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_5382129.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5382129.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5382129.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.49, per 1000 atoms: 0.44 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: 0.30 Conformation dependent library (CDL) restraints added in 126.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 485 0.90 - 1.16: 1157 1.16 - 1.41: 569 1.41 - 1.66: 886 1.66 - 1.91: 56 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 20 " pdb=" O VAL A 20 " ideal model delta sigma weight residual 1.237 0.986 0.251 1.19e-02 7.06e+03 4.45e+02 bond pdb=" C THR A 34 " pdb=" N VAL A 35 " ideal model delta sigma weight residual 1.329 1.538 -0.209 1.15e-02 7.56e+03 3.30e+02 bond pdb=" CE1 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.321 1.501 -0.180 1.00e-02 1.00e+04 3.23e+02 bond pdb=" C THR A 34 " pdb=" O THR A 34 " ideal model delta sigma weight residual 1.236 1.029 0.207 1.17e-02 7.31e+03 3.12e+02 bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.520 1.732 -0.212 1.23e-02 6.61e+03 2.96e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 3268 4.88 - 9.75: 1836 9.75 - 14.62: 581 14.62 - 19.49: 83 19.49 - 24.37: 9 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH2 ARG A 27 " ideal model delta sigma weight residual 119.20 105.62 13.58 9.00e-01 1.23e+00 2.28e+02 angle pdb=" O LEU A 82 " pdb=" C LEU A 82 " pdb=" N SER A 83 " ideal model delta sigma weight residual 122.12 137.98 -15.86 1.06e+00 8.90e-01 2.24e+02 angle pdb=" CA GLY A 40 " pdb=" C GLY A 40 " pdb=" O GLY A 40 " ideal model delta sigma weight residual 121.76 134.45 -12.69 8.70e-01 1.32e+00 2.13e+02 angle pdb=" CA BGLU A 96 " pdb=" C BGLU A 96 " pdb=" O BGLU A 96 " ideal model delta sigma weight residual 120.82 107.13 13.69 1.05e+00 9.07e-01 1.70e+02 angle pdb=" O ALA A 36 " pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 123.22 137.81 -14.59 1.14e+00 7.69e-01 1.64e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.64: 1357 20.64 - 41.28: 88 41.28 - 61.92: 31 61.92 - 82.55: 3 82.55 - 103.19: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -145.39 22.79 0 2.50e+00 1.60e-01 8.31e+01 dihedral pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual 122.80 144.44 -21.64 0 2.50e+00 1.60e-01 7.49e+01 dihedral pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CA ARG A 48 " pdb=" CB ARG A 48 " ideal model delta harmonic sigma weight residual 122.80 142.51 -19.71 0 2.50e+00 1.60e-01 6.22e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.007 - 0.228: 111 0.228 - 0.449: 71 0.449 - 0.670: 44 0.670 - 0.892: 13 0.892 - 1.113: 4 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.40 1.11 2.00e-01 2.50e+01 3.10e+01 chirality pdb=" CA ILE A 102 " pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CB ILE A 102 " both_signs ideal model delta sigma weight residual False 2.43 3.52 -1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA ARG A 48 " pdb=" N ARG A 48 " pdb=" C ARG A 48 " pdb=" CB ARG A 48 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.63e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.007 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG PHE A 164 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.112 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " -0.032 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.112 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.058 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.025 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.066 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.043 2.00e-02 2.50e+03 5.35e-02 