Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5352376.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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5352376.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5352376.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" } 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: 1.91, per 1000 atoms: 0.56 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: 0.59 Conformation dependent library (CDL) restraints added in 125.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.92: 575 0.92 - 1.18: 1088 1.18 - 1.45: 716 1.45 - 1.71: 753 1.71 - 1.97: 21 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.539 1.411 0.128 5.40e-03 3.43e+04 5.60e+02 bond pdb=" CA THR A 125 " pdb=" C THR A 125 " ideal model delta sigma weight residual 1.523 1.778 -0.255 1.24e-02 6.50e+03 4.23e+02 bond pdb=" N LEU A 72 " pdb=" CA LEU A 72 " ideal model delta sigma weight residual 1.463 1.683 -0.220 1.08e-02 8.57e+03 4.16e+02 bond pdb=" C LEU A 38 " pdb=" O LEU A 38 " ideal model delta sigma weight residual 1.236 1.469 -0.233 1.16e-02 7.43e+03 4.04e+02 bond pdb=" C ILE A 9 " pdb=" O ILE A 9 " ideal model delta sigma weight residual 1.237 1.033 0.204 1.10e-02 8.26e+03 3.44e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 2950 4.24 - 8.47: 1875 8.47 - 12.71: 757 12.71 - 16.94: 167 16.94 - 21.18: 28 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O LYS A 89 " pdb=" C LYS A 89 " pdb=" N BGLU A 90 " ideal model delta sigma weight residual 122.09 137.17 -15.08 1.04e+00 9.25e-01 2.10e+02 angle pdb=" O LEU A 92 " pdb=" C LEU A 92 " pdb=" N BLYS A 93 " ideal model delta sigma weight residual 122.15 138.02 -15.87 1.14e+00 7.69e-01 1.94e+02 angle pdb=" O ILE A 21 " pdb=" C ILE A 21 " pdb=" N PRO A 22 " ideal model delta sigma weight residual 120.42 129.31 -8.89 6.40e-01 2.44e+00 1.93e+02 angle pdb=" O ILE A 152 " pdb=" C ILE A 152 " pdb=" N BLEU A 153 " ideal model delta sigma weight residual 122.99 108.81 14.18 1.07e+00 8.73e-01 1.76e+02 angle pdb=" O BLYS A 132 " pdb=" C BLYS A 132 " pdb=" N MET A 133 " ideal model delta sigma weight residual 122.15 136.49 -14.34 1.14e+00 7.69e-01 1.58e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.33: 1318 18.33 - 36.66: 118 36.66 - 54.98: 36 54.98 - 73.31: 8 73.31 - 91.64: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C AGLU A 64 " pdb=" N AGLU A 64 " pdb=" CA AGLU A 64 " pdb=" CB AGLU A 64 " ideal model delta harmonic sigma weight residual -122.60 -141.99 19.39 0 2.50e+00 1.60e-01 6.02e+01 dihedral pdb=" N AGLU A 64 " pdb=" C AGLU A 64 " pdb=" CA AGLU A 64 " pdb=" CB AGLU A 64 " ideal model delta harmonic sigma weight residual 122.80 141.06 -18.26 0 2.50e+00 1.60e-01 5.33e+01 dihedral pdb=" N VAL A 50 " pdb=" C VAL A 50 " pdb=" CA VAL A 50 " pdb=" CB VAL A 50 " ideal model delta harmonic sigma weight residual 123.40 140.79 -17.39 0 2.50e+00 1.60e-01 4.84e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.197: 107 0.197 - 0.392: 61 0.392 - 0.587: 46 0.587 - 0.782: 20 0.782 - 0.977: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA AGLU A 64 " pdb=" N AGLU A 64 " pdb=" C AGLU A 64 " pdb=" CB AGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" CA GLU A 163 " pdb=" N GLU A 163 " pdb=" C GLU A 163 " pdb=" CB GLU A 163 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.97e+01 chirality pdb=" CB VAL A 8 " pdb=" CA VAL A 8 " pdb=" CG1 VAL A 8 " pdb=" CG2 VAL A 8 " both_signs ideal model delta sigma weight residual False -2.63 -1.78 -0.85 2.00e-01 2.50e+01 1.82e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.072 2.00e-02 2.50e+03 5.84e-02 1.02e+02 pdb=" CG PHE A 119 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.087 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.086 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.091 