Starting phenix.refine on Sun Dec 29 09:24:41 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2359181.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=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2359181.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_2359181.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 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: 1.13, per 1000 atoms: 0.33 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: 0.35 Conformation dependent library (CDL) restraints added in 175.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.90: 484 0.90 - 1.15: 1140 1.15 - 1.41: 607 1.41 - 1.66: 864 1.66 - 1.91: 58 Bond restraints: 3153 Sorted by residual: bond pdb=" C GLN A 95 " pdb=" O GLN A 95 " ideal model delta sigma weight residual 1.236 0.915 0.321 1.15e-02 7.56e+03 7.78e+02 bond pdb=" C ALA A 6 " pdb=" O ALA A 6 " ideal model delta sigma weight residual 1.235 1.487 -0.252 1.28e-02 6.10e+03 3.87e+02 bond pdb=" N MET A 134 " pdb=" CA MET A 134 " ideal model delta sigma weight residual 1.457 1.677 -0.220 1.32e-02 5.74e+03 2.77e+02 bond pdb=" N BGLU A 90 " pdb=" CA BGLU A 90 " ideal model delta sigma weight residual 1.459 1.651 -0.192 1.17e-02 7.31e+03 2.68e+02 bond pdb=" NE ARG A 156 " pdb=" CZ ARG A 156 " ideal model delta sigma weight residual 1.326 1.503 -0.177 1.10e-02 8.26e+03 2.60e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.32: 3461 5.32 - 10.64: 1796 10.64 - 15.96: 477 15.96 - 21.28: 40 21.28 - 26.60: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N ILE A 21 " pdb=" CA ILE A 21 " pdb=" CB ILE A 21 " ideal model delta sigma weight residual 110.50 123.40 -12.90 6.30e-01 2.52e+00 4.19e+02 angle pdb=" O VAL A 123 " pdb=" C VAL A 123 " pdb=" N THR A 124 " ideal model delta sigma weight residual 123.00 140.57 -17.57 1.14e+00 7.69e-01 2.37e+02 angle pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" C VAL A 20 " ideal model delta sigma weight residual 110.62 123.94 -13.32 1.02e+00 9.61e-01 1.70e+02 angle pdb=" CA GLY A 174 " pdb=" C GLY A 174 " pdb=" O GLY A 174 " ideal model delta sigma weight residual 122.23 113.29 8.94 6.90e-01 2.10e+00 1.68e+02 angle pdb=" OD1BASN A 97 " pdb=" CG BASN A 97 " pdb=" ND2BASN A 97 " ideal model delta sigma weight residual 122.60 135.43 -12.83 1.00e+00 1.00e+00 1.65e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 1310 17.56 - 35.12: 123 35.12 - 52.68: 33 52.68 - 70.23: 13 70.23 - 87.79: 2 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: 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 -144.46 21.86 0 2.50e+00 1.60e-01 7.65e+01 dihedral pdb=" C BASN A 76 " pdb=" N BASN A 76 " pdb=" CA BASN A 76 " pdb=" CB BASN A 76 " ideal model delta harmonic sigma weight residual -122.60 -142.31 19.71 0 2.50e+00 1.60e-01 6.22e+01 dihedral pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual 122.80 141.78 -18.98 0 2.50e+00 1.60e-01 5.76e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.210: 102 0.210 - 0.420: 67 0.420 - 0.630: 48 0.630 - 0.840: 18 0.840 - 1.050: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.75e+01 chirality pdb=" CB VAL A 70 " pdb=" CA VAL A 70 " pdb=" CG1 VAL A 70 " pdb=" CG2 VAL A 70 " both_signs ideal model delta sigma weight residual False -2.63 -3.62 0.99 2.00e-01 2.50e+01 2.45e+01 chirality pdb=" CA BASN A 76 " pdb=" N BASN A 76 " pdb=" C BASN A 76 " pdb=" CB BASN A 76 " both_signs ideal model delta sigma weight residual False 2.51 1.54 0.97 2.00e-01 2.50e+01 2.35e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.050 2.00e-02 2.50e+03 6.43e-02 1.24e+02 pdb=" CG PHE A 164 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.083 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.028 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.031 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.120 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.041 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.096 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.092 