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_2655235.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" 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" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2655235.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2655235.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 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: 1.56, per 1000 atoms: 0.46 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: 0.32 Conformation dependent library (CDL) restraints added in 138.1 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.90: 478 0.90 - 1.15: 1138 1.15 - 1.40: 568 1.40 - 1.64: 894 1.64 - 1.89: 75 Bond restraints: 3153 Sorted by residual: bond pdb=" CA ILE A 91 " pdb=" CB ILE A 91 " ideal model delta sigma weight residual 1.540 1.301 0.239 1.11e-02 8.12e+03 4.63e+02 bond pdb=" NE ARG A 27 " pdb=" CZ ARG A 27 " ideal model delta sigma weight residual 1.326 1.093 0.233 1.10e-02 8.26e+03 4.47e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.111 0.210 1.00e-02 1.00e+04 4.40e+02 bond pdb=" CA ALA A 167 " pdb=" C ALA A 167 " ideal model delta sigma weight residual 1.523 1.260 0.263 1.30e-02 5.92e+03 4.11e+02 bond pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 1.237 1.422 -0.186 1.07e-02 8.73e+03 3.01e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 2865 4.17 - 8.34: 1869 8.34 - 12.51: 804 12.51 - 16.68: 215 16.68 - 20.85: 24 Bond angle restraints: 5777 Sorted by residual: angle pdb=" OE1AGLN A 80 " pdb=" CD AGLN A 80 " pdb=" NE2AGLN A 80 " ideal model delta sigma weight residual 122.60 139.16 -16.56 1.00e+00 1.00e+00 2.74e+02 angle pdb=" O GLY A 40 " pdb=" C GLY A 40 " pdb=" N BLYS A 41 " ideal model delta sigma weight residual 123.06 109.64 13.42 9.50e-01 1.11e+00 1.99e+02 angle pdb=" O LYS A 182 " pdb=" C LYS A 182 " pdb=" N ALA A 183 " ideal model delta sigma weight residual 122.15 106.60 15.55 1.14e+00 7.69e-01 1.86e+02 angle pdb=" O VAL A 35 " pdb=" C VAL A 35 " pdb=" N ALA A 36 " ideal model delta sigma weight residual 122.62 107.57 15.05 1.17e+00 7.31e-01 1.66e+02 angle pdb=" O SER A 142 " pdb=" C SER A 142 " pdb=" N GLU A 143 " ideal model delta sigma weight residual 123.27 138.96 -15.69 1.22e+00 6.72e-01 1.65e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.91: 1322 17.91 - 35.80: 109 35.80 - 53.69: 34 53.69 - 71.58: 14 71.58 - 89.48: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ILE A 21 " pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual -122.00 -142.55 20.55 0 2.50e+00 1.60e-01 6.76e+01 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 -142.64 20.04 0 2.50e+00 1.60e-01 6.43e+01 dihedral pdb=" N ILE A 21 " pdb=" C ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta harmonic sigma weight residual 123.40 141.68 -18.28 0 2.50e+00 1.60e-01 5.35e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.188: 91 0.188 - 0.373: 75 0.373 - 0.558: 47 0.558 - 0.742: 20 0.742 - 0.927: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA BLYS A 99 " pdb=" N BLYS A 99 " pdb=" C BLYS A 99 " pdb=" CB BLYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.58 0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" CA THR A 140 " pdb=" N THR A 140 " pdb=" C THR A 140 " pdb=" CB THR A 140 " both_signs ideal model delta sigma weight residual False 2.53 1.62 0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA LYS A 62 " pdb=" N LYS A 62 " pdb=" C LYS A 62 " pdb=" CB LYS A 62 " both_signs ideal model delta sigma weight residual False 2.51 1.61 0.90 2.00e-01 2.50e+01 2.04e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.093 2.00e-02 2.50e+03 6.35e-02 1.21e+02 pdb=" CG PHE A 164 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.084 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.047 