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_7650209.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7650209.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_7650209.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.28, per 1000 atoms: 0.38 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 109.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.43 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: 512 0.91 - 1.16: 1114 1.16 - 1.40: 601 1.40 - 1.65: 859 1.65 - 1.90: 67 Bond restraints: 3153 Sorted by residual: bond pdb=" N ALA A 165 " pdb=" CA ALA A 165 " ideal model delta sigma weight residual 1.459 1.184 0.275 1.19e-02 7.06e+03 5.34e+02 bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.509 -0.188 1.00e-02 1.00e+04 3.52e+02 bond pdb=" C ALA A 36 " pdb=" N GLY A 37 " ideal model delta sigma weight residual 1.332 1.489 -0.157 8.60e-03 1.35e+04 3.33e+02 bond pdb=" CA ARG A 48 " pdb=" C ARG A 48 " ideal model delta sigma weight residual 1.526 1.751 -0.225 1.28e-02 6.10e+03 3.10e+02 bond pdb=" C HIS A 126 " pdb=" O HIS A 126 " ideal model delta sigma weight residual 1.234 1.018 0.216 1.27e-02 6.20e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.17: 2849 4.17 - 8.35: 1898 8.35 - 12.52: 807 12.52 - 16.69: 201 16.69 - 20.86: 22 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O ILE A 152 " pdb=" C ILE A 152 " pdb=" N ALEU A 153 " ideal model delta sigma weight residual 122.99 137.39 -14.40 1.07e+00 8.73e-01 1.81e+02 angle pdb=" CA BLEU A 153 " pdb=" C BLEU A 153 " pdb=" O BLEU A 153 " ideal model delta sigma weight residual 120.30 134.14 -13.84 1.07e+00 8.73e-01 1.67e+02 angle pdb=" OD1 ASN A 81 " pdb=" CG ASN A 81 " pdb=" ND2 ASN A 81 " ideal model delta sigma weight residual 122.60 110.15 12.45 1.00e+00 1.00e+00 1.55e+02 angle pdb=" C LEU A 77 " pdb=" N GLY A 78 " pdb=" CA GLY A 78 " ideal model delta sigma weight residual 119.94 133.62 -13.68 1.11e+00 8.12e-01 1.52e+02 angle pdb=" O LEU A 7 " pdb=" C LEU A 7 " pdb=" N VAL A 8 " ideal model delta sigma weight residual 123.27 109.53 13.74 1.13e+00 7.83e-01 1.48e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 1278 16.41 - 32.81: 145 32.81 - 49.21: 37 49.21 - 65.62: 16 65.62 - 82.02: 5 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ALA A 2 " pdb=" C ALA A 2 " pdb=" CA ALA A 2 " pdb=" CB ALA A 2 " ideal model delta harmonic sigma weight residual 122.90 140.97 -18.07 0 2.50e+00 1.60e-01 5.22e+01 dihedral pdb=" C BTYR A 67 " pdb=" N BTYR A 67 " pdb=" CA BTYR A 67 " pdb=" CB BTYR A 67 " ideal model delta harmonic sigma weight residual -122.60 -104.87 -17.73 0 2.50e+00 1.60e-01 5.03e+01 dihedral pdb=" C ASP A 68 " pdb=" N ASP A 68 " pdb=" CA ASP A 68 " pdb=" CB ASP A 68 " ideal model delta harmonic sigma weight residual -122.60 -139.97 17.37 0 2.50e+00 1.60e-01 4.83e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.215: 92 0.215 - 0.424: 79 0.424 - 0.634: 44 0.634 - 0.844: 22 0.844 - 1.053: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 172 " pdb=" CB LEU A 172 " pdb=" CD1 LEU A 172 " pdb=" CD2 LEU A 172 " both_signs ideal model delta sigma weight residual False -2.59 -1.54 -1.05 2.00e-01 2.50e+01 2.77e+01 chirality pdb=" CA BTYR A 67 " pdb=" N BTYR A 67 " pdb=" C BTYR A 67 " pdb=" CB BTYR A 67 " both_signs ideal model delta sigma weight residual False 2.51 3.49 -0.98 2.00e-01 2.50e+01 2.38e+01 chirality pdb=" CA ASP A 68 " pdb=" N ASP A 68 " pdb=" C ASP A 68 " pdb=" CB ASP A 68 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.28e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.110 2.00e-02 2.50e+03 7.83e-02 1.84e+02 pdb=" CG PHE A 119 " -0.167 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " -0.113 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.058 