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.033 2.00e-02 2.50e+03 5.07e-02 7.72e+01 pdb=" CG TYR A 139 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.071 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.035 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.093 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.019 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.015 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " -0.066 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.045 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 98 " -0.068 9.50e-02 1.11e+02 6.18e-02 7.51e+01 pdb=" NE ARG A 98 " -0.069 2.00e-02 2.50e+03 pdb=" CZ ARG A 98 " 0.112 2.00e-02 2.50e+03 pdb=" NH1 ARG A 98 " 0.071 2.00e-02 2.50e+03 pdb=" NH2 ARG A 98 " -0.047 2.00e-02 2.50e+03 pdb="HH11 ARG A 98 " -0.036 2.00e-02 2.50e+03 pdb="HH12 ARG A 98 " -0.038 2.00e-02 2.50e+03 pdb="HH21 ARG A 98 " 0.040 2.00e-02 2.50e+03 pdb="HH22 ARG A 98 " -0.030 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 476 2.21 - 2.81: 7244 2.81 - 3.41: 10799 3.41 - 4.00: 15502 4.00 - 4.60: 22527 Nonbonded interactions: 56548 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.618 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.721 2.100 nonbonded pdb=" HD3 ARG A 5 " pdb="HH11 ARG A 5 " model vdw 1.761 2.270 nonbonded pdb="HD21BASN A 76 " pdb=" O HOH A 304 " model vdw 1.803 2.450 nonbonded pdb=" O GLY A 75 " pdb=" H ALA A 79 " model vdw 1.831 2.450 ... (remaining 56543 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 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 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_2359181_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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2795 r_free= 0.1819 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.403985 | | target function (ml) not normalized (work): 71533.935787 | | target function (ml) not normalized (free): 3268.415195 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3185 0.2118 7.5163 5.0309| | 2: 3.63 - 2.88 1.00 2711 122 0.2652 0.1672 4.328 4.3247| | 3: 2.88 - 2.52 1.00 2682 148 0.2578 0.1762 4.1886 4.1941| | 4: 2.52 - 2.29 1.00 2661 139 0.2557 0.1462 3.5156 3.5368| | 5: 2.29 - 2.13 1.00 2678 122 0.2662 0.1525 3.3915 3.4863| | 6: 2.13 - 2.00 1.00 2692 117 0.2771 0.2027 3.3212 3.4463| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2819 159 0.88 17.68 0.77 0.23 1305.97| | 2: 3.63 - 2.88 2711 122 0.82 24.05 1.32 0.23 1305.97| | 3: 2.88 - 2.52 2682 148 0.73 32.85 1.29 0.23 1305.97| | 4: 2.52 - 2.29 2661 139 0.93 11.36 1.30 0.26 135.33| | 5: 2.29 - 2.13 2678 122 0.92 13.73 1.32 0.26 135.33| | 6: 2.13 - 2.00 2692 117 0.90 16.24 1.34 0.26 135.33| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 135.33 max = 1305.97 mean = 727.17| |figures of merit: min = 0.00 max = 1.00 mean = 0.86| |phase err.(work): min = 0.00 max = 89.95 mean = 19.32| |phase err.(test): min = 0.00 max = 89.12 mean = 19.31| |-----------------------------------------------------------------------------| ----------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 : 0.082 0.321 1557 Z= 5.432 Angle : 5.425 18.199 2118 Z= 3.832 Chirality : 0.393 1.050 243 Planarity : 0.033 0.107 284 Dihedral : 13.757 87.793 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 1.08 % Allowed : 2.70 % Favored : 96.22 % Rotamer: Outliers : 1.24 % Allowed : 4.35 % Favored : 94.41 % Cbeta Deviations : 44.86 % 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: -3.28 (0.45), residues: 224 helix: -3.02 (0.38), residues: 109 sheet: -1.50 (0.82), residues: 28 loop : -0.87 (0.53), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.093 0.023 ARG A 98 TYR 0.077 0.038 TYR A 141 PHE 0.090 0.034 PHE A 119 HIS 0.071 0.024 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: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2795 r_free= 0.1819 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.403985 | | target function (ml) not normalized (work): 71533.935787 | | target function (ml) not normalized (free): 3268.415195 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3219 percent. r_work = 0.2927 r_free = 0.1955 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2874 0.2927 0.1955 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2874 0.2927 0.1955 n_refl.: 17050 remove outliers: r(all,work,free)=0.2169 0.2181 0.1955 n_refl.: 17045 overall B=-0.42 to atoms: r(all,work,free)=0.2141 0.2153 0.1937 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1622 0.1622 0.1620 n_refl.: 17045 remove outliers: r(all,work,free)=0.1620 0.1619 0.1620 n_refl.: 17043 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3924 398.944 360.053 0.660 1.011 0.405 11.894-9.307 99.02 97 4 0.1820 633.617 612.242 0.939 1.012 0.394 9.237-7.194 100.00 213 7 0.2164 518.235 511.482 0.963 1.011 0.345 7.162-5.571 100.00 427 22 0.2334 388.936 375.854 0.926 1.010 0.279 5.546-4.326 100.00 867 58 0.1387 533.946 527.377 0.959 1.009 0.215 4.315-3.360 100.00 1859 96 0.1292 507.788 503.240 1.014 1.006 0.191 3.356-2.611 100.00 3867 181 0.1677 333.588 329.250 1.015 1.001 0.040 2.608-2.000 99.99 8818 434 0.1655 217.442 213.501 1.029 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4870 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1619 r_free=0.1620 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1619 r_free=0.1620 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.737510 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.917064 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1352 0.1643 0.0291 0.009 1.0 1.0 0.5 0.0 0 11.369 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.52 16.43 2.91 3.012 18.442 0.917 0.023 12.79 16.63 3.84 3.662 18.723 0.917 0.020 Individual atomic B min max mean iso aniso Overall: 6.07 113.88 20.00 4.12 1785 0 Protein: 6.07 113.16 17.23 4.12 1519 0 Water: 8.71 113.88 36.12 N/A 258 0 Other: 21.54 37.66 26.59 N/A 8 0 Chain A: 6.07 113.88 20.00 N/A 1785 0 Histogram: Values Number of atoms 6.07 - 16.85 1077 16.85 - 27.63 344 27.63 - 38.41 189 38.41 - 49.19 97 49.19 - 59.98 51 59.98 - 70.76 12 70.76 - 81.54 7 81.54 - 92.32 4 92.32 - 103.10 1 103.10 - 113.88 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1663 r_work=0.1282 r_free=0.1669 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1669 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1276 r_free = 0.1660 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17043 (all), 4.74 % free)------------| | | | r_work= 0.1276 r_free= 0.1660 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.019944 | | target function (ls_wunit_k1) not normalized (work): 323.818755 | | target function (ls_wunit_k1) not normalized (free): 27.642574 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1295 0.1276 0.1660 n_refl.: 17043 re-set all scales: r(all,work,free)=0.1904 0.1902 0.1992 n_refl.: 17043 remove outliers: r(all,work,free)=0.1904 0.1902 0.1992 n_refl.: 17043 overall B=-0.40 to atoms: r(all,work,free)=0.1875 0.1873 0.1975 n_refl.: 17043 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1277 0.1652 n_refl.: 17043 remove outliers: r(all,work,free)=0.1293 0.1275 0.1652 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3441 306.718 281.213 0.626 1.009 0.366 11.894-9.307 99.02 97 4 0.1699 488.034 478.017 0.916 1.010 0.364 9.237-7.194 100.00 213 7 0.1809 399.163 396.548 0.960 1.009 0.341 7.162-5.571 100.00 427 22 0.1833 299.572 294.669 0.933 1.009 0.291 5.546-4.326 100.00 867 58 0.1035 411.264 408.978 0.957 1.007 0.205 4.315-3.360 100.00 1859 96 0.0926 391.117 390.724 1.017 1.004 0.191 3.356-2.611 100.00 3867 181 0.1300 256.941 255.742 1.017 1.000 0.091 2.608-2.000 99.99 8818 434 0.1357 167.482 165.999 1.024 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.4158 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1275 r_free=0.1652 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1275 r_free=0.1652 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1275 r_free=0.1652 | n_water=258 | time (s): 0.880 (total time: 0.880) Filter (dist) r_work=0.1284 r_free=0.1644 | n_water=252 | time (s): 19.020 (total time: 19.900) Filter (q & B) r_work=0.1284 r_free=0.1644 | n_water=250 | time (s): 1.500 (total time: 21.400) Compute maps r_work=0.1284 r_free=0.1644 | n_water=250 | time (s): 0.650 (total time: 22.050) Filter (map) r_work=0.1316 r_free=0.1647 | n_water=213 | time (s): 1.450 (total time: 23.500) Find peaks r_work=0.1316 r_free=0.1647 | n_water=213 | time (s): 0.430 (total time: 23.930) Add new water r_work=0.1541 r_free=0.1886 | n_water=374 | time (s): 1.520 (total time: 25.450) Refine new water occ: r_work=0.1337 r_free=0.1619 adp: r_work=0.1277 r_free=0.1605 occ: r_work=0.1281 r_free=0.1571 adp: r_work=0.1248 r_free=0.1575 occ: r_work=0.1249 r_free=0.1564 adp: r_work=0.1239 r_free=0.1565 ADP+occupancy (water only), MIN, final r_work=0.1239 r_free=0.1565 r_work=0.1239 r_free=0.1565 | n_water=374 | time (s): 14.810 (total time: 40.260) Filter (q & B) r_work=0.1241 r_free=0.1569 | n_water=366 | time (s): 2.040 (total time: 42.300) Filter (dist only) r_work=0.1241 r_free=0.1566 | n_water=365 | time (s): 27.750 (total time: 70.050) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.832599 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.958344 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1211 0.1589 0.0378 0.008 0.9 2.2 0.5 0.0 0 12.416 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 15.89 3.78 4.196 21.097 0.958 0.018 11.97 16.19 4.22 4.139 21.384 0.958 0.018 Individual atomic B min max mean iso aniso Overall: 6.62 107.76 21.43 4.19 1892 0 Protein: 6.62 107.76 17.76 4.18 1519 0 Water: 8.34 66.07 36.48 N/A 365 0 Other: 24.02 44.93 33.53 N/A 8 0 Chain A: 6.62 107.76 19.52 N/A 1740 0 Chain S: 18.26 66.07 43.30 N/A 152 0 Histogram: Values Number of atoms 6.62 - 16.73 1020 16.73 - 26.85 382 26.85 - 36.96 223 36.96 - 47.08 159 47.08 - 57.19 68 57.19 - 67.30 30 67.30 - 77.42 3 77.42 - 87.53 4 87.53 - 97.64 1 97.64 - 107.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.1197 r_free=0.1619 r_work=0.1198 r_free=0.1620 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1198 r_free = 0.1620 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1194 r_free = 0.1604 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1194 r_free= 0.1604 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.016899 | | target function (ls_wunit_k1) not normalized (work): 274.335649 | | target function (ls_wunit_k1) not normalized (free): 24.201229 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1214 0.1194 0.1604 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1749 0.1739 0.1976 n_refl.: 17041 remove outliers: r(all,work,free)=0.1749 0.1739 0.1976 n_refl.: 17041 overall B=-0.39 to atoms: r(all,work,free)=0.1724 0.1713 0.1958 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1207 0.1188 0.1598 n_refl.: 17041 remove outliers: r(all,work,free)=0.1207 0.1188 0.1598 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3243 306.718 286.548 0.614 1.005 0.360 11.894-9.307 99.02 97 4 0.1439 488.034 485.994 0.919 1.005 0.356 9.237-7.194 100.00 213 7 0.1633 399.163 400.908 0.975 1.005 0.300 7.162-5.571 100.00 427 22 0.1550 299.572 295.445 0.934 1.005 0.281 5.546-4.326 100.00 867 58 0.0867 411.264 408.584 0.960 1.004 0.221 4.315-3.360 100.00 1859 96 0.0827 391.117 390.384 1.013 1.003 0.191 3.356-2.611 100.00 3867 181 0.1204 256.941 256.076 1.013 1.001 0.121 2.608-2.000 99.99 8818 434 0.1330 167.482 166.442 1.018 0.997 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3809 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1188 r_free=0.1598 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=0.1188 r_free=0.1597 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1188 r_free=0.1597 | n_water=365 | time (s): 0.880 (total time: 0.880) Filter (dist) r_work=0.1188 r_free=0.1597 | n_water=365 | time (s): 28.630 (total time: 29.510) Filter (q & B) r_work=0.1188 r_free=0.1597 | n_water=365 | time (s): 1.140 (total time: 