Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7509253.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=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7509253.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7509253.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.23, per 1000 atoms: 0.36 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: 0.28 Conformation dependent library (CDL) restraints added in 104.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.62 - 0.91: 515 0.91 - 1.20: 1164 1.20 - 1.48: 846 1.48 - 1.77: 619 1.77 - 2.05: 9 Bond restraints: 3153 Sorted by residual: bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.556 -0.230 1.10e-02 8.26e+03 4.37e+02 bond pdb=" C GLU A 163 " pdb=" N PHE A 164 " ideal model delta sigma weight residual 1.334 1.554 -0.220 1.20e-02 6.94e+03 3.36e+02 bond pdb=" C ALYS A 132 " pdb=" O ALYS A 132 " ideal model delta sigma weight residual 1.236 1.024 0.212 1.16e-02 7.43e+03 3.34e+02 bond pdb=" C SER A 142 " pdb=" O SER A 142 " ideal model delta sigma weight residual 1.234 1.456 -0.222 1.26e-02 6.30e+03 3.10e+02 bond pdb=" CA ALA A 79 " pdb=" C ALA A 79 " ideal model delta sigma weight residual 1.523 1.288 0.235 1.35e-02 5.49e+03 3.04e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.85: 3238 4.85 - 9.70: 1869 9.70 - 14.54: 583 14.54 - 19.39: 79 19.39 - 24.24: 8 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA ALYS A 132 " pdb=" C ALYS A 132 " pdb=" N MET A 133 " ideal model delta sigma weight residual 116.79 99.92 16.87 1.28e+00 6.10e-01 1.74e+02 angle pdb=" CA THR A 140 " pdb=" C THR A 140 " pdb=" O THR A 140 " ideal model delta sigma weight residual 120.36 134.46 -14.10 1.08e+00 8.57e-01 1.70e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.43 132.88 -10.45 8.10e-01 1.52e+00 1.66e+02 angle pdb=" O AGLU A 90 " pdb=" C AGLU A 90 " pdb=" N ILE A 91 " ideal model delta sigma weight residual 122.07 108.94 13.13 1.03e+00 9.43e-01 1.63e+02 angle pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 107.20 95.14 12.06 1.00e+00 1.00e+00 1.45e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 1280 15.53 - 31.06: 134 31.06 - 46.59: 37 46.59 - 62.12: 24 62.12 - 77.65: 6 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N VAL A 23 " pdb=" C VAL A 23 " pdb=" CA VAL A 23 " pdb=" CB VAL A 23 " ideal model delta harmonic sigma weight residual 123.40 106.53 16.87 0 2.50e+00 1.60e-01 4.55e+01 dihedral pdb=" C CYS A 46 " pdb=" N CYS A 46 " pdb=" CA CYS A 46 " pdb=" CB CYS A 46 " ideal model delta harmonic sigma weight residual -122.60 -138.47 15.87 0 2.50e+00 1.60e-01 4.03e+01 dihedral pdb=" C VAL A 123 " pdb=" N VAL A 123 " pdb=" CA VAL A 123 " pdb=" CB VAL A 123 " ideal model delta harmonic sigma weight residual -122.00 -137.47 15.47 0 2.50e+00 1.60e-01 3.83e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.198: 92 0.198 - 0.392: 83 0.392 - 0.587: 41 0.587 - 0.782: 19 0.782 - 0.977: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA SER A 161 " pdb=" N SER A 161 " pdb=" C SER A 161 " pdb=" CB SER A 161 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.38e+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 -1.65 -0.94 2.00e-01 2.50e+01 2.21e+01 chirality pdb=" CB VAL A 23 " pdb=" CA VAL A 23 " pdb=" CG1 VAL A 23 " pdb=" CG2 VAL A 23 " both_signs ideal model delta sigma weight residual False -2.63 -3.51 0.88 2.00e-01 2.50e+01 1.95e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " 0.084 9.50e-02 1.11e+02 7.51e-02 1.10e+02 pdb=" NE ARG A 5 " -0.079 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.128 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.070 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.115 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.032 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB AASN A 97 " -0.069 2.00e-02 2.50e+03 8.55e-02 1.10e+02 pdb=" CG AASN A 97 " 0.109 2.00e-02 2.50e+03 pdb=" OD1AASN A 97 " -0.038 2.00e-02 2.50e+03 pdb=" ND2AASN A 97 " 0.126 2.00e-02 2.50e+03 pdb="HD21AASN A 97 " -0.092 2.00e-02 2.50e+03 pdb="HD22AASN A 97 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 115 " -0.055 2.00e-02 2.50e+03 6.88e-02 1.06e+02 pdb=" CG HIS A 115 " 0.020 2.00e-02 2.50e+03 pdb=" ND1 HIS A 115 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 HIS A 115 " 0.051 2.00e-02 2.50e+03 pdb=" CE1 HIS A 115 " -0.104 2.00e-02 2.50e+03 pdb=" NE2 HIS A 115 " -0.031 2.00e-02 2.50e+03 pdb=" HD2 HIS A 115 " 0.065 2.00e-02 2.50e+03 pdb=" HE1 HIS A 115 " 0.119 2.00e-02 2.50e+03 pdb=" HE2 HIS A 115 " -0.078 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1340 2.37 - 2.92: 8350 2.92 - 3.48: 10476 3.48 - 4.04: 15047 4.04 - 4.60: 21459 Nonbonded interactions: 56672 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.807 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.814 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.827 2.450 nonbonded pdb=" H GLY A 120 " pdb=" O HIS A 138 " model vdw 1.838 2.450 nonbonded pdb=" H VAL A 35 " pdb=" OD2 ASP A 55 " model vdw 1.862 2.450 ... (remaining 56667 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 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 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_7509253_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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2796 r_free= 0.1834 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.411450 | | target function (ml) not normalized (work): 71655.186963 | | target function (ml) not normalized (free): 3271.913007 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3195 0.2119 7.5613 5.0379| | 2: 3.63 - 2.88 1.00 2711 122 0.2631 0.1647 4.3263 4.3168| | 3: 2.88 - 2.52 1.00 2682 148 0.2594 0.1724 4.183 4.1844| | 4: 2.52 - 2.29 1.00 2661 139 0.2590 0.1579 3.5096 3.5456| | 5: 2.29 - 2.13 1.00 2678 122 0.2633 0.1609 3.4022 3.4826| | 6: 2.13 - 2.00 1.00 2692 117 0.2764 0.2034 3.3217 3.4806| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 17.54 0.77 0.23 1291.12| | 2: 3.63 - 2.88 2711 122 0.83 23.76 1.31 0.23 1291.12| | 3: 2.88 - 2.52 2682 148 0.73 32.79 1.29 0.23 1291.12| | 4: 2.52 - 2.29 2661 139 0.93 11.58 1.30 0.26 140.11| | 5: 2.29 - 2.13 2678 122 0.92 13.77 1.32 0.26 140.11| | 6: 2.13 - 2.00 2692 117 0.89 16.78 1.33 0.26 140.11| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 140.11 max = 1291.12 mean = 722.02| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.93 mean = 19.37| |phase err.(test): min = 0.00 max = 89.31 mean = 19.49| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.082 0.249 1557 Z= 5.469 Angle : 5.342 18.550 2118 Z= 3.795 Chirality : 0.368 0.977 243 Planarity : 0.032 0.115 284 Dihedral : 13.964 77.646 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % 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: -2.44 (0.49), residues: 224 helix: -2.44 (0.39), residues: 103 sheet: -0.73 (0.80), residues: 38 loop : -0.56 (0.66), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.021 ARG A 98 TYR 0.108 0.046 TYR A 139 PHE 0.094 0.039 PHE A 164 HIS 0.035 0.016 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2796 r_free= 0.1834 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.411450 | | target function (ml) not normalized (work): 71655.186963 | | target function (ml) not normalized (free): 3271.913007 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3405 percent. r_work = 0.2930 r_free = 0.1992 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2876 0.2930 0.1992 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2876 0.2930 0.1992 n_refl.: 17050 remove outliers: r(all,work,free)=0.2166 0.2177 0.1992 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2138 0.2149 0.1973 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1615 0.1613 0.1660 n_refl.: 17045 remove outliers: r(all,work,free)=0.1613 0.1611 0.1660 n_refl.: 17043 ======================== 