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_6024882.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 { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6024882.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6024882.pdb" 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" } 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 6 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: 2.07, per 1000 atoms: 0.61 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: 0.29 Conformation dependent library (CDL) restraints added in 115.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.91: 489 0.91 - 1.16: 1142 1.16 - 1.41: 599 1.41 - 1.65: 864 1.65 - 1.90: 59 Bond restraints: 3153 Sorted by residual: bond pdb=" N GLY A 108 " pdb=" CA GLY A 108 " ideal model delta sigma weight residual 1.444 1.641 -0.198 8.80e-03 1.29e+04 5.05e+02 bond pdb=" CA GLY A 108 " pdb=" C GLY A 108 " ideal model delta sigma weight residual 1.511 1.385 0.126 6.90e-03 2.10e+04 3.35e+02 bond pdb=" CA VAL A 35 " pdb=" CB VAL A 35 " ideal model delta sigma weight residual 1.533 1.325 0.208 1.14e-02 7.69e+03 3.33e+02 bond pdb=" N GLY A 174 " pdb=" CA GLY A 174 " ideal model delta sigma weight residual 1.447 1.267 0.179 9.90e-03 1.02e+04 3.28e+02 bond pdb=" C LEU A 7 " pdb=" O LEU A 7 " ideal model delta sigma weight residual 1.236 1.035 0.201 1.14e-02 7.69e+03 3.10e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.69: 3154 4.69 - 9.37: 1888 9.37 - 14.06: 613 14.06 - 18.75: 109 18.75 - 23.44: 13 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLY A 108 " pdb=" C GLY A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 121.07 110.85 10.22 3.60e-01 7.72e+00 8.05e+02 angle pdb=" CA GLY A 74 " pdb=" C GLY A 74 " pdb=" O GLY A 74 " ideal model delta sigma weight residual 121.28 137.77 -16.49 1.01e+00 9.80e-01 2.67e+02 angle pdb=" CA ACYS A 53 " pdb=" C ACYS A 53 " pdb=" O ACYS A 53 " ideal model delta sigma weight residual 119.71 107.68 12.03 8.10e-01 1.52e+00 2.20e+02 angle pdb=" OD1 ASN A 173 " pdb=" CG ASN A 173 " pdb=" ND2 ASN A 173 " ideal model delta sigma weight residual 122.60 108.37 14.23 1.00e+00 1.00e+00 2.03e+02 angle pdb=" CA ALA A 56 " pdb=" C ALA A 56 " pdb=" O ALA A 56 " ideal model delta sigma weight residual 121.10 105.54 15.56 1.10e+00 8.26e-01 2.00e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 1367 21.36 - 42.71: 86 42.71 - 64.07: 22 64.07 - 85.43: 4 85.43 - 106.78: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 128 " pdb=" N LEU A 128 " pdb=" CA LEU A 128 " pdb=" CB LEU A 128 " ideal model delta harmonic sigma weight residual -122.60 -146.02 23.42 0 2.50e+00 1.60e-01 8.78e+01 dihedral pdb=" N LEU A 128 " pdb=" C LEU A 128 " pdb=" CA LEU A 128 " pdb=" CB LEU A 128 " ideal model delta harmonic sigma weight residual 122.80 145.80 -23.00 0 2.50e+00 1.60e-01 8.46e+01 dihedral pdb=" N ACYS A 53 " pdb=" C ACYS A 53 " pdb=" CA ACYS A 53 " pdb=" CB ACYS A 53 " ideal model delta harmonic sigma weight residual 122.80 140.89 -18.09 0 2.50e+00 1.60e-01 5.24e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.233: 113 0.233 - 0.462: 76 0.462 - 0.692: 35 0.692 - 0.922: 13 0.922 - 1.151: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA LYS A 32 " pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CB LYS A 32 " both_signs ideal model delta sigma weight residual False 2.51 3.66 -1.15 2.00e-01 2.50e+01 3.31e+01 chirality pdb=" CA LEU A 128 " pdb=" N LEU A 128 " pdb=" C LEU A 128 " pdb=" CB LEU A 128 " both_signs ideal model delta sigma weight residual False 2.51 1.48 1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CG LEU A 112 " pdb=" CB LEU A 112 " pdb=" CD1 LEU A 112 " pdb=" CD2 LEU A 112 " both_signs ideal model delta sigma weight residual False -2.59 -1.57 -1.02 2.00e-01 2.50e+01 