30.650) Compute maps r_work=0.1188 r_free=0.1597 | n_water=365 | time (s): 0.840 (total time: 31.490) Filter (map) r_work=0.1256 r_free=0.1614 | n_water=260 | time (s): 2.030 (total time: 33.520) Find peaks r_work=0.1256 r_free=0.1614 | n_water=260 | time (s): 0.560 (total time: 34.080) Add new water r_work=0.1435 r_free=0.1761 | n_water=395 | time (s): 1.460 (total time: 35.540) Refine new water occ: r_work=0.1244 r_free=0.1582 adp: r_work=0.1237 r_free=0.1580 occ: r_work=0.1218 r_free=0.1566 adp: r_work=0.1209 r_free=0.1563 occ: r_work=0.1200 r_free=0.1551 adp: r_work=0.1191 r_free=0.1550 ADP+occupancy (water only), MIN, final r_work=0.1191 r_free=0.1550 r_work=0.1191 r_free=0.1550 | n_water=395 | time (s): 32.920 (total time: 68.460) Filter (q & B) r_work=0.1193 r_free=0.1551 | n_water=389 | time (s): 1.610 (total time: 70.070) Filter (dist only) r_work=0.1193 r_free=0.1551 | n_water=389 | time (s): 28.470 (total time: 98.540) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.922283 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.192516 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1179 0.1528 0.0349 0.009 1.0 4.2 0.5 0.0 0 0.961 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.79 15.28 3.49 4.293 21.501 0.193 4.992 11.60 15.49 3.89 4.949 21.447 0.193 4.971 Individual atomic B min max mean iso aniso Overall: 6.40 104.86 20.90 4.91 1916 0 Protein: 6.40 104.86 17.07 4.90 1519 0 Water: 8.99 65.02 35.56 N/A 389 0 Other: 25.75 46.27 33.72 N/A 8 0 Chain A: 6.40 104.86 18.81 N/A 1735 0 Chain S: 18.48 65.02 40.90 N/A 181 0 Histogram: Values Number of atoms 6.40 - 16.24 1070 16.24 - 26.09 345 26.09 - 35.94 207 35.94 - 45.78 170 45.78 - 55.63 80 55.63 - 65.48 30 65.48 - 75.32 5 75.32 - 85.17 4 85.17 - 95.01 3 95.01 - 104.86 2 =========================== Idealize ADP of riding H ========================== r_work=0.1160 r_free=0.1549 r_work=0.1161 r_free=0.1549 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1161 r_free = 0.1549 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1151 r_free = 0.1536 target_work(ml) = 4.963 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1151 r_free= 0.1536 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.962852 | | target function (ml) not normalized (work): 80566.942620 | | target function (ml) not normalized (free): 4181.026945 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1170 0.1151 0.1536 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1679 0.1672 0.1871 n_refl.: 17041 remove outliers: r(all,work,free)=0.1679 0.1672 0.1871 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1653 0.1645 0.1858 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1168 0.1149 0.1532 n_refl.: 17041 remove outliers: r(all,work,free)=0.1168 0.1149 0.1532 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3541 306.718 283.164 0.588 1.003 0.350 11.894-9.307 99.02 97 4 0.1624 488.034 482.208 0.920 1.004 0.350 9.237-7.194 100.00 213 7 0.1797 399.163 400.257 0.983 1.004 0.290 7.162-5.571 100.00 427 22 0.1594 299.572 294.509 0.942 1.004 0.251 5.546-4.326 100.00 867 58 0.0933 411.264 407.397 0.963 1.004 0.211 4.315-3.360 100.00 1859 96 0.0912 391.117 388.996 1.010 1.003 0.181 3.356-2.611 100.00 3867 181 0.1290 256.941 254.721 1.012 1.002 0.131 2.608-2.000 99.99 8818 434 0.1090 167.482 166.070 1.013 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-1.3342 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1149 r_free=0.1532 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1149 r_free=0.1532 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1149 r_free=0.1532 | n_water=389 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1155 r_free=0.1526 | n_water=387 | time (s): 31.060 (total time: 31.740) Filter (q & B) r_work=0.1155 r_free=0.1526 | n_water=387 | time (s): 1.190 (total time: 32.930) Compute maps r_work=0.1155 r_free=0.1526 | n_water=387 | time (s): 0.700 (total time: 33.630) Filter (map) r_work=0.1207 r_free=0.1556 | n_water=300 | time (s): 1.920 (total