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_3975290.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3975290.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3975290.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== 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: 1.24, per 1000 atoms: 0.37 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: 0.30 Conformation dependent library (CDL) restraints added in 104.6 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.68 - 0.94: 703 0.94 - 1.20: 1000 1.20 - 1.46: 743 1.46 - 1.73: 696 1.73 - 1.99: 11 Bond restraints: 3153 Sorted by residual: bond pdb=" N LYS A 89 " pdb=" CA LYS A 89 " ideal model delta sigma weight residual 1.459 1.700 -0.241 1.23e-02 6.61e+03 3.83e+02 bond pdb=" CA BLYS A 132 " pdb=" C BLYS A 132 " ideal model delta sigma weight residual 1.524 1.753 -0.229 1.26e-02 6.30e+03 3.30e+02 bond pdb=" N BGLU A 64 " pdb=" CA BGLU A 64 " ideal model delta sigma weight residual 1.456 1.669 -0.213 1.18e-02 7.18e+03 3.26e+02 bond pdb=" N ARG A 28 " pdb=" CA ARG A 28 " ideal model delta sigma weight residual 1.458 1.224 0.233 1.30e-02 5.92e+03 3.22e+02 bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.237 1.437 -0.201 1.13e-02 7.83e+03 3.15e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.84: 3221 4.84 - 9.68: 1828 9.68 - 14.52: 613 14.52 - 19.36: 100 19.36 - 24.20: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ALA A 103 " pdb=" C ALA A 103 " pdb=" N ALA A 104 " ideal model delta sigma weight residual 123.27 144.05 -20.78 1.16e+00 7.43e-01 3.21e+02 angle pdb=" O GLU A 59 " pdb=" C GLU A 59 " pdb=" N ASP A 60 " ideal model delta sigma weight residual 122.12 140.18 -18.06 1.06e+00 8.90e-01 2.90e+02 angle pdb=" C GLY A 40 " pdb=" N ALYS A 41 " pdb=" CA ALYS A 41 " ideal model delta sigma weight residual 120.31 140.41 -20.10 1.52e+00 4.33e-01 1.75e+02 angle pdb=" O GLY A 75 " pdb=" C GLY A 75 " pdb=" N AASN A 76 " ideal model delta sigma weight residual 122.70 105.88 16.82 1.30e+00 5.92e-01 1.67e+02 angle pdb=" O GLY A 157 " pdb=" C GLY A 157 " pdb=" N PRO A 158 " ideal model delta sigma weight residual 121.77 109.05 12.72 1.00e+00 1.00e+00 1.62e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 15.68: 1278 15.68 - 31.35: 133 31.35 - 47.02: 44 47.02 - 62.69: 22 62.69 - 78.37: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C ARG A 98 " pdb=" N ARG A 98 " pdb=" CA ARG A 98 " pdb=" CB ARG A 98 " ideal model delta harmonic sigma weight residual -122.60 -141.12 18.52 0 2.50e+00 1.60e-01 5.49e+01 dihedral pdb=" C ILE A 105 " pdb=" N ILE A 105 " pdb=" CA ILE A 105 " pdb=" CB ILE A 105 " ideal model delta harmonic sigma weight residual -122.00 -140.49 18.49 0 2.50e+00 1.60e-01 5.47e+01 dihedral pdb=" N BLEU A 153 " pdb=" C BLEU A 153 " pdb=" CA BLEU A 153 " pdb=" CB BLEU A 153 " ideal model delta harmonic sigma weight residual 122.80 105.45 17.35 0 2.50e+00 1.60e-01 4.82e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.240: 116 0.240 - 0.479: 67 0.479 - 0.718: 46 0.718 - 0.956: 13 0.956 - 1.195: 1 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 20 " pdb=" CA VAL A 20 " pdb=" CG1 VAL A 20 " pdb=" CG2 VAL A 20 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.57e+01 chirality pdb=" CA LYS A 89 " pdb=" N LYS A 89 " pdb=" C LYS A 89 " pdb=" CB LYS A 89 " both_signs ideal model delta sigma weight residual False 2.51 3.46 -0.95 2.00e-01 2.50e+01 2.25e+01 chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.82 0.90 2.00e-01 2.50e+01 2.03e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 5 " -0.026 9.50e-02 1.11e+02 6.31e-02 8.80e+01 pdb=" NE ARG A 5 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG A 5 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG A 5 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 5 " 0.132 2.00e-02 