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.043 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.010 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " 0.089 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.054 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.066 2.00e-02 2.50e+03 6.78e-02 1.38e+02 pdb=" CG TYR A 139 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.092 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.050 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.119 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.053 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.084 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " 0.005 2.00e-02 2.50e+03 5.59e-02 9.38e+01 pdb=" CG PHE A 164 " 0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.022 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " 0.080 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.052 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.038 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.086 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1035 2.32 - 2.89: 8049 2.89 - 3.46: 10545 3.46 - 4.03: 15207 4.03 - 4.60: 21803 Nonbonded interactions: 56639 Sorted by model distance: nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.748 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.846 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.857 2.450 nonbonded pdb=" O LEU A 92 " pdb=" H AGLU A 96 " model vdw 1.866 2.450 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.866 2.100 ... (remaining 56634 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_7650209_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= 0.3624 r_free= 0.2028 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463362 | | target function (ml) not normalized (work): 22004.373221 | | target function (ml) not normalized (free): 1154.852265 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3813 0.2293 4.853 4.908| | 2: 3.78 - 3.00 1.00 2430 110 0.3394 0.1580 4.0625 4.1629| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.87 0.83 0.13 6604.28| | 2: 3.78 - 3.00 2430 110 0.94 11.16 1.48 0.26 443.60| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 375.40 max = 12071.67 mean = 3567.68| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.28| |phase err.(test): min = 0.00 max = 89.93 mean = 33.24| |-----------------------------------------------------------------------------| ----------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 0.275 1557 Z= 5.637 Angle : 5.171 17.906 2118 Z= 3.655 Chirality : 0.401 1.053 243 Planarity : 0.032 0.108 284 Dihedral : 14.076 82.020 611 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 : 1.86 % Allowed : 2.48 % Favored : 95.65 % Cbeta Deviations : 34.59 % 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: -2.43 (0.46), residues: 224 helix: -2.39 (0.38), residues: 102 sheet: -0.74 (0.75), residues: 38 loop : -0.61 (0.59), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.016 ARG A 156 TYR 0.061 0.025 TYR A 141 PHE 0.151 0.039 PHE A 119 HIS 0.088 0.044 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= 0.3624 r_free= 0.2028 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.463362 | | target function (ml) not normalized (work): 22004.373221 | | target function (ml) not normalized (free): 1154.852265 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3580 0.3657 0.2144 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3580 0.3657 0.2144 n_refl.: 5182 remove outliers: r(all,work,free)=0.2528 0.2551 0.2144 n_refl.: 5178 overall B=-2.83 to atoms: r(all,work,free)=0.2418 0.2438 0.2105 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1561 0.1557 0.1651 n_refl.: 5178 remove outliers: r(all,work,free)=0.1560 0.1555 0.1651 