=0.1361 r_free=0.1806 | n_water=141 | time (s): 0.400 (total time: 25.400) Add new water r_work=0.1739 r_free=0.2136 | n_water=232 | time (s): 1.340 (total time: 26.740) Refine new water occ: r_work=0.1161 r_free=0.1724 adp: r_work=0.1131 r_free=0.1735 occ: r_work=0.1129 r_free=0.1700 adp: r_work=0.1116 r_free=0.1706 occ: r_work=0.1115 r_free=0.1694 adp: r_work=0.1112 r_free=0.1699 ADP+occupancy (water only), MIN, final r_work=0.1112 r_free=0.1699 r_work=0.1112 r_free=0.1699 | n_water=232 | time (s): 3.750 (total time: 30.490) Filter (q & B) r_work=0.1112 r_free=0.1699 | n_water=232 | time (s): 1.170 (total time: 31.660) Filter (dist only) r_work=0.1116 r_free=0.1694 | n_water=230 | time (s): 19.300 (total time: 50.960) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.321151 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.856655 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 0.1002 0.1792 0.0790 0.009 1.0 3.8 0.5 0.6 0 11.161 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.02 17.92 7.90 4.685 16.685 2.857 0.013 9.36 18.15 8.78 5.447 17.075 2.857 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.13 16.53 6.49 1757 0 Protein: 0.00 108.13 14.90 6.47 1519 0 Water: 0.00 62.70 26.97 N/A 230 0 Other: 13.03 39.14 25.35 N/A 8 0 Chain A: 0.00 108.13 15.65 N/A 1666 0 Chain S: 0.00 58.64 32.54 N/A 91 0 Histogram: Values Number of atoms 0.00 - 10.81 702 10.81 - 21.63 649 21.63 - 32.44 212 32.44 - 43.25 109 43.25 - 54.07 45 54.07 - 64.88 25 64.88 - 75.69 8 75.69 - 86.51 3 86.51 - 97.32 2 97.32 - 108.13 2 =========================== Idealize ADP of riding H ========================== r_work=0.0936 r_free=0.1815 r_work=0.0934 r_free=0.1820 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0934 r_free = 0.1820 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0931 r_free = 0.1822 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 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= 0.0931 r_free= 0.1822 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011774 | | target function (ls_wunit_k1) not normalized (work): 57.973562 | | target function (ls_wunit_k1) not normalized (free): 10.225239 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0976 0.0931 0.1822 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2106 0.2110 0.2191 n_refl.: 5176 remove outliers: r(all,work,free)=0.2106 0.2110 0.2191 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2106 0.2110 0.2191 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0977 0.0933 0.1818 n_refl.: 5176 remove outliers: r(all,work,free)=0.0975 0.0931 0.1818 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 0.3230 328.895 316.117 0.676 1.006 0.364 11.894-9.307 99.02 97 4 0.1427 526.914 521.712 0.991 1.007 0.360 9.237-7.194 100.00 213 7 0.1465 430.911 430.977 1.021 1.007 0.300 7.162-5.571 100.00 427 22 0.1403 323.346 320.688 0.990 1.006 0.290 5.546-4.326 100.00 867 58 0.0794 443.909 440.895 1.006 1.004 0.250 4.315-3.360 100.00 1859 96 0.0717 422.162 422.121 1.057 1.000 0.210 3.356-3.002 100.00 1373 60 0.0962 325.167 324.396 1.028 0.997 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.1657 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0931 r_free=0.1819 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A Total number of N/Q/H flips: 2 r_work=0.0934 r_free=0.1819 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0934 r_free=0.1819 | n_water=230 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.0961 r_free=0.1811 | n_water=223 | time (s): 17.800 (total time: 18.290) Filter (q & B) r_work=0.1033 r_free=0.1834 | n_water=219 | time (s): 1.530 (total time: 19.820) Compute maps r_work=0.1033 r_free=0.1834 | n_water=219 | time (s): 0.650 (total time: 20.470) Filter (map) r_work=0.1305 r_free=0.1818 | n_water=145 | time (s): 1.910 (total time: 22.380) Find peaks r_work=0.1305 r_free=0.1818 | n_water=145 | time (s): 0.590 (total time: 22.970) Add new water r_work=0.1714 r_free=0.2209 | n_water=235 | time (s): 1.440 (total time: 24.410) Refine new water occ: r_work=0.1075 r_free=0.1824 adp: r_work=0.1071 r_free=0.1830 occ: r_work=0.1057 r_free=0.1804 adp: r_work=0.1058 r_free=0.1807 occ: r_work=0.1049 r_free=0.1791 adp: r_work=0.1049 r_free=0.1790 ADP+occupancy (water only), MIN, final r_work=0.1049 r_free=0.1790 r_work=0.1049 r_free=0.1790 | n_water=235 | time (s): 12.280 (total time: 36.690) Filter (q & B) r_work=0.1050 r_free=0.1787 | n_water=233 | time (s): 1.160 (total time: 37.850) Filter (dist only) r_work=0.1060 r_free=0.1790 | n_water=231 | time (s): 19.010 (total time: 56.860) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.144523 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.234038 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 0.0940 0.1816 0.0876 0.011 1.1 4.2 0.5 0.6 0 0.572 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.40 18.16 8.76 5.416 17.708 0.234 5.168 8.97 18.46 9.49 7.265 17.722 0.234 5.074 Individual atomic B min max mean iso aniso Overall: 0.00 107.54 16.33 8.96 1758 0 Protein: 0.00 107.54 15.05 8.96 1519 0 Water: 0.00 60.33 24.43 N/A 231 0 Other: 12.06 38.44 25.33 N/A 8 0 Chain A: 0.00 107.54 15.75 N/A 1652 0 Chain S: 0.00 60.33 25.34 N/A 106 0 Histogram: Values Number of atoms 0.00 - 10.75 688 10.75 - 21.51 656 21.51 - 32.26 223 32.26 - 43.01 125 43.01 - 53.77 31 53.77 - 64.52 17 64.52 - 75.28 10 75.28 - 86.03 3 86.03 - 96.78 4 96.78 - 107.54 1 =========================== Idealize ADP of riding H ========================== r_work=0.0897 r_free=0.1846 r_work=0.0902 r_free=0.1856 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0902 r_free = 0.1856 target_work(ml) = 5.078 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0894 r_free = 0.1848 target_work(ml) = 5.073 | | occupancies: max = 1.00 min = 0.23 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= 0.0894 r_free= 0.1848 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.072810 | | target function (ml) not normalized (work): 24973.445643 | | target function (ml) not normalized (free): 1834.744097 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0943 0.0894 0.1848 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2136 0.2143 0.2181 n_refl.: 5175 remove outliers: r(all,work,free)=0.2136 0.2143 0.2181 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2136 0.2143 0.2181 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0936 0.0888 0.1832 n_refl.: 5175 remove outliers: r(all,work,free)=0.0934 0.0886 0.1832 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3450 331.083 300.145 0.601 0.996 0.340 11.894-9.307 99.02 97 4 0.1742 526.914 514.597 0.950 0.999 0.324 9.237-7.194 100.00 213 7 0.1885 430.911 425.901 1.000 1.000 0.295 7.162-5.571 100.00 427 22 0.1882 323.346 315.237 0.973 1.001 0.276 5.546-4.326 100.00 867 58 0.0904 443.909 438.658 0.996 1.002 0.230 4.315-3.360 100.00 1859 96 0.0589 422.162 421.605 1.055 1.002 0.220 3.356-3.002 100.00 1373 60 0.0617 325.167 324.425 1.029 1.003 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.2594 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0886 r_free=0.1832 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0886 r_free=0.1832 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0886 r_free=0.1832 | n_water=231 | time (s): 0.570 (total time: 0.570) Filter (dist) r_work=0.0902 r_free=0.1823 | n_water=227 | time (s): 19.410 (total time: 19.980) Filter (q & B) r_work=0.0931 r_free=0.1837 | n_water=226 | time (s): 1.370 (total time: 21.350) Compute maps r_work=0.0931 r_free=0.1837 | n_water=226 | time (s): 0.460 (total time: 21.810) Filter (map) r_work=0.1223 r_free=0.1892 | n_water=161 | time (s): 1.260 (total time: 23.070) Find peaks r_work=0.1223 r_free=0.1892 | n_water=161 | time (s): 0.440 (total time: 23.510) Add new water r_work=0.1560 r_free=0.2134 | n_water=239 | time (s): 1.460 (total time: 24.970) Refine new water occ: r_work=0.0994 r_free=0.1869 adp: r_work=0.0992 r_free=0.1878 occ: r_work=0.0982 r_free=0.1859 adp: r_work=0.0982 r_free=0.1869 occ: r_work=0.0972 r_free=0.1849 adp: r_work=0.0972 r_free=0.1859 ADP+occupancy (water only), MIN, final r_work=0.0972 r_free=0.1859 r_work=0.0972 r_free=0.1859 | n_water=239 | time (s): 12.200 (total time: 37.170) Filter (q & B) r_work=0.0972 r_free=0.1857 | n_water=238 | time (s): 1.960 (total time: 39.130) Filter (dist only) r_work=0.0978 r_free=0.1873 | n_water=236 | time (s): 18.240 (total time: 57.370) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.997230 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.236515 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 0.0890 0.1889 0.0999 0.011 1.0 5.1 0.5 0.6 0 0.499 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.90 18.89 9.99 6.978 17.908 0.237 5.021 8.68 19.10 10.43 8.116 18.014 0.237 4.959 Individual atomic B min max mean iso aniso Overall: 0.00 107.76 16.65 10.57 1763 0 Protein: 0.00 107.76 15.46 10.58 1519 0 Water: 0.00 56.78 23.96 N/A 236 0 Other: 12.41 41.09 26.99 N/A 8 0 Chain A: 0.00 107.76 16.04 N/A 1644 0 Chain S: 0.93 56.78 25.02 N/A 119 0 Histogram: Values Number of atoms 0.00 - 10.78 658 10.78 - 21.55 673 21.55 - 32.33 239 32.33 - 43.10 112 43.10 - 53.88 46 53.88 - 64.65 14 64.65 - 75.43 12 75.43 - 86.21 3 86.21 - 96.98 4 96.98 - 107.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.0868 r_free=0.1910 r_work=0.0873 r_free=0.1910 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0873 r_free = 0.1910 target_work(ml) = 4.965 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0861 r_free = 0.1900 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0861 r_free= 0.1900 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.957084 | | target function (ml) not normalized (work): 24398.767717 | | target function (ml) not normalized (free): 2132.292787 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0914 0.0861 0.1900 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2066 0.2061 0.2278 n_refl.: 5174 remove outliers: r(all,work,free)=0.2066 0.2061 0.2278 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2066 0.2061 0.2278 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0915 0.0862 0.1906 n_refl.: 5174 remove outliers: r(all,work,free)=0.0915 0.0862 0.1906 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3691 331.083 302.756 0.607 0.988 0.340 11.894-9.307 99.02 97 4 0.1794 526.914 513.074 0.958 0.992 0.333 9.237-7.194 100.00 213 7 0.2115 430.911 421.565 0.998 0.995 0.294 7.162-5.571 100.00 427 22 0.1997 323.346 314.482 0.981 0.997 0.271 5.546-4.326 100.00 867 58 0.0949 443.909 438.452 1.008 0.999 0.225 4.315-3.360 100.00 1859 96 0.0550 422.162 421.349 1.070 1.002 0.220 3.356-3.002 100.00 1373 60 0.0441 325.167 325.028 1.044 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.9499 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0862 r_free=0.1906 After: r_work=0.0864 r_free=0.1906 ================================== NQH flips ================================== r_work=0.0864 r_free=0.1906 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0864 r_free=0.1906 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0864 r_free=0.1906 | n_water=236 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.0875 r_free=0.1890 | n_water=232 | time (s): 19.560 (total time: 20.200) Filter (q & B) r_work=0.0977 r_free=0.1890 | n_water=229 | time (s): 1.780 (total time: 21.980) Compute maps r_work=0.0977 r_free=0.1890 | n_water=229 | time (s): 0.620 (total time: 22.600) Filter (map) r_work=0.1245 r_free=0.1937 | n_water=162 | time (s): 1.830 (total time: 24.430) Find peaks r_work=0.1245 r_free=0.1937 | n_water=162 | time (s): 0.490 (total time: 24.920) Add new water r_work=0.1526 r_free=0.2226 | n_water=231 | time (s): 1.450 (total time: 26.370) Refine new water occ: r_work=0.0990 r_free=0.1867 adp: r_work=0.0981 r_free=0.1886 occ: r_work=0.0974 r_free=0.1868 adp: r_work=0.0974 r_free=0.1878 occ: r_work=0.0969 r_free=0.1860 adp: r_work=0.0968 r_free=0.1872 ADP+occupancy (water only), MIN, final r_work=0.0968 r_free=0.1872 r_work=0.0968 r_free=0.1872 | n_water=231 | time (s): 13.710 (total time: 40.080) Filter (q & B) r_work=0.0969 r_free=0.1871 | n_water=229 | time (s): 1.680 (total time: 41.760) Filter (dist only) r_work=0.0969 r_free=0.1871 | n_water=229 | time (s): 17.430 (total time: 59.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.058403 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.229816 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 0.0906 0.1891 0.0985 0.011 1.2 8.3 0.5 0.6 0 0.529 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.06 18.91 9.85 8.048 18.240 0.230 5.016 8.84 19.14 10.30 8.881 18.345 0.230 4.960 Individual atomic B min max mean iso aniso Overall: 0.00 108.42 16.89 11.78 1756 0 Protein: 0.00 108.42 15.84 11.79 1519 0 Water: 0.00 59.92 23.50 N/A 229 0 Other: 13.99 39.25 26.31 N/A 8 0 Chain A: 0.00 108.42 16.30 N/A 1634 0 Chain S: 0.00 59.92 24.77 N/A 122 0 Histogram: Values Number of atoms 0.00 - 10.84 658 10.84 - 21.68 657 21.68 - 32.53 249 32.53 - 43.37 107 43.37 - 54.21 46 54.21 - 65.05 16 65.05 - 75.89 12 75.89 - 86.73 5 86.73 - 97.58 4 97.58 - 108.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.0884 r_free=0.1914 r_work=0.0887 r_free=0.1914 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0887 r_free = 0.1914 target_work(ml) = 4.965 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0881 r_free = 0.1904 target_work(ml) = 4.960 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0881 r_free= 0.1904 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.960433 | | target function (ml) not normalized (work): 24415.250302 | | target function (ml) not normalized (free): 2258.711786 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1254 0.1862 5.5403 6.249| | 2: 3.78 - 3.00 1.00 2430 110 0.0427 0.1976 4.3658 12.467| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.92 12.17 1.00 0.99 13324.21| | 2: 3.78 - 3.00 2430 110 0.99 1.91 1.00 1.01 919.99| |alpha: min = 0.97 max = 1.01 mean = 1.00| |beta: min = 587.99 max = 22326.31 mean = 7200.22| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.71 mean = 7.10| |phase err.(test): min = 0.00 max = 89.53 mean = 7.91| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0933 0.0881 0.1904 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2101 0.2101 0.2223 n_refl.: 5174 remove outliers: r(all,work,free)=0.2101 0.2101 0.2223 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2101 0.2101 0.2223 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0931 0.0880 0.1891 n_refl.: 5174 remove outliers: r(all,work,free)=0.0931 0.0880 0.1891 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3778 331.083 301.607 0.582 0.989 0.320 11.894-9.307 99.02 97 4 0.1821 526.914 508.470 0.959 0.994 0.320 9.237-7.194 100.00 213 7 0.2197 430.911 421.843 0.999 0.997 0.293 7.162-5.571 100.00 427 22 0.2072 323.346 313.209 0.985 0.998 0.273 5.546-4.326 100.00 867 58 0.1001 443.909 437.789 1.024 1.000 0.229 4.315-3.360 100.00 1859 96 0.0563 422.162 421.893 1.095 1.003 0.227 3.356-3.002 100.00 1373 60 0.0404 325.167 325.453 1.072 