2.59e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.134 2.00e-02 2.50e+03 6.91e-02 1.43e+02 pdb=" CG PHE A 119 " -0.109 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.104 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.043 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " -0.045 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.086 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.022 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.046 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.038 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.102 2.00e-02 2.50e+03 6.56e-02 1.29e+02 pdb=" CG PHE A 164 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.142 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.040 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.026 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " 0.063 9.50e-02 1.11e+02 7.48e-02 1.16e+02 pdb=" NE ARG A 98 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " 0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " 0.077 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.123 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " 0.002 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " -0.100 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " -0.009 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " 0.108 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 1176 2.34 - 2.91: 8301 2.91 - 3.47: 10440 3.47 - 4.04: 15158 4.04 - 4.60: 21573 Nonbonded interactions: 56648 Sorted by model distance: nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.777 2.100 nonbonded pdb=" OE2 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.793 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.836 2.450 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.837 2.450 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.841 2.100 ... (remaining 56643 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_6024882_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= 0.2028 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463650 | | target function (ml) not normalized (work): 22005.795485 | | target function (ml) not normalized (free): 1154.557407 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3812 0.2195 4.8364 4.899| | 2: 3.78 - 3.00 1.00 2430 110 0.3401 0.1746 4.0801 4.1718| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.64 0.83 0.13 6588.00| | 2: 3.78 - 3.00 2430 110 0.94 11.33 1.48 0.26 451.83| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 392.81 max = 12064.32 mean = 3563.48| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.25| |phase err.(test): min = 0.00 max = 89.99 mean = 33.23| |-----------------------------------------------------------------------------| ----------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 0.226 1557 Z= 5.599 Angle : 5.311 18.178 2118 Z= 3.853 Chirality : 0.388 1.151 243 Planarity : 0.032 0.111 284 Dihedral : 14.207 106.782 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 31.89 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.48), residues: 224 helix: -2.67 (0.37), residues: 109 sheet: -0.75 (0.80), residues: 38 loop : -0.49 (0.64), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.016 ARG A 98 TYR 0.077 0.032 TYR A 141 PHE 0.127 0.044 PHE A 119 HIS 0.040 0.023 HIS A 115 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3627 r_free= 0.2028 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463650 | | target function (ml) not normalized (work): 22005.795485 | | target function (ml) not normalized (free): 1154.557407 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3583 0.3662 0.2113 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3583 0.3662 0.2113 n_refl.: 5182 remove outliers: r(all,work,free)=0.2525 0.2550 0.2113 n_refl.: 5178 overall