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 0.3860 398.735 362.299 0.648 1.018 0.397 11.894-9.307 99.02 97 4 0.1839 633.285 614.271 0.930 1.019 0.375 9.237-7.194 100.00 213 7 0.2193 517.963 509.646 0.950 1.018 0.371 7.162-5.571 100.00 427 22 0.2336 388.732 376.345 0.915 1.016 0.321 5.546-4.326 100.00 867 58 0.1374 533.667 528.687 0.954 1.013 0.211 4.315-3.360 100.00 1859 96 0.1310 507.522 503.105 1.017 1.008 0.201 3.356-2.611 100.00 3867 181 0.1640 333.413 329.129 1.013 0.999 0.034 2.608-2.000 99.99 8818 434 0.1650 217.328 213.340 1.037 0.984 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4670 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1611 r_free=0.1660 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1611 r_free=0.1660 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.225157 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.968055 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1348 0.1630 0.0282 0.009 1.0 1.3 0.5 0.0 0 12.113 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.48 16.30 2.82 3.013 18.447 0.968 0.022 12.76 16.50 3.74 3.703 18.743 0.968 0.020 Individual atomic B min max mean iso aniso Overall: 5.97 113.89 20.03 4.14 1785 0 Protein: 5.97 113.16 17.27 4.15 1519 0 Water: 9.12 113.89 36.09 N/A 258 0 Other: 21.47 36.86 26.31 N/A 8 0 Chain A: 5.97 113.89 20.03 N/A 1785 0 Histogram: Values Number of atoms 5.97 - 16.76 1066 16.76 - 27.55 357 27.55 - 38.35 186 38.35 - 49.14 100 49.14 - 59.93 48 59.93 - 70.72 13 70.72 - 81.51 7 81.51 - 92.30 4 92.30 - 103.10 1 103.10 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1276 r_free=0.1650 r_work=0.1280 r_free=0.1656 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1280 r_free = 0.1656 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1275 r_free = 0.1643 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1275 r_free= 0.1643 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019909 | | target function (ls_wunit_k1) not normalized (work): 323.239743 | | target function (ls_wunit_k1) not normalized (free): 26.595594 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1293 0.1275 0.1643 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1910 0.1909 0.1988 n_refl.: 17043 remove outliers: r(all,work,free)=0.1910 0.1909 0.1988 n_refl.: 17043 overall B=-0.39 to atoms: r(all,work,free)=0.1881 0.1880 0.1971 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1293 0.1276 0.1635 n_refl.: 17043 remove outliers: r(all,work,free)=0.1291 0.1274 0.1635 n_refl.: 17041 ======================== 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 0.3424 306.431 281.994 0.632 1.010 0.370 11.894-9.307 99.02 97 4 0.1683 487.577 477.800 0.917 1.010 0.366 9.237-7.194 100.00 213 7 0.1809 398.789 396.240 0.958 1.010 0.351 7.162-5.571 100.00 427 22 0.1847 299.292 293.731 0.929 1.009 0.311 5.546-4.326 100.00 867 58 0.1041 410.879 408.381 0.958 1.007 0.221 4.315-3.360 100.00 1859 96 0.0925 390.750 390.237 1.018 1.005 0.191 3.356-2.611 100.00 3867 181 0.1294 256.701 255.459 1.015 1.000 0.081 2.608-2.000 99.99 8818 434 0.1356 167.325 165.868 1.024 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4073 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1274 r_free=0.1635 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1274 r_free=0.1635 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1274 r_free=0.1635 | n_water=258 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.1281 r_free=0.1623 | n_water=252 | time (s): 18.630 (total time: 19.350) Filter (q & B) r_work=0.1281 r_free=0.1622 | n_water=250 | time (s): 1.560 (total time: 20.910) Compute maps r_work=0.1281 r_free=0.1622 | n_water=250 | time (s): 0.640 (total time: 21.550) Filter (map) r_work=0.1313 r_free=0.1619 | n_water=215 | time (s): 2.220 (total time: 23.770) Find peaks r_work=0.1313 r_free=0.1619 | n_water=215 | time (s): 0.630 (total time: 24.400) Add new water r_work=0.1538 