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_8831905.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8831905.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_8831905.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.96, per 1000 atoms: 0.58 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: 0.50 Conformation dependent library (CDL) restraints added in 148.7 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: 0.63 - 0.90: 446 0.90 - 1.16: 1198 1.16 - 1.43: 666 1.43 - 1.69: 820 1.69 - 1.96: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 1.537 1.667 -0.130 5.00e-03 4.00e+04 6.81e+02 bond pdb=" CA ALA A 183 " pdb=" C ALA A 183 " ideal model delta sigma weight residual 1.521 1.750 -0.229 1.14e-02 7.69e+03 4.05e+02 bond pdb=" C VAL A 23 " pdb=" O VAL A 23 " ideal model delta sigma weight residual 1.237 1.452 -0.215 1.13e-02 7.83e+03 3.63e+02 bond pdb=" N ALA A 61 " pdb=" CA ALA A 61 " ideal model delta sigma weight residual 1.459 1.239 0.220 1.21e-02 6.83e+03 3.30e+02 bond pdb=" C SER A 47 " pdb=" O SER A 47 " ideal model delta sigma weight residual 1.236 1.031 0.205 1.18e-02 7.18e+03 3.02e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.56: 3102 4.56 - 9.11: 1867 9.11 - 13.67: 670 13.67 - 18.23: 122 18.23 - 22.79: 16 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 165 " pdb=" C ALA A 165 " pdb=" N LEU A 166 " ideal model delta sigma weight residual 122.12 135.74 -13.62 1.06e+00 8.90e-01 1.65e+02 angle pdb=" N PRO A 184 " pdb=" CA PRO A 184 " pdb=" CB PRO A 184 " ideal model delta sigma weight residual 103.52 115.46 -11.94 9.50e-01 1.11e+00 1.58e+02 angle pdb=" O TYR A 141 " pdb=" C TYR A 141 " pdb=" N SER A 142 " ideal model delta sigma weight residual 123.10 137.24 -14.14 1.15e+00 7.56e-01 1.51e+02 angle pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " pdb=" NH1 ARG A 156 " ideal model delta sigma weight residual 121.50 133.58 -12.08 1.00e+00 1.00e+00 1.46e+02 angle pdb=" CA ALA A 178 " pdb=" C ALA A 178 " pdb=" O ALA A 178 " ideal model delta sigma weight residual 120.82 133.15 -12.33 1.05e+00 9.07e-01 1.38e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.33: 1297 16.33 - 32.65: 123 32.65 - 48.97: 38 48.97 - 65.29: 20 65.29 - 81.62: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -145.58 22.98 0 2.50e+00 1.60e-01 8.45e+01 dihedral pdb=" C ALA A 6 " pdb=" N ALA A 6 " pdb=" CA ALA A 6 " pdb=" CB ALA A 6 " ideal model delta harmonic sigma weight residual -122.60 -104.70 -17.90 0 2.50e+00 1.60e-01 5.13e+01 dihedral pdb=" C SER A 142 " pdb=" N SER A 142 " pdb=" CA SER A 142 " pdb=" CB SER A 142 " ideal model delta harmonic sigma weight residual -122.60 -105.12 -17.48 0 2.50e+00 1.60e-01 4.89e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.209: 81 0.209 - 0.417: 91 0.417 - 0.626: 42 0.626 - 0.834: 20 0.834 - 1.042: 9 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA SER A 142 " pdb=" N SER A 142 " pdb=" C SER A 142 " pdb=" CB SER A 142 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.72e+01 chirality pdb=" CB VAL A 146 " pdb=" CA VAL A 146 " pdb=" CG1 VAL A 146 " pdb=" CG2 VAL A 146 " both_signs ideal model delta sigma weight residual False -2.63 -1.61 -1.02 2.00e-01 2.50e+01 2.62e+01 chirality pdb=" CG LEU A 10 " pdb=" CB LEU A 10 " pdb=" CD1 LEU A 10 " pdb=" CD2 LEU A 10 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.58e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.153 2.00e-02 2.50e+03 6.28e-02 1.18e+02 pdb=" CG ATYR A 67 " 0.052 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.011 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.100 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.011 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.050 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.065 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.041 