Starting phenix.refine on Sun Dec 29 09:10:03 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2226169.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 { phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2226169.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2226169.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 =============================================================================== 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: 1.42, per 1000 atoms: 0.42 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: 0.31 Conformation dependent library (CDL) restraints added in 135.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.69 - 0.94: 722 0.94 - 1.20: 976 1.20 - 1.46: 712 1.46 - 1.71: 720 1.71 - 1.97: 23 Bond restraints: 3153 Sorted by residual: bond pdb=" CE1 HIS A 126 " pdb=" NE2 HIS A 126 " ideal model delta sigma weight residual 1.321 1.515 -0.194 1.00e-02 1.00e+04 3.77e+02 bond pdb=" CA VAL A 181 " pdb=" CB VAL A 181 " ideal model delta sigma weight residual 1.540 1.775 -0.235 1.29e-02 6.01e+03 3.33e+02 bond pdb=" C ILE A 168 " pdb=" O ILE A 168 " ideal model delta sigma weight residual 1.237 1.424 -0.187 1.13e-02 7.83e+03 2.74e+02 bond pdb=" C LYS A 32 " pdb=" O LYS A 32 " ideal model delta sigma weight residual 1.235 1.430 -0.194 1.19e-02 7.06e+03 2.67e+02 bond pdb=" N HIS A 115 " pdb=" CA HIS A 115 " ideal model delta sigma weight residual 1.456 1.250 0.205 1.26e-02 6.30e+03 2.65e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.76: 3198 4.76 - 9.52: 1843 9.52 - 14.28: 618 14.28 - 19.03: 108 19.03 - 23.79: 10 Bond angle restraints: 5777 Sorted by residual: angle pdb=" NE ARG A 98 " pdb=" CZ ARG A 98 " pdb=" NH2 ARG A 98 " ideal model delta sigma weight residual 119.20 104.39 14.81 9.00e-01 1.23e+00 2.71e+02 angle pdb=" OE1BGLN A 80 " pdb=" CD BGLN A 80 " pdb=" NE2BGLN A 80 " ideal model delta sigma weight residual 122.60 137.81 -15.21 1.00e+00 1.00e+00 2.31e+02 angle pdb=" NE ARG A 28 " pdb=" CZ ARG A 28 " pdb=" NH2 ARG A 28 " ideal model delta sigma weight residual 119.20 132.19 -12.99 9.00e-01 1.23e+00 2.08e+02 angle pdb=" CA ALA A 103 " pdb=" C ALA A 103 " pdb=" N ALA A 104 " ideal model delta sigma weight residual 116.37 132.58 -16.21 1.19e+00 7.06e-01 1.85e+02 angle pdb=" CA LEU A 38 " pdb=" C LEU A 38 " pdb=" O LEU A 38 " ideal model delta sigma weight residual 120.63 106.13 14.50 1.08e+00 8.57e-01 1.80e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 1284 16.26 - 32.51: 136 32.51 - 48.77: 36 48.77 - 65.03: 21 65.03 - 81.28: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N LYS A 32 " pdb=" C LYS A 32 " pdb=" CA LYS A 32 " pdb=" CB LYS A 32 " ideal model delta harmonic sigma weight residual 122.80 102.76 20.04 0 2.50e+00 1.60e-01 6.42e+01 dihedral pdb=" C ALA A 103 " pdb=" N ALA A 103 " pdb=" CA ALA A 103 " pdb=" CB ALA A 103 " ideal model delta harmonic sigma weight residual -122.60 -142.30 19.70 0 2.50e+00 1.60e-01 6.21e+01 dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -142.23 19.63 0 2.50e+00 1.60e-01 6.17e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.185: 66 0.185 - 0.368: 79 0.368 - 0.551: 54 0.551 - 0.734: 30 0.734 - 0.917: 14 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ALA A 103 " pdb=" N ALA A 103 " pdb=" C ALA A 103 " pdb=" CB ALA A 103 " both_signs ideal model delta sigma weight residual False 2.48 1.57 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA LEU A 77 " pdb=" N LEU A 77 " pdb=" C LEU A 77 " pdb=" CB LEU A 77 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.08e+01 chirality pdb=" CA VAL A 169 " pdb=" N VAL A 169 " pdb=" C VAL A 169 " pdb=" CB VAL A 169 " both_signs ideal model delta sigma weight residual False 2.44 3.35 -0.91 2.00e-01 2.50e+01 2.08e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.062 2.00e-02 2.50e+03 6.70e-02 1.35e+02 pdb=" CG TYR A 139 