2.50e+03 pdb="HH11 ARG A 5 " 0.076 2.00e-02 2.50e+03 pdb="HH12 ARG A 5 " -0.057 2.00e-02 2.50e+03 pdb="HH21 ARG A 5 " -0.030 2.00e-02 2.50e+03 pdb="HH22 ARG A 5 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.043 2.00e-02 2.50e+03 5.24e-02 8.23e+01 pdb=" CG BTYR A 67 " -0.038 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " -0.091 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " -0.028 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.086 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " 0.052 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.077 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " -0.057 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " 0.015 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.012 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 156 " -0.148 9.50e-02 1.11e+02 7.69e-02 8.11e+01 pdb=" NE ARG A 156 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 156 " -0.088 2.00e-02 2.50e+03 pdb=" NH1 ARG A 156 " -0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 156 " -0.045 2.00e-02 2.50e+03 pdb="HH11 ARG A 156 " 0.033 2.00e-02 2.50e+03 pdb="HH12 ARG A 156 " 0.071 2.00e-02 2.50e+03 pdb="HH21 ARG A 156 " 0.109 2.00e-02 2.50e+03 pdb="HH22 ARG A 156 " -0.050 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1049 2.32 - 2.89: 8078 2.89 - 3.46: 10513 3.46 - 4.03: 15254 4.03 - 4.60: 21801 Nonbonded interactions: 56695 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.750 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.762 2.450 nonbonded pdb="HH21 ARG A 145 " pdb=" OE2 GLU A 163 " model vdw 1.782 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.784 2.450 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.819 2.450 ... (remaining 56690 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_3975290_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= 0.3612 r_free= 0.1997 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468692 | | target function (ml) not normalized (work): 22030.652057 | | target function (ml) not normalized (free): 1146.250590 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3795 0.2246 4.8495 4.9273| | 2: 3.78 - 3.00 1.00 2430 110 0.3390 0.1576 4.0769 4.0598| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.65 0.83 0.13 6597.41| | 2: 3.78 - 3.00 2430 110 0.94 11.42 1.48 0.26 452.55| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 388.57 max = 12063.60 mean = 3568.61| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.30| |phase err.(test): min = 0.00 max = 89.96 mean = 33.27| |-----------------------------------------------------------------------------| ----------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 : 0.084 0.250 1557 Z= 5.583 Angle : 5.396 20.784 2118 Z= 3.828 Chirality : 0.384 1.195 243 Planarity : 0.030 0.116 284 Dihedral : 13.889 78.366 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.08 % Favored : 97.84 % Rotamer: Outliers : 2.48 % Allowed : 1.24 % Favored : 96.27 % Cbeta Deviations : 30.27 % 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: -2.76 (0.44), residues: 224 helix: -2.90 (0.32), residues: 102 sheet: -2.04 (0.75), residues: 30 loop : -0.04 (0.55), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.067 0.016 ARG A 145 TYR 0.082 0.035 TYR A 139 PHE 0.087 0.030 PHE A 164 HIS 0.050 0.028 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= 0.3612 r_free= 0.1997 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.468692 | | target function (ml) not normalized (work): 22030.652057 | | target function (ml) not normalized (free): 1146.250590 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3569 0.3646 0.2113 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3569 0.3646 0.2113 n_refl.: 5182 remove outliers: r(all,work,free)=0.2520 0.2545 0.2113 n_refl.: 5178 overall