r_free=0.1837 | n_water=371 | time (s): 1.860 (total time: 26.260) Refine new water occ: r_work=0.1340 r_free=0.1600 adp: r_work=0.1280 r_free=0.1582 occ: r_work=0.1285 r_free=0.1572 adp: r_work=0.1251 r_free=0.1567 occ: r_work=0.1251 r_free=0.1563 adp: r_work=0.1240 r_free=0.1561 ADP+occupancy (water only), MIN, final r_work=0.1240 r_free=0.1561 r_work=0.1240 r_free=0.1561 | n_water=371 | time (s): 10.300 (total time: 36.560) Filter (q & B) r_work=0.1241 r_free=0.1563 | n_water=364 | time (s): 1.870 (total time: 38.430) Filter (dist only) r_work=0.1241 r_free=0.1563 | n_water=363 | time (s): 30.480 (total time: 68.910) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.845915 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.990277 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1210 0.1598 0.0387 0.008 0.9 2.2 0.5 0.0 0 12.423 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.10 15.98 3.87 4.213 21.164 0.990 0.018 11.96 16.26 4.30 4.248 21.435 0.990 0.017 Individual atomic B min max mean iso aniso Overall: 6.95 107.76 21.47 4.28 1890 0 Protein: 6.95 107.76 17.79 4.26 1519 0 Water: 8.74 74.65 36.53 N/A 363 0 Other: 24.40 46.90 35.31 N/A 8 0 Chain A: 6.95 107.76 19.61 N/A 1742 0 Chain S: 17.49 67.54 43.35 N/A 148 0 Histogram: Values Number of atoms 6.95 - 17.03 1034 17.03 - 27.11 372 27.11 - 37.19 225 37.19 - 47.27 152 47.27 - 57.36 71 57.36 - 67.44 23 67.44 - 77.52 6 77.52 - 87.60 4 87.60 - 97.68 1 97.68 - 107.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.1196 r_free=0.1626 r_work=0.1197 r_free=0.1628 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1197 r_free = 0.1628 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1193 r_free = 0.1629 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1193 r_free= 0.1629 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016852 | | target function (ls_wunit_k1) not normalized (work): 273.581813 | | target function (ls_wunit_k1) not normalized (free): 25.094650 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1193 0.1629 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1766 0.1755 0.2010 n_refl.: 17041 remove outliers: r(all,work,free)=0.1766 0.1755 0.2010 n_refl.: 17041 overall B=-0.41 to atoms: r(all,work,free)=0.1739 0.1728 0.1990 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1208 0.1187 0.1621 n_refl.: 17041 remove outliers: r(all,work,free)=0.1208 0.1187 0.1621 n_refl.: 17041 ======================== 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 0.3192 306.431 286.354 0.614 1.002 0.350 11.894-9.307 99.02 97 4 0.1490 487.577 483.260 0.917 1.003 0.344 9.237-7.194 100.00 213 7 0.1656 398.789 398.060 0.974 1.003 0.310 7.162-5.571 100.00 427 22 0.1544 299.292 295.065 0.939 1.003 0.283 5.546-4.326 100.00 867 58 0.0888 410.879 406.844 0.959 1.003 0.221 4.315-3.360 100.00 1859 96 0.0819 390.750 389.452 1.018 1.002 0.201 3.356-2.611 100.00 3867 181 0.1193 256.701 256.125 1.014 1.001 0.058 2.608-2.000 99.99 8818 434 0.1334 167.325 166.684 1.019 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.4540 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1187 r_free=0.1621 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1187 r_free=0.1621 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1187 r_free=0.1621 | n_water=363 | time (s): 0.600 (total time: 0.600) Filter (dist) r_work=0.1186 r_free=0.1623 | n_water=362 | time (s): 27.390 (total time: 27.990) Filter (q & B) r_work=0.1186 r_free=0.1623 | n_water=362 | time (s): 1.200 (total time: 29.190) Compute maps r_work=0.1186 r_free=0.1623 | n_water=362 | time (s): 0.780 (total time: 29.970) Filter (map) r_work=0.1249 r_free=0.1635 | n_water=264 | time (s): 2.030 (total time: 32.000) Find peaks r_work=0.1249 r_free=0.1635 | n_water=264 | time (s): 0.680 (total time: 32.680) Add new water r_work=0.1434 r_free=0.1825 | n_water=410 | time (s): 1.990 (total time: 34.670) Refine new water occ: r_work=0.1251 r_free=0.1605 adp: r_work=0.1242 r_free=0.1613 occ: r_work=0.1226 r_free=0.1584 adp: r_work=0.1213 r_free=0.1589 occ: r_work=0.1205 r_free=0.1575 adp: r_work=0.1194 r_free=0.1575 ADP+occupancy (water only), MIN, final r_work=0.1194 r_free=0.1575 r_work=0.1194 r_free=0.1575 | n_water=410 | time (s): 22.840 (total time: 57.510) Filter (q & B) r_work=0.1199 r_free=0.1581 | n_water=396 | time (s): 2.030 (total time: 59.540) Filter (dist only) r_work=0.1199 r_free=0.1581 | n_water=396 | time (s): 29.520 (total time: 89.