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.046 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.072 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.017 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " -0.114 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.133 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " -0.029 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.040 2.00e-02 2.50e+03 5.91e-02 1.05e+02 pdb=" CG ATYR A 67 " 0.094 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.023 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.090 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.012 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.082 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.017 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " -0.023 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.087 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.009 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.087 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 162 " -0.060 2.00e-02 2.50e+03 5.74e-02 9.89e+01 pdb=" CG PHE A 162 " 0.113 2.00e-02 2.50e+03 pdb=" CD1 PHE A 162 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 162 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 PHE A 162 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 162 " 0.070 2.00e-02 2.50e+03 pdb=" CZ PHE A 162 " -0.060 2.00e-02 2.50e+03 pdb=" HD1 PHE A 162 " 0.050 2.00e-02 2.50e+03 pdb=" HD2 PHE A 162 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 PHE A 162 " -0.053 2.00e-02 2.50e+03 pdb=" HE2 PHE A 162 " -0.039 2.00e-02 2.50e+03 pdb=" HZ PHE A 162 " 0.063 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.31: 1001 2.31 - 2.88: 8055 2.88 - 3.46: 10524 3.46 - 4.03: 15242 4.03 - 4.60: 21875 Nonbonded interactions: 56697 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.739 2.100 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.768 2.450 x-y,-y,-z-4/3 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.792 2.450 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.812 2.450 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.821 2.270 ... (remaining 56692 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_2226169_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= 0.3623 r_free= 0.2033 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.462313 | | target function (ml) not normalized (work): 21999.204440 | | target function (ml) not normalized (free): 1149.651244 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.2246 4.8511 4.928| | 2: 3.78 - 3.00 1.00 2430 110 0.3391 0.1674 4.0623 4.0898| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.68 0.83 0.13 6601.00| | 2: 3.78 - 3.00 2430 110 0.94 11.14 1.48 0.26 438.74| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 370.37 max = 12062.48 mean = 3563.62| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.18| |phase err.(test): min = 0.00 max = 89.95 mean = 33.18| |-----------------------------------------------------------------------------| ----------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 : 0.081 0.235 1557 Z= 5.403 Angle : 5.373 18.971 2118 Z= 3.821 Chirality : 0.404 0.917 243 Planarity : 0.031 0.107 284 Dihedral : 13.852 81.283 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.62 % Favored : 97.84 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 36.22 % 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 (0.48), residues: 224 helix: -2.67 (0.36), residues: 108 sheet: 0.02 (0.93), residues: 28 loop : -0.40 (0.60), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.071 0.019 ARG A 48 TYR 0.080 0.032 TYR A 141 PHE 0.117 0.042 PHE A 162 HIS 0.086 0.038 HIS A 138 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= 0.3623 r_free= 0.2033 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.462313 | | target