B=-2.66 to atoms: r(all,work,free)=0.2423 0.2445 0.2075 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1561 0.1557 0.1631 n_refl.: 5178 remove outliers: r(all,work,free)=0.1559 0.1555 0.1631 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 0.3976 445.179 407.501 0.657 1.035 0.400 11.894-9.307 99.02 97 4 0.1800 714.680 689.747 0.934 1.034 0.386 9.237-7.194 100.00 213 7 0.2167 584.466 569.696 0.958 1.030 0.364 7.162-5.571 100.00 427 22 0.2274 438.571 421.745 0.926 1.024 0.358 5.546-4.326 100.00 867 58 0.1368 602.096 592.972 0.963 1.013 0.230 4.315-3.360 100.00 1859 96 0.1298 572.599 567.419 1.026 0.994 0.189 3.356-3.002 100.00 1373 60 0.1634 441.040 435.571 1.026 0.976 0.032 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9170 b_overall=-4.6283 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1555 r_free=0.1631 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 3 r_work=0.1564 r_free=0.1633 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.151482 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.674071 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 0.1164 0.1793 0.0629 0.011 1.0 1.9 0.5 0.0 0 11.076 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.64 17.93 6.29 3.012 16.203 1.674 0.018 10.27 17.84 7.57 4.761 16.445 1.674 0.015 Individual atomic B min max mean iso aniso Overall: 2.63 111.64 17.69 5.14 1785 0 Protein: 2.63 111.38 14.98 5.13 1519 0 Water: 4.27 111.64 33.46 N/A 258 0 Other: 16.66 34.41 23.92 N/A 8 0 Chain A: 2.63 111.64 17.69 N/A 1785 0 Histogram: Values Number of atoms 2.63 - 13.53 928 13.53 - 24.43 478 24.43 - 35.33 192 35.33 - 46.24 99 46.24 - 57.14 58 57.14 - 68.04 13 68.04 - 78.94 8 78.94 - 89.84 5 89.84 - 100.74 1 100.74 - 111.64 3 =========================== Idealize ADP of riding H ========================== r_work=0.1027 r_free=0.1784 r_work=0.1020 r_free=0.1792 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1020 r_free = 0.1792 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1020 r_free = 0.1778 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.24 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= 0.1020 r_free= 0.1778 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.014132 | | target function (ls_wunit_k1) not normalized (work): 69.599934 | | target function (ls_wunit_k1) not normalized (free): 10.504256 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1058 0.1020 0.1778 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2145 0.2146 0.2233 n_refl.: 5177 remove outliers: r(all,work,free)=0.2145 0.2146 0.2233 n_refl.: 5177 overall B=-0.94 to atoms: r(all,work,free)=0.2104 0.2103 0.2220 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1055 0.1016 0.1774 n_refl.: 5177 remove outliers: r(all,work,free)=0.1055 0.1016 0.1774 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 97.92 89 5 0.3423 316.781 301.903 0.638 1.021 0.382 11.894-9.307 99.02 97 4 0.1514 508.553 500.068 0.937 1.022 0.361 9.237-7.194 100.00 213 7 0.1673 415.896 415.900 0.972 1.019 0.323 7.162-5.571 100.00 427 22 0.1615 312.079 308.970 0.940 1.015 0.302 5.546-4.326 100.00 867 58 0.0918 428.440 425.415 0.962 1.008 0.214 4.315-3.360 100.00 1859 96 0.0768 407.451 407.454 1.018 0.996 0.199 3.356-3.002 100.00 1373 60 0.1003 313.836 312.294 1.003 0.985 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-4.2394 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1016 r_free=0.1774 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN Total number of N/Q/H flips: 1 r_work=0.1017 r_free=0.1771 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1017 r_free=0.1771 | n_water=258 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.1048 r_free=0.1762 | n_water=249 | time (s): 20.130 (total time: 20.770) Filter (q & B) r_work=0.1048 r_free=0.1766 | n_water=246 | time (s): 