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_1318715.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_1318715.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_1318715.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: 1.19, per 1000 atoms: 0.35 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: 0.48 Conformation dependent library (CDL) restraints added in 205.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 622 0.93 - 1.20: 1046 1.20 - 1.47: 791 1.47 - 1.74: 681 1.74 - 2.01: 13 Bond restraints: 3153 Sorted by residual: bond pdb=" C VAL A 123 " pdb=" O VAL A 123 " ideal model delta sigma weight residual 1.233 1.043 0.190 1.08e-02 8.57e+03 3.09e+02 bond pdb=" N ATYR A 67 " pdb=" CA ATYR A 67 " ideal model delta sigma weight residual 1.456 1.245 0.211 1.21e-02 6.83e+03 3.05e+02 bond pdb=" C ILE A 152 " pdb=" N ALEU A 153 " ideal model delta sigma weight residual 1.331 1.557 -0.227 1.34e-02 5.57e+03 2.87e+02 bond pdb=" C BASN A 97 " pdb=" N ARG A 98 " ideal model delta sigma weight residual 1.331 1.102 0.229 1.43e-02 4.89e+03 2.57e+02 bond pdb=" CG HIS A 126 " pdb=" ND1 HIS A 126 " ideal model delta sigma weight residual 1.378 1.202 0.176 1.10e-02 8.26e+03 2.56e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 3168 4.66 - 9.33: 1865 9.33 - 13.99: 621 13.99 - 18.65: 108 18.65 - 23.31: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " pdb=" NH1 ARG A 27 " ideal model delta sigma weight residual 121.50 140.97 -19.47 1.00e+00 1.00e+00 3.79e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.18 137.62 -14.44 1.08e+00 8.57e-01 1.79e+02 angle pdb=" NE ARG A 145 " pdb=" CZ ARG A 145 " pdb=" NH2 ARG A 145 " ideal model delta sigma weight residual 119.20 131.14 -11.94 9.00e-01 1.23e+00 1.76e+02 angle pdb=" CA GLU A 170 " pdb=" C GLU A 170 " pdb=" O GLU A 170 " ideal model delta sigma weight residual 120.70 107.95 12.75 1.03e+00 9.43e-01 1.53e+02 angle pdb=" O GLU A 170 " pdb=" C GLU A 170 " pdb=" N ALA A 171 " ideal model delta sigma weight residual 122.09 134.96 -12.87 1.08e+00 8.57e-01 1.42e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 1288 16.66 - 33.31: 142 33.31 - 49.97: 37 49.97 - 66.62: 11 66.62 - 83.28: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 151 " pdb=" N LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual -122.60 -143.81 21.21 0 2.50e+00 1.60e-01 7.20e+01 dihedral pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual 122.80 143.54 -20.74 0 2.50e+00 1.60e-01 6.88e+01 dihedral pdb=" C VAL A 71 " pdb=" N VAL A 71 " pdb=" CA VAL A 71 " pdb=" CB VAL A 71 " ideal model delta harmonic sigma weight residual -122.00 -140.09 18.09 0 2.50e+00 1.60e-01 5.23e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.225: 106 0.225 - 0.450: 78 0.450 - 0.675: 39 0.675 - 0.900: 17 0.900 - 1.124: 3 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LEU A 151 " pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CB LEU A 151 " both_signs ideal model delta sigma weight residual False 2.51 1.39 1.12 2.00e-01 2.50e+01 3.16e+01 chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.48 -1.11 2.00e-01 2.50e+01 3.06e+01 chirality pdb=" CB VAL A 169 " pdb=" CA VAL A 169 " pdb=" CG1 VAL A 169 " pdb=" CG2 VAL A 169 " both_signs ideal model delta sigma weight residual False -2.63 -3.59 0.96 2.00e-01 2.50e+01 2.32e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.110 2.00e-02 2.50e+03 6.74e-02 1.36e+02 pdb=" CG PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.131 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.050 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.015 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.078 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.048 