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.041 2.00e-02 2.50e+03 6.27e-02 1.18e+02 pdb=" CG PHE A 119 " -0.177 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.062 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.017 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " 0.031 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.033 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.010 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " -0.021 2.00e-02 2.50e+03 6.01e-02 1.08e+02 pdb=" CG BTYR A 67 " -0.049 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.050 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.078 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.036 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.103 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.062 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.028 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.034 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.110 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.042 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.35: 1266 2.35 - 2.91: 8328 2.91 - 3.48: 10416 3.48 - 4.04: 15153 4.04 - 4.60: 21502 Nonbonded interactions: 56665 Sorted by model distance: nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.792 2.270 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.809 2.100 nonbonded pdb=" O GLU A 147 " pdb=" H ATHR A 154 " model vdw 1.836 2.450 nonbonded pdb=" HG SER A 47 " pdb="HH11 ARG A 48 " model vdw 1.847 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.858 2.450 ... (remaining 56660 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_8831905_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3619 r_free= 0.2062 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.466487 | | target function (ml) not normalized (work): 22019.779100 | | target function (ml) not normalized (free): 1157.527632 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3797 0.2247 4.8466 4.9155| | 2: 3.78 - 3.00 1.00 2430 110 0.3401 0.1750 4.0754 4.1775| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.78 0.83 0.13 6605.16| | 2: 3.78 - 3.00 2430 110 0.93 11.45 1.48 0.26 450.28| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 382.12 max = 12061.50 mean = 3571.41| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.38| |phase err.(test): min = 0.00 max = 89.90 mean = 33.30| |-----------------------------------------------------------------------------| ----------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 : 0.083 0.229 1557 Z= 5.677 Angle : 5.295 16.972 2118 Z= 3.642 Chirality : 0.407 1.042 243 Planarity : 0.030 0.077 284 Dihedral : 14.023 81.616 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 1.08 % Allowed : 3.24 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 4.97 % Favored : 94.41 % Cbeta Deviations : 31.35 % 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: -3.07 (0.46), residues: 224 helix: -2.72 (0.37), residues: 103 sheet: -0.98 (0.81), residues: 38 loop : -1.28 (0.57), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.097 0.026 ARG A 156 TYR 0.084 0.045 TYR A 139 PHE 0.154 0.048 PHE A 119 HIS 0.060 0.034 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3619 r_free= 0.2062 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.466487 | | target function (ml) not normalized (work): 22019.779100 | | target function (ml) not normalized (free): 1157.527632 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3568 0.3647 0.2151 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3568 0.3647 0.2151 n_refl.: 5182 remove outliers: r(all,work,free)=0.2512 0.2536 0.2151 n_refl.: 5178 overall B=-2.87 to atoms: r(all,work,free)=0.2403 0.2423 0.2110 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1552 