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.069 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.018 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.019 2.00e-02 2.50e+03 5.90e-02 1.04e+02 pdb=" CG BTYR A 67 " 0.013 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.026 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.071 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.096 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.062 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " -0.092 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.010 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.052 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " 0.017 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " 0.014 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " 0.103 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BASN A 97 " -0.003 2.00e-02 2.50e+03 8.06e-02 9.74e+01 pdb=" CG BASN A 97 " 0.098 2.00e-02 2.50e+03 pdb=" OD1BASN A 97 " -0.037 2.00e-02 2.50e+03 pdb=" ND2BASN A 97 " -0.151 2.00e-02 2.50e+03 pdb="HD21BASN A 97 " 0.066 2.00e-02 2.50e+03 pdb="HD22BASN A 97 " 0.028 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.37: 1400 2.37 - 2.93: 8341 2.93 - 3.48: 10427 3.48 - 4.04: 15040 4.04 - 4.60: 21376 Nonbonded interactions: 56584 Sorted by model distance: nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.810 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.823 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.847 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O PHE A 162 " pdb=" H LEU A 166 " model vdw 1.848 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.856 2.100 ... (remaining 56579 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_2655235_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3627 r_free= 0.2071 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.460919 | | target function (ml) not normalized (work): 21992.332443 | | target function (ml) not normalized (free): 1153.067808 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3814 0.2271 4.8556 4.9371| | 2: 3.78 - 3.00 1.00 2430 110 0.3398 0.1733 4.0548 4.109| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.92 0.83 0.13 6614.12| | 2: 3.78 - 3.00 2430 110 0.94 11.19 1.48 0.26 438.30| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 366.22 max = 12077.07 mean = 3570.06| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.32| |phase err.(test): min = 0.00 max = 89.99 mean = 33.09| |-----------------------------------------------------------------------------| ----------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 0.263 1557 Z= 5.670 Angle : 5.286 17.753 2118 Z= 3.726 Chirality : 0.365 0.927 243 Planarity : 0.033 0.083 284 Dihedral : 14.241 89.475 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.54 % Allowed : 2.16 % Favored : 97.30 % Rotamer: Outliers : 1.24 % Allowed : 3.11 % Favored : 95.65 % Cbeta Deviations : 32.97 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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: -2.84 (0.47), residues: 224 helix: -2.55 (0.37), residues: 107 sheet: -0.26 (0.83), residues: 38 loop : -1.38 (0.58), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.085 0.022 ARG A 5 TYR 0.058 0.025 TYR A 139 PHE 0.058 0.025 PHE A 164 HIS 0.053 0.025 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3627 r_free= 0.2071 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.460919 | | target function (ml) not normalized (work): 21992.332443 | | target function (ml) not normalized (free): 1153.067808 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3578 0.3658 0.2143 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3578 0.3658 0.2143 n_refl.: 5182 remove outliers: r(all,work,free)=0.2533 0.2557 0.2143 