1.590 (total time: 22.360) Compute maps r_work=0.1048 r_free=0.1766 | n_water=246 | time (s): 0.430 (total time: 22.790) Filter (map) r_work=0.1364 r_free=0.1866 | n_water=143 | time (s): 1.270 (total time: 24.060) Find peaks r_work=0.1364 r_free=0.1866 | n_water=143 | time (s): 0.450 (total time: 24.510) Add new water r_work=0.1729 r_free=0.2117 | n_water=234 | time (s): 1.490 (total time: 26.000) Refine new water occ: r_work=0.1163 r_free=0.1711 adp: r_work=0.1135 r_free=0.1719 occ: r_work=0.1132 r_free=0.1683 adp: r_work=0.1119 r_free=0.1694 occ: r_work=0.1118 r_free=0.1675 adp: r_work=0.1115 r_free=0.1677 ADP+occupancy (water only), MIN, final r_work=0.1115 r_free=0.1677 r_work=0.1115 r_free=0.1677 | n_water=234 | time (s): 4.940 (total time: 30.940) Filter (q & B) r_work=0.1115 r_free=0.1677 | n_water=234 | time (s): 0.930 (total time: 31.870) Filter (dist only) r_work=0.1120 r_free=0.1677 | n_water=231 | time (s): 19.100 (total time: 50.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.475730 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.656183 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 0.1013 0.1809 0.0796 0.009 1.0 4.5 0.5 0.6 0 11.238 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.13 18.09 7.96 4.588 17.125 2.656 0.014 9.47 18.52 9.06 5.339 17.486 2.656 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.36 16.90 6.32 1758 0 Protein: 0.00 107.36 15.25 6.32 1519 0 Water: 0.00 62.98 27.67 N/A 231 0 Other: 12.44 28.49 20.42 N/A 8 0 Chain A: 0.00 107.36 15.97 N/A 1667 0 Chain S: 0.00 59.74 34.11 N/A 91 0 Histogram: Values Number of atoms 0.00 - 10.74 644 10.74 - 21.47 698 21.47 - 32.21 209 32.21 - 42.94 119 42.94 - 53.68 44 53.68 - 64.41 30 64.41 - 75.15 7 75.15 - 85.88 3 85.88 - 96.62 2 96.62 - 107.36 2 =========================== Idealize ADP of riding H ========================== r_work=0.0947 r_free=0.1852 r_work=0.0943 r_free=0.1851 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0943 r_free = 0.1851 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0941 r_free = 0.1838 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.0941 r_free= 0.1838 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.012015 | | target function (ls_wunit_k1) not normalized (work): 59.173752 | | target function (ls_wunit_k1) not normalized (free): 10.180292 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0987 0.0941 0.1838 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2173 0.2179 0.2206 n_refl.: 5177 remove outliers: r(all,work,free)=0.2173 0.2179 0.2206 n_refl.: 5177 overall B=-0.00 to atoms: r(all,work,free)=0.2173 0.2179 0.2206 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.0989 0.0942 0.1863 n_refl.: 5177 remove outliers: r(all,work,free)=0.0989 0.0942 0.1863 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 97.92 89 5 0.3322 316.781 306.095 0.687 1.012 0.387 11.894-9.307 99.02 97 4 0.1415 508.553 503.965 0.989 1.013 0.370 9.237-7.194 100.00 213 7 0.1479 415.896 416.943 1.014 1.012 0.300 7.162-5.571 100.00 427 22 0.1437 312.079 310.283 0.991 1.010 0.300 5.546-4.326 100.00 867 58 0.0808 428.440 426.109 1.007 1.005 0.240 4.315-3.360 100.00 1859 96 0.0724 407.451 407.128 1.062 0.998 0.203 3.356-3.002 100.00 1373 60 0.0965 313.836 312.499 1.046 0.991 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.4915 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0942 r_free=0.1863 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0942 r_free=0.1863 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0942 r_free=0.1863 | n_water=231 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.0951 r_free=0.1844 | n_water=228 | time (s): 17.110 (total time: 17.600) Filter (q & B) r_work=0.1018 r_free=0.1850 | n_water=225 | time (s): 1.700 (total time: 19.300) Compute maps r_work=0.1018 