8.59e+01 pdb=" CG BTYR A 67 " 0.073 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.025 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " -0.086 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.093 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.028 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.019 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.075 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 49 " -0.052 2.00e-02 2.50e+03 9.22e-02 8.51e+01 pdb=" C ASP A 49 " 0.160 2.00e-02 2.50e+03 pdb=" O ASP A 49 " -0.053 2.00e-02 2.50e+03 pdb=" N VAL A 50 " -0.055 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1282 2.35 - 2.91: 8208 2.91 - 3.48: 10502 3.48 - 4.04: 15144 4.04 - 4.60: 21424 Nonbonded interactions: 56560 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.788 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.795 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.820 2.100 nonbonded pdb=" H LEU A 72 " pdb=" O ALA A 103 " model vdw 1.837 2.450 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.839 2.100 ... (remaining 56555 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_5382129_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= 0.3617 r_free= 0.1982 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.472409 | | target function (ml) not normalized (work): 22048.974847 | | target function (ml) not normalized (free): 1142.903925 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3798 0.2157 4.8474 4.8942| | 2: 3.78 - 3.00 1.00 2430 110 0.3397 0.1687 4.0867 4.0721| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 6612.74| | 2: 3.78 - 3.00 2430 110 0.94 11.41 1.48 0.26 454.99| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 387.96 max = 12069.88 mean = 3577.59| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.38| |phase err.(test): min = 0.00 max = 89.93 mean = 33.21| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.258 1557 Z= 5.355 Angle : 5.248 15.864 2118 Z= 3.666 Chirality : 0.382 1.113 243 Planarity : 0.031 0.092 284 Dihedral : 14.092 103.191 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.16 % Favored : 96.76 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 32.43 % 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: -1.73 (0.51), residues: 224 helix: -1.88 (0.44), residues: 102 sheet: -2.14 (0.85), residues: 28 loop : 0.45 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.121 0.024 ARG A 48 TYR 0.089 0.028 TYR A 141 PHE 0.078 0.032 PHE A 119 HIS 0.069 0.031 HIS A 126 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= 0.3617 r_free= 0.1982 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.472409 | | target function (ml) not normalized (work): 22048.974847 | | target function (ml) not normalized (free): 1142.903925 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3572 0.3650 0.2072 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3572 0.3650 0.2072 n_refl.: 5182 remove outliers: r(all,work,free)=0.2519 0.2546 0.2072 n_refl.: 5178 overall B=-2.89 to atoms: r(all,work,free)=0.2410 0.2434 0.2020 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1565 0.1567 0.1537 n_refl.: 5178 remove outliers: r(all,work,free)=0.1561 0.1562 0.1537 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 0.3911 449.635 407.380 0.667 1.054 0.392 11.894-9.307 99.02 97 4 0.1886 714.280 693.208 0.952 1.052 0.373 9.237-7.194 100.00 213 7 0.2190 584.140 575.308 0.984 1.047 0.348 7.162-5.571 100.00 427 22 0.2291 438.326 423.497 0.943 1.037 0.294 5.546-4.326 100.00 867 58 0.1386 601.759 594.320 0.987 1.020 0.226 4.315-3.360 100.00 1859 96 0.1306 572.279 566.155 1.053 0.992 0.200 3.356-3.002 100.00 1373 60 0.1616 