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.958662 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.146819 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1180 0.1567 0.0387 0.009 1.0 4.8 0.5 0.0 0 0.979 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.80 15.67 3.87 4.342 21.560 0.147 4.999 11.60 15.78 4.18 4.841 21.524 0.147 4.976 Individual atomic B min max mean iso aniso Overall: 6.46 105.10 20.99 4.67 1923 0 Protein: 6.46 105.10 17.11 4.66 1519 0 Water: 8.95 69.25 35.64 N/A 396 0 Other: 24.75 46.26 33.58 N/A 8 0 Chain A: 6.46 105.10 18.89 N/A 1737 0 Chain S: 18.71 65.58 40.62 N/A 186 0 Histogram: Values Number of atoms 6.46 - 16.33 1059 16.33 - 26.19 357 26.19 - 36.05 222 36.05 - 45.92 166 45.92 - 55.78 72 55.78 - 65.65 33 65.65 - 75.51 6 75.51 - 85.37 4 85.37 - 95.24 2 95.24 - 105.10 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1578 r_work=0.1160 r_free=0.1579 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1160 r_free = 0.1579 target_work(ml) = 4.976 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1153 r_free = 0.1580 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1153 r_free= 0.1580 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.971662 | | target function (ml) not normalized (work): 80709.956928 | | target function (ml) not normalized (free): 4193.746827 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1174 0.1153 0.1580 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1687 0.1679 0.1885 n_refl.: 17041 remove outliers: r(all,work,free)=0.1687 0.1679 0.1885 n_refl.: 17041 overall B=-0.39 to atoms: r(all,work,free)=0.1659 0.1651 0.1870 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1170 0.1150 0.1576 n_refl.: 17041 remove outliers: r(all,work,free)=0.1170 0.1150 0.1576 n_refl.: 17041 ======================== 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 0.3498 306.431 284.426 0.594 1.006 0.360 11.894-9.307 99.02 97 4 0.1653 487.577 481.431 0.906 1.007 0.338 9.237-7.194 100.00 213 7 0.1788 398.789 399.034 0.979 1.007 0.269 7.162-5.571 100.00 427 22 0.1599 299.292 293.797 0.935 1.006 0.224 5.546-4.326 100.00 867 58 0.0941 410.879 406.891 0.960 1.005 0.209 4.315-3.360 100.00 1859 96 0.0906 390.750 388.245 1.012 1.004 0.201 3.356-2.611 100.00 3867 181 0.1291 256.701 254.322 1.013 1.001 0.142 2.608-2.000 99.99 8818 434 0.1091 167.325 165.937 1.020 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3950 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1150 r_free=0.1576 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1150 r_free=0.1576 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1150 r_free=0.1576 | n_water=396 | time (s): 0.920 (total time: 0.920) Filter (dist) r_work=0.1153 r_free=0.1574 | n_water=395 | time (s): 32.980 (total time: 33.900) Filter (q & B) r_work=0.1153 r_free=0.1574 | n_water=395 | time (s): 0.930 (total time: 34.830) Compute maps r_work=0.1153 r_free=0.1574 | n_water=395 | time (s): 0.720 (total time: 35.550) Filter (map) r_work=0.1205 r_free=0.1619 | n_water=307 | time (s): 2.160 (total time: 37.710) Find peaks r_work=0.1205 r_free=0.1619 | n_water=307 | time (s): 0.420 (total time: 38.130) Add new water r_work=0.1352 r_free=0.1762 | n_water=451 | time (s): 1.890 (total time: 40.020) Refine new water occ: r_work=0.1186 r_free=0.1555 adp: r_work=0.1179 r_free=0.1568 occ: r_work=0.1161 r_free=0.1529 adp: r_work=0.1152 r_free=0.1539 occ: r_work=0.1144 r_free=0.1511 adp: r_work=0.1136 r_free=0.1519 ADP+occupancy (water only), MIN, final r_work=0.1136 r_free=0.1519 r_work=0.1136 r_free=0.1519 | n_water=451 | time (s): 33.020 (total time: 73.040) Filter (q & B) r_work=0.1140 r_free=0.1520 | n_water=444 | time (s): 1.970 (total time: 75.010) Filter (dist only) r_work=0.1140 r_free=0.1520 | n_water=444 | time (s): 33.050 (total time: 108.060) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.031959 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.161844 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1123 0.1568 0.0446 0.010 1.0 5.1 0.5 0.0 0 1.016 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.23 15.68 4.46 4.497 21.265 0.162 4.965 11.12 15.66 4.53 4.646 21.304 0.162 4.959 Individual atomic B min max mean iso aniso Overall: 6.10 103.49 21.23 4.82 1971 0 Protein: 6.10 103.49 16.74 4.81 1519 0 Water: 8.74 63.86 36.45 N/A 444 0 Other: 23.73 42.31 30.76 N/A 8 0 Chain A: 6.10 103.49 18.44 N/A 1735 0 Chain S: 18.48 62.25 41.78 N/A 236 0 Histogram: Values Number of atoms 6.10 - 15.84 1053 15.84 - 25.57 361 25.57 - 35.31 219 35.31 - 45.05 181 45.05 - 54.79 106 54.79 - 64.53 38 64.53 - 74.27 3 74.27 - 84.01 5 84.01 - 93.75 2 93.75 - 103.49 3 =========================== Idealize ADP of riding H ========================== r_work=0.1112 r_free=0.1566 r_work=0.1113 r_free=0.1566 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1113 r_free = 0.1566 target_work(ml) = 4.959 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1104 r_free = 0.1565 target_work(ml) = 4.953 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1104 r_free= 0.1565 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.952785 | | target function (ml) not normalized (work): 80403.511287 | | target function (ml) not normalized (free): 4193.106287 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1126 0.1104 0.1565 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1606 0.1591 0.1928 n_refl.: 17041 remove outliers: r(all,work,free)=0.1606 0.1591 0.1928 n_refl.: 17041 overall B=-0.33 to atoms: r(all,work,free)=0.1585 0.1569 0.1915 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1125 0.1102 0.1562 n_refl.: 17041 remove outliers: r(all,work,free)=0.1125 0.1102 0.1562 n_refl.: 17041 ======================== 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 0.3604 306.431 281.919 0.568 1.001 0.350 11.894-9.307 99.02 97 4 0.1716 487.577 481.383 0.910 1.003 0.330 9.237-7.194 100.00 213 7 0.1730 398.789 400.597 0.986 1.003 0.235 7.162-5.571 100.00 427 22 0.1540 299.292 293.679 0.940 1.003 0.215 5.546-4.326 100.00 867 58 0.0894 410.879 407.151 0.964 1.003 0.200 4.315-3.360 100.00 1859 96 0.0868 390.750 388.536 1.010 1.002 0.191 3.356-2.611 100.00 3867 181 0.1231 256.701 254.525 1.008 1.001 0.141 2.608-2.000 99.99 8818 434 0.1043 167.325 166.088 1.008 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.1299 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1102 r_free=0.1562 After: r_work=0.1105 r_free=0.1561 ================================== NQH flips ================================== r_work=0.1105 r_free=0.1561 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1105 r_free=0.1561 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1105 r_free=0.1561 | n_water=444 | time (s): 0.930 (total time: 0.930) Filter (dist) r_work=0.1105 r_free=0.1561 | n_water=444 | time (s): 34.820 (total time: 35.750) Filter (q & B) r_work=0.1105 r_free=0.1561 | n_water=444 | time (s): 1.510 (total time: 37.260) Compute maps r_work=0.1105 r_free=0.1561 | n_water=444 | time (s): 0.720 (total time: 37.980) Filter (map) r_work=0.1181 r_free=0.1597 | n_water=337 | time (s): 2.050 (total time: 40.030) Find peaks r_work=0.1181 r_free=0.1597 | n_water=337 | time (s): 0.640 (total time: 40.670) Add new water r_work=0.1302 r_free=0.1721 | n_water=477 | time (s): 2.020 (total time: 42.690) Refine