r_free=0.1850 | n_water=225 | time (s): 0.640 (total time: 19.940) Filter (map) r_work=0.1307 r_free=0.1884 | n_water=144 | time (s): 1.760 (total time: 21.700) Find peaks r_work=0.1307 r_free=0.1884 | n_water=144 | time (s): 0.440 (total time: 22.140) Add new water r_work=0.1684 r_free=0.2239 | n_water=229 | time (s): 1.270 (total time: 23.410) Refine new water occ: r_work=0.1081 r_free=0.1846 adp: r_work=0.1075 r_free=0.1860 occ: r_work=0.1064 r_free=0.1839 adp: r_work=0.1064 r_free=0.1846 occ: r_work=0.1055 r_free=0.1826 adp: r_work=0.1054 r_free=0.1833 ADP+occupancy (water only), MIN, final r_work=0.1054 r_free=0.1833 r_work=0.1054 r_free=0.1833 | n_water=229 | time (s): 13.180 (total time: 36.590) Filter (q & B) r_work=0.1054 r_free=0.1833 | n_water=229 | time (s): 0.810 (total time: 37.400) Filter (dist only) r_work=0.1065 r_free=0.1845 | n_water=227 | time (s): 18.000 (total time: 55.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.111476 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.229420 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 0.0961 0.1849 0.0888 0.011 1.1 4.2 0.5 0.6 0 0.556 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.61 18.49 8.88 5.320 17.966 0.229 5.150 9.16 18.42 9.26 7.101 17.975 0.229 5.054 Individual atomic B min max mean iso aniso Overall: 0.00 105.45 16.57 8.74 1754 0 Protein: 0.00 105.45 15.40 8.74 1519 0 Water: 0.00 57.98 24.22 N/A 227 0 Other: 11.60 34.18 22.25 N/A 8 0 Chain A: 0.00 105.45 16.09 N/A 1655 0 Chain S: 0.00 51.49 24.70 N/A 99 0 Histogram: Values Number of atoms 0.00 - 10.54 632 10.54 - 21.09 689 21.09 - 31.63 239 31.63 - 42.18 118 42.18 - 52.72 42 52.72 - 63.27 16 63.27 - 73.81 8 73.81 - 84.36 5 84.36 - 94.90 3 94.90 - 105.45 2 =========================== Idealize ADP of riding H ========================== r_work=0.0916 r_free=0.1842 r_work=0.0921 r_free=0.1848 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0921 r_free = 0.1848 target_work(ml) = 5.057 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0913 r_free = 0.1837 target_work(ml) = 5.052 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.0913 r_free= 0.1837 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 5.051957 | | target function (ml) not normalized (work): 24880.890657 | | target function (ml) not normalized (free): 1805.561452 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0961 0.0913 0.1837 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2198 0.2209 0.2154 n_refl.: 5177 remove outliers: r(all,work,free)=0.2198 0.2209 0.2154 n_refl.: 5177 overall B=-0.00 to atoms: r(all,work,free)=0.2198 0.2209 0.2154 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.0953 0.0906 0.1823 n_refl.: 5177 remove outliers: r(all,work,free)=0.0949 0.0902 0.1823 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 0.3660 316.130 288.780 0.604 0.998 0.350 11.894-9.307 99.02 97 4 0.1880 508.553 494.385 0.948 1.001 0.350 9.237-7.194 100.00 213 7 0.1954 415.896 409.782 1.000 1.002 0.295 7.162-5.571 100.00 427 22 0.1879 312.079 303.717 0.979 1.002 0.290 5.546-4.326 100.00 867 58 0.0916 428.440 423.703 1.003 1.002 0.250 4.315-3.360 100.00 1859 96 0.0594 407.451 407.091 1.063 1.001 0.210 3.356-3.002 100.00 1373 60 0.0624 313.836 312.745 1.046 1.001 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9175 b_overall=-6.7139 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0902 r_free=0.1823 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.0902 r_free=0.1826 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0902 r_free=0.1826 | n_water=227 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.0922 r_free=0.1825 | n_water=223 | time (s): 17.440 (total time: 17.960) Filter (q & B) r_work=0.0952 r_free=0.1831 | n_water=222 | time (s): 1.760 (total time: 19.720) Compute maps r_work=0.0952 