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 0.3987 445.341 412.787 0.660 1.072 0.398 11.894-9.307 99.02 97 4 0.1913 714.940 695.775 0.936 1.069 0.383 9.237-7.194 100.00 213 7 0.2156 584.679 574.705 0.969 1.062 0.384 7.162-5.571 100.00 427 22 0.2319 438.731 424.285 0.938 1.048 0.336 5.546-4.326 100.00 867 58 0.1398 602.315 594.170 0.974 1.026 0.215 4.315-3.360 100.00 1859 96 0.1290 572.808 566.205 1.055 0.989 0.189 3.356-3.002 100.00 1373 60 0.1591 441.201 433.487 1.070 0.952 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.6384 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1555 r_free=0.1651 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1555 r_free=0.1651 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.805827 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.713473 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 0.1159 0.1804 0.0644 0.010 1.0 2.6 0.5 0.0 0 9.403 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.59 18.04 6.44 3.013 16.028 1.713 0.018 10.23 18.04 7.81 4.819 16.206 1.713 0.015 Individual atomic B min max mean iso aniso Overall: 2.25 111.47 17.39 5.18 1785 0 Protein: 2.25 110.69 14.71 5.17 1519 0 Water: 4.03 111.47 33.00 N/A 258 0 Other: 16.25 38.33 23.71 N/A 8 0 Chain A: 2.25 111.47 17.39 N/A 1785 0 Histogram: Values Number of atoms 2.25 - 13.17 925 13.17 - 24.09 480 24.09 - 35.02 186 35.02 - 45.94 106 45.94 - 56.86 56 56.86 - 67.78 15 67.78 - 78.70 8 78.70 - 89.62 5 89.62 - 100.55 1 100.55 - 111.47 3 =========================== Idealize ADP of riding H ========================== r_work=0.1023 r_free=0.1804 r_work=0.1017 r_free=0.1811 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1017 r_free = 0.1811 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 = 0.1011 r_free = 0.1792 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1011 r_free= 0.1792 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.014031 | | target function (ls_wunit_k1) not normalized (work): 69.101928 | | target function (ls_wunit_k1) not normalized (free): 10.319584 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1050 0.1011 0.1792 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2111 0.2110 0.2245 n_refl.: 5177 remove outliers: r(all,work,free)=0.2111 0.2110 0.2245 n_refl.: 5177 overall B=-0.98 to atoms: r(all,work,free)=0.2069 0.2066 0.2234 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1052 0.1013 0.1792 n_refl.: 5177 remove outliers: r(all,work,free)=0.1050 0.1011 0.1792 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 0.3432 323.809 308.747 0.669 1.009 0.375 11.894-9.307 99.02 97 4 0.1543 524.310 515.860 0.987 1.011 0.364 9.237-7.194 100.00 213 7 0.1700 428.782 428.115 1.024 1.010 0.329 7.162-5.571 100.00 427 22 0.1628 321.749 318.167 0.986 1.008 0.302 5.546-4.326 100.00 867 58 0.0906 441.715 438.989 0.995 1.005 0.202 4.315-3.360 100.00 1859 96 0.0761 420.076 419.830 1.044 0.998 0.193 3.356-3.002 100.00 1373 60 0.0994 323.560 321.886 1.018 0.992 0.061 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.5017 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1011 r_free=0.1792 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=0.1012 r_free=0.1792 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1012 r_free=0.1792 | n_water=258 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.1027 r_free=0.1770 | n_water=252 | time (s): 21.540 (total time: 22.010) Filter (q & B) r_work=0.1026 r_free=0.1771 | n_water=249 | time (s): 1.500 (total time: 23.510) Compute maps r_work=0.1026 r_free=0.1771 | n_water=249 | time (s): 0.600 (total time: 24.110) Filter (map) r_work=0.1317 r_free=0.1853 | n_water=151 | time (s): 1.900 (total time: 26.010) Find peaks r_work=0.1317 r_free=0.1853 | n_water=151 | time (s): 0.570 (total time: 26.580) Add new water