n_refl.: 5178 overall B=-2.82 to atoms: r(all,work,free)=0.2424 0.2446 0.2092 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1556 0.1553 0.1602 n_refl.: 5178 remove outliers: r(all,work,free)=0.1554 0.1551 0.1602 n_refl.: 5177 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.4112 444.940 407.332 0.648 1.100 0.409 11.894-9.307 99.02 97 4 0.1906 714.296 693.916 0.915 1.093 0.401 9.237-7.194 100.00 213 7 0.2190 584.153 573.582 0.953 1.082 0.369 7.162-5.571 100.00 427 22 0.2331 438.336 422.742 0.914 1.064 0.308 5.546-4.326 100.00 867 58 0.1365 601.772 593.888 0.966 1.035 0.226 4.315-3.360 100.00 1859 96 0.1316 572.292 565.115 1.061 0.985 0.200 3.356-3.002 100.00 1373 60 0.1541 440.803 433.438 1.089 0.936 0.082 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.6305 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1551 r_free=0.1602 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1551 r_free=0.1602 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.776995 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.858131 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 0.1158 0.1803 0.0644 0.010 1.0 2.9 0.5 0.0 0 9.388 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 18.03 6.44 3.013 16.034 1.858 0.018 10.22 17.88 7.66 4.789 16.164 1.858 0.015 Individual atomic B min max mean iso aniso Overall: 2.20 111.54 17.31 5.22 1785 0 Protein: 2.20 111.54 14.59 5.21 1519 0 Water: 4.04 111.47 33.12 N/A 258 0 Other: 17.74 37.20 23.74 N/A 8 0 Chain A: 2.20 111.54 17.31 N/A 1785 0 Histogram: Values Number of atoms 2.20 - 13.14 929 13.14 - 24.07 474 24.07 - 35.00 187 35.00 - 45.94 110 45.94 - 56.87 56 56.87 - 67.81 12 67.81 - 78.74 8 78.74 - 89.67 5 89.67 - 100.61 1 100.61 - 111.54 3 =========================== Idealize ADP of riding H ========================== r_work=0.1022 r_free=0.1788 r_work=0.1016 r_free=0.1795 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1016 r_free = 0.1795 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 = 0.1027 r_free = 0.1808 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1027 r_free= 0.1808 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.014416 | | target function (ls_wunit_k1) not normalized (work): 70.997716 | | target function (ls_wunit_k1) not normalized (free): 10.662530 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1067 0.1027 0.1808 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2116 0.2115 0.2240 n_refl.: 5177 remove outliers: r(all,work,free)=0.2116 0.2115 0.2240 n_refl.: 5177 overall B=-0.99 to atoms: r(all,work,free)=0.2073 0.2071 0.2231 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1075 0.1035 0.1816 n_refl.: 5177 remove outliers: r(all,work,free)=0.1073 0.1033 0.1816 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 0.3409 324.605 308.994 0.663 1.003 0.365 11.894-9.307 99.02 97 4 0.1521 525.599 517.874 0.988 1.005 0.361 9.237-7.194 100.00 213 7 0.1721 429.835 429.348 1.036 1.005 0.341 7.162-5.571 100.00 427 22 0.1672 322.539 319.320 0.989 1.004 0.302 5.546-4.326 100.00 867 58 0.0944 442.801 439.637 0.998 1.002 0.207 4.315-3.360 100.00 1859 96 0.0783 421.108 420.830 1.046 0.999 0.193 3.356-3.002 100.00 1373 60 0.1003 324.355 322.254 1.013 0.996 0.062 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.5349 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1033 r_free=0.1816 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1033 r_free=0.1816 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1033 r_free=0.1816 | n_water=258 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.1069 r_free=0.1815 | n_water=247 | time (s): 20.530 (total time: 21.090) Filter (q & B) r_work=0.1067 r_free=0.1814 | n_water=244 | time (s): 1.400 (total time: 22.490) Compute maps r_work=0.1067 r_free=0.1814 | n_water=244 | time (s): 0.450 (total time: 22.940) Filter (map) r_work=0.1345 r_free=0.1897 | n_water=146 | time (s): 1.540 (total time: 24.480) Find peaks r_work=0.1345 r_free=0.1897 | n_water=146 | time (s): 0.500 (total time: 24.980) Add new water r_work=0.1677 r_free=0.2175 | n_water=225 | time (s): 1.780 (total time: 26.760) Refine new water occ: r_work=0.1174 r_free=0.1706 adp: r_work=0.1151 r_free=0.1710 occ: r_work=0.1148 r_free=0.1698 adp: r_work=0.1138 r_free=0.1698 occ: r_work=0.1137 r_free=0.1687 adp: r_work=0.1135 r_free=0.1691 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1691 r_work=0.1135 r_free=0.1691 | n_water=225 | time (s): 3.510 (total time: 30.270) Filter (q & B) r_work=0.1135 r_free=0.1691 | n_water=225 | time (s): 0.920 (total time: 31.190) Filter (dist only) r_work=0.1137 r_free=0.1695 | n_water=223 | time (s): 18.170 (total time: 49.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.421294 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.735273 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 0.1030 0.1830 0.0800 0.009 1.0 4.2 0.5 0.0 0 11.211 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.30 18.30 8.00 4.612 16.551 2.735 0.014 9.60 18.56 8.96 5.482 16.916 2.735 0.013 Individual atomic B min max mean iso aniso Overall: 0.00 107.03 16.25 6.45 1750 0 Protein: 0.00 107.03 14.75 6.43 1519 0 Water: 0.00 62.76 26.04 N/A 223 0 Other: 11.97 43.62 26.69 N/A 8 0 Chain A: 0.00 107.03 15.52 N/A 1671 0 Chain S: 0.00 56.20 31.58 N/A 79 0 Histogram: Values Number of atoms 0.00 - 10.70 694 10.70 - 21.41 651 21.41 - 32.11 210 32.11 - 42.81 118 42.81 - 53.52 42 53.52 - 64.22 23 64.22 - 74.92 5 74.92 - 85.63 3 85.63 - 96.33 2 96.33 - 107.03 2 =========================== Idealize ADP of riding H ========================== r_work=0.0960 r_free=0.1856 r_work=0.0957 r_free=0.1857 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0957 r_free = 0.1857 target_work(ls_wunit_k1) = 0.013 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0948 r_free = 0.1853 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0948 r_free= 0.1853 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.012320 | | target function (ls_wunit_k1) not normalized (work): 60.664526 | | target function (ls_wunit_k1) not normalized (free): 10.274160 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0994 0.0948 0.1853 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2145 0.2148 0.2232 n_refl.: 5176 remove outliers: r(all,work,free)=0.2145 0.2148 0.2232 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2145 0.2148 0.2232 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0993 0.0947 0.1858 n_refl.: 5176 remove outliers: r(all,work,free)=0.0993 0.0947 0.1858 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 0.3456 324.605 308.565 0.663 1.007 0.360 11.894-9.307 99.02 97 4 0.1474 525.599 518.756 0.982 1.008 0.350 9.237-7.194 100.00 213 7 0.1491 429.835 429.169 1.026 1.008 0.340 7.162-5.571 100.00 427 22 0.1431 322.539 320.277 0.996 1.007 0.300 5.546-4.326 100.00 867 58 0.0813 442.801 440.468 1.004 1.004 0.230 4.315-3.360 100.00 1859 96 0.0726 421.108 421.013 1.056 0.999 0.210 3.356-3.002 100.00 1373 60 0.0966 324.355 323.120 1.030 0.995 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.1437 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0947 r_free=0.1858 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0947 r_free=0.1858 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0947 r_free=0.1858 | n_water=223 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.0969 r_free=0.1833 | n_water=217 | time (s): 17.830 (total time: 18.390) Filter (q & B) r_work=0.1034 r_free=0.1844 | n_water=214 | time (s): 1.390 (total time: 19.780) Compute maps r_work=0.1034 r_free=0.1844 | n_water=214 | time (s): 0.530 (total