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.014 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.096 2.00e-02 2.50e+03 6.49e-02 1.26e+02 pdb=" CG PHE A 164 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.085 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.055 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.060 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.128 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.110 2.00e-02 2.50e+03 6.12e-02 1.12e+02 pdb=" CG ATYR A 67 " 0.092 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.019 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.008 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.026 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.085 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.005 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.069 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.042 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.32: 1008 2.32 - 2.89: 8110 2.89 - 3.46: 10496 3.46 - 4.03: 15289 4.03 - 4.60: 21737 Nonbonded interactions: 56640 Sorted by model distance: nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.745 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.745 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.767 2.100 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.784 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.832 2.100 ... (remaining 56635 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_1318715_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= 0.3627 r_free= 0.2013 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464084 | | target function (ml) not normalized (work): 22007.935922 | | target function (ml) not normalized (free): 1148.084053 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.79 1.00 2500 142 0.3805 0.2177 4.8536 4.8958| | 2: 3.78 - 3.00 1.00 2430 110 0.3409 0.1736 4.0634 4.1171| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.49 48.99 0.83 0.13 6624.21| | 2: 3.78 - 3.00 2430 110 0.94 11.10 1.49 0.26 436.06| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 362.39 max = 12081.65 mean = 3574.07| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.31| |phase err.(test): min = 0.00 max = 89.99 mean = 33.06| |-----------------------------------------------------------------------------| ----------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 0.261 1557 Z= 5.359 Angle : 5.264 19.467 2118 Z= 3.738 Chirality : 0.385 1.124 243 Planarity : 0.031 0.082 284 Dihedral : 13.552 83.279 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.70 % Favored : 96.76 % Rotamer: Outliers : 2.48 % Allowed : 2.48 % Favored : 95.03 % Cbeta Deviations : 31.89 % 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: -2.42 (0.45), residues: 224 helix: -2.45 (0.36), residues: 108 sheet: -0.48 (0.90), residues: 28 loop : -0.50 (0.54), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.018 ARG A 98 TYR 0.107 0.039 TYR A 141 PHE 0.096 0.035 PHE A 119 HIS 0.067 0.035 HIS A 138 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3627 r_free= 0.2013 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464084 | | target function (ml) not normalized (work): 22007.935922 | | target function (ml) not normalized (free): 1148.084053 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3585 0.3662 0.2101 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3585 0.3662 0.2101 n_refl.: 5182 remove outliers: r(all,work,free)=0.2535 0.2560 0.2101 n_refl.: 5178 overall B=-2.52 to atoms: r(all,work,free)=0.2436 0.2458 0.2057 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1558 0.1557 0.1575 n_refl.: 5178 remove outliers: r(all,work,free)=0.1556 0.1555 0.1575 n_refl.: 5177 