440.794 432.844 1.058 0.964 0.054 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6981 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1562 r_free=0.1537 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1562 r_free=0.1537 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.246652 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.071196 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 0.1154 0.1791 0.0637 0.010 1.0 3.2 0.5 0.0 0 9.623 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.54 17.91 6.37 3.013 15.966 2.071 0.018 10.15 17.78 7.63 4.937 16.139 2.071 0.014 Individual atomic B min max mean iso aniso Overall: 2.04 111.54 17.32 5.35 1785 0 Protein: 2.04 111.54 14.60 5.34 1519 0 Water: 3.97 111.41 33.12 N/A 258 0 Other: 17.37 37.86 24.27 N/A 8 0 Chain A: 2.04 111.54 17.32 N/A 1785 0 Histogram: Values Number of atoms 2.04 - 12.99 914 12.99 - 23.94 482 23.94 - 34.89 190 34.89 - 45.84 110 45.84 - 56.79 56 56.79 - 67.74 16 67.74 - 78.69 8 78.69 - 89.64 5 89.64 - 100.59 1 100.59 - 111.54 3 =========================== Idealize ADP of riding H ========================== r_work=0.1015 r_free=0.1778 r_work=0.1010 r_free=0.1780 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1010 r_free = 0.1780 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 = 0.1003 r_free = 0.1773 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.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1003 r_free= 0.1773 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013686 | | target function (ls_wunit_k1) not normalized (work): 67.391228 | | target function (ls_wunit_k1) not normalized (free): 10.432229 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1043 0.1003 0.1773 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2078 0.2075 0.2238 n_refl.: 5176 remove outliers: r(all,work,free)=0.2078 0.2075 0.2238 n_refl.: 5176 overall B=-0.94 to atoms: r(all,work,free)=0.2039 0.2034 0.2227 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1049 0.1010 0.1780 n_refl.: 5176 remove outliers: r(all,work,free)=0.1049 0.1010 0.1780 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 0.3313 331.144 323.470 0.706 0.999 0.381 11.894-9.307 99.02 97 4 0.1514 526.050 517.784 0.994 1.001 0.361 9.237-7.194 100.00 213 7 0.1631 430.204 431.486 1.028 1.002 0.310 7.162-5.571 100.00 427 22 0.1606 322.816 318.982 0.984 1.001 0.292 5.546-4.326 100.00 867 58 0.0901 443.180 439.781 0.998 1.001 0.202 4.315-3.360 100.00 1859 96 0.0767 421.469 421.403 1.040 0.999 0.193 3.356-3.002 100.00 1373 60 0.1007 324.633 322.935 1.010 0.998 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3851 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1010 r_free=0.1780 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1010 r_free=0.1780 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1010 r_free=0.1780 | n_water=258 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1039 r_free=0.1762 | n_water=248 | time (s): 22.230 (total time: 22.890) Filter (q & B) r_work=0.1039 r_free=0.1760 | n_water=245 | time (s): 1.390 (total time: 24.280) Compute maps r_work=0.1039 r_free=0.1760 | n_water=245 | time (s): 0.450 (total time: 24.730) Filter (map) r_work=0.1348 r_free=0.1823 | n_water=147 | time (s): 1.370 (total time: 26.100) Find peaks r_work=0.1348 r_free=0.1823 | n_water=147 | time (s): 0.480 (total time: 26.580) Add new water r_work=0.1701 r_free=0.2093 | n_water=234 | time (s): 1.720 (total time: 28.300) Refine new water occ: r_work=0.1140 r_free=0.1648 adp: r_work=0.1116 r_free=0.1667 occ: r_work=0.1113 r_free=0.1637 adp: r_work=0.1102 r_free=0.1653 occ: r_work=0.1102 r_free=0.1638 adp: r_work=0.1099 r_free=0.1644 ADP+occupancy (water only), MIN, final r_work=0.1099 r_free=0.1644 r_work=0.1099 r_free=0.1644 | n_water=234 | time (s): 3.980 (total time: 32.280) Filter (q & B) r_work=0.1099 r_free=0.1644 | n_water=234 | time (s): 1.120 (total time: 33.400) Filter (dist only) r_work=0.1102 r_free=0.1633 | n_water=231 | time (s): 17.700 (total time: 51.