B=-2.87 to atoms: r(all,work,free)=0.2409 0.2431 0.2070 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1563 0.1562 0.1585 n_refl.: 5178 remove outliers: r(all,work,free)=0.1559 0.1557 0.1585 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3864 450.219 408.420 0.667 1.060 0.398 11.894-9.307 99.02 97 4 0.1857 715.210 697.306 0.947 1.057 0.383 9.237-7.194 100.00 213 7 0.2181 584.899 577.837 0.980 1.051 0.348 7.162-5.571 100.00 427 22 0.2352 438.896 423.660 0.944 1.040 0.326 5.546-4.326 100.00 867 58 0.1348 602.542 596.428 0.983 1.022 0.210 4.315-3.360 100.00 1859 96 0.1323 573.024 567.177 1.053 0.991 0.190 3.356-3.002 100.00 1373 60 0.1590 441.367 433.424 1.062 0.960 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9556 b_overall=-3.6723 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1557 r_free=0.1585 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1557 r_free=0.1585 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.591572 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.872653 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 0.1162 0.1775 0.0613 0.010 1.0 2.6 0.5 0.0 0 9.796 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.62 17.75 6.13 3.013 15.987 1.873 0.018 10.21 17.61 7.40 4.957 16.206 1.873 0.015 Individual atomic B min max mean iso aniso Overall: 2.10 111.70 17.43 5.30 1785 0 Protein: 2.10 111.70 14.73 5.30 1519 0 Water: 3.99 111.43 33.08 N/A 258 0 Other: 17.19 36.70 24.41 N/A 8 0 Chain A: 2.10 111.70 17.43 N/A 1785 0 Histogram: Values Number of atoms 2.10 - 13.06 911 13.06 - 24.02 490 24.02 - 34.98 186 34.98 - 45.94 109 45.94 - 56.90 53 56.90 - 67.86 20 67.86 - 78.82 7 78.82 - 89.78 5 89.78 - 100.74 1 100.74 - 111.70 3 =========================== Idealize ADP of riding H ========================== r_work=0.1021 r_free=0.1761 r_work=0.1015 r_free=0.1765 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1015 r_free = 0.1765 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1008 r_free = 0.1766 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.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1008 r_free= 0.1766 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.013878 | | target function (ls_wunit_k1) not normalized (work): 68.335094 | | target function (ls_wunit_k1) not normalized (free): 10.102404 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1047 0.1008 0.1766 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2085 0.2083 0.2232 n_refl.: 5176 remove outliers: r(all,work,free)=0.2085 0.2083 0.2232 n_refl.: 5176 overall B=-0.95 to atoms: r(all,work,free)=0.2045 0.2042 0.2219 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1048 0.1009 0.1765 n_refl.: 5176 remove outliers: r(all,work,free)=0.1048 0.1009 0.1765 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 0.3346 330.620 313.045 0.672 1.021 0.383 11.894-9.307 99.02 97 4 0.1528 525.217 516.440 0.978 1.021 0.364 9.237-7.194 100.00 213 7 0.1648 429.523 430.686 1.012 1.019 0.320 7.162-5.571 100.00 427 22 0.1600 322.305 319.203 0.973 1.015 0.302 5.546-4.326 100.00 867 58 0.0900 442.479 439.393 0.993 1.008 0.207 4.315-3.360 100.00 1859 96 0.0766 420.802 420.791 1.044 0.996 0.193 3.356-3.002 100.00 1373 60 0.1006 324.120 322.415 1.026 0.984 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.4207 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1009 r_free=0.1765 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=0.1010 r_free=0.1765 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1010 r_free=0.1765 | n_water=258 | time (s): 0.620 (total time: 0.620) Filter (dist) r_work=0.1035 r_free=0.1762 | n_water=248 | time (s): 20.570 (total time: 21.190) Filter (q & B) r_work=0.1035 r_free=0.1762 | n_water=245 | time (s): 1.470 (total time: 22.660) Compute maps r_work=0.1035 r_free=0.1762 | n_water=245 | time (s): 0.460 (total time: 23.120) Filter (map) r_work=0.1341 r_free=0.1827 | n_water=145 | time (s): 1.440 (total time: 24.560) Find peaks r_work=0.1341 r_free=0.1827 | n_water=145 | time (s): 0.520 (total time: 25.080) Add new water r_work=0.1713 r_free=0.2044 | n_water=235 | time (s): 1.660 (total time: 26.740) Refine new water occ: r_work=0.1144 r_free=0.1625 adp: r_work=0.1119 r_free=0.1624 occ: r_work=0.1115 r_free=0.1612 adp: r_work=0.1105 r_free=0.1613 occ: r_work=0.1104 r_free=0.1614 adp: r_work=0.1104 r_free=0.1614 ADP+occupancy (water only), MIN, final r_work=0.1104 r_free=0.1614 r_work=0.1104 r_free=0.1614 | n_water=235 | time (s): 6.210 (total time: 32.950) Filter (q & B) r_work=0.1104 r_free=0.1614 | n_water=235 | time (s): 1.160 (total time: 34.110) Filter (dist only) r_work=0.1109 r_free=0.1603 | n_water=232 | time (s): 19.450 (total time: 53.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.153567 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.852963 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 0.0991 0.1765 0.0774 0.009 1.0 3.8 0.5 0.6 0 12.077 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.91 17.65 7.74 4.678 16.762 2.853 0.013 9.27 18.09 8.82 5.355 17.131 2.853 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 109.43 16.47 6.41 1759 0 Protein: 0.00 109.43 14.97 6.40 1519 0 Water: 0.00 62.75 25.98 N/A 232 0 Other: 14.45 36.35 24.47 N/A 8 0 Chain A: 0.00 109.43 15.71 N/A 1669 0 Chain S: 2.75 59.22 30.44 N/A 90 0 Histogram: Values Number of atoms 0.00 - 10.94 690 10.94 - 21.89 672 21.89 - 32.83 208 32.83 - 43.77 118 43.77 - 54.72 37 54.72 - 65.66 23 65.66 - 76.60 4 76.60 - 87.55 4 87.55 - 98.49 1 98.49 - 109.43 2 =========================== Idealize ADP of riding H ========================== r_work=0.0927 r_free=0.1809 r_work=0.0925 r_free=0.1814 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0925 r_free = 0.1814 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0924 r_free = 0.1791 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.28 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= 0.0924 r_free= 0.1791 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011556 | | target function (ls_wunit_k1) not normalized (work): 56.902339 | | target function (ls_wunit_k1) not normalized (free): 9.731002 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0968 0.0924 0.1791 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2107 0.2110 0.2204 n_refl.: 5176 remove outliers: r(all,work,free)=0.2107 0.2110 0.2204 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2107 0.2110 0.2204 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0970 0.0927 0.1800 n_refl.: 5176 remove outliers: r(all,work,free)=0.0970 0.0927 0.1800 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 0.3315 330.620 313.261 0.697 1.003 0.377 11.894-9.307 99.02 97 4 0.1356 525.217 521.369 0.990 1.005 0.360 9.237-7.194 100.00 213 7 0.1430 429.523 431.074 1.020 1.005 0.310 7.162-5.571 100.00 427 22 0.1376 322.305 319.777 0.992 1.004 0.300 5.546-4.326 100.00 867 58 0.0792 442.479 439.954 1.004 1.002 0.219 4.315-3.360 100.00 1859 96 0.0720 420.802 420.927 1.049 0.999 0.200 3.356-3.002 100.00 1373 60 0.0954 324.120 322.619 1.025 0.995 0.073 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.8930 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0927 r_free=0.1800 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 76 ASN B A 80 GLN A Total number of N/Q/H flips: 3 r_work=0.0928 r_free=0.1801 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0928 r_free=0.1801 | n_water=232 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.0944 r_free=0.1806 | n_water=229 | time (s): 18.700 (total time: 19.280) Filter (q & B) r_work=0.1004 r_free=0.1826 | n_water=227 | time (s): 1.440 (total time: 20.720) Compute maps