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4026 444.930 407.499 0.641 1.045 0.394 11.894-9.307 99.02 97 4 0.1867 714.280 696.258 0.925 1.044 0.382 9.237-7.194 100.00 213 7 0.2196 584.139 574.833 0.963 1.039 0.373 7.162-5.571 100.00 427 22 0.2352 438.326 423.552 0.915 1.031 0.302 5.546-4.326 100.00 867 58 0.1380 601.759 594.995 0.956 1.017 0.215 4.315-3.360 100.00 1859 96 0.1304 572.279 566.122 1.022 0.993 0.188 3.356-3.002 100.00 1373 60 0.1568 440.793 432.808 1.026 0.970 0.096 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.3847 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1555 r_free=0.1575 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 80 GLN A A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1563 r_free=0.1580 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.640392 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.625740 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 0.1159 0.1770 0.0611 0.009 1.0 3.2 0.5 0.0 0 9.320 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 17.70 6.11 3.013 16.342 1.626 0.018 10.20 17.60 7.40 4.752 16.564 1.626 0.015 Individual atomic B min max mean iso aniso Overall: 2.56 111.78 17.79 5.12 1785 0 Protein: 2.56 111.11 15.11 5.12 1519 0 Water: 4.35 111.78 33.38 N/A 258 0 Other: 17.42 34.85 23.55 N/A 8 0 Chain A: 2.56 111.78 17.79 N/A 1785 0 Histogram: Values Number of atoms 2.56 - 13.49 910 13.49 - 24.41 491 24.41 - 35.33 190 35.33 - 46.25 108 46.25 - 57.17 55 57.17 - 68.10 14 68.10 - 79.02 8 79.02 - 89.94 5 89.94 - 100.86 1 100.86 - 111.78 3 =========================== Idealize ADP of riding H ========================== r_work=0.1020 r_free=0.1760 r_work=0.1013 r_free=0.1765 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1013 r_free = 0.1765 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 = 0.1014 r_free = 0.1777 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1014 r_free= 0.1777 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014143 | | target function (ls_wunit_k1) not normalized (work): 69.655298 | | target function (ls_wunit_k1) not normalized (free): 10.206533 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1052 0.1014 0.1777 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2121 0.2119 0.2259 n_refl.: 5177 remove outliers: r(all,work,free)=0.2121 0.2119 0.2259 n_refl.: 5177 overall B=-0.96 to atoms: r(all,work,free)=0.2080 0.2076 0.2247 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1053 0.1015 0.1782 n_refl.: 5177 remove outliers: r(all,work,free)=0.1051 0.1013 0.1782 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 96.88 88 5 0.3392 312.606 297.684 0.626 1.016 0.365 11.894-9.307 99.02 97 4 0.1517 506.169 498.017 0.945 1.016 0.361 9.237-7.194 100.00 213 7 0.1734 413.946 412.896 0.988 1.015 0.310 7.162-5.571 100.00 427 22 0.1638 310.616 307.273 0.945 1.012 0.292 5.546-4.326 100.00 867 58 0.0898 426.432 423.670 0.964 1.006 0.197 4.315-3.360 100.00 1859 96 0.0763 405.541 405.514 1.018 0.997 0.193 3.356-3.002 100.00 1373 60 0.0999 312.365 310.911 1.001 0.988 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.2871 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1013 r_free=0.1782 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN Total number of N/Q/H flips: 1 r_work=0.1015 r_free=0.1786 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1015 r_free=0.1786 | n_water=258 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.1050 r_free=0.1778 | n_water=248 | time (s): 18.790 (total time: 19.380) Filter (q & B) r_work=0.1050 r_free=0.1782 | n_water=245 | time (s): 1.230 (total time: 20.610) Compute maps r_work=0.1050 r_free=0.1782 | n_water=245 | time (s): 0.470 (total time: 21.080) Filter (map) r_work=0.1336 r_free=0.1853 | n_water=149 | time (s): 1.910 (total time: 22.990) Find peaks r_work=0.1336 r_free=0.1853 | n_water=149 | time (s): 0.610 (total time: 23.600) Add new water r_work=0.1695 r_free=0.2146 | n_water=240 | time (s): 1.710 (total time: 25.310) Refine new water occ: r_work=0.1169 r_free=0.1674 adp: r_work=0.1140 r_free=0.1674 occ: r_work=0.1137 r_free=0.1655 adp: r_work=0.1124 r_free=0.1661 occ: r_work=0.1124 r_free=0.1651 adp: r_work=0.1120 r_free=0.1653 ADP+occupancy (water only), MIN, final r_work=0.1120 r_free=0.1653 r_work=0.1120 r_free=0.1653 | n_water=240 | time (s): 4.260 (total time: 29.570) Filter (q & B) r_work=0.1120 r_free=0.1653 | n_water=240 | time (s): 0.840 (total time: 30.410) Filter (dist only) r_work=0.1127 r_free=0.1630 | n_water=237 | time (s): 18.780 (total time: 49.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.742028 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.480972 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 0.1006 0.1802 0.0796 0.009 1.0 4.8 0.5 0.6 0 11.871 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.06 18.02 7.96 4.586 17.269 2.481 0.014 9.37 18.13 8.75 5.448 17.631 2.481 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.03 17.09 6.38 1764 0 Protein: 0.00 107.03 15.37 6.38 1519 0 Water: 0.00 63.11 27.94 N/A 237 0 Other: 11.46 32.61 20.89 N/A 8 0 Chain A: 0.00 107.03 16.12 N/A 1674 0 Chain S: 3.81 59.49 35.04 N/A 90 0 Histogram: Values Number of atoms 0.00 - 10.70 636 10.70 - 21.41 704 21.41 - 32.11 215 32.11 - 42.81 111 42.81 - 53.52 52 53.52 - 64.22 34 64.22 - 74.92 5 74.92 - 85.63 2 85.63 - 96.33 3 96.33 - 107.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.0937 r_free=0.1813 r_work=0.0934 r_free=0.1811 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0934 r_free = 0.1811 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0929 r_free = 0.1810 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 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= 0.0929 r_free= 0.1810 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011927 | | target function (ls_wunit_k1) not normalized (work): 58.726214 | | target function (ls_wunit_k1) not normalized (free): 9.719606 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0974 0.0929 0.1810 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2127 0.2128 0.2246 n_refl.: 5176 remove outliers: r(all,work,free)=0.2127 0.2128 0.2246 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2127 0.2128 0.2246 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0972 0.0927 0.1819 n_refl.: 5176 remove outliers: r(all,work,free)=0.0972 0.0927 0.1819 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 0.3321 312.606 299.610 0.650 1.014 0.358 11.894-9.307 99.02 97 4 0.1412 506.169 503.147 0.979 1.015 0.350 9.237-7.194 100.00 213 7 0.1487 413.946 413.314 1.031 1.014 0.300 7.162-5.571 100.00 427 22 0.1400 310.616 308.685 0.991 1.011 0.290 5.546-4.326 100.00 867 58 0.0770 426.432 424.327 1.014 1.007 0.230 4.315-3.360 100.00 1859 96 0.0713 405.541 404.892 1.070 0.998 0.200 3.356-3.002 100.00 1373 60 0.0965 312.365 311.222 1.056 0.990 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.9132 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0927 r_free=0.1819 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.0930 r_free=0.1818 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0930 r_free=0.1818 | n_water=237 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.0950 r_free=0.1799 | n_water=232 | time (s): 18.300 (total time: 19.010) Filter (q & B) r_work=0.1036 r_free=0.1771 | n_water=229 | time (s): 1.180 (total time: 20.190) Compute maps r_work=0.1036 r_free=0.1771 | n_water=229 | time (s): 0.420 (total time: 20.610) Filter (map) r_work=0.1312 