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.863403 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.884072 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 0.0989 0.1735 0.0745 0.009 1.0 3.5 0.5 0.6 0 11.432 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.89 17.35 7.45 4.694 16.696 2.884 0.013 9.23 17.88 8.65 5.527 17.146 2.884 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.64 16.64 6.65 1758 0 Protein: 0.00 106.64 15.07 6.63 1519 0 Water: 0.00 63.89 26.72 N/A 231 0 Other: 11.43 36.90 24.10 N/A 8 0 Chain A: 0.00 106.64 15.83 N/A 1672 0 Chain S: 5.64 61.04 32.42 N/A 86 0 Histogram: Values Number of atoms 0.00 - 10.66 673 10.66 - 21.33 678 21.33 - 31.99 195 31.99 - 42.66 126 42.66 - 53.32 42 53.32 - 63.98 27 63.98 - 74.65 10 74.65 - 85.31 4 85.31 - 95.98 1 95.98 - 106.64 2 =========================== Idealize ADP of riding H ========================== r_work=0.0923 r_free=0.1788 r_work=0.0921 r_free=0.1790 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0921 r_free = 0.1790 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0919 r_free = 0.1796 target_work(ls_wunit_k1) = 0.011 | | 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= 0.0919 r_free= 0.1796 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011418 | | target function (ls_wunit_k1) not normalized (work): 56.223640 | | target function (ls_wunit_k1) not normalized (free): 9.672103 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0963 0.0919 0.1796 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2090 0.2097 0.2124 n_refl.: 5176 remove outliers: r(all,work,free)=0.2090 0.2097 0.2124 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2090 0.2097 0.2124 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0962 0.0918 0.1797 n_refl.: 5176 remove outliers: r(all,work,free)=0.0960 0.0916 0.1797 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 0.3289 328.356 313.080 0.678 1.006 0.364 11.894-9.307 99.02 97 4 0.1356 526.050 522.778 0.992 1.007 0.360 9.237-7.194 100.00 213 7 0.1393 430.204 431.326 1.022 1.007 0.304 7.162-5.571 100.00 427 22 0.1383 322.816 319.949 0.994 1.006 0.290 5.546-4.326 100.00 867 58 0.0782 443.180 439.970 1.004 1.004 0.220 4.315-3.360 100.00 1859 96 0.0708 421.469 421.360 1.056 1.000 0.210 3.356-3.002 100.00 1373 60 0.0948 324.633 323.834 1.030 0.996 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-4.1544 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0916 r_free=0.1797 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=0.0917 r_free=0.1801 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0917 r_free=0.1801 | n_water=231 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.0931 r_free=0.1780 | n_water=227 | time (s): 18.120 (total time: 18.590) Filter (q & B) r_work=0.0992 r_free=0.1790 | n_water=225 | time (s): 1.260 (total time: 19.850) Compute maps r_work=0.0992 r_free=0.1790 | n_water=225 | time (s): 0.490 (total time: 20.340) Filter (map) r_work=0.1249 r_free=0.1814 | n_water=154 | time (s): 1.640 (total time: 21.980) Find peaks r_work=0.1249 r_free=0.1814 | n_water=154 | time (s): 0.520 (total time: 22.500) Add new water r_work=0.1645 r_free=0.2150 | n_water=236 | time (s): 1.400 (total time: 23.900) Refine new water occ: r_work=0.1060 r_free=0.1801 adp: r_work=0.1054 r_free=0.1803 occ: r_work=0.1042 r_free=0.1790 adp: r_work=0.1042 r_free=0.1794 occ: r_work=0.1032 r_free=0.1778 adp: r_work=0.1031 r_free=0.1782 ADP+occupancy (water only), MIN, final r_work=0.1031 r_free=0.1782 r_work=0.1031 r_free=0.1782 | n_water=236 | time (s): 19.080 (total time: 42.980) Filter (q & B) r_work=0.1031 r_free=0.1782 | n_water=236 | time (s): 0.830 (total time: 43.810) Filter (dist only) r_work=0.1048 r_free=0.1796 | n_water=233 | time (s): 17.900 (total time: 61.