r_work=0.1652 r_free=0.2108 | n_water=235 | time (s): 1.820 (total time: 28.400) Refine new water occ: r_work=0.1144 r_free=0.1670 adp: r_work=0.1119 r_free=0.1692 occ: r_work=0.1116 r_free=0.1660 adp: r_work=0.1105 r_free=0.1679 occ: r_work=0.1104 r_free=0.1665 adp: r_work=0.1101 r_free=0.1670 ADP+occupancy (water only), MIN, final r_work=0.1101 r_free=0.1670 r_work=0.1101 r_free=0.1670 | n_water=235 | time (s): 6.010 (total time: 34.410) Filter (q & B) r_work=0.1101 r_free=0.1670 | n_water=235 | time (s): 1.020 (total time: 35.430) Filter (dist only) r_work=0.1109 r_free=0.1658 | n_water=231 | time (s): 18.760 (total time: 54.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.368660 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.734824 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 0.1004 0.1744 0.0740 0.009 1.0 4.5 0.5 0.6 0 12.184 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.04 17.44 7.40 4.590 16.779 2.735 0.014 9.38 17.71 8.34 5.445 17.130 2.735 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.50 16.57 6.44 1758 0 Protein: 0.00 108.50 14.91 6.43 1519 0 Water: 0.00 62.77 27.28 N/A 231 0 Other: 11.31 32.35 21.63 N/A 8 0 Chain A: 0.00 108.50 15.66 N/A 1675 0 Chain S: 6.26 60.13 34.96 N/A 83 0 Histogram: Values Number of atoms 0.00 - 10.85 695 10.85 - 21.70 660 21.70 - 32.55 207 32.55 - 43.40 114 43.40 - 54.25 44 54.25 - 65.10 28 65.10 - 75.95 3 75.95 - 86.80 4 86.80 - 97.65 1 97.65 - 108.50 2 =========================== Idealize ADP of riding H ========================== r_work=0.0938 r_free=0.1771 r_work=0.0934 r_free=0.1772 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0934 r_free = 0.1772 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0936 r_free = 0.1776 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 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= 0.0936 r_free= 0.1776 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012143 | | target function (ls_wunit_k1) not normalized (work): 59.793656 | | target function (ls_wunit_k1) not normalized (free): 9.759473 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0979 0.0936 0.1776 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2117 0.2124 0.2115 n_refl.: 5176 remove outliers: r(all,work,free)=0.2117 0.2124 0.2115 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2117 0.2124 0.2115 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0977 0.0935 0.1773 n_refl.: 5176 remove outliers: r(all,work,free)=0.0977 0.0935 0.1773 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 0.3435 323.809 306.333 0.652 1.006 0.360 11.894-9.307 99.02 97 4 0.1508 524.310 520.380 0.990 1.007 0.349 9.237-7.194 100.00 213 7 0.1483 428.782 429.046 1.025 1.007 0.320 7.162-5.571 100.00 427 22 0.1464 321.749 319.082 0.999 1.006 0.290 5.546-4.326 100.00 867 58 0.0788 441.715 439.075 1.008 1.004 0.220 4.315-3.360 100.00 1859 96 0.0707 420.076 420.093 1.057 1.000 0.210 3.356-3.002 100.00 1373 60 0.0956 323.560 322.413 1.031 0.996 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.2648 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0935 r_free=0.1773 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=0.0935 r_free=0.1775 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0935 r_free=0.1775 | n_water=231 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0952 r_free=0.1744 | n_water=227 | time (s): 18.520 (total time: 19.030) Filter (q & B) r_work=0.0981 r_free=0.1770 | n_water=226 | time (s): 1.390 (total time: 20.420) Compute maps r_work=0.0981 r_free=0.1770 | n_water=226 | time (s): 0.500 (total time: 20.920) Filter (map) r_work=0.1249 r_free=0.1829 | n_water=152 | time (s): 1.520 (total time: 22.440) Find peaks r_work=0.1249 r_free=0.1829 | n_water=152 | time (s): 0.410 (total time: 