r_free=0.1792 | n_water=153 | time (s): 1.310 (total time: 21.920) Find peaks r_work=0.1312 r_free=0.1792 | n_water=153 | time (s): 0.420 (total time: 22.340) Add new water r_work=0.1697 r_free=0.2138 | n_water=242 | time (s): 1.670 (total time: 24.010) Refine new water occ: r_work=0.1044 r_free=0.1700 adp: r_work=0.1035 r_free=0.1727 occ: r_work=0.1025 r_free=0.1701 adp: r_work=0.1024 r_free=0.1713 occ: r_work=0.1015 r_free=0.1690 adp: r_work=0.1013 r_free=0.1701 ADP+occupancy (water only), MIN, final r_work=0.1013 r_free=0.1701 r_work=0.1013 r_free=0.1701 | n_water=242 | time (s): 12.660 (total time: 36.670) Filter (q & B) r_work=0.1013 r_free=0.1701 | n_water=242 | time (s): 1.150 (total time: 37.820) Filter (dist only) r_work=0.1021 r_free=0.1710 | n_water=239 | time (s): 17.960 (total time: 55.780) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.056255 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.213594 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 0.0930 0.1722 0.0792 0.011 1.1 4.5 0.5 0.6 0 0.528 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.30 17.22 7.92 5.368 18.213 0.214 5.113 8.85 17.27 8.42 7.249 18.238 0.214 5.013 Individual atomic B min max mean iso aniso Overall: 0.00 107.94 16.88 8.94 1766 0 Protein: 0.00 107.94 15.53 8.93 1519 0 Water: 0.00 59.36 25.38 N/A 239 0 Other: 6.46 35.50 20.64 N/A 8 0 Chain A: 0.00 107.94 16.28 N/A 1662 0 Chain S: 0.00 58.39 26.57 N/A 104 0 Histogram: Values Number of atoms 0.00 - 10.79 636 10.79 - 21.59 695 21.59 - 32.38 240 32.38 - 43.17 116 43.17 - 53.97 42 53.97 - 64.76 20 64.76 - 75.55 10 75.55 - 86.35 2 86.35 - 97.14 4 97.14 - 107.94 1 =========================== Idealize ADP of riding H ========================== r_work=0.0885 r_free=0.1727 r_work=0.0890 r_free=0.1734 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0890 r_free = 0.1734 target_work(ml) = 5.016 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0877 r_free = 0.1724 target_work(ml) = 5.008 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0877 r_free= 0.1724 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.007636 | | target function (ml) not normalized (work): 24657.597576 | | target function (ml) not normalized (free): 1816.211520 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0920 0.0877 0.1724 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2128 0.2137 0.2105 n_refl.: 5176 remove outliers: r(all,work,free)=0.2128 0.2137 0.2105 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2128 0.2137 0.2105 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0916 0.0874 0.1715 n_refl.: 5176 remove outliers: r(all,work,free)=0.0914 0.0872 0.1715 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 0.3677 314.648 285.716 0.593 0.995 0.337 11.894-9.307 99.02 97 4 0.1754 506.169 495.492 0.948 0.999 0.320 9.237-7.194 100.00 213 7 0.1872 413.946 408.591 1.009 1.000 0.300 7.162-5.571 100.00 427 22 0.1822 310.616 302.444 0.979 1.001 0.290 5.546-4.326 100.00 867 58 0.0897 426.432 422.522 1.007 1.001 0.224 4.315-3.360 100.00 1859 96 0.0577 405.541 404.845 1.063 1.001 0.210 3.356-3.002 100.00 1373 60 0.0588 312.365 312.201 1.045 1.001 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.7657 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0872 r_free=0.1715 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=0.0873 r_free=0.1712 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0873 r_free=0.1712 | n_water=239 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0878 r_free=0.1709 | n_water=237 | time (s): 18.530 (total time: 19.080) Filter (q & B) r_work=0.0975 r_free=0.1743 | n_water=233 | time (s): 1.210 (total time: 20.290) Compute maps r_work=0.0975 r_free=0.1743 | n_water=233 | time (s): 