r_work=0.1004 r_free=0.1826 | n_water=227 | time (s): 0.440 (total time: 21.160) Filter (map) r_work=0.1270 r_free=0.1856 | n_water=154 | time (s): 1.360 (total time: 22.520) Find peaks r_work=0.1270 r_free=0.1856 | n_water=154 | time (s): 0.400 (total time: 22.920) Add new water r_work=0.1668 r_free=0.2186 | n_water=241 | time (s): 1.340 (total time: 24.260) Refine new water occ: r_work=0.1054 r_free=0.1743 adp: r_work=0.1049 r_free=0.1753 occ: r_work=0.1036 r_free=0.1731 adp: r_work=0.1037 r_free=0.1740 occ: r_work=0.1025 r_free=0.1717 adp: r_work=0.1025 r_free=0.1726 ADP+occupancy (water only), MIN, final r_work=0.1025 r_free=0.1726 r_work=0.1025 r_free=0.1726 | n_water=241 | time (s): 12.570 (total time: 36.830) Filter (q & B) r_work=0.1025 r_free=0.1732 | n_water=240 | time (s): 1.500 (total time: 38.330) Filter (dist only) r_work=0.1028 r_free=0.1725 | n_water=238 | time (s): 19.230 (total time: 57.560) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.079280 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.218229 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 0.0926 0.1767 0.0841 0.011 1.1 3.5 0.5 0.6 0 0.540 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.26 17.67 8.41 5.371 17.800 0.218 5.152 8.82 17.83 9.01 7.264 17.815 0.218 5.055 Individual atomic B min max mean iso aniso Overall: 0.00 108.00 16.44 8.94 1765 0 Protein: 0.00 108.00 15.09 8.92 1519 0 Water: 0.00 57.75 24.70 N/A 238 0 Other: 10.68 41.17 25.95 N/A 8 0 Chain A: 0.00 108.00 15.80 N/A 1658 0 Chain S: 0.00 54.95 26.31 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.80 695 10.80 - 21.60 649 21.60 - 32.40 229 32.40 - 43.20 120 43.20 - 54.00 36 54.00 - 64.80 16 64.80 - 75.60 14 75.60 - 86.40 1 86.40 - 97.20 4 97.20 - 108.00 1 =========================== Idealize ADP of riding H ========================== r_work=0.0882 r_free=0.1783 r_work=0.0887 r_free=0.1788 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0887 r_free = 0.1788 target_work(ml) = 5.060 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0875 r_free = 0.1771 target_work(ml) = 5.053 | | occupancies: max = 1.00 min = 0.11 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= 0.0875 r_free= 0.1771 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.052584 | | target function (ml) not normalized (work): 24878.921386 | | target function (ml) not normalized (free): 1822.382431 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0920 0.0875 0.1771 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2106 0.2119 0.2018 n_refl.: 5176 remove outliers: r(all,work,free)=0.2106 0.2119 0.2018 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2106 0.2119 0.2018 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0914 0.0870 0.1763 n_refl.: 5176 remove outliers: r(all,work,free)=0.0910 0.0865 0.1763 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3701 330.016 295.429 0.599 0.993 0.344 11.894-9.307 99.02 97 4 0.1717 525.217 513.933 0.962 0.996 0.340 9.237-7.194 100.00 213 7 0.1851 429.523 424.599 1.006 0.998 0.299 7.162-5.571 100.00 427 22 0.1773 322.305 314.260 0.978 0.999 0.283 5.546-4.326 100.00 867 58 0.0883 442.479 436.748 0.997 1.000 0.224 4.315-3.360 100.00 1859 96 0.0566 420.802 420.461 1.049 1.002 0.210 3.356-3.002 100.00 1373 60 0.0611 324.120 323.474 1.026 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9176 b_overall=-6.0885 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0865 r_free=0.1763 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0865 r_free=0.1763 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0865 r_free=0.1763 | n_water=238 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.0874 r_free=0.1759 | n_water=237 | time (s): 18.350 (total time: 18.820) Filter (q & B) r_work=0.0976 r_free=0.1797 | n_water=233 | time (s): 1.660 (total time: 