function (ml) not normalized (work): 21999.204440 | | target function (ml) not normalized (free): 1149.651244 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3579 0.3656 0.2135 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3579 0.3656 0.2135 n_refl.: 5182 remove outliers: r(all,work,free)=0.2521 0.2544 0.2135 n_refl.: 5178 overall B=-2.88 to atoms: r(all,work,free)=0.2411 0.2430 0.2082 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1562 0.1559 0.1632 n_refl.: 5178 remove outliers: r(all,work,free)=0.1560 0.1556 0.1632 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 0.4054 444.668 409.360 0.674 1.052 0.403 11.894-9.307 99.02 97 4 0.1866 713.860 698.749 0.952 1.049 0.398 9.237-7.194 100.00 213 7 0.2109 583.796 576.033 0.987 1.044 0.374 7.162-5.571 100.00 427 22 0.2315 438.068 423.736 0.944 1.035 0.326 5.546-4.326 100.00 867 58 0.1384 601.405 593.627 0.990 1.019 0.248 4.315-3.360 100.00 1859 96 0.1310 571.942 565.511 1.049 0.993 0.195 3.356-3.002 100.00 1373 60 0.1587 440.534 432.347 1.055 0.967 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.7014 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1556 r_free=0.1632 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.1558 r_free=0.1639 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.780618 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.668248 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 0.1165 0.1793 0.0628 0.009 1.0 2.2 0.5 0.0 0 9.390 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.65 17.93 6.28 3.013 15.979 1.668 0.018 10.34 17.83 7.49 4.563 16.112 1.668 0.015 Individual atomic B min max mean iso aniso Overall: 2.30 111.42 17.26 4.99 1785 0 Protein: 2.30 110.57 14.56 4.98 1519 0 Water: 3.99 111.42 32.95 N/A 258 0 Other: 16.34 37.78 23.17 N/A 8 0 Chain A: 2.30 111.42 17.26 N/A 1785 0 Histogram: Values Number of atoms 2.30 - 13.21 939 13.21 - 24.12 479 24.12 - 35.03 179 35.03 - 45.94 105 45.94 - 56.86 53 56.86 - 67.77 14 67.77 - 78.68 7 78.68 - 89.59 5 89.59 - 100.51 1 100.51 - 111.42 3 =========================== Idealize ADP of riding H ========================== r_work=0.1034 r_free=0.1783 r_work=0.1028 r_free=0.1787 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1028 r_free = 0.1787 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 = 0.1030 r_free = 0.1788 target_work(ls_wunit_k1) = 0.015 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1030 r_free= 0.1788 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.014528 | | target function (ls_wunit_k1) not normalized (work): 71.549691 | | target function (ls_wunit_k1) not normalized (free): 10.463571 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1068 0.1030 0.1788 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2115 0.2116 0.2222 n_refl.: 5177 remove outliers: r(all,work,free)=0.2115 0.2116 0.2222 n_refl.: 5177 overall B=-1.00 to atoms: r(all,work,free)=0.2073 0.2072 0.2209 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1067 0.1029 0.1773 n_refl.: 5177 remove outliers: r(all,work,free)=0.1065 0.1027 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 0.3403 324.605 306.237 0.668 1.001 0.370 11.894-9.307 99.02 97 4 0.1597 525.599 516.642 0.992 1.003 0.351 9.237-7.194 100.00 213 7 0.1721 429.836 429.337 1.035 1.003 0.325 7.162-5.571 100.00 427 22 0.1643 322.539 319.119 0.985 1.003 0.302 5.546-4.326 100.00 867 58 0.0922 442.801 439.838 1.005 1.002 0.217 4.315-3.360 100.00 1859 96 0.0774 421.109 421.218 1.043 1.000 0.204 3.356-3.002 100.00 1373 60 0.1012 324.355 322.603 1.014 0.998 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.5661 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1027 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=0.1029 r_free=0.1774 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1029 r_free=0.1774 | n_water=258 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1048 