0.1547 0.1644 n_refl.: 5178 remove outliers: r(all,work,free)=0.1548 0.1543 0.1644 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3834 449.751 406.690 0.662 1.064 0.398 11.894-9.307 99.02 97 4 0.1857 714.465 695.028 0.941 1.061 0.383 9.237-7.194 100.00 213 7 0.2176 584.291 574.602 0.973 1.054 0.384 7.162-5.571 100.00 427 22 0.2309 438.439 422.117 0.937 1.042 0.283 5.546-4.326 100.00 867 58 0.1346 601.915 594.894 0.984 1.023 0.247 4.315-3.360 100.00 1859 96 0.1303 572.428 566.336 1.057 0.990 0.211 3.356-3.002 100.00 1373 60 0.1580 440.908 433.843 1.062 0.958 0.087 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6649 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1543 r_free=0.1644 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 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 r_work=0.1546 r_free=0.1653 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.237210 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.993084 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 0.1169 0.1797 0.0628 0.010 1.0 2.6 0.5 0.0 0 9.619 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.69 17.97 6.28 3.013 15.993 1.993 0.018 10.26 18.00 7.74 4.950 16.157 1.993 0.015 Individual atomic B min max mean iso aniso Overall: 1.91 112.09 17.33 5.36 1785 0 Protein: 1.91 112.09 14.64 5.35 1519 0 Water: 4.00 111.43 32.97 N/A 258 0 Other: 16.75 37.91 24.28 N/A 8 0 Chain A: 1.91 112.09 17.33 N/A 1785 0 Histogram: Values Number of atoms 1.91 - 12.93 912 12.93 - 23.95 490 23.95 - 34.96 182 34.96 - 45.98 114 45.98 - 57.00 55 57.00 - 68.02 16 68.02 - 79.03 7 79.03 - 90.05 5 90.05 - 101.07 1 101.07 - 112.09 3 =========================== Idealize ADP of riding H ========================== r_work=0.1026 r_free=0.1800 r_work=0.1021 r_free=0.1809 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1021 r_free = 0.1809 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 = 0.1800 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1014 r_free= 0.1800 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.014014 | | target function (ls_wunit_k1) not normalized (work): 69.005156 | | target function (ls_wunit_k1) not normalized (free): 10.507999 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1055 0.1014 0.1800 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2090 0.2089 0.2233 n_refl.: 5176 remove outliers: r(all,work,free)=0.2090 0.2089 0.2233 n_refl.: 5176 overall B=-0.93 to atoms: r(all,work,free)=0.2052 0.2049 0.2223 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1055 0.1015 0.1797 n_refl.: 5176 remove outliers: r(all,work,free)=0.1055 0.1015 0.1797 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 0.3343 330.823 314.131 0.684 1.009 0.387 11.894-9.307 99.02 97 4 0.1525 525.539 518.568 0.983 1.010 0.371 9.237-7.194 100.00 213 7 0.1701 429.787 428.901 1.021 1.009 0.351 7.162-5.571 100.00 427 22 0.1598 322.503 319.870 0.978 1.007 0.292 5.546-4.326 100.00 867 58 0.0904 442.751 439.681 0.995 1.004 0.222 4.315-3.360 100.00 1859 96 0.0774 421.061 421.176 1.043 0.998 0.214 3.356-3.002 100.00 1373 60 0.1000 324.319 322.536 1.012 0.993 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.3407 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1015 r_free=0.1797 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1015 r_free=0.1797 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1015 r_free=0.1797 | n_water=258 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.1043 r_free=0.1807 | n_water=246 | time (s): 19.050 (total time: 19.710) Filter (q & B) r_work=0.1043 r_free=0.1810 | n_water=243 | time (s): 1.460 (total time: 21.170) Compute maps r_work=0.1043 r_free=0.1810 | n_water=243 | time (s): 0.490 (total time: 21.660) Filter (map) r_work=0.1347 r_free=0.1854 | n_water=143 | time (s): 1.360 (total time: 23.020) Find peaks