time: 35.550) Find peaks r_work=0.1207 r_free=0.1556 | n_water=300 | time (s): 0.630 (total time: 36.180) Add new water r_work=0.1366 r_free=0.1697 | n_water=450 | time (s): 1.900 (total time: 38.080) Refine new water occ: r_work=0.1191 r_free=0.1541 adp: r_work=0.1183 r_free=0.1540 occ: r_work=0.1164 r_free=0.1519 adp: r_work=0.1155 r_free=0.1515 occ: r_work=0.1147 r_free=0.1509 adp: r_work=0.1138 r_free=0.1502 ADP+occupancy (water only), MIN, final r_work=0.1138 r_free=0.1502 r_work=0.1138 r_free=0.1502 | n_water=450 | time (s): 37.180 (total time: 75.260) Filter (q & B) r_work=0.1140 r_free=0.1508 | n_water=440 | time (s): 1.470 (total time: 76.730) Filter (dist only) r_work=0.1140 r_free=0.1512 | n_water=439 | time (s): 33.200 (total time: 109.930) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.981677 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.185891 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1126 0.1570 0.0444 0.010 1.0 3.2 0.5 0.0 0 0.991 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.70 4.44 4.624 21.202 0.186 4.969 11.19 15.72 4.54 4.784 21.218 0.186 4.963 Individual atomic B min max mean iso aniso Overall: 5.75 103.40 21.09 5.03 1966 0 Protein: 5.75 103.40 16.67 5.02 1519 0 Water: 8.76 63.98 36.19 N/A 439 0 Other: 24.51 45.37 32.45 N/A 8 0 Chain A: 5.75 103.40 18.33 N/A 1732 0 Chain S: 20.45 63.98 41.56 N/A 234 0 Histogram: Values Number of atoms 5.75 - 15.51 1032 15.51 - 25.28 374 25.28 - 35.04 211 35.04 - 44.81 199 44.81 - 54.57 104 54.57 - 64.34 32 64.34 - 74.10 4 74.10 - 83.87 5 83.87 - 93.63 3 93.63 - 103.40 2 =========================== Idealize ADP of riding H ========================== r_work=0.1119 r_free=0.1572 r_work=0.1119 r_free=0.1574 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1119 r_free = 0.1574 target_work(ml) = 4.964 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1110 r_free = 0.1582 target_work(ml) = 4.961 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1110 r_free= 0.1582 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.960623 | | target function (ml) not normalized (work): 80530.751339 | | target function (ml) not normalized (free): 4206.921185 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1132 0.1110 0.1582 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1605 0.1592 0.1903 n_refl.: 17041 remove outliers: r(all,work,free)=0.1605 0.1592 0.1903 n_refl.: 17041 overall B=-0.31 to atoms: r(all,work,free)=0.1585 0.1572 0.1891 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1129 0.1106 0.1576 n_refl.: 17041 remove outliers: r(all,work,free)=0.1129 0.1106 0.1576 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3644 306.718 281.034 0.567 1.002 0.350 11.894-9.307 99.02 97 4 0.1751 488.034 481.572 0.916 1.003 0.330 9.237-7.194 100.00 213 7 0.1734 399.163 400.833 0.988 1.003 0.246 7.162-5.571 100.00 427 22 0.1544 299.572 294.193 0.942 1.003 0.227 5.546-4.326 100.00 867 58 0.0918 411.264 408.214 0.963 1.003 0.195 4.315-3.360 100.00 1859 96 0.0865 391.117 388.780 1.008 1.002 0.181 3.356-2.611 100.00 3867 181 0.1255 256.941 254.762 1.006 1.001 0.121 2.608-2.000 99.99 8818 434 0.1030 167.482 166.319 1.005 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0685 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1106 r_free=0.1576 After: r_work=0.1108 r_free=0.1574 ================================== NQH flips ================================== r_work=0.1108 r_free=0.1574 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1108 r_free=0.1574 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1108 r_free=0.1574 | n_water=439 | time (s): 0.920 (total time: 0.920) Filter (dist) r_work=0.1110 r_free=0.1572 | n_water=438 | time (s): 34.540 (total time: 35.460) Filter (q & B) r_work=0.1110 r_free=0.1572 | n_water=438 | time (s): 0.850 (total time: 36.310) Compute maps r_work=0.1110 r_free=0.1572 | n_water=438 | time (s): 0.630 (total time: 36.940) Filter (map) r_work=0.1185 r_free=0.1581 | n_water=335 | time (s): 1.830 (total time: 