r_free=0.1831 | n_water=222 | time (s): 0.570 (total time: 20.290) Filter (map) r_work=0.1234 r_free=0.1952 | n_water=155 | time (s): 1.400 (total time: 21.690) Find peaks r_work=0.1234 r_free=0.1952 | n_water=155 | time (s): 0.390 (total time: 22.080) Add new water r_work=0.1564 r_free=0.2292 | n_water=234 | time (s): 1.220 (total time: 23.300) Refine new water occ: r_work=0.1013 r_free=0.1826 adp: r_work=0.1010 r_free=0.1839 occ: r_work=0.1002 r_free=0.1825 adp: r_work=0.1000 r_free=0.1834 occ: r_work=0.0993 r_free=0.1819 adp: r_work=0.0991 r_free=0.1828 ADP+occupancy (water only), MIN, final r_work=0.0991 r_free=0.1828 r_work=0.0991 r_free=0.1828 | n_water=234 | time (s): 11.770 (total time: 35.070) Filter (q & B) r_work=0.0991 r_free=0.1830 | n_water=233 | time (s): 1.340 (total time: 36.410) Filter (dist only) r_work=0.0994 r_free=0.1819 | n_water=231 | time (s): 18.700 (total time: 55.110) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.041289 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.265324 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 0.0902 0.1816 0.0915 0.011 1.1 4.2 0.5 0.0 0 0.521 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.02 18.16 9.15 6.847 18.203 0.265 5.004 8.80 18.33 9.53 7.990 18.309 0.265 4.948 Individual atomic B min max mean iso aniso Overall: 0.00 105.96 16.93 10.38 1758 0 Protein: 0.00 105.96 15.78 10.38 1519 0 Water: 0.00 61.95 24.23 N/A 231 0 Other: 12.35 35.66 22.73 N/A 8 0 Chain A: 0.00 105.96 16.33 N/A 1642 0 Chain S: 0.32 61.95 25.34 N/A 116 0 Histogram: Values Number of atoms 0.00 - 10.60 625 10.60 - 21.19 689 21.19 - 31.79 241 31.79 - 42.38 116 42.38 - 52.98 49 52.98 - 63.57 19 63.57 - 74.17 8 74.17 - 84.76 7 84.76 - 95.36 1 95.36 - 105.96 3 =========================== Idealize ADP of riding H ========================== r_work=0.0880 r_free=0.1833 r_work=0.0883 r_free=0.1840 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0883 r_free = 0.1840 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0873 r_free = 0.1824 target_work(ml) = 4.944 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0873 r_free= 0.1824 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.943689 | | target function (ml) not normalized (work): 24337.782643 | | target function (ml) not normalized (free): 2062.383737 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0922 0.0873 0.1824 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2122 0.2124 0.2217 n_refl.: 5175 remove outliers: r(all,work,free)=0.2122 0.2124 0.2217 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2122 0.2124 0.2217 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0920 0.0871 0.1816 n_refl.: 5175 remove outliers: r(all,work,free)=0.0920 0.0871 0.1816 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 0.3872 316.130 290.002 0.596 0.990 0.326 11.894-9.307 99.02 97 4 0.1866 508.553 492.000 0.950 0.995 0.311 9.237-7.194 100.00 213 7 0.2031 415.896 408.191 1.006 0.997 0.295 7.162-5.571 100.00 427 22 0.2005 312.079 302.750 0.989 0.999 0.274 5.546-4.326 100.00 867 58 0.0948 428.440 423.669 1.013 1.000 0.260 4.315-3.360 100.00 1859 96 0.0559 407.451 407.052 1.077 1.002 0.220 3.356-3.002 100.00 1373 60 0.0462 313.836 313.215 1.062 1.004 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.5211 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0871 r_free=0.1816 After: r_work=0.0875 r_free=0.1814 ================================== NQH flips ================================== r_work=0.0875 r_free=0.1814 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0875 r_free=0.1814 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0875 r_free=0.1814 | n_water=231 | time (s): 0.530 (total time: 0.530) Filter (dist) r_work=0.0896 r_free=0.1833 | n_water=226 | time (s): 19.620 (total time: 20.150) Filter (q & B) r_work=0.1017 r_free=0.1860 | n_water=222 | time (s): 1.420 (total time: 21.570) Compute maps r_work=0.1017 r_free=0.1860 | n_water=222 | time (s): 0.490 (total time: 22.060) Filter (map) r_work=0.1250 r_free=0.1944 | n_water=160 | time (s): 1.260 (total time: 23.320) Find peaks r_work=0.1250 r_free=0.1944 | n_water=160 | time (s): 0.510 (total time: 23.830) Add new water r_work=0.1521 r_free=0.2200 | n_water=226 | time (s): 1.290 (total time: 25.120) Refine new water occ: r_work=0.1000 r_free=0.1818 adp: r_work=0.0991 r_free=0.1837 occ: r_work=0.0984 r_free=0.1819 adp: r_work=0.0982 r_free=0.1828 occ: r_work=0.0977 r_free=0.1813 adp: r_work=0.0976 r_free=0.1820 ADP+occupancy (water only), MIN, final r_work=0.0976 r_free=0.1820 r_work=0.0976 r_free=0.1820 | n_water=226 | time (s): 10.830 (total time: 35.950) Filter (q & B) r_work=0.0977 r_free=0.1819 | n_water=225 | time (s): 1.600 (total time: 37.550) Filter (dist only) r_work=0.0983 r_free=0.1814 | n_water=224 | time (s): 16.500 (total time: 54.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.008307 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.250999 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 0.0917 0.1855 0.0938 0.011 1.1 6.4 0.5 0.0 0 0.504 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.17 18.55 9.38 7.927 18.487 0.251 4.999 8.94 18.74 9.80 8.775 18.586 0.251 4.943 Individual atomic B min max mean iso aniso Overall: 0.00 106.71 17.16 11.60 1751 0 Protein: 0.00 106.71 16.17 11.61 1519 0 Water: 1.45 59.48 23.68 N/A 224 0 Other: 15.10 35.36 23.21 N/A 8 0 Chain A: 0.00 106.71 16.63 N/A 1635 0 Chain S: 1.71 59.48 24.69 N/A 116 0 Histogram: Values Number of atoms 0.00 - 10.67 619 10.67 - 21.34 663 21.34 - 32.01 270 32.01 - 42.68 110 42.68 - 53.36 48 53.36 - 64.03 16 64.03 - 74.70 12 74.70 - 85.37 6 85.37 - 96.04 4 96.04 - 106.71 3 =========================== Idealize ADP of riding H ========================== r_work=0.0894 r_free=0.1874 r_work=0.0897 r_free=0.1874 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0897 r_free = 0.1874 target_work(ml) = 4.948 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0890 r_free = 0.1866 target_work(ml) = 4.943 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0890 r_free= 0.1866 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.943151 | | target function (ml) not normalized (work): 24335.133296 | | target function (ml) not normalized (free): 2174.936582 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1256 0.1856 5.4989 6.1672| | 2: 3.78 - 3.00 1.00 2430 110 0.0443 0.1883 4.373 11.811| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.92 11.87 1.00 0.95 11849.42| | 2: 3.78 - 3.00 2430 110 0.99 2.03 1.00 0.97 935.10| |alpha: min = 0.94 max = 0.97 mean = 0.96| |beta: min = 606.76 max = 19593.26 mean = 6462.10| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.66 mean = 7.01| |phase err.(test): min = 0.00 max = 80.56 mean = 7.12| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0939 0.0890 0.1866 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2157 0.2156 0.2274 n_refl.: 5175 remove outliers: r(all,work,free)=0.2157 0.2156 0.2274 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2157 0.2156 0.2274 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0938 0.0889 0.1869 n_refl.: 5175 remove outliers: r(all,work,free)=0.0938 0.0889 0.1869 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 0.3900 316.130 291.340 0.593 0.991 0.324 11.894-9.307 99.02 97 4 0.1834 508.553 494.643 0.964 0.995 0.320 9.237-7.194 100.00 213 7 0.2106 415.896 408.140 1.013 0.998 0.290 7.162-5.571 100.00 427 22 0.2082 312.079 301.893 0.989 0.999 0.275 5.546-4.326 100.00 867 58 0.0995 428.440 422.742 1.019 1.000 0.270 4.315-3.360 100.00 1859 96 0.0574 407.451 406.994 1.090 1.002 0.222 3.356-3.002 100.00 1373 