new water occ: r_work=0.1151 r_free=0.1534 adp: r_work=0.1145 r_free=0.1541 occ: r_work=0.1127 r_free=0.1508 adp: r_work=0.1120 r_free=0.1515 occ: r_work=0.1111 r_free=0.1496 adp: r_work=0.1104 r_free=0.1498 ADP+occupancy (water only), MIN, final r_work=0.1104 r_free=0.1498 r_work=0.1104 r_free=0.1498 | n_water=477 | time (s): 25.090 (total time: 67.780) Filter (q & B) r_work=0.1107 r_free=0.1510 | n_water=467 | time (s): 1.570 (total time: 69.350) Filter (dist only) r_work=0.1107 r_free=0.1510 | n_water=467 | time (s): 37.740 (total time: 107.090) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.044908 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.175242 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1129 0.1524 0.0395 0.010 1.1 10.9 0.5 0.0 0 1.022 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.29 15.24 3.95 4.543 21.111 0.175 4.949 11.19 15.20 4.01 4.605 21.235 0.175 4.942 Individual atomic B min max mean iso aniso Overall: 5.57 102.91 21.43 5.08 1994 0 Protein: 5.57 102.91 16.55 5.07 1519 0 Water: 7.94 69.37 37.17 N/A 467 0 Other: 23.34 40.46 30.32 N/A 8 0 Chain A: 5.57 102.91 18.23 N/A 1735 0 Chain S: 18.99 69.37 42.90 N/A 259 0 Histogram: Values Number of atoms 5.57 - 15.31 1029 15.31 - 25.04 375 25.04 - 34.78 213 34.78 - 44.51 195 44.51 - 54.24 130 54.24 - 63.98 30 63.98 - 73.71 12 73.71 - 83.45 3 83.45 - 93.18 3 93.18 - 102.91 4 =========================== Idealize ADP of riding H ========================== r_work=0.1119 r_free=0.1520 r_work=0.1119 r_free=0.1520 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1119 r_free = 0.1520 target_work(ml) = 4.942 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1112 r_free = 0.1513 target_work(ml) = 4.936 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1112 r_free= 0.1513 coordinate error (max.-lik. estimate): 0.08 A | | | | normalized target function (ml) (work): 4.935952 | | target function (ml) not normalized (work): 80130.252377 | | target function (ml) not normalized (free): 4161.335260 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1107 0.1412 5.4538 5.6885| | 2: 3.63 - 2.88 1.00 2711 122 0.1097 0.1505 5.2199 5.3256| | 3: 2.88 - 2.52 1.00 2681 148 0.1382 0.1636 5.1338 5.1743| | 4: 2.52 - 2.29 1.00 2661 139 0.0940 0.1474 4.6265 4.9268| | 5: 2.29 - 2.13 1.00 2678 122 0.0969 0.1461 4.5777 4.8718| | 6: 2.13 - 2.00 1.00 2692 117 0.1139 0.1832 4.5745 4.8048| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2811 159 0.95 9.00 1.00 0.96 6333.64| | 2: 3.63 - 2.88 2711 122 0.92 12.77 1.01 0.96 6333.64| | 3: 2.88 - 2.52 2681 148 0.87 19.02 0.99 0.96 6333.64| | 4: 2.52 - 2.29 2661 139 0.93 11.93 1.01 0.98 2099.41| | 5: 2.29 - 2.13 2678 122 0.91 14.08 1.00 0.98 2099.41| | 6: 2.13 - 2.00 2692 117 0.89 16.81 0.99 0.98 2099.41| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2099.41 max = 6333.64 mean = 4238.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.97 mean = 13.90| |phase err.(test): min = 0.00 max = 87.57 mean = 13.60| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1131 0.1112 0.1513 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1600 0.1586 0.1883 n_refl.: 17041 remove outliers: r(all,work,free)=0.1600 0.1586 0.1883 n_refl.: 17041 overall B=-0.28 to atoms: r(all,work,free)=0.1582 0.1568 0.1871 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1131 0.1112 0.1514 n_refl.: 17041 remove outliers: r(all,work,free)=0.1131 0.1111 0.1514 n_refl.: 17040 ======================== 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 93.75 85 5 0.3507 302.941 284.259 0.571 1.003 0.350 11.894-9.307 99.02 97 4 0.1707 487.577 481.974 0.908 1.004 0.340 9.237-7.194 100.00 213 7 0.1686 398.789 399.955 0.987 1.005 0.229 7.162-5.571 100.00 427 22 0.1500 299.292 293.978 0.936 1.004 0.227 5.546-4.326 100.00 867 58 0.0923 410.879 407.679 0.963 1.004 0.201 4.315-3.360 100.00 1859 96 0.0881 390.750 388.519 1.005 1.003 0.191 3.356-2.611 100.00 