22.850) Add new water r_work=0.1609 r_free=0.2068 | n_water=233 | time (s): 1.200 (total time: 24.050) Refine new water occ: r_work=0.1047 r_free=0.1721 adp: r_work=0.1044 r_free=0.1721 occ: r_work=0.1033 r_free=0.1708 adp: r_work=0.1033 r_free=0.1713 occ: r_work=0.1024 r_free=0.1702 adp: r_work=0.1024 r_free=0.1707 ADP+occupancy (water only), MIN, final r_work=0.1024 r_free=0.1707 r_work=0.1024 r_free=0.1707 | n_water=233 | time (s): 9.770 (total time: 33.820) Filter (q & B) r_work=0.1024 r_free=0.1707 | n_water=233 | time (s): 1.000 (total time: 34.820) Filter (dist only) r_work=0.1030 r_free=0.1712 | n_water=231 | time (s): 16.970 (total time: 51.790) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.079639 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.216414 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 0.0939 0.1768 0.0829 0.011 1.1 5.1 0.5 0.6 0 0.540 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.39 17.68 8.29 5.376 17.676 0.216 5.160 8.96 17.79 8.83 7.229 17.682 0.216 5.064 Individual atomic B min max mean iso aniso Overall: 0.00 108.03 16.32 8.95 1758 0 Protein: 0.00 108.03 15.04 8.95 1519 0 Water: 0.00 63.59 24.50 N/A 231 0 Other: 13.54 36.29 23.57 N/A 8 0 Chain A: 0.00 108.03 15.68 N/A 1661 0 Chain S: 0.00 63.59 27.24 N/A 97 0 Histogram: Values Number of atoms 0.00 - 10.80 699 10.80 - 21.61 643 21.61 - 32.41 227 32.41 - 43.21 128 43.21 - 54.02 27 54.02 - 64.82 15 64.82 - 75.62 11 75.62 - 86.42 3 86.42 - 97.23 4 97.23 - 108.03 1 =========================== Idealize ADP of riding H ========================== r_work=0.0896 r_free=0.1779 r_work=0.0901 r_free=0.1795 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0901 r_free = 0.1795 target_work(ml) = 5.068 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0893 r_free = 0.1781 target_work(ml) = 5.064 | | 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.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0893 r_free= 0.1781 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.063677 | | target function (ml) not normalized (work): 24933.544726 | | target function (ml) not normalized (free): 1770.521798 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0938 0.0893 0.1781 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2120 0.2131 0.2096 n_refl.: 5176 remove outliers: r(all,work,free)=0.2120 0.2131 0.2096 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2120 0.2131 0.2096 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0932 0.0887 0.1775 n_refl.: 5176 remove outliers: r(all,work,free)=0.0929 0.0885 0.1775 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 0.3788 325.925 290.891 0.587 0.992 0.338 11.894-9.307 99.02 97 4 0.1859 524.310 508.804 0.960 0.995 0.337 9.237-7.194 100.00 213 7 0.1835 428.782 422.929 1.005 0.998 0.305 7.162-5.571 100.00 427 22 0.1844 321.749 313.498 0.985 0.999 0.300 5.546-4.326 100.00 867 58 0.0902 441.715 436.771 0.999 1.000 0.227 4.315-3.360 100.00 1859 96 0.0582 420.076 419.841 1.054 1.003 0.220 3.356-3.002 100.00 1373 60 0.0613 323.560 323.625 1.030 1.005 0.064 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.3439 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0885 r_free=0.1775 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B Total number of N/Q/H flips: 1 r_work=0.0885 r_free=0.1771 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0885 r_free=0.1771 | n_water=231 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.0894 r_free=0.1780 | n_water=228 | time (s): 18.270 (total time: 18.930) Filter (q & B) r_work=0.0930 r_free=0.1805 | n_water=227 | time (s): 1.720 (total time: 20.650) Compute maps r_work=0.0930 r_free=0.1805 | n_water=227 | time (s): 0.560 (total time: 21.210) Filter (map) r_work=0.1222 r_free=0.1831 | n_water=159 | time (s): 