r_free=0.1779 | n_water=250 | time (s): 21.760 (total time: 22.470) Filter (q & B) r_work=0.1048 r_free=0.1782 | n_water=247 | time (s): 1.340 (total time: 23.810) Compute maps r_work=0.1048 r_free=0.1782 | n_water=247 | time (s): 0.440 (total time: 24.250) Filter (map) r_work=0.1331 r_free=0.1846 | n_water=146 | time (s): 1.500 (total time: 25.750) Find peaks r_work=0.1331 r_free=0.1846 | n_water=146 | time (s): 0.560 (total time: 26.310) Add new water r_work=0.1655 r_free=0.2067 | n_water=232 | time (s): 1.830 (total time: 28.140) Refine new water occ: r_work=0.1163 r_free=0.1698 adp: r_work=0.1138 r_free=0.1695 occ: r_work=0.1139 r_free=0.1690 adp: r_work=0.1126 r_free=0.1697 occ: r_work=0.1127 r_free=0.1691 adp: r_work=0.1124 r_free=0.1697 ADP+occupancy (water only), MIN, final r_work=0.1124 r_free=0.1697 r_work=0.1124 r_free=0.1697 | n_water=232 | time (s): 4.170 (total time: 32.310) Filter (q & B) r_work=0.1124 r_free=0.1697 | n_water=232 | time (s): 1.120 (total time: 33.430) Filter (dist only) r_work=0.1133 r_free=0.1690 | n_water=228 | time (s): 17.590 (total time: 51.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 23.343314 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.762163 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 0.1025 0.1820 0.0795 0.010 1.0 4.5 0.5 0.0 0 11.672 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.25 18.20 7.95 4.464 16.543 2.762 0.014 9.49 18.19 8.70 5.383 16.920 2.762 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 106.31 16.36 6.37 1755 0 Protein: 0.00 106.31 14.74 6.34 1519 0 Water: 0.00 62.70 26.67 N/A 228 0 Other: 19.65 46.67 29.67 N/A 8 0 Chain A: 0.00 106.31 15.46 N/A 1669 0 Chain S: 1.78 58.28 33.75 N/A 86 0 Histogram: Values Number of atoms 0.00 - 10.63 690 10.63 - 21.26 659 21.26 - 31.89 211 31.89 - 42.52 109 42.52 - 53.15 47 53.15 - 63.78 26 63.78 - 74.41 6 74.41 - 85.04 3 85.04 - 95.68 2 95.68 - 106.31 2 =========================== Idealize ADP of riding H ========================== r_work=0.0949 r_free=0.1819 r_work=0.0947 r_free=0.1817 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0947 r_free = 0.1817 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0945 r_free = 0.1824 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.19 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= 0.0945 r_free= 0.1824 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012048 | | target function (ls_wunit_k1) not normalized (work): 59.324390 | | target function (ls_wunit_k1) not normalized (free): 10.308707 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0989 0.0945 0.1824 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2139 0.2143 0.2222 n_refl.: 5176 remove outliers: r(all,work,free)=0.2139 0.2143 0.2222 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2139 0.2143 0.2222 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0988 0.0944 0.1833 n_refl.: 5176 remove outliers: r(all,work,free)=0.0988 0.0944 0.1833 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 0.3295 324.605 309.525 0.681 0.999 0.370 11.894-9.307 99.02 97 4 0.1467 525.599 517.354 0.993 1.001 0.360 9.237-7.194 100.00 213 7 0.1513 429.836 428.435 1.029 1.002 0.309 7.162-5.571 100.00 427 22 0.1456 322.539 318.205 0.997 1.002 0.290 5.546-4.326 100.00 867 58 0.0799 442.801 439.572 1.013 1.001 0.240 4.315-3.360 100.00 1859 96 0.0728 421.109 421.272 1.055 1.001 0.200 3.356-3.002 100.00 1373 60 0.0962 324.355 324.453 1.030 1.000 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.3004 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0944 r_free=0.1833 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=0.0946 r_free=0.1829 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0946 r_free=0.1829 | n_water=228 | time (s): 0.590 (total time: 0.590) Filter (dist) r_work=0.0964 r_free=0.1810 | n_water=222 | time (s): 18.840 (total time: 19.430) Filter (q & B) r_work=0.1022 r_free=0.1840 | n_water=220 | time (s): 1.660 (total time: 21.090) Compute maps r_work=0.1022 r_free=0.1840 | n_water=220 | time (s): 0.480 (total time: 21.570) Filter (map) r_work=0.1294 r_free=0.1882 | n_water=143 | time (s): 1.540 (total time: 23.110) Find peaks r_work=0.1294 r_free=0.1882 | n_water=143 | time (s): 0.570 (total time: 23.680) Add new water r_work=0.1679 r_free=0.2212 | n_water=231 | time (s): 1.830 (total time: 25.510) Refine new water occ: r_work=0.1070 r_free=0.1723 adp: r_work=0.1064 r_free=0.1738 occ: r_work=0.1052 r_free=0.1718 adp: r_work=0.1051 r_free=0.1727 occ: r_work=0.1041 r_free=0.1708 adp: r_work=0.1039 r_free=0.1717 ADP+occupancy (water only), MIN, final r_work=0.1039 r_free=0.1717 r_work=0.1039 r_free=0.1717 | n_water=231 | time (s): 11.070 (total time: 36.580) Filter (q & B) r_work=0.1039 r_free=0.1718 | n_water=230 | time (s): 1.740 (total time: 38.320) Filter (dist only) r_work=0.1054 r_free=0.1743 | n_water=227 | time (s): 18.230 (total time: 56.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.101542 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.249581 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 0.0952 0.1842 0.0890 0.011 1.0 3.8 0.5 0.6 0 0.551 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.52 18.42 8.90 5.321 17.510 0.250 5.168 9.12 18.53 9.41 7.092 17.549 0.250 5.075 Individual atomic B min max mean iso aniso Overall: 0.00 105.89 16.19 8.76 1754 0 Protein: 0.00 105.89 14.94 8.74 1519 0 Water: 0.00 58.86 24.06 N/A 227 0 Other: 17.68 48.57 30.61 N/A 8 0 Chain A: 0.00 105.89 15.63 N/A 1655 0 Chain S: 0.00 58.86 25.59 N/A 99 0 Histogram: Values Number of atoms 0.00 - 10.59 674 10.59 - 21.18 658 21.18 - 31.77 231 31.77 - 42.35 114 42.35 - 52.94 39 52.94 - 63.53 20 63.53 - 74.12 9 74.12 - 84.71 4 84.71 - 95.30 4 95.30 - 105.89 1 =========================== Idealize ADP of riding H ========================== r_work=0.0912 r_free=0.1853 r_work=0.0919 r_free=0.1866 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0919 r_free = 0.1866 target_work(ml) = 5.080 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0910 r_free = 0.1843 target_work(ml) = 5.074 | | occupancies: max = 1.00 min = 0.21 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= 0.0910 r_free= 0.1843 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.073540 | | target function (ml) not normalized (work): 24982.109070 | | target function (ml) not normalized (free): 1830.382325 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0957 0.0910 0.1843 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2150 0.2163 0.2091 n_refl.: 5176 remove outliers: r(all,work,free)=0.2150 0.2163 0.2091 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2150 0.2163 0.2091 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0951 0.0904 0.1847 n_refl.: 5176 remove outliers: r(all,work,free)=0.0949 0.0903 0.1847 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 0.3761 326.726 296.887 0.608 0.994 0.350 11.894-9.307 99.02 97 4 0.1813 525.599 510.930 0.953 0.997 0.335 9.237-7.194 100.00 213 7 0.1890 429.836 424.011 1.002 0.999 0.315 7.162-5.571 100.00 427 22 0.1864 322.539 312.549 0.978 1.000 0.310 5.546-4.326 100.00 867 58 0.0940 442.801 437.709 0.998 1.001 0.247 4.315-3.360 100.00 1859 96 0.0593 421.109 420.782 1.051 1.003 0.210 3.356-3.002 100.00 1373 60 0.0626 324.355 324.253 1.029 1.004 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.2368 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0903 r_free=0.1847 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 Total number of N/Q/H flips: 2 r_work=0.0904 r_free=0.1840 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0904 r_free=0.1840 | n_water=227 | time (s): 0.510 (total time: 0.510) Filter (dist) r_work=0.0906 r_free=0.1851 | n_water=226 | time (s): 18.120 (total time: 18.630) Filter (q & B) r_work=0.0942 r_free=0.1866 | n_water=225 | time (s): 1.310 (total time: 19.940) Compute maps r_work=0.0942 r_free=0.1866 | n_water=225 | time (s): 0.560 (total time: 20.500) Filter (map) r_work=0.1225 r_free=0.1980 | n_water=154 | time (s): 1.410 (total time: 21.910) Find peaks r_work=0.1225 r_free=0.1980 | n_water=154 | time (s): 0.390 (total time: 22.300) Add new water r_work=0.1570 r_free=0.2314 | n_water=230 | time (s): 1.210 (total time: 23.510) Refine new water occ: r_work=0.1020 r_free=0.1909 adp: r_work=0.1015 r_free=0.1921 occ: r_work=0.1004 r_free=0.1895 adp: r_work=0.1003 r_free=0.1907 occ: r_work=0.0993 r_free=0.1881 adp: r_work=0.0992 r_free=0.1892 ADP+occupancy (water only), MIN, final r_work=0.0992 r_free=0.1892 r_work=0.0992 r_free=0.1892 | n_water=230 | time (s): 9.630 (total time: 33.140) Filter (q & B) r_work=0.0993 r_free=0.1892 | n_water=229 | time (s): 1.320 (total time: 34.460) Filter (dist only) r_work=0.0992 r_free=0.1889 | n_water=228 | time (s): 18.390 (total time: 52.850) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.036034 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.268864 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.0905 0.1971 0.1067 0.011 1.1 4.8 0.5 1.2 0 0.518 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.05 19.71 10.67 6.838 17.766 0.269 5.028 8.82 20.04 11.21 8.112 17.886 0.269 4.967 Individual atomic B min max mean iso aniso Overall: 0.00 105.58 16.50 10.55 1755 0 Protein: 0.00 105.58 15.34 10.53 1519 0 Water: 0.00 58.11 23.69 N/A 228 0 Other: 16.03 51.20 31.57 N/A 8 0 Chain A: 0.00 105.58 15.92 N/A 1647 0 Chain S: 0.00 55.00 25.41 N/A 108 0 Histogram: Values Number of atoms 0.00 - 10.56 665 10.56 - 21.12 634 21.12 - 31.68 255 31.68 - 42.23 124 42.23 - 52.79 42 52.79 - 63.35 17 63.35 - 73.91 6 73.91 - 84.47 6 84.47 - 95.03 4 95.03 - 105.58 2 =========================== Idealize ADP of riding H ========================== r_work=0.0882 r_free=0.2004 r_work=0.0886 r_free=0.2009 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0886 r_free = 0.2009 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0871 r_free = 0.1995 target_work(ml) = 4.962 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0871 r_free= 0.1995 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.962308 | | target function (ml) not normalized (work): 24429.443353 | | target function (ml) not normalized (free): 2235.627709 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0927 0.0871 0.1995 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2127 0.2128 0.2245 n_refl.: 5175 remove outliers: r(all,work,free)=0.2127 0.2128 0.2245 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2127 0.2128 0.2245 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0923 0.0868 0.1966 n_refl.: 5175 remove outliers: r(all,work,free)=0.0923 0.0868 0.1966 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 0.3827 326.726 298.849 0.585 0.990 0.320 11.894-9.307 99.02 97 4 0.1983 525.599 510.925 0.945 0.994 0.318 9.237-7.194 100.00 213 7 0.2059 429.836 420.746 1.006 0.997 0.308 7.162-5.571 100.00 427 22 0.2026 322.539 311.126 0.987 0.999 0.269 5.546-4.326 100.00 867 58 0.0954 442.801 437.268 1.017 1.000 0.223 4.315-3.360 100.00 1859 96 0.0541 421.109 421.049 1.078 1.003 0.208 3.356-3.002 100.00 1373 60 0.0454 324.355 324.449 1.058 1.005 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.5165 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0868 r_free=0.1966 After: r_work=0.0872 r_free=0.1965 ================================== NQH flips ================================== r_work=0.0872 r_free=0.1965 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A Total number of N/Q/H flips: 1 r_work=0.0873 r_free=0.1969 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0873 r_free=0.1969 | n_water=228 | time (s): 0.520 (total time: 0.520) Filter (dist) r_work=0.0885 r_free=0.1974 | n_water=223 | time (s): 17.660 (total time: 18.180) Filter (q & B) r_work=0.1036 r_free=0.1959 | n_water=218 | time (s): 1.520 (total time: 19.700) Compute maps r_work=0.1036 r_free=0.1959 | n_water=218 | time (s): 0.490 (total time: 20.190) Filter (map) r_work=0.1284 r_free=0.2014 | n_water=152 | time (s): 1.310 (total time: 21.500) Find peaks r_work=0.1284 r_free=0.2014 | n_water=152 | time (s): 0.400 (total time: 21.900) Add new water r_work=0.1576 r_free=0.2240 | n_water=226 | time (s): 1.770 (total time: 23.670) Refine new water occ: r_work=0.1009 r_free=0.1963 adp: r_work=0.0997 r_free=0.1970 occ: r_work=0.0990 r_free=0.1960 adp: r_work=0.0990 r_free=0.1963 occ: r_work=0.0983 r_free=0.1953 adp: r_work=0.0983 r_free=0.1957 ADP+occupancy (water only), MIN, final r_work=0.0983 r_free=0.1957 r_work=0.0983 r_free=0.1957 | n_water=226 | time (s): 17.910 (total time: 41.580) Filter (q & B) r_work=0.0984 r_free=0.1955 | n_water=224 | time (s): 1.350 (total time: 42.930) Filter (dist only) r_work=0.0983 r_free=0.1962 | n_water=222 | time (s): 16.360 (total time: 59.290) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.959936 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.229858 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 0.0920 0.1924 0.1004 0.011 1.1 7.0 0.5 0.6 0 0.480 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.20 19.24 10.04 8.026 18.131 0.230 5.005 9.00 19.34 10.34 8.807 18.241 0.230 4.952 Individual atomic B min max mean iso aniso Overall: 0.00 106.48 16.73 11.69 1749 0 Protein: 0.00 106.48 15.75 11.66 1519 0 Water: 0.00 57.26 22.88 N/A 222 0 Other: 17.84 48.97 32.51 N/A 8 0 Chain A: 0.00 106.48 16.21 N/A 1638 0 Chain S: 0.00 53.99 24.40 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.65 657 10.65 - 21.30 623 21.30 - 31.94 265 31.94 - 42.59 125 42.59 - 53.24 38 53.24 - 63.89 23 63.89 - 74.53 4 74.53 - 85.18 7 85.18 - 95.83 5 95.83 - 106.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.0900 r_free=0.1934 r_work=0.0903 r_free=0.1934 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0903 r_free = 0.1934 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0897 r_free = 0.1928 target_work(ml) = 4.953 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0897 r_free= 0.1928 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ml) (work): 4.952761 | | target function (ml) not normalized (work): 24382.440904 | | target function (ml) not normalized (free): 2330.784967 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1291 0.1881 5.5519 6.3302| | 2: 3.78 - 3.00 1.00 2430 110 0.0417 0.2008 4.3381 13.017| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.91 12.58 1.00 0.97 13910.91| | 2: 3.78 - 3.00 2430 110 0.99 1.75 1.01 1.00 875.12| |alpha: min = 0.96 max = 1.00 mean = 0.99| |beta: min = 551.78 max = 23422.81 mean = 7476.43| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.82 mean = 7.23| |phase err.(test): min = 0.00 max = 85.39 mean = 7.29| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0949 0.0897 0.1928 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2152 0.2156 0.2206 n_refl.: 5175 remove outliers: r(all,work,free)=0.2152 0.2156 0.2206 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2152 0.2156 0.2206 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0948 0.0895 0.1938 n_refl.: 5175 remove outliers: r(all,work,free)=0.0948 0.0895 0.1938 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 0.3956 326.726 289.290 0.588 0.985 0.314 11.894-9.307 99.02 97 4 0.1998 525.599 510.836 0.996 0.991 0.305 9.237-7.194 100.00 213 7 0.2277 429.836 419.583 1.058 0.995 0.295 7.162-5.571 100.00 427 22 0.2114 322.539 311.787 1.040 0.997 0.290 5.546-4.326 100.00 867 58 0.1011 442.801 436.218 1.073 0.999 0.224 4.315-3.360 100.00 1859 96 0.0562 421.109 