38.770) Find peaks r_work=0.1185 r_free=0.1581 | n_water=335 | time (s): 0.450 (total time: 39.220) Add new water r_work=0.1305 r_free=0.1716 | n_water=466 | time (s): 1.840 (total time: 41.060) Refine new water occ: r_work=0.1154 r_free=0.1546 adp: r_work=0.1147 r_free=0.1547 occ: r_work=0.1132 r_free=0.1517 adp: r_work=0.1123 r_free=0.1519 occ: r_work=0.1116 r_free=0.1500 adp: r_work=0.1109 r_free=0.1502 ADP+occupancy (water only), MIN, final r_work=0.1109 r_free=0.1502 r_work=0.1109 r_free=0.1502 | n_water=466 | time (s): 20.960 (total time: 62.020) Filter (q & B) r_work=0.1113 r_free=0.1513 | n_water=455 | time (s): 1.680 (total time: 63.700) Filter (dist only) r_work=0.1113 r_free=0.1513 | n_water=455 | time (s): 37.060 (total time: 100.760) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.938188 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.169651 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 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 0.1130 0.1550 0.0420 0.010 1.0 4.2 0.5 0.0 0 0.969 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.30 15.50 4.20 4.653 20.959 0.170 4.960 11.18 15.33 4.15 4.700 21.041 0.170 4.951 Individual atomic B min max mean iso aniso Overall: 5.73 102.43 21.14 5.09 1982 0 Protein: 5.73 102.43 16.38 5.08 1519 0 Water: 8.28 65.56 36.82 N/A 455 0 Other: 24.07 43.45 31.34 N/A 8 0 Chain A: 5.73 102.43 18.00 N/A 1732 0 Chain S: 18.48 65.56 42.83 N/A 250 0 Histogram: Values Number of atoms 5.73 - 15.40 1048 15.40 - 25.07 362 25.07 - 34.74 205 34.74 - 44.41 197 44.41 - 54.08 113 54.08 - 63.75 39 63.75 - 73.42 8 73.42 - 83.09 4 83.09 - 92.76 2 92.76 - 102.43 4 =========================== Idealize ADP of riding H ========================== r_work=0.1118 r_free=0.1533 r_work=0.1118 r_free=0.1531 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1118 r_free = 0.1531 target_work(ml) = 4.951 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1111 r_free = 0.1526 target_work(ml) = 4.945 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1111 r_free= 0.1526 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.945262 | | target function (ml) not normalized (work): 80281.376610 | | target function (ml) not normalized (free): 4181.853319 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2811 159 0.1129 0.1431 5.4708 5.7102| | 2: 3.63 - 2.88 1.00 2711 122 0.1098 0.1488 5.2289 5.343| | 3: 2.88 - 2.52 1.00 2681 148 0.1355 0.1661 5.1481 5.2226| | 4: 2.52 - 2.29 1.00 2661 139 0.0938 0.1534 4.6325 4.9766| | 5: 2.29 - 2.13 1.00 2678 122 0.0961 0.1515 4.5858 4.9048| | 6: 2.13 - 2.00 1.00 2692 117 0.1113 0.1740 4.5755 4.7778| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 - 3.64 2811 159 0.94 9.35 1.00 0.96 6756.48| | 2: 3.63 - 2.88 2711 122 0.92 13.25 1.01 0.96 6756.48| | 3: 2.88 - 2.52 2681 148 0.87 19.51 0.99 0.96 6756.48| | 4: 2.52 - 2.29 2661 139 0.93 12.23 1.01 0.98 2158.91| | 5: 2.29 - 2.13 2678 122 0.91 14.31 1.00 0.98 2158.91| | 6: 2.13 - 2.00 2692 117 0.89 16.98 0.99 0.98 2158.91| |alpha: min = 0.96 max = 0.98 mean = 0.97| |beta: min = 2158.91 max = 6756.48 mean = 4482.05| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.99 mean = 14.24| |phase err.(test): min = 0.00 max = 89.96 mean = 13.88| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1131 0.1111 0.1526 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1579 0.1567 0.1834 n_refl.: 17041 remove outliers: r(all,work,free)=0.1579 0.1567 0.1834 n_refl.: 17041 overall B=-0.24 to atoms: r(all,work,free)=0.1564 0.1552 0.1824 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1131 0.1111 0.1529 n_refl.: 17041 remove outliers: r(all,work,free)=0.1131 0.1111 0.1529 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3706 306.718 281.618 0.555 1.004 0.334 11.894-9.307 99.02 97 4 0.1773 488.034 480.605 0.910 1.005 0.330 9.237-7.194 100.00 213 7 0.1746 399.163 400.059 0.982 1.006 0.225 7.162-5.571 100.00 427 22 0.1546 299.572 294.211 0.937 1.005 0.220 5.546-4.326 100.00 867 58 0.0933 411.264 407.869 0.961 