1.540 (total time: 22.750) Find peaks r_work=0.1222 r_free=0.1831 | n_water=159 | time (s): 0.600 (total time: 23.350) Add new water r_work=0.1556 r_free=0.2122 | n_water=242 | time (s): 1.740 (total time: 25.090) Refine new water occ: r_work=0.1000 r_free=0.1756 adp: r_work=0.0997 r_free=0.1766 occ: r_work=0.0987 r_free=0.1749 adp: r_work=0.0987 r_free=0.1756 occ: r_work=0.0978 r_free=0.1739 adp: r_work=0.0978 r_free=0.1747 ADP+occupancy (water only), MIN, final r_work=0.0978 r_free=0.1747 r_work=0.0978 r_free=0.1747 | n_water=242 | time (s): 11.940 (total time: 37.030) Filter (q & B) r_work=0.0978 r_free=0.1747 | n_water=242 | time (s): 0.810 (total time: 37.840) Filter (dist only) r_work=0.0977 r_free=0.1753 | n_water=241 | time (s): 18.460 (total time: 56.300) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.018238 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.223923 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 0.0904 0.1789 0.0885 0.011 1.1 5.8 0.5 0.0 0 0.509 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.04 17.89 8.85 6.963 17.901 0.224 5.025 8.82 18.37 9.54 8.282 18.020 0.224 4.967 Individual atomic B min max mean iso aniso Overall: 0.00 107.19 16.70 10.86 1768 0 Protein: 0.00 107.19 15.45 10.87 1519 0 Water: 0.00 59.94 24.25 N/A 241 0 Other: 15.69 39.44 25.86 N/A 8 0 Chain A: 0.00 107.19 16.01 N/A 1651 0 Chain S: 0.00 59.94 26.45 N/A 117 0 Histogram: Values Number of atoms 0.00 - 10.72 669 10.72 - 21.44 630 21.44 - 32.16 266 32.16 - 42.88 126 42.88 - 53.60 42 53.60 - 64.32 14 64.32 - 75.04 10 75.04 - 85.76 6 85.76 - 96.47 3 96.47 - 107.19 2 =========================== Idealize ADP of riding H ========================== r_work=0.0882 r_free=0.1837 r_work=0.0887 r_free=0.1843 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0887 r_free = 0.1843 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0875 r_free = 0.1828 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.24 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= 0.0875 r_free= 0.1828 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.964259 | | target function (ml) not normalized (work): 24439.048728 | | target function (ml) not normalized (free): 2101.816845 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0922 0.0875 0.1828 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2067 0.2070 0.2172 n_refl.: 5175 remove outliers: r(all,work,free)=0.2067 0.2070 0.2172 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2067 0.2070 0.2172 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0922 0.0874 0.1830 n_refl.: 5175 remove outliers: r(all,work,free)=0.0922 0.0874 0.1830 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 0.3882 325.925 285.982 0.559 0.988 0.318 11.894-9.307 99.02 97 4 0.2024 524.310 507.498 0.955 0.993 0.317 9.237-7.194 100.00 213 7 0.2083 428.782 422.804 1.014 0.996 0.290 7.162-5.571 100.00 427 22 0.2054 321.749 312.744 0.998 0.998 0.280 5.546-4.326 100.00 867 58 0.0957 441.715 435.298 1.014 1.000 0.225 4.315-3.360 100.00 1859 96 0.0542 420.076 420.019 1.079 1.003 0.220 3.356-3.002 100.00 1373 60 0.0451 323.560 323.406 1.057 1.006 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.5328 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0874 r_free=0.1830 After: r_work=0.0878 r_free=0.1830 ================================== NQH flips ================================== r_work=0.0878 r_free=0.1830 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B A 135 ASN Total number of N/Q/H flips: 2 r_work=0.0886 r_free=0.1832 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0886 r_free=0.1832 | n_water=241 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.0900 r_free=0.1827 | n_water=236 | time (s): 21.270 (total time: 21.910) Filter (q & B) r_work=0.1053 r_free=0.1883 | n_water=231 | time (s): 1.620 (total time: 23.530) Compute maps r_work=0.1053 r_free=0.1883 | n_water=231 | time (s): 0.470 (total time: 24.000) Filter (map) r_work=0.1266 r_free=0.1932 | n_water=160 | time (s): 1.400 (total time: 25.400) Find peaks r_work=0.1266 r_free=0.1932 | n_water=160 | time (s): 0.460 (total time: 25.860) Add new water r_work=0.1530 r_free=0.2140 | n_water=230 | time (s): 1.590 (total time: 27.450) Refine new water occ: r_work=0.1007 r_free=0.1830 adp: r_work=0.0998 r_free=0.1814 occ: r_work=0.0989 r_free=0.1812 adp: r_work=0.0990 r_free=0.1810 occ: r_work=0.0982 r_free=0.1809 adp: r_work=0.0983 r_free=0.1806 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1806 r_work=0.0983 r_free=0.1806 | n_water=230 | time (s): 11.820 (total time: 39.270) Filter (q & B) r_work=0.0983 r_free=0.1801 | n_water=229 | time (s): 1.320 (total time: 40.590) Filter (dist only) r_work=0.0991 r_free=0.1797 | n_water=228 | time (s): 17.930 (total time: 58.520) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.973621 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.228076 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 0.0921 0.1823 0.0902 0.011 1.1 9.6 0.5 0.6 0 0.487 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.21 18.23 9.02 8.242 18.269 0.228 5.034 8.99 18.41 9.43 8.863 18.356 0.228 4.977 Individual atomic B min max mean iso aniso Overall: 0.00 107.89 16.85 11.68 1755 0 Protein: 0.00 107.89 15.79 11.69 1519 0 Water: 0.00 62.80 23.56 N/A 228 0 Other: 18.36 37.01 26.15 N/A 8 0 Chain A: 0.00 107.89 16.24 N/A 1641 0 Chain S: 0.00 58.40 25.52 N/A 114 0 Histogram: Values Number of atoms 0.00 - 10.79 660 10.79 - 21.58 631 21.58 - 32.37 270 32.37 - 43.16 125 43.16 - 53.95 36 53.95 - 64.74 11 64.74 - 75.52 9 75.52 - 86.31 7 86.31 - 97.10 4 97.10 - 107.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.0899 r_free=0.1841 r_work=0.0902 r_free=0.1839 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0902 r_free = 0.1839 target_work(ml) = 4.981 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0893 r_free = 0.1829 target_work(ml) = 4.976 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0893 r_free= 0.1829 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.975825 | | target function (ml) not normalized (work): 24495.987975 | | target function (ml) not normalized (free): 2096.125196 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1258 0.1806 5.5318 6.1568| | 2: 3.78 - 3.00 1.00 2430 110 0.0449 0.1868 4.4054 11.108| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 12.11 1.00 0.97 13085.60| | 2: 3.78 - 3.00 2430 110 0.99 2.00 1.00 0.99 987.81| |alpha: min = 0.96 max = 0.99 mean = 0.98| |beta: min = 641.58 max = 21810.59 mean = 7114.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.66 mean = 7.12| |phase err.(test): min = 0.00 max = 88.66 mean = 7.27| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0941 0.0893 0.1829 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2129 0.2132 0.2189 n_refl.: 5175 remove outliers: r(all,work,free)=0.2129 0.2132 0.2189 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2129 0.2132 0.2189 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0939 0.0891 0.1836 n_refl.: 5175 remove outliers: r(all,work,free)=0.0939 0.0891 0.1836 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 0.3890 325.925 295.782 0.579 0.987 0.320 11.894-9.307 99.02 97 4 0.1856 524.310 507.963 0.958 0.993 0.320 9.237-7.194 100.00 213 7 0.2080 428.782 417.625 1.003 0.997 0.310 7.162-5.571 100.00 427 22 0.2097 321.749 311.497 0.997 0.998 0.310 5.546-4.326 100.00 867 58 0.1009 441.715 435.670 1.018 1.000 0.240 4.315-3.360 100.00 1859 96 0.0575 420.076 419.849 1.087 1.003 0.220 3.356-3.002 100.00 1373 60 0.0429 323.560 323.913 1.069 1.006 