421.595 1.149 1.002 0.210 3.356-3.002 100.00 1373 60 0.0400 324.355 324.266 1.129 1.005 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.5640 ================= 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 : 0.3623 0.2033 0.081 5.373 8.8 119.3 19.9 258 0.000 1_bss: 0.1556 0.1632 0.081 5.373 6.0 116.4 17.0 258 0.000 1_settarget: 0.1556 0.1632 0.081 5.373 6.0 116.4 17.0 258 0.000 1_nqh: 0.1558 0.1639 0.081 5.373 6.0 116.4 17.0 258 0.003 1_weight: 0.1558 0.1639 0.081 5.373 6.0 116.4 17.0 258 0.003 1_xyzrec: 0.1165 0.1793 0.009 0.967 6.0 116.4 17.0 258 0.214 1_adp: 0.1034 0.1783 0.009 0.967 2.3 111.4 17.3 258 0.214 1_regHadp: 0.1028 0.1787 0.009 0.967 2.3 111.4 17.3 258 0.214 1_occ: 0.1030 0.1788 0.009 0.967 2.3 111.4 17.3 258 0.214 2_bss: 0.1027 0.1773 0.009 0.967 1.3 110.4 16.3 258 0.214 2_settarget: 0.1027 0.1773 0.009 0.967 1.3 110.4 16.3 258 0.214 2_updatecdl: 0.1027 0.1773 0.009 0.991 1.3 110.4 16.3 258 0.214 2_nqh: 0.1029 0.1774 0.009 0.991 1.3 110.4 16.3 258 0.217 2_sol: 0.1133 0.1690 0.009 0.991 1.0 109.6 15.6 228 n/a 2_weight: 0.1133 0.1690 0.009 0.991 1.0 109.6 15.6 228 n/a 2_xyzrec: 0.1025 0.1820 0.010 1.003 1.0 109.6 15.6 228 n/a 2_adp: 0.0949 0.1819 0.010 1.003 0.0 106.3 16.4 228 n/a 2_regHadp: 0.0947 0.1817 0.010 1.003 0.0 106.3 16.4 228 n/a 2_occ: 0.0945 0.1824 0.010 1.003 0.0 106.3 16.4 228 n/a 3_bss: 0.0944 0.1833 0.010 1.003 0.0 106.3 16.4 228 n/a 3_settarget: 0.0944 0.1833 0.010 1.003 0.0 106.3 16.4 228 n/a 3_updatecdl: 0.0944 0.1833 0.010 1.007 0.0 106.3 16.4 228 n/a 3_nqh: 0.0946 0.1829 0.010 1.007 0.0 106.3 16.4 228 n/a 3_sol: 0.1054 0.1743 0.010 1.007 0.0 106.3 16.1 227 n/a 3_weight: 0.1054 0.1743 0.010 1.007 0.0 106.3 16.1 227 n/a 3_xyzrec: 0.0952 0.1842 0.011 1.042 0.0 106.3 16.1 227 n/a 3_adp: 0.0912 0.1853 0.011 1.042 0.0 105.9 16.2 227 n/a 3_regHadp: 0.0919 0.1866 0.011 1.042 0.0 105.9 16.2 227 n/a 3_occ: 0.0910 0.1843 0.011 1.042 0.0 105.9 16.2 227 n/a 4_bss: 0.0903 0.1847 0.011 1.042 0.0 105.9 16.2 227 n/a 4_settarget: 0.0903 0.1847 0.011 1.042 0.0 105.9 16.2 227 n/a 4_updatecdl: 0.0903 0.1847 0.011 1.053 0.0 105.9 16.2 227 n/a 4_nqh: 0.0904 0.1840 0.011 1.053 0.0 105.9 16.2 227 n/a 4_sol: 0.0992 0.1889 0.011 1.053 0.0 105.9 16.3 228 n/a 4_weight: 0.0992 0.1889 0.011 1.053 0.0 105.9 16.3 228 n/a 4_xyzrec: 0.0905 0.1971 0.011 1.052 0.0 105.9 16.3 228 n/a 4_adp: 0.0882 0.2004 0.011 1.052 0.0 105.6 16.5 228 n/a 4_regHadp: 0.0886 0.2009 0.011 1.052 0.0 105.6 16.5 228 n/a 4_occ: 0.0871 0.1995 0.011 1.052 0.0 105.6 16.5 228 n/a 5_bss: 0.0868 0.1966 0.011 1.052 0.0 105.6 16.5 228 n/a 5_settarget: 0.0868 0.1966 0.011 1.052 0.0 105.6 16.5 228 n/a 5_updatecdl: 0.0868 0.1966 0.011 1.060 0.0 105.6 16.5 228 n/a 5_setrh: 0.0872 0.1965 0.011 1.060 0.0 105.6 16.5 228 n/a 5_nqh: 0.0873 0.1969 0.011 1.060 0.0 105.6 16.5 228 n/a 5_sol: 0.0983 0.1962 0.011 1.060 0.0 105.6 16.5 222 n/a 5_weight: 0.0983 0.1962 0.011 1.060 0.0 105.6 16.5 222 n/a 5_xyzrec: 0.0920 0.1924 0.011 1.092 0.0 105.6 16.5 222 n/a 5_adp: 0.0900 0.1934 0.011 1.092 0.0 106.5 16.7 222 n/a 5_regHadp: 0.0903 0.1934 0.011 1.092 0.0 106.5 16.7 222 n/a 5_occ: 0.0897 0.1928 0.011 1.092 0.0 106.5 16.7 222 n/a end: 0.0895 0.1938 0.011 1.092 0.0 106.5 16.7 222 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2226169_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_2226169_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1800 Refinement macro-cycles (run) : 494.3200 Write final files (write_after_run_outputs) : 9.7500 Total : 507.2500 Total CPU time: 8.80 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:09 PST -0800 (1735492749.86 s) Start R-work = 0.1556, R-free = 0.1632 Final R-work = 0.0895, R-free = 0.1938 =============================================================================== Job complete usr+sys time: 536.21 seconds wall clock time: 9 minutes 18.63 seconds (558.63 seconds total)