0.420 (total time: 20.710) Filter (map) r_work=0.1242 r_free=0.1837 | n_water=165 | time (s): 1.480 (total time: 22.190) Find peaks r_work=0.1242 r_free=0.1837 | n_water=165 | time (s): 0.480 (total time: 22.670) Add new water r_work=0.1563 r_free=0.2097 | n_water=239 | time (s): 1.650 (total time: 24.320) Refine new water r_work=0.1563 r_free=0.2097 | n_water=239 | time (s): 0.100 (total time: 24.420) Filter (q & B) r_work=0.1242 r_free=0.1837 | n_water=165 | time (s): 1.700 (total time: 26.120) Filter (dist only) r_work=0.1259 r_free=0.1840 | n_water=160 | time (s): 13.030 (total time: 39.150) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.367441 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.257725 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 0.1114 0.1927 0.0813 0.012 1.1 6.1 0.5 1.2 0 0.684 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.14 19.27 8.13 6.977 18.169 0.258 5.310 10.51 19.53 9.01 8.197 18.132 0.258 5.223 Individual atomic B min max mean iso aniso Overall: 0.00 106.68 16.36 10.23 1687 0 Protein: 0.00 106.68 15.55 10.23 1519 0 Water: 2.77 54.36 23.83 N/A 160 0 Other: 10.49 41.12 21.89 N/A 8 0 Chain A: 0.00 106.68 16.15 N/A 1648 0 Chain S: 3.66 47.19 25.26 N/A 39 0 Histogram: Values Number of atoms 0.00 - 10.67 645 10.67 - 21.34 631 21.34 - 32.00 233 32.00 - 42.67 97 42.67 - 53.34 46 53.34 - 64.01 16 64.01 - 74.68 11 74.68 - 85.35 3 85.35 - 96.01 3 96.01 - 106.68 2 =========================== Idealize ADP of riding H ========================== r_work=0.1051 r_free=0.1953 r_work=0.1054 r_free=0.1964 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1054 r_free = 0.1964 target_work(ml) = 5.226 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1051 r_free = 0.1960 target_work(ml) = 5.223 | | occupancies: max = 1.00 min = 0.25 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= 0.1051 r_free= 0.1960 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 5.223206 | | target function (ml) not normalized (work): 25713.845269 | | target function (ml) not normalized (free): 1697.032811 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1097 0.1051 0.1960 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2344 0.2340 0.2510 n_refl.: 5175 remove outliers: r(all,work,free)=0.2344 0.2340 0.2510 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2344 0.2340 0.2510 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1078 0.1032 0.1959 n_refl.: 5175 remove outliers: r(all,work,free)=0.1078 0.1032 0.1959 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 0.3658 314.648 292.108 0.664 0.994 0.360 11.894-9.307 99.02 97 4 0.1655 506.169 494.748 0.982 0.998 0.350 9.237-7.194 100.00 213 7 0.1923 413.946 404.032 1.008 1.000 0.350 7.162-5.571 100.00 427 22 0.1912 310.616 304.597 0.979 1.000 0.300 5.546-4.326 100.00 867 58 0.1098 426.432 420.641 0.997 1.001 0.254 4.315-3.360 100.00 1859 96 0.0747 405.541 404.189 1.078 1.001 0.240 3.356-3.002 100.00 1373 60 0.0782 312.365 311.630 1.070 1.001 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.5275 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1032 r_free=0.1959 After: r_work=0.1035 r_free=0.1958 ================================== NQH flips ================================== r_work=0.1035 r_free=0.1958 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1036 r_free=0.1960 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1036 r_free=0.1960 | n_water=160 | time (s): 0.480 (total time: 0.480) Filter (dist) r_work=0.1045 r_free=0.1950 | n_water=158 | time (s): 12.500 (total time: 12.980) Filter (q & B) r_work=0.1045 r_free=0.1950 | n_water=158 | time (s): 0.840 (total time: 13.820) Compute maps r_work=0.1045 r_free=0.1950 | n_water=158 | time (s): 0.500 (total