r_work=0.1347 r_free=0.1854 | n_water=143 | time (s): 0.390 (total time: 23.410) Add new water r_work=0.1698 r_free=0.2177 | n_water=228 | time (s): 1.190 (total time: 24.600) Refine new water occ: r_work=0.1172 r_free=0.1720 adp: r_work=0.1148 r_free=0.1718 occ: r_work=0.1148 r_free=0.1691 adp: r_work=0.1136 r_free=0.1690 occ: r_work=0.1136 r_free=0.1680 adp: r_work=0.1134 r_free=0.1681 ADP+occupancy (water only), MIN, final r_work=0.1134 r_free=0.1681 r_work=0.1134 r_free=0.1681 | n_water=228 | time (s): 4.510 (total time: 29.110) Filter (q & B) r_work=0.1134 r_free=0.1681 | n_water=228 | time (s): 1.010 (total time: 30.120) Filter (dist only) r_work=0.1139 r_free=0.1668 | n_water=226 | time (s): 18.170 (total time: 48.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.711602 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.832250 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 0.1023 0.1828 0.0805 0.009 1.0 4.5 0.5 0.6 0 11.356 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.23 18.28 8.05 4.702 16.758 2.832 0.014 9.56 18.41 8.86 5.448 17.109 2.832 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 109.67 16.49 6.47 1753 0 Protein: 0.00 109.67 14.89 6.45 1519 0 Water: 0.00 62.78 26.91 N/A 226 0 Other: 13.95 41.24 25.67 N/A 8 0 Chain A: 0.00 109.67 15.62 N/A 1669 0 Chain S: 5.07 60.82 33.75 N/A 84 0 Histogram: Values Number of atoms 0.00 - 10.97 724 10.97 - 21.93 643 21.93 - 32.90 201 32.90 - 43.87 105 43.87 - 54.83 38 54.83 - 65.80 30 65.80 - 76.77 6 76.77 - 87.73 3 87.73 - 98.70 1 98.70 - 109.67 2 =========================== Idealize ADP of riding H ========================== r_work=0.0956 r_free=0.1841 r_work=0.0952 r_free=0.1842 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0952 r_free = 0.1842 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0947 r_free = 0.1827 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.29 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= 0.0947 r_free= 0.1827 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ls_wunit_k1) (work): 0.012402 | | target function (ls_wunit_k1) not normalized (work): 61.065740 | | target function (ls_wunit_k1) not normalized (free): 10.144605 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0991 0.0947 0.1827 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2123 0.2126 0.2216 n_refl.: 5176 remove outliers: r(all,work,free)=0.2123 0.2126 0.2216 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2123 0.2126 0.2216 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0991 0.0946 0.1830 n_refl.: 5176 remove outliers: r(all,work,free)=0.0991 0.0946 0.1830 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 0.3296 330.823 311.837 0.704 0.998 0.387 11.894-9.307 99.02 97 4 0.1420 525.539 518.965 0.989 1.001 0.370 9.237-7.194 100.00 213 7 0.1511 429.787 427.433 1.026 1.001 0.340 7.162-5.571 100.00 427 22 0.1411 322.503 318.402 0.994 1.001 0.290 5.546-4.326 100.00 867 58 0.0809 442.751 439.599 1.007 1.001 0.229 4.315-3.360 100.00 1859 96 0.0729 421.061 420.875 1.057 1.001 0.220 3.356-3.002 100.00 1373 60 0.0976 324.319 324.540 1.026 1.000 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.2327 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0946 r_free=0.1830 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=0.0948 r_free=0.1825 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0948 r_free=0.1825 | n_water=226 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.0959 r_free=0.1830 | n_water=223 | time (s): 18.270 (total time: 18.820) Filter (q & B) r_work=0.1016 r_free=0.1809 | n_water=221 | time (s): 1.160 (total time: 19.980) Compute maps r_work=0.1016 r_free=0.1809 | n_water=221 | time (s): 0.480 (total time: 20.460) Filter (map) r_work=0.1293 r_free=0.1926 | n_water=145 | time (s): 1.330 (total time: 21.790) Find