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.082 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.024 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " -0.037 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.024 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.040 2.00e-02 2.50e+03 5.68e-02 9.67e+01 pdb=" CG TYR A 139 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.084 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.084 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.013 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.088 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.062 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.005 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.046 2.00e-02 2.50e+03 5.34e-02 8.55e+01 pdb=" CG ATYR A 67 " 0.019 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.083 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " 0.057 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.075 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.025 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.038 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.084 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.004 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 1151 2.33 - 2.90: 8199 2.90 - 3.47: 10484 3.47 - 4.03: 15169 4.03 - 4.60: 21583 Nonbonded interactions: 56586 Sorted by model distance: nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.768 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.799 2.100 nonbonded pdb=" HB3 LYS A 188 " pdb=" HE2 LYS A 188 " model vdw 1.808 2.440 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.815 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.821 2.100 ... (remaining 56581 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_5352376_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= 0.2046 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.470405 | | target function (ml) not normalized (work): 22039.095085 | | target function (ml) not normalized (free): 1154.305560 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2255 4.8535 4.9121| | 2: 3.78 - 3.00 1.00 2430 110 0.3395 0.1692 4.0763 4.1526| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.91 0.83 0.13 6615.73| | 2: 3.78 - 3.00 2430 110 0.94 11.39 1.48 0.26 449.47| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 381.01 max = 12080.43 mean = 3576.37| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.41| |phase err.(test): min = 0.00 max = 89.94 mean = 33.53| |-----------------------------------------------------------------------------| ----------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 0.255 1557 Z= 5.584 Angle : 5.278 20.057 2118 Z= 3.756 Chirality : 0.368 0.977 243 Planarity : 0.030 0.080 284 Dihedral : 13.689 91.641 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 4.97 % Favored : 93.79 % Cbeta Deviations : 27.03 % 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: -2.80 (0.44), residues: 224 helix: -2.46 (0.36), residues: 108 sheet: -1.01 (0.72), residues: 38 loop : -0.95 (0.56), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.082 0.019 ARG A 27 TYR 0.085 0.033 TYR A 139 PHE 0.108 0.042 PHE A 119 HIS 0.053 0.025 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= 0.2046 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.470405 | | target function (ml) not normalized (work): 22039.095085 | | target function (ml) not normalized (free): 1154.305560 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3576 0.3651 0.2139 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3576 0.3651 0.2139 n_refl.: 5182 remove outliers: r(all,work,free)=0.2528 0.2551 0.2139 n_refl.: 5178 overall B=-2.46 to atoms: r(all,work,free)=0.2434 0.2454 0.2102 