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.082738 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.239591 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 0.0946 0.1830 0.0883 0.010 1.0 2.9 0.5 0.6 0 0.541 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.46 18.30 8.83 5.522 17.889 0.240 5.166 9.00 18.37 9.37 7.278 17.858 0.240 5.065 Individual atomic B min max mean iso aniso Overall: 0.00 106.36 16.43 8.98 1760 0 Protein: 0.00 106.36 15.14 8.95 1519 0 Water: 0.00 58.89 24.58 N/A 233 0 Other: 9.40 40.08 25.21 N/A 8 0 Chain A: 0.00 106.36 15.82 N/A 1656 0 Chain S: 0.00 57.62 26.19 N/A 104 0 Histogram: Values Number of atoms 0.00 - 10.64 681 10.64 - 21.27 654 21.27 - 31.91 220 31.91 - 42.55 131 42.55 - 53.18 37 53.18 - 63.82 19 63.82 - 74.46 10 74.46 - 85.09 3 85.09 - 95.73 4 95.73 - 106.36 1 =========================== Idealize ADP of riding H ========================== r_work=0.0900 r_free=0.1837 r_work=0.0905 r_free=0.1840 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0905 r_free = 0.1840 target_work(ml) = 5.068 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0895 r_free = 0.1822 target_work(ml) = 5.063 | | 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= 0.0895 r_free= 0.1822 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.062899 | | target function (ml) not normalized (work): 24924.653572 | | target function (ml) not normalized (free): 1854.116768 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0942 0.0895 0.1822 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2099 0.2110 0.2088 n_refl.: 5175 remove outliers: r(all,work,free)=0.2099 0.2110 0.2088 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2099 0.2110 0.2088 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0932 0.0886 0.1815 n_refl.: 5175 remove outliers: r(all,work,free)=0.0930 0.0884 0.1815 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 0.3722 330.539 292.580 0.587 0.993 0.340 11.894-9.307 99.02 97 4 0.1820 526.050 512.230 0.954 0.997 0.320 9.237-7.194 100.00 213 7 0.1899 430.204 421.644 1.008 0.999 0.300 7.162-5.571 100.00 427 22 0.1849 322.816 313.372 0.978 1.000 0.290 5.546-4.326 100.00 867 58 0.0906 443.180 438.599 1.006 1.001 0.217 4.315-3.360 100.00 1859 96 0.0581 421.469 421.187 1.064 1.003 0.213 3.356-3.002 100.00 1373 60 0.0599 324.633 324.277 1.043 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.8107 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0884 r_free=0.1815 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0884 r_free=0.1815 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0884 r_free=0.1815 | n_water=233 | time (s): 0.480 (total time: 0.480) Filter (dist) r_work=0.0896 r_free=0.1820 | n_water=230 | time (s): 18.120 (total time: 18.600) Filter (q & B) r_work=0.0957 r_free=0.1858 | n_water=228 | time (s): 1.470 (total time: 20.070) Compute maps r_work=0.0957 r_free=0.1858 | n_water=228 | time (s): 0.600 (total time: 20.670) Filter (map) r_work=0.1236 r_free=0.1873 | n_water=154 | time (s): 1.520 (total time: 22.190) Find peaks r_work=0.1236 r_free=0.1873 | n_water=154 | time (s): 0.390 (total time: 22.580) Add new water r_work=0.1559 r_free=0.2148 | n_water=228 | time (s): 1.370 (total time: 23.950) Refine new water occ: r_work=0.1019 r_free=0.1812 adp: r_work=0.1014 r_free=0.1821 occ: r_work=0.1005 r_free=0.1801 adp: r_work=0.1005 r_free=0.1813 occ: r_work=0.0997 r_free=0.1791 adp: r_work=0.0997 r_free=0.1803 ADP+occupancy (water only), MIN, final r_work=0.0997 r_free=0.1803 r_work=0.0997 r_free=0.1803 | n_water=228 | time (s): 11.520 (total time: 35.470) Filter (q & B) r_work=0.0998 r_free=0.1802 | n_water=227 | time (s): 1.490 (total time: 36.960) Filter (dist only) r_work=0.1007 r_free=0.1796 | n_water=224 | time (s): 17.840 (total time: 54.