peaks r_work=0.1293 r_free=0.1926 | n_water=145 | time (s): 0.480 (total time: 22.270) Add new water r_work=0.1698 r_free=0.2264 | n_water=239 | time (s): 1.330 (total time: 23.600) Refine new water occ: r_work=0.1067 r_free=0.1724 adp: r_work=0.1062 r_free=0.1741 occ: r_work=0.1051 r_free=0.1711 adp: r_work=0.1052 r_free=0.1725 occ: r_work=0.1043 r_free=0.1695 adp: r_work=0.1042 r_free=0.1709 ADP+occupancy (water only), MIN, final r_work=0.1042 r_free=0.1709 r_work=0.1042 r_free=0.1709 | n_water=239 | time (s): 12.200 (total time: 35.800) Filter (q & B) r_work=0.1043 r_free=0.1714 | n_water=237 | time (s): 1.560 (total time: 37.360) Filter (dist only) r_work=0.1045 r_free=0.1720 | n_water=236 | time (s): 18.270 (total time: 55.630) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.064317 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.204561 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 0.0937 0.1822 0.0885 0.010 1.0 3.5 0.5 0.6 0 0.532 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.37 18.22 8.85 5.406 17.704 0.205 5.162 8.97 18.27 9.30 7.166 17.742 0.205 5.069 Individual atomic B min max mean iso aniso Overall: 0.00 109.27 16.35 8.80 1763 0 Protein: 0.00 109.27 15.07 8.78 1519 0 Water: 0.00 59.98 24.18 N/A 236 0 Other: 14.86 47.86 27.84 N/A 8 0 Chain A: 0.00 109.27 15.76 N/A 1652 0 Chain S: 0.00 59.98 25.12 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.93 696 10.93 - 21.85 662 21.85 - 32.78 230 32.78 - 43.71 105 43.71 - 54.63 35 54.63 - 65.56 18 65.56 - 76.49 11 76.49 - 87.41 2 87.41 - 98.34 3 98.34 - 109.27 1 =========================== Idealize ADP of riding H ========================== r_work=0.0897 r_free=0.1827 r_work=0.0902 r_free=0.1840 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0902 r_free = 0.1840 target_work(ml) = 5.072 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0891 r_free = 0.1817 target_work(ml) = 5.065 | | occupancies: max = 1.00 min = 0.25 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= 0.0891 r_free= 0.1817 coordinate error (max.-lik. estimate): 0.24 A | | | | normalized target function (ml) (work): 5.065323 | | target function (ml) not normalized (work): 24941.650865 | | target function (ml) not normalized (free): 1828.958534 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0937 0.0891 0.1817 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2150 0.2160 0.2113 n_refl.: 5176 remove outliers: r(all,work,free)=0.2150 0.2160 0.2113 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2150 0.2160 0.2113 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0932 0.0888 0.1790 n_refl.: 5176 remove outliers: r(all,work,free)=0.0928 0.0883 0.1790 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3691 330.219 294.770 0.598 0.994 0.343 11.894-9.307 99.02 97 4 0.1762 525.539 513.325 0.944 0.997 0.339 9.237-7.194 100.00 213 7 0.1910 429.787 424.172 0.999 0.999 0.300 7.162-5.571 100.00 427 22 0.1861 322.503 313.597 0.976 0.999 0.264 5.546-4.326 100.00 867 58 0.0906 442.751 437.741 1.000 1.001 0.240 4.315-3.360 100.00 1859 96 0.0581 421.061 420.663 1.056 1.003 0.230 3.356-3.002 100.00 1373 60 0.0602 324.319 324.267 1.025 1.005 0.078 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9176 b_overall=-6.2321 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0883 r_free=0.1790 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN B Total number of N/Q/H flips: 2 r_work=0.0887 r_free=0.1795 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0887 r_free=0.1795 | n_water=236 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.0900 r_free=0.1787 | n_water=234 | time (s): 18.160 (total time: 18.770) Filter (q & B) r_work=0.0968 r_free=0.1814 | n_water=232 | time (s): 1.520 (total time: 20.290) Compute maps r_work=0.0968 r_free=0.1814 | n_water=232 | time (s): 0.640 (total time: 20.930) Filter (map) r_work=0.1251 r_free=0.1888 | n_water=154 | time (s): 1.720 (total time: 22.650) Find peaks r_work=0.1251 r_free=0.1888 | n_water=154 | time (s): 0.380 (total time: 23.030) Add new water r_work=0.1608 r_free=0.2255 | n_water=239 | time (s): 1.350 (total time: 24.380) Refine new water occ: r_work=0.1026 r_free=0.1837 adp: r_work=0.1020 r_free=0.1838 occ: r_work=0.1009 r_free=0.1819 adp: r_work=0.1009 r_free=0.1827 occ: r_work=0.0999 r_free=0.1807 adp: r_work=0.0999 r_free=0.1814 ADP+occupancy (water only), MIN, final r_work=0.0999 r_free=0.1814 r_work=0.0999 r_free=0.1814 | n_water=239 | time (s): 8.800 (total time: 33.180) Filter (q & B) r_work=0.0999 r_free=0.1818 | n_water=237 | time (s): 1.730 (total time: 34.910) Filter (dist only) r_work=0.1008 r_free=0.1828 | n_water=236 | time (s): 16.230 (total time: 51.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.998870 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.223441 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 0.1849 0.0934 0.010 1.0 4.8 0.5 0.0 0 0.499 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.16 18.49 9.34 6.880 17.918 0.223 5.054 8.91 19.09 10.17 8.132 18.037 0.223 4.987 Individual atomic B min max mean iso aniso Overall: 0.00 111.36 16.68 10.57 1763 0 Protein: 0.00 111.36 15.48 10.53 1519 0 Water: 0.00 55.63 23.97 N/A 236 0 Other: 13.42 54.90 29.04 N/A 8 0 Chain A: 0.00 111.36 16.06 N/A 1640 0 Chain S: 0.00 55.63 24.94 N/A 123 0 Histogram: Values Number of atoms 0.00 - 11.14 699 11.14 - 22.27 651 22.27 - 33.41 235 33.41 - 44.55 105 44.55 - 55.68 39 55.68 - 66.82 15 66.82 - 77.95 9 77.95 - 89.09 7 89.09 - 100.23 2 100.23 - 111.36 1 =========================== Idealize ADP of riding H ========================== r_work=0.0891 r_free=0.1909 r_work=0.0895 r_free=0.1920 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0895 r_free = 0.1920 target_work(ml) = 4.992 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0881 r_free = 0.1903 target_work(ml) = 4.983 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0881 r_free= 0.1903 coordinate error (max.-lik. estimate): 0.26 A | | | | normalized target function (ml) (work): 4.982659 | | target function (ml) not normalized (work): 24524.648848 | | target function (ml) not normalized (free): 2090.366039 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0933 0.0881 0.1903 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2085 0.2085 0.2220 n_refl.: 5174 remove outliers: r(all,work,free)=0.2085 0.2085 0.2220 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2085 0.2085 0.2220 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0932 0.0881 0.1898 n_refl.: 5174 remove outliers: r(all,work,free)=0.0932 0.0881 0.1898 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3909 330.219 297.378 0.577 0.990 0.315 11.894-9.307 99.02 97 4 0.1973 525.539 510.977 0.939 0.993 0.311 9.237-7.194 100.00 213 7 0.2161 429.787 418.679 1.000 0.996 0.290 7.162-5.571 100.00 427 22 0.2072 322.503 312.021 0.990 0.998 0.270 5.546-4.326 100.00 867 58 0.0950 442.751 437.687 1.019 1.000 0.230 4.315-3.360 100.00 1859 96 0.0548 421.061 420.479 1.084 1.003 0.230 3.356-3.002 100.00 1373 60 0.0460 324.319 324.341 1.056 1.006 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.6092 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0881 r_free=0.1898 After: r_work=0.0884 r_free=0.1897 ================================== NQH flips ================================== r_work=0.0884 r_free=0.1897 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=0.0885 r_free=0.1895 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0885 r_free=0.1895 | n_water=236 | time (s): 0.540 (total time: 0.540) Filter (dist) r_work=0.0899 r_free=0.1894 | n_water=230 | time (s): 18.640 (total time: 19.180) Filter (q & B) r_work=0.0975 r_free=0.1917 | n_water=228 | time (s): 1.680 (total time: 20.860) Compute maps r_work=0.0975 r_free=0.1917 | n_water=228 | time (s): 0.670 (total time: 21.530) Filter (map) r_work=0.1240 r_free=0.1955 | n_water=162 | time (s): 1.580 (total time: 23.110) Find peaks r_work=0.1240 r_free=0.1955 | n_water=162 | time (s): 0.530 (total time: 23.640) Add new water r_work=0.1538 r_free=0.2205 | n_water=234 | time (s): 1.850 (total time: 25.490) Refine new water occ: r_work=0.1002 r_free=0.1882 adp: r_work=0.0998 r_free=0.1885 occ: r_work=0.0990 r_free=0.1873 adp: r_work=0.0990 r_free=0.1878 occ: r_work=0.0985 r_free=0.1869 adp: r_work=0.0984 r_free=0.1875 ADP+occupancy (water only), MIN, final r_work=0.0984 r_free=0.1875 r_work=0.0984 r_free=0.1875 | n_water=234 | time (s): 8.330 (total time: 33.820) Filter (q & B) r_work=0.0985 r_free=0.1877 | n_water=233 | time (s): 1.610 (total time: 35.430) Filter (dist only) r_work=0.0984 r_free=0.1884 | n_water=232 | time (s): 18.330 (total time: 53.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.992698 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.220660 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 0.0925 0.1912 0.0986 0.010 1.1 6.7 0.5 0.0 0 0.496 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.25 19.12 9.86 8.052 18.225 0.221 5.021 9.07 19.43 10.36 9.079 18.346 0.221 4.963 Individual atomic B min max mean iso aniso Overall: 0.00 113.77 16.92 11.99 1759 0 Protein: 0.00 113.77 15.86 11.94 1519 0 Water: 0.79 55.83 23.46 N/A 232 0 Other: 9.14 51.03 28.71 N/A 8 0 Chain A: 0.00 113.77 16.37 N/A 1634 0 Chain S: 0.79 50.99 24.12 N/A 125 0 Histogram: Values Number of atoms 0.00 - 11.38 710 11.38 - 22.75 625 22.75 - 34.13 254 34.13 - 45.51 96 45.51 - 56.89 40 56.89 - 68.26 17 68.26 - 79.64 7 79.64 - 91.02 4 91.02 - 102.39 4 102.39 - 113.77 2 =========================== Idealize ADP of riding H ========================== r_work=0.0907 r_free=0.1943 r_work=0.0912 r_free=0.1945 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0912 r_free = 0.1945 target_work(ml) = 4.970 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0904 r_free = 0.1926 target_work(ml) = 4.963 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0904 r_free= 0.1926 coordinate error (max.-lik. estimate): 0.25 A | | | | normalized target function (ml) (work): 4.962751 | | target function (ml) not normalized (work): 24426.659836 | | target function (ml) not normalized (free): 2266.109269 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1298 0.1899 5.5597 6.2677| | 2: 3.78 - 3.00 1.00 2430 110 0.0423 0.1972 4.3506 12.51| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.91 12.63 1.00 0.97 14419.08| | 2: 3.78 - 3.00 2430 110 0.99 1.86 1.00 0.99 896.32| |alpha: min = 0.96 max = 1.00 mean = 0.98| |beta: min = 566.60 max = 24416.85 mean = 7742.87| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.59 mean = 7.32| |phase err.(test): min = 0.00 max = 74.46 mean = 7.14| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0955 0.0904 0.1926 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2137 0.2139 0.2267 n_refl.: 5174 remove outliers: r(all,work,free)=0.2137 0.2139 0.2267 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2137 0.2139 0.2267 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0952 0.0902 0.1926 n_refl.: 5174 remove outliers: r(all,work,free)=0.0952 0.0902 0.1926 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.4040 330.219 294.790 0.609 0.986 0.319 11.894-9.307 99.02 97 4 0.1944 525.539 511.289 0.987 0.992 0.319 9.237-7.194 100.00 213 7 0.2264 429.787 416.635 1.043 0.995 0.310 7.162-5.571 100.00 427 22 0.2134 322.503 312.831 1.029 0.997 0.270 5.546-4.326 100.00 867 58 0.1029 442.751 437.482 1.070 1.000 0.236 4.315-3.360 100.00 1859 96 0.0568 421.061 420.608 1.147 1.003 0.230 