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9291 ================= 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 : 0.3624 0.2028 0.084 5.171 8.8 119.3 19.9 258 0.000 1_bss: 0.1555 0.1651 0.084 5.171 6.0 116.5 17.1 258 0.000 1_settarget: 0.1555 0.1651 0.084 5.171 6.0 116.5 17.1 258 0.000 1_nqh: 0.1555 0.1651 0.084 5.171 6.0 116.5 17.1 258 0.000 1_weight: 0.1555 0.1651 0.084 5.171 6.0 116.5 17.1 258 0.000 1_xyzrec: 0.1159 0.1804 0.010 0.958 6.0 116.5 17.1 258 0.206 1_adp: 0.1023 0.1804 0.010 0.958 2.2 111.5 17.4 258 0.206 1_regHadp: 0.1017 0.1811 0.010 0.958 2.2 111.5 17.4 258 0.206 1_occ: 0.1011 0.1792 0.010 0.958 2.2 111.5 17.4 258 0.206 2_bss: 0.1011 0.1792 0.010 0.958 1.3 110.5 16.4 258 0.206 2_settarget: 0.1011 0.1792 0.010 0.958 1.3 110.5 16.4 258 0.206 2_updatecdl: 0.1011 0.1792 0.010 0.982 1.3 110.5 16.4 258 0.206 2_nqh: 0.1012 0.1792 0.010 0.982 1.3 110.5 16.4 258 0.208 2_sol: 0.1109 0.1658 0.010 0.982 1.3 109.7 15.9 231 n/a 2_weight: 0.1109 0.1658 0.010 0.982 1.3 109.7 15.9 231 n/a 2_xyzrec: 0.1004 0.1744 0.009 1.009 1.3 109.7 15.9 231 n/a 2_adp: 0.0938 0.1771 0.009 1.009 0.0 108.5 16.6 231 n/a 2_regHadp: 0.0934 0.1772 0.009 1.009 0.0 108.5 16.6 231 n/a 2_occ: 0.0936 0.1776 0.009 1.009 0.0 108.5 16.6 231 n/a 3_bss: 0.0935 0.1773 0.009 1.009 0.0 108.5 16.6 231 n/a 3_settarget: 0.0935 0.1773 0.009 1.009 0.0 108.5 16.6 231 n/a 3_updatecdl: 0.0935 0.1773 0.009 1.016 0.0 108.5 16.6 231 n/a 3_nqh: 0.0935 0.1775 0.009 1.016 0.0 108.5 16.6 231 n/a 3_sol: 0.1030 0.1712 0.009 1.016 0.0 108.5 16.3 231 n/a 3_weight: 0.1030 0.1712 0.009 1.016 0.0 108.5 16.3 231 n/a 3_xyzrec: 0.0939 0.1768 0.011 1.075 0.0 108.5 16.3 231 n/a 3_adp: 0.0896 0.1779 0.011 1.075 0.0 108.0 16.3 231 n/a 3_regHadp: 0.0901 0.1795 0.011 1.075 0.0 108.0 16.3 231 n/a 3_occ: 0.0893 0.1781 0.011 1.075 0.0 108.0 16.3 231 n/a 4_bss: 0.0885 0.1775 0.011 1.075 0.0 108.0 16.3 231 n/a 4_settarget: 0.0885 0.1775 0.011 1.075 0.0 108.0 16.3 231 n/a 4_updatecdl: 0.0885 0.1775 0.011 1.086 0.0 108.0 16.3 231 n/a 4_nqh: 0.0885 0.1771 0.011 1.086 0.0 108.0 16.3 231 n/a 4_sol: 0.0977 0.1753 0.011 1.086 0.0 108.0 16.5 241 n/a 4_weight: 0.0977 0.1753 0.011 1.086 0.0 108.0 16.5 241 n/a 4_xyzrec: 0.0904 0.1789 0.011 1.061 0.0 108.0 16.5 241 n/a 4_adp: 0.0882 0.1837 0.011 1.061 0.0 107.2 16.7 241 n/a 4_regHadp: 0.0887 0.1843 0.011 1.061 0.0 107.2 16.7 241 n/a 4_occ: 0.0875 0.1828 0.011 1.061 0.0 107.2 16.7 241 n/a 5_bss: 0.0874 0.1830 0.011 1.061 0.0 107.2 16.7 241 n/a 5_settarget: 0.0874 0.1830 0.011 1.061 0.0 107.2 16.7 241 n/a 5_updatecdl: 0.0874 0.1830 0.011 1.071 0.0 107.2 16.7 241 n/a 5_setrh: 0.0878 0.1830 0.011 1.071 0.0 107.2 16.7 241 n/a 5_nqh: 0.0886 0.1832 0.011 1.071 0.0 107.2 16.7 241 n/a 5_sol: 0.0991 0.1797 0.011 1.071 0.0 107.2 16.7 228 n/a 5_weight: 0.0991 0.1797 0.011 1.071 0.0 107.2 16.7 228 n/a 5_xyzrec: 0.0921 0.1823 0.011 1.105 0.0 107.2 16.7 228 n/a 5_adp: 0.0899 0.1841 0.011 1.105 0.0 107.9 16.8 228 n/a 5_regHadp: 0.0902 0.1839 0.011 1.105 0.0 107.9 16.8 228 n/a 5_occ: 0.0893 0.1829 0.011 1.105 0.0 107.9 16.8 228 n/a end: 0.0891 0.1836 0.011 1.105 0.0 107.9 16.8 228 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7650209_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_7650209_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.8200 Refinement macro-cycles (run) : 488.0000 Write final files (write_after_run_outputs) : 11.1100 Total : 502.9300 Total CPU time: 8.72 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:04 PST -0800 (1735492744.05 s) Start R-work = 0.1555, R-free = 0.1651 Final R-work = 0.0891, R-free = 0.1836 =============================================================================== Job complete usr+sys time: 530.94 seconds wall clock time: 9 minutes 12.43 seconds (552.43 seconds total)