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1568 0.1564 0.1647 n_refl.: 5178 remove outliers: r(all,work,free)=0.1563 0.1558 0.1647 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 97.87 87 5 0.3898 444.286 404.628 0.607 1.089 0.381 11.894-9.307 99.02 97 4 0.1818 714.717 694.988 0.888 1.085 0.381 9.237-7.194 100.00 213 7 0.2146 584.496 578.793 0.926 1.075 0.354 7.162-5.571 100.00 427 22 0.2295 438.593 424.373 0.895 1.059 0.304 5.546-4.326 100.00 867 58 0.1388 602.127 594.830 0.939 1.032 0.229 4.315-3.360 100.00 1859 96 0.1320 572.629 566.089 1.025 0.987 0.197 3.356-3.002 100.00 1373 60 0.1592 441.063 433.082 1.058 0.942 0.054 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9177 b_overall=-4.2510 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1558 r_free=0.1647 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A A 80 GLN B Total number of N/Q/H flips: 2 r_work=0.1558 r_free=0.1641 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.499425 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.635851 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 0.1151 0.1763 0.0612 0.010 1.0 2.6 0.5 0.0 0 9.750 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.51 17.63 6.12 3.013 16.397 1.636 0.018 10.12 17.71 7.59 4.814 16.620 1.636 0.014 Individual atomic B min max mean iso aniso Overall: 2.66 111.84 17.85 5.16 1785 0 Protein: 2.66 111.63 15.16 5.16 1519 0 Water: 4.40 111.84 33.43 N/A 258 0 Other: 17.49 35.43 24.56 N/A 8 0 Chain A: 2.66 111.84 17.85 N/A 1785 0 Histogram: Values Number of atoms 2.66 - 13.58 912 13.58 - 24.50 492 24.50 - 35.42 187 35.42 - 46.33 110 46.33 - 57.25 50 57.25 - 68.17 17 68.17 - 79.09 8 79.09 - 90.00 5 90.00 - 100.92 1 100.92 - 111.84 3 =========================== Idealize ADP of riding H ========================== r_work=0.1012 r_free=0.1771 r_work=0.1004 r_free=0.1777 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1004 r_free = 0.1777 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 = 0.0997 r_free = 0.1761 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0997 r_free= 0.1761 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013671 | | target function (ls_wunit_k1) not normalized (work): 67.302028 | | target function (ls_wunit_k1) not normalized (free): 10.136766 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1036 0.0997 0.1761 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2019 0.2011 0.2247 n_refl.: 5175 remove outliers: r(all,work,free)=0.2019 0.2011 0.2247 n_refl.: 5175 overall B=-1.07 to atoms: r(all,work,free)=0.1976 0.1966 0.2234 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1043 0.1005 0.1769 n_refl.: 5175 remove outliers: r(all,work,free)=0.1043 0.1005 0.1769 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 0.3239 313.858 297.957 0.659 1.009 0.360 11.894-9.307 99.02 97 4 0.1549 504.898 497.350 0.988 1.011 0.356 9.237-7.194 100.00 213 7 0.1655 412.906 413.906 1.027 1.010 0.320 7.162-5.571 100.00 427 22 0.1604 309.836 306.453 0.987 1.008 0.302 5.546-4.326 100.00 867 58 0.0892 425.361 422.884 1.001 1.004 0.207 4.315-3.360 100.00 1859 96 0.0766 404.523 404.316 1.050 0.998 0.194 3.356-3.002 100.00 1373 60 0.0996 311.581 309.873 1.030 0.991 0.041 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.8460 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1005 r_free=0.1769 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN B Total number of N/Q/H flips: 1 r_work=0.1005 r_free=0.1771 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1005 r_free=0.1771 | n_water=258 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.1030 r_free=0.1766 | n_water=248 | time (s): 18.960 (total time: 19.520) Filter (q & B) r_work=0.1031 r_free=0.1767 | n_water=245 | time (s): 1.900 (total time: 21.420) Compute maps r_work=0.1031 r_free=0.1767 | n_water=245 | time (s): 0.640 (total time: 22.060) Filter (map) r_work=0.1336 r_free=0.1871 | n_water=146 | time (s): 1.730 (total time: 23.790) Find peaks r_work=0.1336 r_free=0.1871 | n_water=146 | time (s): 0.400 (total time: 24.190) Add new water r_work=0.1689 r_free=0.2148 | n_water=235 | time (s): 1.870 (total time: 26.060) Refine new water occ: r_work=0.1147 r_free=0.1633 adp: r_work=0.1118 r_free=0.1654 occ: r_work=0.1115 r_free=0.1625 adp: r_work=0.1102 r_free=0.1643 occ: r_work=0.1101 r_free=0.1628 adp: r_work=0.1098 r_free=0.1634 ADP+occupancy (water only), MIN, final r_work=0.1098 r_free=0.1634 r_work=0.1098 r_free=0.1634 | n_water=235 | time (s): 6.720 (total time: 32.780) Filter (q & B) r_work=0.1098 r_free=0.1634 | n_water=235 | time (s): 0.870 (total time: 33.650) Filter (dist only) r_work=0.1104 r_free=0.1648 | n_water=231 | time (s): 17.730 (total time: 51.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.393423 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.696006 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 0.0993 0.1785 0.0792 0.009 1.0 4.5 0.5 0.0 0 12.197 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.93 17.85 7.92 4.617 17.128 2.696 0.013 9.27 17.90 8.62 5.347 17.450 2.696 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.41 16.77 6.31 1758 0 Protein: 0.00 106.41 15.15 6.29 1519 0 Water: 0.00 63.05 26.91 N/A 231 0 Other: 20.86 42.54 30.26 N/A 8 0 Chain A: 0.00 106.41 15.92 N/A 1670 0 Chain S: 2.63 58.39 32.93 N/A 88 0 Histogram: Values Number of atoms 0.00 - 10.64 652 10.64 - 21.28 686 21.28 - 31.92 217 31.92 - 42.56 119 42.56 - 53.20 42 53.20 - 63.84 28 63.84 - 74.48 7 74.48 - 85.12 3 85.12 - 95.77 2 95.77 - 106.41 2 =========================== Idealize ADP of riding H ========================== r_work=0.0927 r_free=0.1790 r_work=0.0925 r_free=0.1790 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0925 r_free = 0.1790 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0922 r_free = 0.1789 target_work(ls_wunit_k1) = 0.011 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0922 r_free= 0.1789 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011450 | | target function (ls_wunit_k1) not normalized (work): 56.369079 | | target function (ls_wunit_k1) not normalized (free): 9.820020 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0966 0.0922 0.1789 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2035 0.2033 0.2165 n_refl.: 5175 remove outliers: r(all,work,free)=0.2035 0.2033 0.2165 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2035 0.2033 0.2165 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0966 0.0922 0.1794 n_refl.: 5175 remove outliers: r(all,work,free)=0.0966 0.0922 0.1794 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 0.3158 313.858 298.071 0.661 1.010 0.350 11.894-9.307 99.02 97 4 0.1479 504.898 500.361 0.985 1.012 0.340 9.237-7.194 100.00 213 7 0.1461 412.906 414.299 1.020 1.012 0.305 7.162-5.571 100.00 427 22 0.1368 309.836 307.289 0.992 1.010 0.300 5.546-4.326 100.00 867 58 0.0790 425.361 423.087 1.008 1.005 0.240 4.315-3.360 100.00 1859 96 0.0721 404.523 403.958 1.059 0.998 0.200 3.356-3.002 100.00 1373 60 0.0930 311.581 310.540 1.043 0.990 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.3669 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0922 r_free=0.1794 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B A 80 GLN A Total number of N/Q/H flips: 3 r_work=0.0924 r_free=0.1797 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0924 r_free=0.1797 | n_water=231 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.0939 r_free=0.1799 | n_water=228 | time (s): 18.440 (total time: 19.060) Filter (q & B) r_work=0.1001 r_free=0.1810 | n_water=226 | time (s): 1.810 (total time: 20.870) Compute maps r_work=0.1001 r_free=0.1810 | n_water=226 | time (s): 0.510 (total time: 21.380) Filter (map) r_work=0.1234 r_free=0.1923 | n_water=160 | time (s): 1.350 (total time: 22.730) Find peaks r_work=0.1234 r_free=0.1923 | n_water=160 | time (s): 0.520 (total time: 23.250) Add new water r_work=0.1554 r_free=0.2213 | n_water=233 | time (s): 1.510 (total time: 24.760) Refine new water occ: r_work=0.1037 r_free=0.1733 adp: r_work=0.1030 r_free=0.1750 occ: r_work=0.1020 r_free=0.1726 adp: r_work=0.1019 r_free=0.1738 occ: r_work=0.1009 r_free=0.1715 adp: r_work=0.1008 r_free=0.1725 ADP+occupancy (water only), MIN, final r_work=0.1008 r_free=0.1725 r_work=0.1008 r_free=0.1725 | n_water=233 | time (s): 12.160 (total time: 36.920) Filter (q & B) r_work=0.1008 r_free=0.1725 | n_water=233 | time (s): 0.680 (total time: 37.600) Filter (dist only) r_work=0.1015 r_free=0.1737 | n_water=232 | time (s): 17.080 (total time: 54.680) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.081847 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.220662 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 0.0916 0.1781 0.0865 0.011 1.1 4.8 0.5 0.0 0 0.541 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.16 17.81 8.65 5.313 18.009 0.221 5.102 8.72 17.85 9.13 7.089 18.006 0.221 5.009 Individual atomic B min max mean iso aniso Overall: 0.00 104.89 16.61 8.74 1759 0 Protein: 0.00 104.89 15.25 8.72 1519 0 Water: 0.00 58.05 24.90 N/A 232 0 Other: 21.66 47.50 33.42 N/A 8 0 Chain A: 0.00 104.89 15.99 N/A 1662 0 Chain S: 0.00 55.00 27.17 N/A 97 0 Histogram: Values Number of atoms 0.00 - 10.49 645 10.49 - 20.98 669 20.98 - 31.47 229 31.47 - 41.95 131 41.95 - 52.44 45 52.44 - 62.93 22 62.93 - 73.42 9 73.42 - 83.91 4 83.91 - 94.40 3 94.40 - 104.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.0872 r_free=0.1785 r_work=0.0876 r_free=0.1793 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0876 r_free = 0.1793 target_work(ml) = 5.011 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0866 r_free = 0.1769 target_work(ml) = 5.005 | | occupancies: max = 1.00 min = 0.20 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= 0.0866 r_free= 0.1769 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.004524 | | target function (ml) not normalized (work): 24637.273029 | | target function (ml) not normalized (free): 1778.702431 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0912 0.0866 0.1769 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2044 0.2046 0.2142 n_refl.: 5175 remove outliers: r(all,work,free)=0.2044 0.2046 0.2142 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2044 0.2046 0.2142 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0906 0.0860 0.1777 n_refl.: 5175 remove outliers: r(all,work,free)=0.0906 0.0860 0.1777 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 0.3560 313.858 289.250 0.606 0.993 0.330 11.894-9.307 99.02 97 4 0.1747 504.898 492.673 0.963 0.996 0.330 9.237-7.194 100.00 213 7 0.1780 412.906 407.240 1.002 0.998 0.310 7.162-5.571 100.00 427 22 0.1716 309.836 301.532 0.980 0.999 0.300 5.546-4.326 100.00 867 58 0.0891 425.361 421.237 0.998 1.000 0.248 4.315-3.360 100.00 1859 96 0.0573 404.523 403.707 1.050 1.002 0.210 3.356-3.002 100.00 1373 60 0.0613 311.581 311.385 1.032 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-6.2585 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0860 r_free=0.1777 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0860 r_free=0.1777 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0860 r_free=0.1777 | n_water=232 | time (s): 0.700 (total time: 0.700) Filter (dist) r_work=0.0874 r_free=0.1783 | n_water=229 | time (s): 17.950 (total time: 18.650) Filter (q & B) r_work=0.0948 r_free=0.1834 | n_water=225 | time (s): 1.650 (total time: 20.300) Compute maps r_work=0.0948 r_free=0.1834 | n_water=225 | time (s): 0.660 (total time: 20.960) Filter (map) r_work=0.1201 r_free=0.1903 | n_water=157 | time (s): 1.810 (total time: 22.770) Find peaks r_work=0.1201 r_free=0.1903 | n_water=157 | time (s): 0.540 (total time: 23.310) Add new water r_work=0.1512 r_free=0.2200 | n_water=233 | time (s): 1.490 (total time: 24.800) Refine new water occ: r_work=0.1010 r_free=0.1836 adp: r_work=0.1005 r_free=0.1845 occ: r_work=0.0994 r_free=0.1819 adp: r_work=0.0993 r_free=0.1828 occ: r_work=0.0982 r_free=0.1801 adp: r_work=0.0981 r_free=0.1809 ADP+occupancy (water only), MIN, final r_work=0.0981 r_free=0.1809 r_work=0.0981 r_free=0.1809 | n_water=233 | time (s): 11.860 (total time: 36.660) Filter (q & B) r_work=0.0981 r_free=0.1816 | n_water=232 | time (s): 1.800 (total time: 38.460) Filter (dist only) r_work=0.0993 r_free=0.1821 | n_water=231 | time (s): 17.100 (total time: 55.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.034681 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.214771 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 0.0888 0.1888 0.1001 0.011 1.0 5.8 0.5 0.0 0 0.517 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.88 18.88 10.01 6.843 18.138 0.215 4.996 8.61 19.24 10.63 8.104 18.247 0.215 4.927 Individual atomic B min max mean iso aniso Overall: 0.00 104.96 16.90 10.53 1758 0 Protein: 0.00 104.96 15.66 10.53 1519 0 Water: 0.29 61.05 24.51 N/A 231 0 Other: 19.30 49.19 33.69 N/A 8 0 Chain A: 0.00 104.96 16.27 N/A 1651 0 Chain S: 1.31 61.05 26.64 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.50 639 10.50 - 20.99 647 20.99 - 31.49 255 31.49 - 41.99 127 41.99 - 52.48 49 52.48 - 62.98 21 62.98 - 73.47 7 73.47 - 83.97 7 83.97 - 94.47 4 94.47 - 104.96 2 =========================== Idealize ADP of riding H ========================== r_work=0.0861 r_free=0.1924 r_work=0.0865 r_free=0.1925 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0865 r_free = 0.1925 target_work(ml) = 4.932 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0853 r_free = 0.1899 target_work(ml) = 4.924 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0853 r_free= 0.1899 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 4.923549 | | target function (ml) not normalized (work): 24238.633774 | | target function (ml) not normalized (free): 2186.443099 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0908 0.0853 0.1899 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2087 0.2087 0.2220 n_refl.: 5175 remove outliers: r(all,work,free)=0.2087 0.2087 0.2220 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2087 0.2087 0.2220 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0905 0.0851 0.1895 n_refl.: 5175 remove outliers: r(all,work,free)=0.0905 0.0851 0.1895 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 0.3685 313.858 284.250 0.578 0.988 0.319 11.894-9.307 99.02 97 4 0.1814 504.898 489.016 0.961 0.993 0.319 9.237-7.194 100.00 213 7 0.2047 412.906 404.766 1.013 0.995 0.310 7.162-5.571 100.00 427 22 0.1861 309.836 302.563 0.992 0.997 0.300 5.546-4.326 100.00 867 58 0.0962 425.361 420.890 1.017 0.999 0.260 4.315-3.360 100.00 1859 96 0.0542 404.523 403.838 1.076 1.002 0.219 3.356-3.002 100.00 1373 60 0.0451 311.581 311.684 1.060 1.005 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.4702 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0851 r_free=0.1896 After: r_work=0.0854 r_free=0.1896 ================================== NQH flips ================================== r_work=0.0854 r_free=0.1896 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=0.0855 r_free=0.1897 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0855 r_free=0.1897 | n_water=231 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.0860 r_free=0.1895 | n_water=229 | time (s): 17.840 (total time: 18.400) Filter (q & B) r_work=0.0883 