time: 20.310) Filter (map) r_work=0.1289 r_free=0.1882 | n_water=147 | time (s): 1.620 (total time: 21.930) Find peaks r_work=0.1289 r_free=0.1882 | n_water=147 | time (s): 0.500 (total time: 22.430) Add new water r_work=0.1682 r_free=0.2247 | n_water=234 | time (s): 1.460 (total time: 23.890) Refine new water occ: r_work=0.1064 r_free=0.1840 adp: r_work=0.1057 r_free=0.1851 occ: r_work=0.1046 r_free=0.1830 adp: r_work=0.1046 r_free=0.1837 occ: r_work=0.1036 r_free=0.1818 adp: r_work=0.1035 r_free=0.1827 ADP+occupancy (water only), MIN, final r_work=0.1035 r_free=0.1827 r_work=0.1035 r_free=0.1827 | n_water=234 | time (s): 12.530 (total time: 36.420) Filter (q & B) r_work=0.1036 r_free=0.1826 | n_water=233 | time (s): 1.280 (total time: 37.700) Filter (dist only) r_work=0.1033 r_free=0.1827 | n_water=232 | time (s): 17.660 (total time: 55.360) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.109291 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.213201 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 0.0944 0.1871 0.0927 0.011 1.1 4.5 0.5 0.0 0 0.555 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.44 18.71 9.27 5.384 17.539 0.213 5.163 9.06 18.77 9.70 7.178 17.549 0.213 5.071 Individual atomic B min max mean iso aniso Overall: 0.00 105.69 16.14 8.78 1759 0 Protein: 0.00 105.69 14.91 8.76 1519 0 Water: 0.00 58.71 23.88 N/A 232 0 Other: 8.72 42.27 26.24 N/A 8 0 Chain A: 0.00 105.69 15.56 N/A 1657 0 Chain S: 0.00 58.71 25.55 N/A 102 0 Histogram: Values Number of atoms 0.00 - 10.57 686 10.57 - 21.14 659 21.14 - 31.71 226 31.71 - 42.28 117 42.28 - 52.85 36 52.85 - 63.42 17 63.42 - 73.99 8 73.99 - 84.56 5 84.56 - 95.13 4 95.13 - 105.69 1 =========================== Idealize ADP of riding H ========================== r_work=0.0906 r_free=0.1877 r_work=0.0912 r_free=0.1885 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0912 r_free = 0.1885 target_work(ml) = 5.074 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0903 r_free = 0.1859 target_work(ml) = 5.067 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0903 r_free= 0.1859 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.067016 | | target function (ml) not normalized (work): 24949.984339 | | target function (ml) not normalized (free): 1896.481783 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0951 0.0903 0.1859 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2154 0.2162 0.2165 n_refl.: 5176 remove outliers: r(all,work,free)=0.2154 0.2162 0.2165 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2154 0.2162 0.2165 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0941 0.0895 0.1831 n_refl.: 5176 remove outliers: r(all,work,free)=0.0939 0.0893 0.1831 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3728 326.726 293.907 0.574 0.996 0.324 11.894-9.307 99.02 97 4 0.1906 525.599 509.643 0.939 1.000 0.315 9.237-7.194 100.00 213 7 0.1958 429.835 422.033 1.009 1.001 0.310 7.162-5.571 100.00 427 22 0.1878 322.539 313.371 0.987 1.001 0.289 5.546-4.326 100.00 867 58 0.0906 442.801 437.989 0.999 1.002 0.230 4.315-3.360 100.00 1859 96 0.0570 421.108 420.888 1.058 1.002 0.220 3.356-3.002 100.00 1373 60 0.0626 324.355 323.566 1.032 1.001 0.071 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9172 b_overall=-6.3654 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0893 r_free=0.1831 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0893 r_free=0.1831 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0893 r_free=0.1831 | n_water=232 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.0907 r_free=0.1839 | n_water=228 | time (s): 19.160 (total time: 19.750) Filter (q & B) r_work=0.0986 r_free=0.1867 | n_water=225 | time (s): 1.570 (total time: 21.320) Compute maps r_work=0.0986 r_free=0.1867 | n_water=225 | time (s): 0.500 (total time: 21.820) Filter (map) r_work=0.1264 r_free=0.1938 | n_water=152 | time (s): 1.540 (total time: 23.360) Find peaks r_work=0.1264 r_free=0.1938 | n_water=152 | time (s): 0.470 (total time: 23.830) Add new water r_work=0.1584 r_free=0.2299 | n_water=231 | time (s): 1.450 (total time: 25.280) Refine new water occ: r_work=0.0998 r_free=0.1793 adp: r_work=0.0991 r_free=0.1793 occ: r_work=0.0985 r_free=0.1782 adp: r_work=0.0983 r_free=0.1784 occ: r_work=0.0978 r_free=0.1772 adp: r_work=0.0976 r_free=0.1774 ADP+occupancy (water only), MIN, final r_work=0.0976 r_free=0.1774 r_work=0.0976 r_free=0.1774 | n_water=231 | time (s): 19.370 (total time: 44.650) Filter (q & B) r_work=0.0977 r_free=0.1781 | n_water=228 | time (s): 1.430 (total time: 46.080) Filter (dist only) r_work=0.0984 r_free=0.1775 | n_water=224 | time (s): 18.180 (total time: 64.260) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.982680 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.254001 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 0.0898 0.1888 0.0990 0.011 1.0 5.1 0.5 0.6 0 0.491 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.98 18.88 9.90 6.851 17.624 0.254 5.046 8.75 19.22 10.47 8.226 17.740 0.254 4.979 Individual atomic B min max mean iso aniso Overall: 0.00 104.96 16.35 10.72 1751 0 Protein: 0.00 104.96 15.34 10.72 1519 0 Water: 0.00 57.62 22.87 N/A 224 0 Other: 12.72 41.94 25.92 N/A 8 0 Chain A: 0.00 104.96 15.85 N/A 1644 0 Chain S: 0.00 57.62 24.08 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.50 674 10.50 - 20.99 620 20.99 - 31.49 260 31.49 - 41.98 121 41.98 - 52.48 42 52.48 - 62.98 15 62.98 - 73.47 8 73.47 - 83.97 6 83.97 - 94.46 4 94.46 - 104.96 1 =========================== Idealize ADP of riding H ========================== r_work=0.0875 r_free=0.1922 r_work=0.0879 r_free=0.1928 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0879 r_free = 0.1928 target_work(ml) = 4.985 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0871 r_free = 0.1924 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0871 r_free= 0.1924 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.978040 | | target function (ml) not normalized (work): 24506.892450 | | target function (ml) not normalized (free): 2188.589057 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0924 0.0871 0.1924 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2136 0.2135 0.2297 n_refl.: 5175 remove outliers: r(all,work,free)=0.2136 0.2135 0.2297 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2136 0.2135 0.2297 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0923 0.0870 0.1934 n_refl.: 5175 remove outliers: r(all,work,free)=0.0923 0.0870 0.1934 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3706 326.726 291.284 0.576 0.988 0.320 11.894-9.307 99.02 97 4 0.1946 525.599 510.927 0.947 0.993 0.320 9.237-7.194 100.00 213 7 0.2069 429.835 421.912 1.013 0.996 0.320 7.162-5.571 100.00 427 22 0.1995 322.539 313.526 1.000 0.998 0.310 5.546-4.326 100.00 867 58 0.0963 442.801 436.737 1.007 1.000 0.230 4.315-3.360 100.00 1859 96 0.0537 421.108 420.857 1.072 1.002 0.220 3.356-3.002 100.00 1373 60 0.0478 324.355 323.818 1.049 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.1473 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0870 r_free=0.1934 After: r_work=0.0873 r_free=0.1932 ================================== NQH flips ================================== r_work=0.0873 r_free=0.1932 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0873 r_free=0.1932 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0873 r_free=0.1932 | n_water=224 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.0895 r_free=0.1928 | n_water=220 | time (s): 17.930 (total time: 18.490) Filter (q & B) r_work=0.1011 r_free=0.1937 | n_water=217 | time (s): 1.460 (total time: 19.950) Compute maps r_work=0.1011 r_free=0.1937 | n_water=217 | time (s): 0.550 (total time: 20.500) Filter (map) r_work=0.1272 r_free=0.1966 | n_water=157 | time (s): 1.870 (total time: 22.370) Find peaks r_work=0.1272 r_free=0.1966 | n_water=157 | time (s): 0.390 (total time: 22.760) Add new water r_work=0.1576 r_free=0.2193 | n_water=228 | time (s): 1.330 (total time: 24.090) Refine new water occ: r_work=0.1006 r_free=0.1889 adp: r_work=0.0996 r_free=0.1901 occ: r_work=0.0989 r_free=0.1883 adp: r_work=0.0988 r_free=0.1893 occ: r_work=0.0981 r_free=0.1877 adp: r_work=0.0980 r_free=0.1884 ADP+occupancy (water only), MIN, final r_work=0.0980 r_free=0.1884 r_work=0.0980 r_free=0.1884 | n_water=228 | time (s): 11.840 (total time: 35.930) Filter (q & B) r_work=0.0980 r_free=0.1889 | n_water=227 | time (s): 1.430 (total time: 37.360) Filter (dist only) r_work=0.0977 r_free=0.1888 | n_water=226 | time (s): 17.940 (total time: 55.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.004032 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.221526 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 0.0905 0.1918 0.1014 0.011 1.1 7.4 0.5 0.6 0 0.502 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.05 19.18 10.14 8.137 18.118 0.222 5.010 8.86 19.44 10.58 9.081 18.235 0.222 4.960 Individual atomic B min max mean iso aniso Overall: 0.00 109.78 16.77 12.00 1753 0 Protein: 0.00 109.78 15.77 12.00 1519 0 Water: 0.00 59.64 23.15 N/A 226 0 Other: 11.47 41.01 26.82 N/A 8 0 Chain A: 0.00 109.78 16.21 N/A 1635 0 Chain S: 0.00 59.64 24.51 N/A 118 0 Histogram: Values Number of atoms 0.00 - 10.98 692 10.98 - 21.96 614 21.96 - 32.94 261 32.94 - 43.91 109 43.91 - 54.89 40 54.89 - 65.87 17 65.87 - 76.85 10 76.85 - 87.83 4 87.83 - 98.81 4 98.81 - 109.78 2 =========================== Idealize ADP of riding H ========================== r_work=0.0886 r_free=0.1944 r_work=0.0890 r_free=0.1949 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0890 r_free = 0.1949 target_work(ml) = 4.968 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0881 r_free = 0.1937 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0881 r_free= 0.1937 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.962147 | | target function (ml) not normalized (work): 24428.648081 | | target function (ml) not normalized (free): 2256.511559 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1245 0.1895 5.5192 6.2832| | 2: 3.78 - 3.00 1.00 2430 110 0.0436 0.2007 4.3907 12.403| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.91 12.18 1.00 0.98 13294.62| | 2: 3.78 - 3.00 2430 110 0.99 1.91 1.00 1.00 952.97| |alpha: min = 0.97 max = 1.01 mean = 0.99| |beta: min = 621.86 max = 22412.26 mean = 7202.76| |figures of merit: min = 0.01 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.52 mean = 7.11| |phase err.(test): min = 0.00 max = 89.20 mean = 7.71| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0933 0.0881 0.1937 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2167 0.2166 0.2330 n_refl.: 5175 remove outliers: r(all,work,free)=0.2167 0.2166 0.2330 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2167 0.2166 0.2330 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0931 0.0879 0.1931 n_refl.: 5175 remove outliers: r(all,work,free)=0.0931 0.0879 0.1931 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3714 326.726 299.300 0.596 0.986 0.320 11.894-9.307 99.02 97 4 0.1915 525.599 510.075 0.952 0.992 0.320 9.237-7.194 100.00 213 7 0.2150 429.835 418.314 1.008 0.996 0.312 7.162-5.571 100.00 427 22 0.2077 322.539 311.325 0.995 0.998 0.305 5.546-4.326 100.00 867 58 0.1003 442.801 437.188 1.018 1.000 0.230 4.315-3.360 100.00 1859 96 0.0553 421.108 420.695 1.090 1.003 0.230 3.356-3.002 100.00 1373 60 