time: 14.320) Filter (map) r_work=0.1093 r_free=0.1907 | n_water=146 | time (s): 1.580 (total time: 15.900) Find peaks r_work=0.1093 r_free=0.1907 | n_water=146 | time (s): 0.390 (total time: 16.290) Add new water r_work=0.1391 r_free=0.2167 | n_water=213 | time (s): 1.170 (total time: 17.460) Refine new water occ: r_work=0.1093 r_free=0.1954 adp: r_work=0.1096 r_free=0.1975 occ: r_work=0.1078 r_free=0.1933 adp: r_work=0.1081 r_free=0.1954 occ: r_work=0.1064 r_free=0.1911 adp: r_work=0.1067 r_free=0.1930 ADP+occupancy (water only), MIN, final r_work=0.1067 r_free=0.1930 r_work=0.1067 r_free=0.1930 | n_water=213 | time (s): 10.980 (total time: 28.440) Filter (q & B) r_work=0.1068 r_free=0.1933 | n_water=211 | time (s): 1.950 (total time: 30.390) Filter (dist only) r_work=0.1065 r_free=0.1925 | n_water=209 | time (s): 17.460 (total time: 47.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.140058 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.225263 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 0.1026 0.1903 0.0876 0.011 1.2 8.3 0.5 1.2 0 0.570 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.26 19.03 8.76 7.816 18.329 0.225 5.136 10.03 19.07 9.04 8.726 18.433 0.225 5.084 Individual atomic B min max mean iso aniso Overall: 0.00 106.83 17.12 11.40 1736 0 Protein: 0.00 106.83 15.94 11.40 1519 0 Water: 1.48 57.72 25.51 N/A 209 0 Other: 10.84 42.16 22.16 N/A 8 0 Chain A: 0.00 106.83 16.43 N/A 1640 0 Chain S: 1.48 57.72 28.90 N/A 96 0 Histogram: Values Number of atoms 0.00 - 10.68 640 10.68 - 21.37 626 21.37 - 32.05 264 32.05 - 42.73 123 42.73 - 53.42 44 53.42 - 64.10 20 64.10 - 74.78 8 74.78 - 85.47 7 85.47 - 96.15 2 96.15 - 106.83 2 =========================== Idealize ADP of riding H ========================== r_work=0.1003 r_free=0.1907 r_work=0.1008 r_free=0.1905 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1008 r_free = 0.1905 target_work(ml) = 5.090 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0967 r_free = 0.1827 target_work(ml) = 5.063 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0967 r_free= 0.1827 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.063491 | | target function (ml) not normalized (work): 24927.568553 | | target function (ml) not normalized (free): 1794.317424 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1305 0.1785 5.5392 5.9711| | 2: 3.78 - 3.00 1.00 2430 110 0.0556 0.1897 4.5755 8.6038| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.91 12.58 1.00 0.94 12337.28| | 2: 3.78 - 3.00 2430 110 0.98 2.90 1.01 0.97 1346.20| |alpha: min = 0.93 max = 0.97 mean = 0.96| |beta: min = 915.02 max = 19817.84 mean = 6912.06| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.93 mean = 7.80| |phase err.(test): min = 0.00 max = 80.41 mean = 7.87| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1011 0.0967 0.1827 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2269 0.2274 0.2277 n_refl.: 5175 remove outliers: r(all,work,free)=0.2269 0.2274 0.2277 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2269 0.2274 0.2277 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.1004 0.0961 0.1820 n_refl.: 5175 remove outliers: r(all,work,free)=0.1004 0.0961 0.1820 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 0.3795 314.648 285.776 0.626 0.988 0.320 11.894-9.307 99.02 97 4 0.1787 506.169 491.966 1.019 0.993 0.320 9.237-7.194 100.00 213 7 0.2090 413.946 405.864 1.069 0.996 0.317 7.162-5.571 100.00 427 22 0.2066 310.616 302.380 1.032 0.998 0.270 5.546-4.326 100.00 867 58 0.1089 426.432 420.758 1.071 1.000 0.254 4.315-3.360 100.00 1859 96 0.0661 405.541 404.856 1.165 1.003 0.248 3.356-3.002 100.00 1373 60 0.0532 312.365 312.355 1.154 1.006 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-9.3432 ================= 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 : 0.3627 0.2013 0.081 5.264 8.8 119.3 19.9 258 0.000 1_bss: 0.1555 0.1575 0.081 5.264 6.3 116.8 17.4 258 0.000 1_settarget: 0.1555 0.1575 0.081 5.264 6.3 116.8 17.4 258 0.000 1_nqh: 0.1563 0.1580 0.081 5.264 6.3 116.8 17.4 258 0.013 1_weight: 0.1563 0.1580 0.081 5.264 6.3 116.8 17.4 258 0.013 1_xyzrec: 0.1159 0.1770 0.009 0.955 6.3 116.8 17.4 258 0.222 1_adp: 0.1020 0.1760 0.009 0.955 2.6 111.8 17.8 258 0.222 1_regHadp: 0.1013 0.1765 0.009 0.955 2.6 111.8 17.8 258 0.222 1_occ: 0.1014 0.1777 0.009 0.955 2.6 111.8 17.8 258 0.222 2_bss: 0.1013 0.1782 0.009 0.955 1.6 110.8 16.8 258 0.222 2_settarget: 0.1013 0.1782 0.009 0.955 1.6 110.8 16.8 258 0.222 2_updatecdl: 0.1013 0.1782 0.009 0.992 1.6 110.8 16.8 258 0.222 2_nqh: 0.1015 0.1786 0.009 0.992 1.6 110.8 16.8 258 0.219 2_sol: 0.1127 0.1630 0.009 0.992 1.0 110.2 16.4 237 n/a 2_weight: 0.1127 0.1630 0.009 0.992 1.0 110.2 16.4 237 n/a 2_xyzrec: 0.1006 0.1802 0.009 0.997 1.0 110.2 16.4 237 n/a 2_adp: 0.0937 0.1813 0.009 0.997 0.0 107.0 17.1 237 n/a 2_regHadp: 0.0934 0.1811 0.009 0.997 0.0 107.0 17.1 237 n/a 2_occ: 0.0929 0.1810 0.009 0.997 0.0 107.0 17.1 237 n/a 3_bss: 0.0927 0.1819 0.009 0.997 0.0 107.0 17.1 237 n/a 3_settarget: 0.0927 0.1819 0.009 0.997 0.0 107.0 17.1 237 n/a 3_updatecdl: 0.0927 0.1819 0.009 1.012 0.0 107.0 17.1 237 n/a 3_nqh: 0.0930 0.1818 0.009 1.012 0.0 107.0 17.1 237 n/a 3_sol: 0.1021 0.1710 0.009 1.012 0.0 107.0 16.8 239 n/a 3_weight: 0.1021 0.1710 0.009 1.012 0.0 107.0 16.8 239 n/a 3_xyzrec: 0.0930 0.1722 0.011 1.066 0.0 107.0 16.8 239 n/a 3_adp: 0.0885 0.1727 0.011 1.066 0.0 107.9 16.9 239 n/a 3_regHadp: 0.0890 0.1734 0.011 1.066 0.0 107.9 16.9 239 n/a 3_occ: 0.0877 0.1724 0.011 1.066 0.0 107.9 16.9 239 n/a 4_bss: 0.0872 0.1715 0.011 1.066 0.0 107.9 16.9 239 n/a 4_settarget: 0.0872 0.1715 0.011 1.066 0.0 107.9 16.9 239 n/a 4_updatecdl: 0.0872 0.1715 0.011 1.071 0.0 107.9 16.9 239 n/a 4_nqh: 0.0873 0.1712 0.011 1.071 0.0 107.9 16.9 239 n/a 4_sol: 0.1259 0.1840 0.011 1.071 0.0 107.9 16.4 160 n/a 4_weight: 0.1259 0.1840 0.011 1.071 0.0 107.9 16.4 160 n/a 4_xyzrec: 0.1114 0.1927 0.012 1.086 0.0 107.9 16.4 160 n/a 4_adp: 0.1051 0.1953 0.012 1.086 0.0 106.7 16.4 160 n/a 4_regHadp: 0.1054 0.1964 0.012 1.086 0.0 106.7 16.4 160 n/a 4_occ: 0.1051 0.1960 0.012 1.086 0.0 106.7 16.4 160 n/a 5_bss: 0.1032 0.1959 0.012 1.086 0.0 106.7 16.4 160 n/a 5_settarget: 0.1032 0.1959 0.012 1.086 0.0 106.7 16.4 160 n/a 5_updatecdl: 0.1032 0.1959 0.012 1.094 0.0 106.7 16.4 160 n/a 5_setrh: 0.1035 0.1958 0.012 1.094 0.0 106.7 16.4 160 n/a 5_nqh: 0.1036 0.1960 0.012 1.094 0.0 106.7 16.4 160 n/a 5_sol: 0.1065 0.1925 0.012 1.094 0.0 106.7 16.9 209 n/a 5_weight: 0.1065 0.1925 0.012 1.094 0.0 106.7 16.9 209 n/a 5_xyzrec: 0.1026 0.1903 0.011 1.177 0.0 106.7 16.9 209 n/a 5_adp: 0.1003 0.1907 0.011 1.177 0.0 106.8 17.1 209 n/a 5_regHadp: 0.1008 0.1905 0.011 1.177 0.0 106.8 17.1 209 n/a 5_occ: 0.0967 0.1827 0.011 1.177 0.0 106.8 17.1 209 n/a end: 0.0961 0.1820 0.011 1.177 0.0 106.8 17.1 209 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1318715_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_1318715_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9400 Refinement macro-cycles (run) : 458.0600 Write final files (write_after_run_outputs) : 11.8100 Total : 472.8100 Total CPU time: 8.25 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:36 PST -0800 (1735492716.10 s) Start R-work = 0.1555, R-free = 0.1575 Final R-work = 0.0961, R-free = 0.1820 =============================================================================== Job complete usr+sys time: 503.66 seconds wall clock time: 8 minutes 45.40 seconds (525.40 seconds total)