r_free=0.1919 | n_water=227 | time (s): 1.630 (total time: 20.030) Compute maps r_work=0.0883 r_free=0.1919 | n_water=227 | time (s): 0.540 (total time: 20.570) Filter (map) r_work=0.1176 r_free=0.1992 | n_water=161 | time (s): 1.410 (total time: 21.980) Find peaks r_work=0.1176 r_free=0.1992 | n_water=161 | time (s): 0.380 (total time: 22.360) Add new water r_work=0.1465 r_free=0.2234 | n_water=229 | time (s): 1.420 (total time: 23.780) Refine new water occ: r_work=0.0967 r_free=0.1943 adp: r_work=0.0966 r_free=0.1948 occ: r_work=0.0959 r_free=0.1936 adp: r_work=0.0958 r_free=0.1941 occ: r_work=0.0953 r_free=0.1929 adp: r_work=0.0952 r_free=0.1934 ADP+occupancy (water only), MIN, final r_work=0.0952 r_free=0.1934 r_work=0.0952 r_free=0.1934 | n_water=229 | time (s): 9.190 (total time: 32.970) Filter (q & B) r_work=0.0952 r_free=0.1938 | n_water=227 | time (s): 1.420 (total time: 34.390) Filter (dist only) r_work=0.0974 r_free=0.1942 | n_water=222 | time (s): 17.550 (total time: 51.940) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.040197 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.241054 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 0.0914 0.1935 0.1021 0.011 1.1 6.1 0.5 0.0 0 0.520 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.14 19.35 10.21 8.027 18.444 0.241 4.997 8.98 19.65 10.67 8.939 18.569 0.241 4.949 Individual atomic B min max mean iso aniso Overall: 0.00 105.63 17.09 11.82 1749 0 Protein: 0.00 105.63 16.07 11.82 1519 0 Water: 0.00 61.61 23.50 N/A 222 0 Other: 18.43 53.46 33.33 N/A 8 0 Chain A: 0.00 105.63 16.62 N/A 1644 0 Chain S: 0.00 52.21 24.50 N/A 105 0 Histogram: Values Number of atoms 0.00 - 10.56 635 10.56 - 21.13 625 21.13 - 31.69 278 31.69 - 42.25 121 42.25 - 52.81 50 52.81 - 63.38 18 63.38 - 73.94 8 73.94 - 84.50 8 84.50 - 95.06 3 95.06 - 105.63 3 =========================== Idealize ADP of riding H ========================== r_work=0.0898 r_free=0.1965 r_work=0.0901 r_free=0.1967 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0901 r_free = 0.1967 target_work(ml) = 4.954 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0893 r_free = 0.1947 target_work(ml) = 4.949 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0893 r_free= 0.1947 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 4.948952 | | target function (ml) not normalized (work): 24363.690305 | | target function (ml) not normalized (free): 2172.709870 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1253 0.1944 5.5031 6.2737| | 2: 3.78 - 3.00 1.00 2430 110 0.0454 0.1952 4.3804 11.653| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.92 11.96 1.00 0.94 11988.04| | 2: 3.78 - 3.00 2430 110 0.99 2.07 1.00 0.96 935.60| |alpha: min = 0.93 max = 0.96 mean = 0.95| |beta: min = 605.97 max = 19842.99 mean = 6532.54| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.68 mean = 7.08| |phase err.(test): min = 0.00 max = 89.24 mean = 7.77| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0947 0.0893 0.1947 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2167 0.2167 0.2294 n_refl.: 5175 remove outliers: r(all,work,free)=0.2167 0.2167 0.2294 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2167 0.2167 0.2294 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0946 0.0892 0.1952 n_refl.: 5175 remove outliers: r(all,work,free)=0.0946 0.0892 0.1952 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 0.3750 313.858 283.255 0.580 0.989 0.320 11.894-9.307 99.02 97 4 0.1811 504.898 491.610 0.973 0.995 0.325 9.237-7.194 100.00 213 7 0.2132 412.906 404.545 1.009 0.997 0.324 7.162-5.571 100.00 427 22 0.1996 309.836 301.590 0.994 0.998 0.320 5.546-4.326 100.00 867 58 0.1019 425.361 420.714 1.022 1.000 0.260 4.315-3.360 100.00 1859 96 0.0588 404.523 403.942 1.093 1.002 0.224 3.356-3.002 100.00 