0.0417 324.355 324.346 1.071 1.006 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.0697 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3627 0.2071 0.083 5.286 8.8 119.3 19.9 258 0.000 1_bss: 0.1551 0.1602 0.083 5.286 6.0 116.5 17.1 258 0.000 1_settarget: 0.1551 0.1602 0.083 5.286 6.0 116.5 17.1 258 0.000 1_nqh: 0.1551 0.1602 0.083 5.286 6.0 116.5 17.1 258 0.000 1_weight: 0.1551 0.1602 0.083 5.286 6.0 116.5 17.1 258 0.000 1_xyzrec: 0.1158 0.1803 0.010 0.956 6.0 116.5 17.1 258 0.209 1_adp: 0.1022 0.1788 0.010 0.956 2.2 111.5 17.3 258 0.209 1_regHadp: 0.1016 0.1795 0.010 0.956 2.2 111.5 17.3 258 0.209 1_occ: 0.1027 0.1808 0.010 0.956 2.2 111.5 17.3 258 0.209 2_bss: 0.1033 0.1816 0.010 0.956 1.2 110.5 16.3 258 0.209 2_settarget: 0.1033 0.1816 0.010 0.956 1.2 110.5 16.3 258 0.209 2_updatecdl: 0.1033 0.1816 0.010 0.976 1.2 110.5 16.3 258 0.209 2_nqh: 0.1033 0.1816 0.010 0.976 1.2 110.5 16.3 258 0.209 2_sol: 0.1137 0.1695 0.010 0.976 1.0 110.5 15.5 223 n/a 2_weight: 0.1137 0.1695 0.010 0.976 1.0 110.5 15.5 223 n/a 2_xyzrec: 0.1030 0.1830 0.009 0.977 1.0 110.5 15.5 223 n/a 2_adp: 0.0960 0.1856 0.009 0.977 0.0 107.0 16.2 223 n/a 2_regHadp: 0.0957 0.1857 0.009 0.977 0.0 107.0 16.2 223 n/a 2_occ: 0.0948 0.1853 0.009 0.977 0.0 107.0 16.2 223 n/a 3_bss: 0.0947 0.1858 0.009 0.977 0.0 107.0 16.2 223 n/a 3_settarget: 0.0947 0.1858 0.009 0.977 0.0 107.0 16.2 223 n/a 3_updatecdl: 0.0947 0.1858 0.009 0.981 0.0 107.0 16.2 223 n/a 3_nqh: 0.0947 0.1858 0.009 0.981 0.0 107.0 16.2 223 n/a 3_sol: 0.1033 0.1827 0.009 0.981 0.0 107.0 16.1 232 n/a 3_weight: 0.1033 0.1827 0.009 0.981 0.0 107.0 16.1 232 n/a 3_xyzrec: 0.0944 0.1871 0.011 1.070 0.0 107.0 16.1 232 n/a 3_adp: 0.0906 0.1877 0.011 1.070 0.0 105.7 16.1 232 n/a 3_regHadp: 0.0912 0.1885 0.011 1.070 0.0 105.7 16.1 232 n/a 3_occ: 0.0903 0.1859 0.011 1.070 0.0 105.7 16.1 232 n/a 4_bss: 0.0893 0.1831 0.011 1.070 0.0 105.7 16.1 232 n/a 4_settarget: 0.0893 0.1831 0.011 1.070 0.0 105.7 16.1 232 n/a 4_updatecdl: 0.0893 0.1831 0.011 1.077 0.0 105.7 16.1 232 n/a 4_nqh: 0.0893 0.1831 0.011 1.077 0.0 105.7 16.1 232 n/a 4_sol: 0.0984 0.1775 0.011 1.077 0.0 105.7 16.1 224 n/a 4_weight: 0.0984 0.1775 0.011 1.077 0.0 105.7 16.1 224 n/a 4_xyzrec: 0.0898 0.1888 0.011 1.048 0.0 105.7 16.1 224 n/a 4_adp: 0.0875 0.1922 0.011 1.048 0.0 105.0 16.4 224 n/a 4_regHadp: 0.0879 0.1928 0.011 1.048 0.0 105.0 16.4 224 n/a 4_occ: 0.0871 0.1924 0.011 1.048 0.0 105.0 16.4 224 n/a 5_bss: 0.0870 0.1934 0.011 1.048 0.0 105.0 16.4 224 n/a 5_settarget: 0.0870 0.1934 0.011 1.048 0.0 105.0 16.4 224 n/a 5_updatecdl: 0.0870 0.1934 0.011 1.053 0.0 105.0 16.4 224 n/a 5_setrh: 0.0873 0.1932 0.011 1.053 0.0 105.0 16.4 224 n/a 5_nqh: 0.0873 0.1932 0.011 1.053 0.0 105.0 16.4 224 n/a 5_sol: 0.0977 0.1888 0.011 1.053 0.0 105.0 16.5 226 n/a 5_weight: 0.0977 0.1888 0.011 1.053 0.0 105.0 16.5 226 n/a 5_xyzrec: 0.0905 0.1918 0.011 1.112 0.0 105.0 16.5 226 n/a 5_adp: 0.0886 0.1944 0.011 1.112 0.0 109.8 16.8 226 n/a 5_regHadp: 0.0890 0.1949 0.011 1.112 0.0 109.8 16.8 226 n/a 5_occ: 0.0881 0.1937 0.011 1.112 0.0 109.8 16.8 226 n/a end: 0.0879 0.1931 0.011 1.112 0.0 109.8 16.8 226 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2655235_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2655235_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1500 Refinement macro-cycles (run) : 490.0800 Write final files (write_after_run_outputs) : 10.0000 Total : 503.2300 Total CPU time: 8.72 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:03 PST -0800 (1735492743.81 s) Start R-work = 0.1551, R-free = 0.1602 Final R-work = 0.0879, R-free = 0.1931 =============================================================================== Job complete usr+sys time: 530.28 seconds wall clock time: 9 minutes 11.73 seconds (551.73 seconds total)