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.1268 ================= 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 : 0.3619 0.1996 0.082 5.461 8.8 119.3 19.9 258 0.000 1_bss: 0.1555 0.1595 0.082 5.461 5.9 116.4 16.9 258 0.000 1_settarget: 0.1555 0.1595 0.082 5.461 5.9 116.4 16.9 258 0.000 1_nqh: 0.1556 0.1591 0.082 5.461 5.9 116.4 16.9 258 0.003 1_weight: 0.1556 0.1591 0.082 5.461 5.9 116.4 16.9 258 0.003 1_xyzrec: 0.1162 0.1781 0.010 0.997 5.9 116.4 16.9 258 0.197 1_adp: 0.1018 0.1778 0.010 0.997 1.8 111.4 17.3 258 0.197 1_regHadp: 0.1013 0.1783 0.010 0.997 1.8 111.4 17.3 258 0.197 1_occ: 0.1007 0.1778 0.010 0.997 1.8 111.4 17.3 258 0.197 2_bss: 0.1011 0.1782 0.010 0.997 0.8 110.4 16.4 258 0.197 2_settarget: 0.1011 0.1782 0.010 0.997 0.8 110.4 16.4 258 0.197 2_updatecdl: 0.1011 0.1782 0.010 1.023 0.8 110.4 16.4 258 0.197 2_nqh: 0.1011 0.1782 0.010 1.023 0.8 110.4 16.4 258 0.197 2_sol: 0.1116 0.1694 0.010 1.023 0.8 110.4 15.8 230 n/a 2_weight: 0.1116 0.1694 0.010 1.023 0.8 110.4 15.8 230 n/a 2_xyzrec: 0.1002 0.1792 0.009 0.965 0.8 110.4 15.8 230 n/a 2_adp: 0.0936 0.1815 0.009 0.965 0.0 108.1 16.5 230 n/a 2_regHadp: 0.0934 0.1820 0.009 0.965 0.0 108.1 16.5 230 n/a 2_occ: 0.0931 0.1822 0.009 0.965 0.0 108.1 16.5 230 n/a 3_bss: 0.0931 0.1819 0.009 0.965 0.0 108.1 16.5 230 n/a 3_settarget: 0.0931 0.1819 0.009 0.965 0.0 108.1 16.5 230 n/a 3_updatecdl: 0.0931 0.1819 0.009 0.968 0.0 108.1 16.5 230 n/a 3_nqh: 0.0934 0.1819 0.009 0.968 0.0 108.1 16.5 230 n/a 3_sol: 0.1060 0.1790 0.009 0.968 0.0 108.1 16.3 231 n/a 3_weight: 0.1060 0.1790 0.009 0.968 0.0 108.1 16.3 231 n/a 3_xyzrec: 0.0940 0.1816 0.011 1.063 0.0 108.1 16.3 231 n/a 3_adp: 0.0897 0.1846 0.011 1.063 0.0 107.5 16.3 231 n/a 3_regHadp: 0.0902 0.1856 0.011 1.063 0.0 107.5 16.3 231 n/a 3_occ: 0.0894 0.1848 0.011 1.063 0.0 107.5 16.3 231 n/a 4_bss: 0.0886 0.1832 0.011 1.063 0.0 107.5 16.3 231 n/a 4_settarget: 0.0886 0.1832 0.011 1.063 0.0 107.5 16.3 231 n/a 4_updatecdl: 0.0886 0.1832 0.011 1.073 0.0 107.5 16.3 231 n/a 4_nqh: 0.0886 0.1832 0.011 1.073 0.0 107.5 16.3 231 n/a 4_sol: 0.0978 0.1873 0.011 1.073 0.0 107.5 16.4 236 n/a 4_weight: 0.0978 0.1873 0.011 1.073 0.0 107.5 16.4 236 n/a 4_xyzrec: 0.0890 0.1889 0.011 1.035 0.0 107.5 16.4 236 n/a 4_adp: 0.0868 0.1910 0.011 1.035 0.0 107.8 16.6 236 n/a 4_regHadp: 0.0873 0.1910 0.011 1.035 0.0 107.8 16.6 236 n/a 4_occ: 0.0861 0.1900 0.011 1.035 0.0 107.8 16.6 236 n/a 5_bss: 0.0862 0.1906 0.011 1.035 0.0 107.8 16.6 236 n/a 5_settarget: 0.0862 0.1906 0.011 1.035 0.0 107.8 16.6 236 n/a 5_updatecdl: 0.0862 0.1906 0.011 1.043 0.0 107.8 16.6 236 n/a 5_setrh: 0.0864 0.1906 0.011 1.043 0.0 107.8 16.6 236 n/a 5_nqh: 0.0864 0.1906 0.011 1.043 0.0 107.8 16.6 236 n/a 5_sol: 0.0969 0.1871 0.011 1.043 0.0 107.8 16.7 229 n/a 5_weight: 0.0969 0.1871 0.011 1.043 0.0 107.8 16.7 229 n/a 5_xyzrec: 0.0906 0.1891 0.011 1.163 0.0 107.8 16.7 229 n/a 5_adp: 0.0884 0.1914 0.011 1.163 0.0 108.4 16.9 229 n/a 5_regHadp: 0.0887 0.1914 0.011 1.163 0.0 108.4 16.9 229 n/a 5_occ: 0.0881 0.1904 0.011 1.163 0.0 108.4 16.9 229 n/a end: 0.0880 0.1891 0.011 1.163 0.0 108.4 16.9 229 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2514713_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2514713_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8400 Refinement macro-cycles (run) : 496.9400 Write final files (write_after_run_outputs) : 8.6100 Total : 509.3900 Total CPU time: 8.86 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:12 PST -0800 (1735492752.37 s) Start R-work = 0.1555, R-free = 0.1595 Final R-work = 0.0880, R-free = 0.1891 =============================================================================== Job complete usr+sys time: 538.47 seconds wall clock time: 9 minutes 20.22 seconds (560.22 seconds total)