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.023464 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.226045 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 0.0907 0.1870 0.0962 0.010 1.0 4.2 0.5 0.6 0 0.512 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.07 18.70 9.62 6.992 17.928 0.226 5.052 8.85 18.91 10.06 8.159 17.996 0.226 4.982 Individual atomic B min max mean iso aniso Overall: 0.00 106.19 16.57 10.59 1751 0 Protein: 0.00 106.19 15.46 10.57 1519 0 Water: 0.00 53.89 23.73 N/A 224 0 Other: 12.41 39.90 26.36 N/A 8 0 Chain A: 0.00 106.19 16.01 N/A 1641 0 Chain S: 0.00 52.16 24.87 N/A 110 0 Histogram: Values Number of atoms 0.00 - 10.62 666 10.62 - 21.24 646 21.24 - 31.86 235 31.86 - 42.48 120 42.48 - 53.09 46 53.09 - 63.71 17 63.71 - 74.33 12 74.33 - 84.95 4 84.95 - 95.57 4 95.57 - 106.19 1 =========================== Idealize ADP of riding H ========================== r_work=0.0885 r_free=0.1891 r_work=0.0889 r_free=0.1892 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0889 r_free = 0.1892 target_work(ml) = 4.986 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0877 r_free = 0.1879 target_work(ml) = 4.977 | | occupancies: max = 1.00 min = 0.22 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= 0.0877 r_free= 0.1879 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.977034 | | target function (ml) not normalized (work): 24496.961784 | | target function (ml) not normalized (free): 2182.555811 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0929 0.0877 0.1879 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2083 0.2083 0.2191 n_refl.: 5174 remove outliers: r(all,work,free)=0.2083 0.2083 0.2191 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2083 0.2083 0.2191 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0927 0.0875 0.1881 n_refl.: 5174 remove outliers: r(all,work,free)=0.0927 0.0875 0.1881 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 0.3836 330.539 297.886 0.575 0.986 0.318 11.894-9.307 99.02 97 4 0.1856 526.050 511.253 0.959 0.991 0.316 9.237-7.194 100.00 213 7 0.2014 430.204 420.156 1.014 0.994 0.302 7.162-5.571 100.00 427 22 0.1964 322.816 312.539 0.993 0.996 0.300 5.546-4.326 100.00 867 58 0.0988 443.180 437.955 1.017 0.999 0.230 4.315-3.360 100.00 1859 96 0.0564 421.469 421.186 1.083 1.002 0.220 3.356-3.002 100.00 1373 60 0.0455 324.633 324.528 1.063 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.6695 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0875 r_free=0.1881 After: r_work=0.0878 r_free=0.1880 ================================== NQH flips ================================== r_work=0.0878 r_free=0.1880 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0880 r_free=0.1877 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0880 r_free=0.1877 | n_water=224 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.0884 r_free=0.1879 | n_water=222 | time (s): 16.090 (total time: 16.630) Filter (q & B) r_work=0.1020 r_free=0.1919 | n_water=217 | time (s): 1.420 (total time: 18.050) Compute maps r_work=0.1020 r_free=0.1919 | n_water=217 | time (s): 0.560 (total time: 18.610) Filter (map) r_work=0.1257 r_free=0.1954 | n_water=152 | time (s): 1.230 (total time: 19.840) Find peaks r_work=0.1257 r_free=0.1954 | n_water=152 | time (s): 0.410 (total time: 20.250) Add new water r_work=0.1551 r_free=0.2194 | n_water=219 | time (s): 1.350 (total time: 21.600) Refine new water occ: r_work=0.1025 r_free=0.1881 adp: r_work=0.1018 r_free=0.1898 occ: r_work=0.1011 r_free=0.1874 adp: r_work=0.1009 r_free=0.1888 occ: r_work=0.1004 r_free=0.1863 adp: r_work=0.1002 r_free=0.1876 ADP+occupancy (water only), MIN, final r_work=0.1002 r_free=0.1876 r_work=0.1002 r_free=0.1876 | n_water=219 | time (s): 12.340 (total time: 33.940) Filter (q & B) r_work=0.1002 r_free=0.1876 | n_water=219 | time (s): 1.140 (total time: 35.080) Filter (dist only) r_work=0.0999 r_free=0.1867 | n_water=216 | time (s): 16.710 (total time: 51.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.979001 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.218123 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 0.0939 0.1880 0.0941 0.010 1.1 7.7 0.5 0.6 0 0.490 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.39 18.80 9.41 8.059 18.201 0.218 5.079 9.13 18.57 9.44 8.974 18.326 0.218 5.020 Individual atomic B min max mean iso aniso Overall: 0.00 108.75 16.88 11.83 1743 0 Protein: 0.00 108.75 15.89 11.81 1519 0 Water: 0.64 63.80 23.51 N/A 216 0 Other: 8.75 35.54 25.03 N/A 8 0 Chain A: 0.00 108.75 16.35 N/A 1631 0 Chain S: 0.64 63.80 24.55 N/A 112 0 Histogram: Values Number of atoms 0.00 - 10.88 655 10.88 - 21.75 653 21.75 - 32.63 233 32.63 - 43.50 123 43.50 - 54.38 39 54.38 - 65.25 18 65.25 - 76.13 12 76.13 - 87.00 4 87.00 - 97.88 4 97.88 - 108.75 2 =========================== Idealize ADP of riding H ========================== r_work=0.0913 r_free=0.1857 r_work=0.0916 r_free=0.1858 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0916 r_free = 0.1858 target_work(ml) = 5.024 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0910 r_free = 0.1849 target_work(ml) = 5.021 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0910 r_free= 0.1849 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.020715 | | target function (ml) not normalized (work): 24711.957965 | | target function (ml) not normalized (free): 1991.055738 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1267 0.1864 5.5582 6.1554| | 2: 3.78 - 3.00 1.00 2430 110 0.0473 0.1826 4.4696 10.154| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.98 13132.81| | 2: 3.78 - 3.00 2430 110 0.99 2.31 1.00 1.00 1123.81| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 736.64 max = 21570.85 mean = 7203.95| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.83 mean = 7.30| |phase err.(test): min = 0.00 max = 88.38 mean = 7.68| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0957 0.0910 0.1849 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2158 0.2163 0.2201 n_refl.: 5174 remove outliers: r(all,work,free)=0.2158 0.2163 0.2201 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2158 0.2163 0.2201 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0956 0.0909 0.1852 n_refl.: 5174 remove outliers: r(all,work,free)=0.0956 0.0909 0.1852 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 0.3854 330.539 299.260 0.611 0.984 0.317 11.894-9.307 99.02 97 4 0.1840 526.050 511.553 1.008 0.991 0.316 9.237-7.194 100.00 213 7 0.2129 430.204 419.848 1.051 0.995 0.300 7.162-5.571 100.00 427 22 0.1967 322.816 313.686 1.040 0.996 0.300 5.546-4.326 100.00 867 58 0.1041 443.180 437.157 1.064 0.999 0.236 4.315-3.360 100.00 1859 96 0.0600 421.469 421.350 1.146 1.002 0.231 3.356-3.002 100.00 1373 60 0.0467 324.633 325.160 1.127 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.4173 ================= 