3867 181 0.1252 256.701 254.261 1.005 1.000 0.121 2.608-2.000 99.99 8818 434 0.1047 167.325 165.899 1.001 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9582 b_overall=-0.9491 ================= 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 : 0.2796 0.1834 0.082 5.342 8.8 119.3 19.9 258 0.000 1_bss: 0.1611 0.1660 0.082 5.342 8.4 118.9 19.5 258 0.000 1_settarget: 0.1611 0.1660 0.082 5.342 8.4 118.9 19.5 258 0.000 1_nqh: 0.1611 0.1660 0.082 5.342 8.4 118.9 19.5 258 0.000 1_weight: 0.1611 0.1660 0.082 5.342 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1348 0.1630 0.009 0.993 8.4 118.9 19.5 258 0.143 1_adp: 0.1276 0.1650 0.009 0.993 6.0 113.9 20.0 258 0.143 1_regHadp: 0.1280 0.1656 0.009 0.993 6.0 113.9 20.0 258 0.143 1_occ: 0.1275 0.1643 0.009 0.993 6.0 113.9 20.0 258 0.143 2_bss: 0.1274 0.1635 0.009 0.993 5.6 113.5 19.6 258 0.143 2_settarget: 0.1274 0.1635 0.009 0.993 5.6 113.5 19.6 258 0.143 2_updatecdl: 0.1274 0.1635 0.009 1.007 5.6 113.5 19.6 258 0.143 2_nqh: 0.1274 0.1635 0.009 1.007 5.6 113.5 19.6 258 0.143 2_sol: 0.1241 0.1563 0.009 1.007 5.6 112.8 21.0 363 n/a 2_weight: 0.1241 0.1563 0.009 1.007 5.6 112.8 21.0 363 n/a 2_xyzrec: 0.1210 0.1598 0.008 0.933 5.6 112.8 21.0 363 n/a 2_adp: 0.1196 0.1626 0.008 0.933 6.9 107.8 21.5 363 n/a 2_regHadp: 0.1197 0.1628 0.008 0.933 6.9 107.8 21.5 363 n/a 2_occ: 0.1193 0.1629 0.008 0.933 6.9 107.8 21.5 363 n/a 3_bss: 0.1187 0.1621 0.008 0.933 6.5 107.4 21.1 363 n/a 3_settarget: 0.1187 0.1621 0.008 0.933 6.5 107.4 21.1 363 n/a 3_updatecdl: 0.1187 0.1621 0.008 0.931 6.5 107.4 21.1 363 n/a 3_nqh: 0.1187 0.1621 0.008 0.931 6.5 107.4 21.1 363 n/a 3_sol: 0.1199 0.1581 0.008 0.931 6.5 107.4 21.1 396 n/a 3_weight: 0.1199 0.1581 0.008 0.931 6.5 107.4 21.1 396 n/a 3_xyzrec: 0.1180 0.1567 0.009 0.970 6.5 107.4 21.1 396 n/a 3_adp: 0.1160 0.1578 0.009 0.970 6.5 105.1 21.0 396 n/a 3_regHadp: 0.1160 0.1579 0.009 0.970 6.5 105.1 21.0 396 n/a 3_occ: 0.1153 0.1580 0.009 0.970 6.5 105.1 21.0 396 n/a 4_bss: 0.1150 0.1576 0.009 0.970 6.1 104.7 20.6 396 n/a 4_settarget: 0.1150 0.1576 0.009 0.970 6.1 104.7 20.6 396 n/a 4_updatecdl: 0.1150 0.1576 0.009 0.970 6.1 104.7 20.6 396 n/a 4_nqh: 0.1150 0.1576 0.009 0.970 6.1 104.7 20.6 396 n/a 4_sol: 0.1140 0.1520 0.009 0.970 6.1 104.7 21.2 444 n/a 4_weight: 0.1140 0.1520 0.009 0.970 6.1 104.7 21.2 444 n/a 4_xyzrec: 0.1123 0.1568 0.010 0.993 6.1 104.7 21.2 444 n/a 4_adp: 0.1112 0.1566 0.010 0.993 6.1 103.5 21.2 444 n/a 4_regHadp: 0.1113 0.1566 0.010 0.993 6.1 103.5 21.2 444 n/a 4_occ: 0.1104 0.1565 0.010 0.993 6.1 103.5 21.2 444 n/a 5_bss: 0.1102 0.1562 0.010 0.993 5.8 103.2 20.9 444 n/a 5_settarget: 0.1102 0.1562 0.010 0.993 5.8 103.2 20.9 444 n/a 5_updatecdl: 0.1102 0.1562 0.010 0.995 5.8 103.2 20.9 444 n/a 5_setrh: 0.1105 0.1561 0.010 0.995 5.8 103.2 20.9 444 n/a 5_nqh: 0.1105 0.1561 0.010 0.995 5.8 103.2 20.9 444 n/a 5_sol: 0.1107 0.1510 0.010 0.995 5.8 103.2 21.2 467 n/a 5_weight: 0.1107 0.1510 0.010 0.995 5.8 103.2 21.2 467 n/a 5_xyzrec: 0.1129 0.1524 0.010 1.062 5.8 103.2 21.2 467 n/a 5_adp: 0.1119 0.1520 0.010 1.062 5.6 102.9 21.4 467 n/a 5_regHadp: 0.1119 0.1520 0.010 1.062 5.6 102.9 21.4 467 n/a 5_occ: 0.1112 0.1513 0.010 1.062 5.6 102.9 21.4 467 n/a end: 0.1111 0.1514 0.010 1.062 5.3 102.6 21.2 467 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7509253_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_7509253_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1300 Refinement macro-cycles (run) : 903.4800 Write final files (write_after_run_outputs) : 23.9800 Total : 931.5900 Total CPU time: 15.90 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:55 PST -0800 (1735494055.82 s) Start R-work = 0.1611, R-free = 0.1660 Final R-work = 0.1111, R-free = 0.1514 =============================================================================== Job complete usr+sys time: 980.69 seconds wall clock time: 16 minutes 43.70 seconds (1003.70 seconds total)