1373 60 0.0436 311.581 311.204 1.081 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.2414 ================= 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 0.2046 0.082 5.278 8.8 119.3 19.9 258 0.000 1_bss: 0.1558 0.1647 0.082 5.278 6.4 116.8 17.4 258 0.000 1_settarget: 0.1558 0.1647 0.082 5.278 6.4 116.8 17.4 258 0.000 1_nqh: 0.1558 0.1641 0.082 5.278 6.4 116.8 17.4 258 0.007 1_weight: 0.1558 0.1641 0.082 5.278 6.4 116.8 17.4 258 0.007 1_xyzrec: 0.1151 0.1763 0.010 0.986 6.4 116.8 17.4 258 0.205 1_adp: 0.1012 0.1771 0.010 0.986 2.7 111.8 17.8 258 0.205 1_regHadp: 0.1004 0.1777 0.010 0.986 2.7 111.8 17.8 258 0.205 1_occ: 0.0997 0.1761 0.010 0.986 2.7 111.8 17.8 258 0.205 2_bss: 0.1005 0.1769 0.010 0.986 1.6 110.8 16.8 258 0.205 2_settarget: 0.1005 0.1769 0.010 0.986 1.6 110.8 16.8 258 0.205 2_updatecdl: 0.1005 0.1769 0.010 1.007 1.6 110.8 16.8 258 0.205 2_nqh: 0.1005 0.1771 0.010 1.007 1.6 110.8 16.8 258 0.202 2_sol: 0.1104 0.1648 0.010 1.007 1.0 110.6 16.2 231 n/a 2_weight: 0.1104 0.1648 0.010 1.007 1.0 110.6 16.2 231 n/a 2_xyzrec: 0.0993 0.1785 0.009 0.999 1.0 110.6 16.2 231 n/a 2_adp: 0.0927 0.1790 0.009 0.999 0.0 106.4 16.8 231 n/a 2_regHadp: 0.0925 0.1790 0.009 0.999 0.0 106.4 16.8 231 n/a 2_occ: 0.0922 0.1789 0.009 0.999 0.0 106.4 16.8 231 n/a 3_bss: 0.0922 0.1794 0.009 0.999 0.0 106.4 16.8 231 n/a 3_settarget: 0.0922 0.1794 0.009 0.999 0.0 106.4 16.8 231 n/a 3_updatecdl: 0.0922 0.1794 0.009 1.008 0.0 106.4 16.8 231 n/a 3_nqh: 0.0924 0.1797 0.009 1.008 0.0 106.4 16.8 231 n/a 3_sol: 0.1015 0.1737 0.009 1.008 0.0 106.4 16.6 232 n/a 3_weight: 0.1015 0.1737 0.009 1.008 0.0 106.4 16.6 232 n/a 3_xyzrec: 0.0916 0.1781 0.011 1.073 0.0 106.4 16.6 232 n/a 3_adp: 0.0872 0.1785 0.011 1.073 0.0 104.9 16.6 232 n/a 3_regHadp: 0.0876 0.1793 0.011 1.073 0.0 104.9 16.6 232 n/a 3_occ: 0.0866 0.1769 0.011 1.073 0.0 104.9 16.6 232 n/a 4_bss: 0.0860 0.1777 0.011 1.073 0.0 104.9 16.6 232 n/a 4_settarget: 0.0860 0.1777 0.011 1.073 0.0 104.9 16.6 232 n/a 4_updatecdl: 0.0860 0.1777 0.011 1.078 0.0 104.9 16.6 232 n/a 4_nqh: 0.0860 0.1777 0.011 1.078 0.0 104.9 16.6 232 n/a 4_sol: 0.0993 0.1821 0.011 1.078 0.0 104.9 16.7 231 n/a 4_weight: 0.0993 0.1821 0.011 1.078 0.0 104.9 16.7 231 n/a 4_xyzrec: 0.0888 0.1888 0.011 1.048 0.0 104.9 16.7 231 n/a 4_adp: 0.0861 0.1924 0.011 1.048 0.0 105.0 16.9 231 n/a 4_regHadp: 0.0865 0.1925 0.011 1.048 0.0 105.0 16.9 231 n/a 4_occ: 0.0853 0.1899 0.011 1.048 0.0 105.0 16.9 231 n/a 5_bss: 0.0851 0.1896 0.011 1.048 0.0 105.0 16.9 231 n/a 5_settarget: 0.0851 0.1896 0.011 1.048 0.0 105.0 16.9 231 n/a 5_updatecdl: 0.0851 0.1896 0.011 1.054 0.0 105.0 16.9 231 n/a 5_setrh: 0.0854 0.1896 0.011 1.054 0.0 105.0 16.9 231 n/a 5_nqh: 0.0855 0.1897 0.011 1.054 0.0 105.0 16.9 231 n/a 5_sol: 0.0974 0.1942 0.011 1.054 0.0 105.0 16.8 222 n/a 5_weight: 0.0974 0.1942 0.011 1.054 0.0 105.0 16.8 222 n/a 5_xyzrec: 0.0914 0.1935 0.011 1.128 0.0 105.0 16.8 222 n/a 5_adp: 0.0898 0.1965 0.011 1.128 0.0 105.6 17.1 222 n/a 5_regHadp: 0.0901 0.1967 0.011 1.128 0.0 105.6 17.1 222 n/a 5_occ: 0.0893 0.1947 0.011 1.128 0.0 105.6 17.1 222 n/a end: 0.0892 0.1952 0.011 1.128 0.0 105.6 17.1 222 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5352376_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5352376_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9600 Refinement macro-cycles (run) : 487.5900 Write final files (write_after_run_outputs) : 9.6900 Total : 501.2400 Total CPU time: 8.72 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:04 PST -0800 (1735492744.59 s) Start R-work = 0.1558, R-free = 0.1647 Final R-work = 0.0892, R-free = 0.1952 =============================================================================== Job complete usr+sys time: 530.41 seconds wall clock time: 9 minutes 12.70 seconds (552.70 seconds total)