1.005 0.211 4.315-3.360 100.00 1859 96 0.0876 391.117 389.359 1.003 1.003 0.191 3.356-2.611 100.00 3867 181 0.1249 256.941 254.564 1.002 1.001 0.063 2.608-2.000 99.99 8818 434 0.1034 167.482 166.228 0.995 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8427 ================= 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 : 0.2795 0.1819 0.082 5.425 8.8 119.3 19.9 258 0.000 1_bss: 0.1619 0.1620 0.082 5.425 8.4 118.9 19.5 258 0.000 1_settarget: 0.1619 0.1620 0.082 5.425 8.4 118.9 19.5 258 0.000 1_nqh: 0.1619 0.1620 0.082 5.425 8.4 118.9 19.5 258 0.000 1_weight: 0.1619 0.1620 0.082 5.425 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1352 0.1643 0.009 0.974 8.4 118.9 19.5 258 0.152 1_adp: 0.1279 0.1663 0.009 0.974 6.1 113.9 20.0 258 0.152 1_regHadp: 0.1282 0.1669 0.009 0.974 6.1 113.9 20.0 258 0.152 1_occ: 0.1276 0.1660 0.009 0.974 6.1 113.9 20.0 258 0.152 2_bss: 0.1275 0.1652 0.009 0.974 5.7 113.5 19.6 258 0.152 2_settarget: 0.1275 0.1652 0.009 0.974 5.7 113.5 19.6 258 0.152 2_updatecdl: 0.1275 0.1652 0.009 0.986 5.7 113.5 19.6 258 0.152 2_nqh: 0.1275 0.1652 0.009 0.986 5.7 113.5 19.6 258 0.152 2_sol: 0.1241 0.1566 0.009 0.986 5.7 112.8 20.9 365 n/a 2_weight: 0.1241 0.1566 0.009 0.986 5.7 112.8 20.9 365 n/a 2_xyzrec: 0.1211 0.1589 0.008 0.934 5.7 112.8 20.9 365 n/a 2_adp: 0.1197 0.1619 0.008 0.934 6.6 107.8 21.4 365 n/a 2_regHadp: 0.1198 0.1620 0.008 0.934 6.6 107.8 21.4 365 n/a 2_occ: 0.1194 0.1604 0.008 0.934 6.6 107.8 21.4 365 n/a 3_bss: 0.1188 0.1598 0.008 0.934 6.2 107.4 21.0 365 n/a 3_settarget: 0.1188 0.1598 0.008 0.934 6.2 107.4 21.0 365 n/a 3_updatecdl: 0.1188 0.1598 0.008 0.939 6.2 107.4 21.0 365 n/a 3_nqh: 0.1188 0.1597 0.008 0.939 6.2 107.4 21.0 365 n/a 3_sol: 0.1193 0.1551 0.008 0.939 6.2 107.4 21.0 389 n/a 3_weight: 0.1193 0.1551 0.008 0.939 6.2 107.4 21.0 389 n/a 3_xyzrec: 0.1179 0.1528 0.009 0.975 6.2 107.4 21.0 389 n/a 3_adp: 0.1160 0.1549 0.009 0.975 6.4 104.9 20.9 389 n/a 3_regHadp: 0.1161 0.1549 0.009 0.975 6.4 104.9 20.9 389 n/a 3_occ: 0.1151 0.1536 0.009 0.975 6.4 104.9 20.9 389 n/a 4_bss: 0.1149 0.1532 0.009 0.975 6.0 104.5 20.5 389 n/a 4_settarget: 0.1149 0.1532 0.009 0.975 6.0 104.5 20.5 389 n/a 4_updatecdl: 0.1149 0.1532 0.009 0.973 6.0 104.5 20.5 389 n/a 4_nqh: 0.1149 0.1532 0.009 0.973 6.0 104.5 20.5 389 n/a 4_sol: 0.1140 0.1512 0.009 0.973 6.0 104.5 21.1 439 n/a 4_weight: 0.1140 0.1512 0.009 0.973 6.0 104.5 21.1 439 n/a 4_xyzrec: 0.1126 0.1570 0.010 0.980 6.0 104.5 21.1 439 n/a 4_adp: 0.1119 0.1572 0.010 0.980 5.7 103.4 21.1 439 n/a 4_regHadp: 0.1119 0.1574 0.010 0.980 5.7 103.4 21.1 439 n/a 4_occ: 0.1110 0.1582 0.010 0.980 5.7 103.4 21.1 439 n/a 5_bss: 0.1106 0.1576 0.010 0.980 5.4 103.1 20.8 439 n/a 5_settarget: 0.1106 0.1576 0.010 0.980 5.4 103.1 20.8 439 n/a 5_updatecdl: 0.1106 0.1576 0.010 0.978 5.4 103.1 20.8 439 n/a 5_setrh: 0.1108 0.1574 0.010 0.978 5.4 103.1 20.8 439 n/a 5_nqh: 0.1108 0.1574 0.010 0.978 5.4 103.1 20.8 439 n/a 5_sol: 0.1113 0.1513 0.010 0.978 5.4 103.1 21.0 455 n/a 5_weight: 0.1113 0.1513 0.010 0.978 5.4 103.1 21.0 455 n/a 5_xyzrec: 0.1130 0.1550 0.010 1.019 5.4 103.1 21.0 455 n/a 5_adp: 0.1118 0.1533 0.010 1.019 5.7 102.4 21.1 455 n/a 5_regHadp: 0.1118 0.1531 0.010 1.019 5.7 102.4 21.1 455 n/a 5_occ: 0.1111 0.1526 0.010 1.019 5.7 102.4 21.1 455 n/a end: 0.1111 0.1529 0.010 1.019 5.5 102.2 20.9 455 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2359181_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_2359181_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.6200 Refinement macro-cycles (run) : 891.0700 Write final files (write_after_run_outputs) : 20.7100 Total : 915.4000 Total CPU time: 15.62 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:40:38 PST -0800 (1735494038.14 s) Start R-work = 0.1619, R-free = 0.1620 Final R-work = 0.1111, R-free = 0.1529 =============================================================================== Job complete usr+sys time: 962.79 seconds wall clock time: 16 minutes 25.25 seconds (985.25 seconds total)