20.480) Compute maps r_work=0.0976 r_free=0.1797 | n_water=233 | time (s): 0.680 (total time: 21.160) Filter (map) r_work=0.1245 r_free=0.1875 | n_water=160 | time (s): 1.760 (total time: 22.920) Find peaks r_work=0.1245 r_free=0.1875 | n_water=160 | time (s): 0.460 (total time: 23.380) Add new water r_work=0.1564 r_free=0.2169 | n_water=233 | time (s): 1.320 (total time: 24.700) Refine new water occ: r_work=0.0996 r_free=0.1803 adp: r_work=0.0991 r_free=0.1806 occ: r_work=0.0984 r_free=0.1787 adp: r_work=0.0983 r_free=0.1793 occ: r_work=0.0976 r_free=0.1773 adp: r_work=0.0976 r_free=0.1779 ADP+occupancy (water only), MIN, final r_work=0.0976 r_free=0.1779 r_work=0.0976 r_free=0.1779 | n_water=233 | time (s): 15.670 (total time: 40.370) Filter (q & B) r_work=0.0976 r_free=0.1779 | n_water=233 | time (s): 1.210 (total time: 41.580) Filter (dist only) r_work=0.0987 r_free=0.1786 | n_water=230 | time (s): 18.770 (total time: 60.350) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.000087 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.258597 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 0.0893 0.1823 0.0929 0.011 1.0 4.2 0.5 0.0 0 0.500 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.93 18.23 9.29 6.970 17.896 0.259 5.030 8.73 18.38 9.66 8.188 17.996 0.259 4.967 Individual atomic B min max mean iso aniso Overall: 0.00 108.62 16.60 10.71 1757 0 Protein: 0.00 108.62 15.48 10.69 1519 0 Water: 0.00 54.43 23.62 N/A 230 0 Other: 13.82 44.28 27.29 N/A 8 0 Chain A: 0.00 108.62 16.06 N/A 1643 0 Chain S: 0.00 50.30 24.34 N/A 114 0 Histogram: Values Number of atoms 0.00 - 10.86 690 10.86 - 21.72 635 21.72 - 32.59 241 32.59 - 43.45 114 43.45 - 54.31 44 54.31 - 65.17 11 65.17 - 76.03 11 76.03 - 86.90 6 86.90 - 97.76 3 97.76 - 108.62 2 =========================== Idealize ADP of riding H ========================== r_work=0.0873 r_free=0.1838 r_work=0.0877 r_free=0.1841 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0877 r_free = 0.1841 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0867 r_free = 0.1824 target_work(ml) = 4.963 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0867 r_free= 0.1824 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.963405 | | target function (ml) not normalized (work): 24429.881261 | | target function (ml) not normalized (free): 2066.664100 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0914 0.0867 0.1824 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2059 0.2065 0.2113 n_refl.: 5174 remove outliers: r(all,work,free)=0.2059 0.2065 0.2113 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2059 0.2065 0.2113 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0913 0.0866 0.1828 n_refl.: 5174 remove outliers: r(all,work,free)=0.0913 0.0866 0.1828 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3934 330.016 296.091 0.577 0.988 0.318 11.894-9.307 99.02 97 4 0.1835 525.217 508.915 0.956 0.992 0.316 9.237-7.194 100.00 213 7 0.2031 429.523 420.031 1.005 0.995 0.297 7.162-5.571 100.00 427 22 0.1995 322.305 311.724 0.994 0.997 0.282 5.546-4.326 100.00 867 58 0.0949 442.479 436.875 1.014 0.999 0.229 4.315-3.360 100.00 1859 96 0.0546 420.802 420.903 1.074 1.002 0.220 3.356-3.002 100.00 1373 60 0.0464 324.120 323.628 1.054 1.005 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.3224 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0866 r_free=0.1828 After: r_work=0.0869 r_free=0.1829 ================================== NQH flips ================================== r_work=0.0869 r_free=0.1829 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0869 r_free=0.1829 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0869 r_free=0.1829 | n_water=230 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.0881 r_free=0.1842 | n_water=226 | time (s): 17.700 (total time: 18.410) Filter (q & B) r_work=0.0965 r_free=0.1887 | n_water=222 | time (s): 1.420 (total time: 19.830) Compute maps r_work=0.0965 r_free=0.1887 | n_water=222 | time (s): 0.440 (total time: 20.270) Filter (map) r_work=0.1243 r_free=0.1899 | n_water=160 | time (s): 1.550 (total time: 21.820) Find peaks r_work=0.1243 r_free=0.1899 | n_water=160 | time (s): 0.540 (total time: 22.360) Add new water r_work=0.1525 r_free=0.2147 | n_water=231 | time (s): 1.830 (total time: 24.190) Refine new water occ: r_work=0.0992 r_free=0.1776 adp: r_work=0.0989 r_free=0.1784 occ: r_work=0.0982 r_free=0.1762 adp: r_work=0.0981 r_free=0.1773 occ: r_work=0.0974 r_free=0.1751 adp: r_work=0.0973 r_free=0.1763 ADP+occupancy (water only), MIN, final r_work=0.0973 r_free=0.1763 r_work=0.0973 r_free=0.1763 | n_water=231 | time (s): 10.500 (total time: 34.690) Filter (q & B) r_work=0.0973 r_free=0.1767 | n_water=230 | time (s): 1.610 (total time: 36.300) Filter (dist only) r_work=0.0981 r_free=0.1768 | n_water=228 | time (s): 18.990 (total time: 55.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.094845 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.235928 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 0.0918 0.1774 0.0856 0.011 1.1 7.0 0.5 0.0 0 0.547 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.18 17.74 8.56 8.146 18.308 0.236 5.029 9.00 17.94 8.94 8.970 18.435 0.236 4.975 Individual atomic B min max mean iso aniso Overall: 0.00 109.00 16.99 11.88 1755 0 Protein: 0.00 109.00 15.89 11.86 1519 0 Water: 0.00 60.34 23.99 N/A 228 0 Other: 12.01 45.50 27.14 N/A 8 0 Chain A: 0.00 109.00 16.41 N/A 1636 0 Chain S: 0.00 58.37 24.97 N/A 119 0 Histogram: Values Number of atoms 0.00 - 10.90 669 10.90 - 21.80 624 21.80 - 32.70 271 32.70 - 43.60 103 43.60 - 54.50 50 54.50 - 65.40 14 65.40 - 76.30 11 76.30 - 87.20 9 87.20 - 98.10 2 98.10 - 109.00 2 =========================== Idealize ADP of riding H ========================== r_work=0.0900 r_free=0.1794 r_work=0.0904 r_free=0.1793 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0904 r_free = 0.1793 target_work(ml) = 4.981 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0895 r_free = 0.1786 target_work(ml) = 4.975 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0895 r_free= 0.1786 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.974804 | | target function (ml) not normalized (work): 24485.985628 | | target function (ml) not normalized (free): 2148.282565 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1263 0.1775 5.5349 6.1062| | 2: 3.78 - 3.00 1.00 2430 110 0.0447 0.1806 4.4005 11.647| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.92 12.09 1.00 0.98 13047.87| | 2: 3.78 - 3.00 2430 110 0.99 1.97 1.01 1.00 986.00| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 637.96 max = 21703.36 mean = 7092.90| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.88 mean = 7.09| |phase err.(test): min = 0.00 max = 86.90 mean = 7.56| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0940 0.0895 0.1786 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2111 0.2119 0.2103 n_refl.: 5174 remove outliers: r(all,work,free)=0.2111 0.2119 0.2103 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2111 0.2119 0.2103 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0939 0.0894 0.1788 n_refl.: 5174 remove outliers: r(all,work,free)=0.0939 0.0894 0.1788 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.4033 330.016 285.198 0.578 0.986 0.309 11.894-9.307 99.02 97 4 0.1818 525.217 516.856 1.021 0.992 0.309 9.237-7.194 100.00 213 7 0.2106 429.523 421.884 1.060 0.995 0.300 7.162-5.571 100.00 427 22 0.2043 322.305 313.005 1.044 0.997 0.300 5.546-4.326 100.00 867 58 0.1018 442.479 435.263 1.064 1.000 0.220 4.315-3.360 100.00 1859 96 0.0577 420.802 421.125 1.142 1.003 0.220 3.356-3.002 100.00 1373 