3.356-3.002 100.00 1373 60 0.0401 324.319 324.183 1.119 1.007 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.3552 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3619 0.2062 0.083 5.295 8.8 119.3 19.9 258 0.000 1_bss: 0.1543 0.1644 0.083 5.295 6.0 116.4 17.0 258 0.000 1_settarget: 0.1543 0.1644 0.083 5.295 6.0 116.4 17.0 258 0.000 1_nqh: 0.1546 0.1653 0.083 5.295 6.0 116.4 17.0 258 0.007 1_weight: 0.1546 0.1653 0.083 5.295 6.0 116.4 17.0 258 0.007 1_xyzrec: 0.1169 0.1797 0.010 0.985 6.0 116.4 17.0 258 0.206 1_adp: 0.1026 0.1800 0.010 0.985 1.9 112.1 17.3 258 0.206 1_regHadp: 0.1021 0.1809 0.010 0.985 1.9 112.1 17.3 258 0.206 1_occ: 0.1014 0.1800 0.010 0.985 1.9 112.1 17.3 258 0.206 2_bss: 0.1015 0.1797 0.010 0.985 1.0 111.2 16.4 258 0.206 2_settarget: 0.1015 0.1797 0.010 0.985 1.0 111.2 16.4 258 0.206 2_updatecdl: 0.1015 0.1797 0.010 1.011 1.0 111.2 16.4 258 0.206 2_nqh: 0.1015 0.1797 0.010 1.011 1.0 111.2 16.4 258 0.206 2_sol: 0.1139 0.1668 0.010 1.011 1.0 111.2 15.8 226 n/a 2_weight: 0.1139 0.1668 0.010 1.011 1.0 111.2 15.8 226 n/a 2_xyzrec: 0.1023 0.1828 0.009 0.962 1.0 111.2 15.8 226 n/a 2_adp: 0.0956 0.1841 0.009 0.962 0.0 109.7 16.5 226 n/a 2_regHadp: 0.0952 0.1842 0.009 0.962 0.0 109.7 16.5 226 n/a 2_occ: 0.0947 0.1827 0.009 0.962 0.0 109.7 16.5 226 n/a 3_bss: 0.0946 0.1830 0.009 0.962 0.0 109.7 16.5 226 n/a 3_settarget: 0.0946 0.1830 0.009 0.962 0.0 109.7 16.5 226 n/a 3_updatecdl: 0.0946 0.1830 0.009 0.967 0.0 109.7 16.5 226 n/a 3_nqh: 0.0948 0.1825 0.009 0.967 0.0 109.7 16.5 226 n/a 3_sol: 0.1045 0.1720 0.009 0.967 0.0 109.7 16.3 236 n/a 3_weight: 0.1045 0.1720 0.009 0.967 0.0 109.7 16.3 236 n/a 3_xyzrec: 0.0937 0.1822 0.010 1.015 0.0 109.7 16.3 236 n/a 3_adp: 0.0897 0.1827 0.010 1.015 0.0 109.3 16.3 236 n/a 3_regHadp: 0.0902 0.1840 0.010 1.015 0.0 109.3 16.3 236 n/a 3_occ: 0.0891 0.1817 0.010 1.015 0.0 109.3 16.3 236 n/a 4_bss: 0.0883 0.1790 0.010 1.015 0.0 109.3 16.3 236 n/a 4_settarget: 0.0883 0.1790 0.010 1.015 0.0 109.3 16.3 236 n/a 4_updatecdl: 0.0883 0.1790 0.010 1.016 0.0 109.3 16.3 236 n/a 4_nqh: 0.0887 0.1795 0.010 1.016 0.0 109.3 16.3 236 n/a 4_sol: 0.1008 0.1828 0.010 1.016 0.0 109.3 16.5 236 n/a 4_weight: 0.1008 0.1828 0.010 1.016 0.0 109.3 16.5 236 n/a 4_xyzrec: 0.0916 0.1849 0.010 1.006 0.0 109.3 16.5 236 n/a 4_adp: 0.0891 0.1909 0.010 1.006 0.0 111.4 16.7 236 n/a 4_regHadp: 0.0895 0.1920 0.010 1.006 0.0 111.4 16.7 236 n/a 4_occ: 0.0881 0.1903 0.010 1.006 0.0 111.4 16.7 236 n/a 5_bss: 0.0881 0.1898 0.010 1.006 0.0 111.4 16.7 236 n/a 5_settarget: 0.0881 0.1898 0.010 1.006 0.0 111.4 16.7 236 n/a 5_updatecdl: 0.0881 0.1898 0.010 1.016 0.0 111.4 16.7 236 n/a 5_setrh: 0.0884 0.1897 0.010 1.016 0.0 111.4 16.7 236 n/a 5_nqh: 0.0885 0.1895 0.010 1.016 0.0 111.4 16.7 236 n/a 5_sol: 0.0984 0.1884 0.010 1.016 0.0 111.4 16.7 232 n/a 5_weight: 0.0984 0.1884 0.010 1.016 0.0 111.4 16.7 232 n/a 5_xyzrec: 0.0925 0.1912 0.010 1.117 0.0 111.4 16.7 232 n/a 5_adp: 0.0907 0.1943 0.010 1.117 0.0 113.8 16.9 232 n/a 5_regHadp: 0.0912 0.1945 0.010 1.117 0.0 113.8 16.9 232 n/a 5_occ: 0.0904 0.1926 0.010 1.117 0.0 113.8 16.9 232 n/a end: 0.0902 0.1926 0.010 1.117 0.0 113.8 16.9 232 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8831905_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_8831905_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0700 Refinement macro-cycles (run) : 475.7900 Write final files (write_after_run_outputs) : 12.0500 Total : 490.9100 Total CPU time: 8.56 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:54 PST -0800 (1735492734.94 s) Start R-work = 0.1543, R-free = 0.1644 Final R-work = 0.0902, R-free = 0.1926 =============================================================================== Job complete usr+sys time: 522.08 seconds wall clock time: 9 minutes 4.20 seconds (544.20 seconds total)