60 0.0435 313.836 313.346 1.079 1.003 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.1236 ================= 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 0.2028 0.083 5.311 8.8 119.3 19.9 258 0.000 1_bss: 0.1555 0.1631 0.083 5.311 6.2 116.6 17.2 258 0.000 1_settarget: 0.1555 0.1631 0.083 5.311 6.2 116.6 17.2 258 0.000 1_nqh: 0.1564 0.1633 0.083 5.311 6.2 116.6 17.2 258 0.010 1_weight: 0.1564 0.1633 0.083 5.311 6.2 116.6 17.2 258 0.010 1_xyzrec: 0.1164 0.1793 0.011 1.032 6.2 116.6 17.2 258 0.195 1_adp: 0.1027 0.1784 0.011 1.032 2.6 111.6 17.7 258 0.195 1_regHadp: 0.1020 0.1792 0.011 1.032 2.6 111.6 17.7 258 0.195 1_occ: 0.1020 0.1778 0.011 1.032 2.6 111.6 17.7 258 0.195 2_bss: 0.1016 0.1774 0.011 1.032 1.7 110.7 16.7 258 0.195 2_settarget: 0.1016 0.1774 0.011 1.032 1.7 110.7 16.7 258 0.195 2_updatecdl: 0.1016 0.1774 0.011 1.062 1.7 110.7 16.7 258 0.195 2_nqh: 0.1017 0.1771 0.011 1.062 1.7 110.7 16.7 258 0.192 2_sol: 0.1120 0.1677 0.011 1.062 1.0 110.4 16.2 231 n/a 2_weight: 0.1120 0.1677 0.011 1.062 1.0 110.4 16.2 231 n/a 2_xyzrec: 0.1013 0.1809 0.009 0.988 1.0 110.4 16.2 231 n/a 2_adp: 0.0947 0.1852 0.009 0.988 0.0 107.4 16.9 231 n/a 2_regHadp: 0.0943 0.1851 0.009 0.988 0.0 107.4 16.9 231 n/a 2_occ: 0.0941 0.1838 0.009 0.988 0.0 107.4 16.9 231 n/a 3_bss: 0.0942 0.1863 0.009 0.988 0.0 107.4 16.9 231 n/a 3_settarget: 0.0942 0.1863 0.009 0.988 0.0 107.4 16.9 231 n/a 3_updatecdl: 0.0942 0.1863 0.009 0.995 0.0 107.4 16.9 231 n/a 3_nqh: 0.0942 0.1863 0.009 0.995 0.0 107.4 16.9 231 n/a 3_sol: 0.1065 0.1845 0.009 0.995 0.0 107.4 16.6 227 n/a 3_weight: 0.1065 0.1845 0.009 0.995 0.0 107.4 16.6 227 n/a 3_xyzrec: 0.0961 0.1849 0.011 1.073 0.0 107.4 16.6 227 n/a 3_adp: 0.0916 0.1842 0.011 1.073 0.0 105.4 16.6 227 n/a 3_regHadp: 0.0921 0.1848 0.011 1.073 0.0 105.4 16.6 227 n/a 3_occ: 0.0913 0.1837 0.011 1.073 0.0 105.4 16.6 227 n/a 4_bss: 0.0902 0.1823 0.011 1.073 0.0 105.4 16.6 227 n/a 4_settarget: 0.0902 0.1823 0.011 1.073 0.0 105.4 16.6 227 n/a 4_updatecdl: 0.0902 0.1823 0.011 1.085 0.0 105.4 16.6 227 n/a 4_nqh: 0.0902 0.1826 0.011 1.085 0.0 105.4 16.6 227 n/a 4_sol: 0.0994 0.1819 0.011 1.085 0.0 105.4 16.7 231 n/a 4_weight: 0.0994 0.1819 0.011 1.085 0.0 105.4 16.7 231 n/a 4_xyzrec: 0.0902 0.1816 0.011 1.078 0.0 105.4 16.7 231 n/a 4_adp: 0.0880 0.1833 0.011 1.078 0.0 106.0 16.9 231 n/a 4_regHadp: 0.0883 0.1840 0.011 1.078 0.0 106.0 16.9 231 n/a 4_occ: 0.0873 0.1824 0.011 1.078 0.0 106.0 16.9 231 n/a 5_bss: 0.0871 0.1816 0.011 1.078 0.0 106.0 16.9 231 n/a 5_settarget: 0.0871 0.1816 0.011 1.078 0.0 106.0 16.9 231 n/a 5_updatecdl: 0.0871 0.1816 0.011 1.083 0.0 106.0 16.9 231 n/a 5_setrh: 0.0875 0.1814 0.011 1.083 0.0 106.0 16.9 231 n/a 5_nqh: 0.0875 0.1814 0.011 1.083 0.0 106.0 16.9 231 n/a 5_sol: 0.0983 0.1814 0.011 1.083 0.0 106.0 17.0 224 n/a 5_weight: 0.0983 0.1814 0.011 1.083 0.0 106.0 17.0 224 n/a 5_xyzrec: 0.0917 0.1855 0.011 1.130 0.0 106.0 17.0 224 n/a 5_adp: 0.0894 0.1874 0.011 1.130 0.0 106.7 17.2 224 n/a 5_regHadp: 0.0897 0.1874 0.011 1.130 0.0 106.7 17.2 224 n/a 5_occ: 0.0890 0.1866 0.011 1.130 0.0 106.7 17.2 224 n/a end: 0.0889 0.1869 0.011 1.130 0.0 106.7 17.2 224 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6024882_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6024882_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.7100 Refinement macro-cycles (run) : 489.2700 Write final files (write_after_run_outputs) : 9.8900 Total : 501.8700 Total CPU time: 8.73 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:04 PST -0800 (1735492744.93 s) Start R-work = 0.1555, R-free = 0.1631 Final R-work = 0.0889, R-free = 0.1869 =============================================================================== Job complete usr+sys time: 531.23 seconds wall clock time: 9 minutes 13.28 seconds (553.28 seconds total)