60 0.0435 324.120 323.624 1.124 1.006 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.3563 ================= 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 : 0.3612 0.1997 0.084 5.396 8.8 119.3 19.9 258 0.000 1_bss: 0.1557 0.1585 0.084 5.396 6.0 116.4 17.0 258 0.000 1_settarget: 0.1557 0.1585 0.084 5.396 6.0 116.4 17.0 258 0.000 1_nqh: 0.1557 0.1585 0.084 5.396 6.0 116.4 17.0 258 0.000 1_weight: 0.1557 0.1585 0.084 5.396 6.0 116.4 17.0 258 0.000 1_xyzrec: 0.1162 0.1775 0.010 0.984 6.0 116.4 17.0 258 0.193 1_adp: 0.1021 0.1761 0.010 0.984 2.1 111.7 17.4 258 0.193 1_regHadp: 0.1015 0.1765 0.010 0.984 2.1 111.7 17.4 258 0.193 1_occ: 0.1008 0.1766 0.010 0.984 2.1 111.7 17.4 258 0.193 2_bss: 0.1009 0.1765 0.010 0.984 1.1 110.7 16.5 258 0.193 2_settarget: 0.1009 0.1765 0.010 0.984 1.1 110.7 16.5 258 0.193 2_updatecdl: 0.1009 0.1765 0.010 1.004 1.1 110.7 16.5 258 0.193 2_nqh: 0.1010 0.1765 0.010 1.004 1.1 110.7 16.5 258 0.196 2_sol: 0.1109 0.1603 0.010 1.004 1.1 110.7 15.8 232 n/a 2_weight: 0.1109 0.1603 0.010 1.004 1.1 110.7 15.8 232 n/a 2_xyzrec: 0.0991 0.1765 0.009 0.973 1.1 110.7 15.8 232 n/a 2_adp: 0.0927 0.1809 0.009 0.973 0.0 109.4 16.5 232 n/a 2_regHadp: 0.0925 0.1814 0.009 0.973 0.0 109.4 16.5 232 n/a 2_occ: 0.0924 0.1791 0.009 0.973 0.0 109.4 16.5 232 n/a 3_bss: 0.0927 0.1800 0.009 0.973 0.0 109.4 16.5 232 n/a 3_settarget: 0.0927 0.1800 0.009 0.973 0.0 109.4 16.5 232 n/a 3_updatecdl: 0.0927 0.1800 0.009 0.986 0.0 109.4 16.5 232 n/a 3_nqh: 0.0928 0.1801 0.009 0.986 0.0 109.4 16.5 232 n/a 3_sol: 0.1028 0.1725 0.009 0.986 0.0 109.4 16.4 238 n/a 3_weight: 0.1028 0.1725 0.009 0.986 0.0 109.4 16.4 238 n/a 3_xyzrec: 0.0926 0.1767 0.011 1.076 0.0 109.4 16.4 238 n/a 3_adp: 0.0882 0.1783 0.011 1.076 0.0 108.0 16.4 238 n/a 3_regHadp: 0.0887 0.1788 0.011 1.076 0.0 108.0 16.4 238 n/a 3_occ: 0.0875 0.1771 0.011 1.076 0.0 108.0 16.4 238 n/a 4_bss: 0.0865 0.1763 0.011 1.076 0.0 108.0 16.4 238 n/a 4_settarget: 0.0865 0.1763 0.011 1.076 0.0 108.0 16.4 238 n/a 4_updatecdl: 0.0865 0.1763 0.011 1.082 0.0 108.0 16.4 238 n/a 4_nqh: 0.0865 0.1763 0.011 1.082 0.0 108.0 16.4 238 n/a 4_sol: 0.0987 0.1786 0.011 1.082 0.0 108.0 16.4 230 n/a 4_weight: 0.0987 0.1786 0.011 1.082 0.0 108.0 16.4 230 n/a 4_xyzrec: 0.0893 0.1823 0.011 1.034 0.0 108.0 16.4 230 n/a 4_adp: 0.0873 0.1838 0.011 1.034 0.0 108.6 16.6 230 n/a 4_regHadp: 0.0877 0.1841 0.011 1.034 0.0 108.6 16.6 230 n/a 4_occ: 0.0867 0.1824 0.011 1.034 0.0 108.6 16.6 230 n/a 5_bss: 0.0866 0.1828 0.011 1.034 0.0 108.6 16.6 230 n/a 5_settarget: 0.0866 0.1828 0.011 1.034 0.0 108.6 16.6 230 n/a 5_updatecdl: 0.0866 0.1828 0.011 1.042 0.0 108.6 16.6 230 n/a 5_setrh: 0.0869 0.1829 0.011 1.042 0.0 108.6 16.6 230 n/a 5_nqh: 0.0869 0.1829 0.011 1.042 0.0 108.6 16.6 230 n/a 5_sol: 0.0981 0.1768 0.011 1.042 0.0 108.6 16.7 228 n/a 5_weight: 0.0981 0.1768 0.011 1.042 0.0 108.6 16.7 228 n/a 5_xyzrec: 0.0918 0.1774 0.011 1.149 0.0 108.6 16.7 228 n/a 5_adp: 0.0900 0.1794 0.011 1.149 0.0 109.0 17.0 228 n/a 5_regHadp: 0.0904 0.1793 0.011 1.149 0.0 109.0 17.0 228 n/a 5_occ: 0.0895 0.1786 0.011 1.149 0.0 109.0 17.0 228 n/a end: 0.0894 0.1788 0.011 1.149 0.0 109.0 17.0 228 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3975290_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_3975290_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.9500 Refinement macro-cycles (run) : 496.7400 Write final files (write_after_run_outputs) : 9.3000 Total : 508.9900 Total CPU time: 8.81 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:10 PST -0800 (1735492750.69 s) Start R-work = 0.1557, R-free = 0.1585 Final R-work = 0.0894, R-free = 0.1788 =============================================================================== Job complete usr+sys time: 536.07 seconds wall clock time: 9 minutes 19.09 seconds (559.09 seconds total)