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 : 0.3617 0.1982 0.081 5.248 8.8 119.3 19.9 258 0.000 1_bss: 0.1562 0.1537 0.081 5.248 6.0 116.4 17.0 258 0.000 1_settarget: 0.1562 0.1537 0.081 5.248 6.0 116.4 17.0 258 0.000 1_nqh: 0.1562 0.1537 0.081 5.248 6.0 116.4 17.0 258 0.000 1_weight: 0.1562 0.1537 0.081 5.248 6.0 116.4 17.0 258 0.000 1_xyzrec: 0.1154 0.1791 0.010 0.981 6.0 116.4 17.0 258 0.204 1_adp: 0.1015 0.1778 0.010 0.981 2.0 111.5 17.3 258 0.204 1_regHadp: 0.1010 0.1780 0.010 0.981 2.0 111.5 17.3 258 0.204 1_occ: 0.1003 0.1773 0.010 0.981 2.0 111.5 17.3 258 0.204 2_bss: 0.1010 0.1780 0.010 0.981 1.1 110.6 16.4 258 0.204 2_settarget: 0.1010 0.1780 0.010 0.981 1.1 110.6 16.4 258 0.204 2_updatecdl: 0.1010 0.1780 0.010 1.005 1.1 110.6 16.4 258 0.204 2_nqh: 0.1010 0.1780 0.010 1.005 1.1 110.6 16.4 258 0.204 2_sol: 0.1102 0.1633 0.010 1.005 1.1 110.6 15.8 231 n/a 2_weight: 0.1102 0.1633 0.010 1.005 1.1 110.6 15.8 231 n/a 2_xyzrec: 0.0989 0.1735 0.009 0.967 1.1 110.6 15.8 231 n/a 2_adp: 0.0923 0.1788 0.009 0.967 0.0 106.6 16.6 231 n/a 2_regHadp: 0.0921 0.1790 0.009 0.967 0.0 106.6 16.6 231 n/a 2_occ: 0.0919 0.1796 0.009 0.967 0.0 106.6 16.6 231 n/a 3_bss: 0.0916 0.1797 0.009 0.967 0.0 106.6 16.6 231 n/a 3_settarget: 0.0916 0.1797 0.009 0.967 0.0 106.6 16.6 231 n/a 3_updatecdl: 0.0916 0.1797 0.009 0.970 0.0 106.6 16.6 231 n/a 3_nqh: 0.0917 0.1801 0.009 0.970 0.0 106.6 16.6 231 n/a 3_sol: 0.1048 0.1796 0.009 0.970 0.0 106.6 16.5 233 n/a 3_weight: 0.1048 0.1796 0.009 0.970 0.0 106.6 16.5 233 n/a 3_xyzrec: 0.0946 0.1830 0.010 1.045 0.0 106.6 16.5 233 n/a 3_adp: 0.0900 0.1837 0.010 1.045 0.0 106.4 16.4 233 n/a 3_regHadp: 0.0905 0.1840 0.010 1.045 0.0 106.4 16.4 233 n/a 3_occ: 0.0895 0.1822 0.010 1.045 0.0 106.4 16.4 233 n/a 4_bss: 0.0884 0.1815 0.010 1.045 0.0 106.4 16.4 233 n/a 4_settarget: 0.0884 0.1815 0.010 1.045 0.0 106.4 16.4 233 n/a 4_updatecdl: 0.0884 0.1815 0.010 1.061 0.0 106.4 16.4 233 n/a 4_nqh: 0.0884 0.1815 0.010 1.061 0.0 106.4 16.4 233 n/a 4_sol: 0.1007 0.1796 0.010 1.061 0.0 106.4 16.4 224 n/a 4_weight: 0.1007 0.1796 0.010 1.061 0.0 106.4 16.4 224 n/a 4_xyzrec: 0.0907 0.1870 0.010 1.041 0.0 106.4 16.4 224 n/a 4_adp: 0.0885 0.1891 0.010 1.041 0.0 106.2 16.6 224 n/a 4_regHadp: 0.0889 0.1892 0.010 1.041 0.0 106.2 16.6 224 n/a 4_occ: 0.0877 0.1879 0.010 1.041 0.0 106.2 16.6 224 n/a 5_bss: 0.0875 0.1881 0.010 1.041 0.0 106.2 16.6 224 n/a 5_settarget: 0.0875 0.1881 0.010 1.041 0.0 106.2 16.6 224 n/a 5_updatecdl: 0.0875 0.1881 0.010 1.041 0.0 106.2 16.6 224 n/a 5_setrh: 0.0878 0.1880 0.010 1.041 0.0 106.2 16.6 224 n/a 5_nqh: 0.0880 0.1877 0.010 1.041 0.0 106.2 16.6 224 n/a 5_sol: 0.0999 0.1867 0.010 1.041 0.0 106.2 16.6 216 n/a 5_weight: 0.0999 0.1867 0.010 1.041 0.0 106.2 16.6 216 n/a 5_xyzrec: 0.0939 0.1880 0.010 1.099 0.0 106.2 16.6 216 n/a 5_adp: 0.0913 0.1857 0.010 1.099 0.0 108.7 16.9 216 n/a 5_regHadp: 0.0916 0.1858 0.010 1.099 0.0 108.7 16.9 216 n/a 5_occ: 0.0910 0.1849 0.010 1.099 0.0 108.7 16.9 216 n/a end: 0.0909 0.1852 0.010 1.099 0.0 108.7 16.9 216 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5382129_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5382129_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9100 Refinement macro-cycles (run) : 483.6600 Write final files (write_after_run_outputs) : 10.4700 Total : 498.0400 Total CPU time: 8.65 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:00 PST -0800 (1735492740.91 s) Start R-work = 0.1562, R-free = 0.1537 Final R-work = 0.0909, R-free = 0.1852 =============================================================================== Job complete usr+sys time: 526.10 seconds wall clock time: 9 minutes 8.68 seconds (548.68 seconds total)