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_6369642.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6369642.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_6369642.pdb" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" 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" } 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: 2.12, per 1000 atoms: 0.63 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: 0.36 Conformation dependent library (CDL) restraints added in 104.8 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.65 - 0.91: 537 0.91 - 1.18: 1122 1.18 - 1.44: 687 1.44 - 1.71: 785 1.71 - 1.97: 22 Bond restraints: 3153 Sorted by residual: bond pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " ideal model delta sigma weight residual 1.354 1.113 0.241 1.10e-02 8.26e+03 4.82e+02 bond pdb=" C LEU A 92 " pdb=" O LEU A 92 " ideal model delta sigma weight residual 1.237 0.992 0.244 1.17e-02 7.31e+03 4.37e+02 bond pdb=" N ILE A 52 " pdb=" CA ILE A 52 " ideal model delta sigma weight residual 1.459 1.223 0.236 1.24e-02 6.50e+03 3.62e+02 bond pdb=" N ALA A 114 " pdb=" CA ALA A 114 " ideal model delta sigma weight residual 1.459 1.683 -0.224 1.20e-02 6.94e+03 3.49e+02 bond pdb=" N ALA A 36 " pdb=" CA ALA A 36 " ideal model delta sigma weight residual 1.456 1.233 0.223 1.23e-02 6.61e+03 3.29e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.63: 3164 4.63 - 9.26: 1869 9.26 - 13.89: 611 13.89 - 18.52: 118 18.52 - 23.15: 15 Bond angle restraints: 5777 Sorted by residual: angle pdb=" ND1 HIS A 126 " pdb=" CG HIS A 126 " pdb=" CD2 HIS A 126 " ideal model delta sigma weight residual 106.10 122.14 -16.04 1.00e+00 1.00e+00 2.57e+02 angle pdb=" CA SER A 3 " pdb=" C SER A 3 " pdb=" O SER A 3 " ideal model delta sigma weight residual 121.56 140.37 -18.81 1.21e+00 6.83e-01 2.42e+02 angle pdb=" O GLU A 116 " pdb=" C GLU A 116 " pdb=" N ILE A 117 " ideal model delta sigma weight residual 122.55 140.44 -17.89 1.24e+00 6.50e-01 2.08e+02 angle pdb=" O GLY A 174 " pdb=" C GLY A 174 " pdb=" N ALYS A 175 " ideal model delta sigma weight residual 122.87 137.51 -14.64 1.04e+00 9.25e-01 1.98e+02 angle pdb=" O ALA A 79 " pdb=" C ALA A 79 " pdb=" N AGLN A 80 " ideal model delta sigma weight residual 122.22 138.07 -15.85 1.17e+00 7.31e-01 1.83e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 1300 16.81 - 33.61: 123 33.61 - 50.41: 37 50.41 - 67.21: 18 67.21 - 84.02: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CA ASP A 60 " pdb=" CB ASP A 60 " ideal model delta harmonic sigma weight residual 122.80 143.97 -21.17 0 2.50e+00 1.60e-01 7.17e+01 dihedral pdb=" C ASP A 60 " pdb=" N ASP A 60 " pdb=" CA ASP A 60 " pdb=" CB ASP A 60 " ideal model delta harmonic sigma weight residual -122.60 -142.39 19.79 0 2.50e+00 1.60e-01 6.27e+01 dihedral pdb=" C BLYS A 99 " pdb=" N BLYS A 99 " pdb=" CA BLYS A 99 " pdb=" CB BLYS A 99 " ideal model delta harmonic sigma weight residual -122.60 -140.23 17.63 0 2.50e+00 1.60e-01 4.97e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.226: 118 0.226 - 0.447: 65 0.447 - 0.668: 37 0.668 - 0.889: 17 0.889 - 1.110: 6 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA ASP A 60 " pdb=" N ASP A 60 " pdb=" C ASP A 60 " pdb=" CB ASP A 60 " both_signs ideal model delta sigma weight residual False 2.51 1.40 1.11 2.00e-01 2.50e+01 3.08e+01 chirality pdb=" CB ILE A 117 " pdb=" CA ILE A 117 " pdb=" CG1 ILE A 117 " pdb=" CG2 ILE A 117 " both_signs ideal model delta sigma weight residual False 2.64 1.57 1.07 2.00e-01 2.50e+01 2.86e+01 chirality pdb=" CA BGLU A 64 " pdb=" N BGLU A 64 " pdb=" C BGLU A 64 " pdb=" CB BGLU A 64 " both_signs ideal model delta sigma weight residual False 2.51 3.54 -1.03 2.00e-01 2.50e+01 2.66e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.048 2.00e-02 2.50e+03 6.79e-02 1.38e+02 pdb=" CG PHE A 119 " -0.134 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.111 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.066 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " -0.090 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " -0.084 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.029 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.017 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.003 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.020 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " 0.019 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 141 " -0.086 2.00e-02 2.50e+03 6.35e-02 1.21e+02 pdb=" CG TYR A 141 " 0.103 2.00e-02 2.50e+03 pdb=" CD1 TYR A 141 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TYR A 141 " 0.086 2.00e-02 2.50e+03 pdb=" CE1 TYR A 141 " -0.066 2.00e-02 2.50e+03 pdb=" CE2 TYR A 141 " -0.033 2.00e-02 2.50e+03 pdb=" CZ TYR A 141 " -0.044 2.00e-02 2.50e+03 pdb=" OH TYR A 141 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 TYR A 141 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 TYR A 141 " -0.081 2.00e-02 2.50e+03 pdb=" HE1 TYR A 141 " -0.016 2.00e-02 2.50e+03 pdb=" HE2 TYR A 141 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.076 2.00e-02 2.50e+03 6.67e-02 1.00e+02 pdb=" CG HIS A 138 " 0.062 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.065 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.059 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.109 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.068 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " 0.016 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 1365 2.36 - 2.92: 8328 2.92 - 3.48: 10431 3.48 - 4.04: 15189 4.04 - 4.60: 21318 Nonbonded interactions: 56631 Sorted by model distance: nonbonded pdb=" O ALA A 14 " pdb=" H SER A 47 " model vdw 1.802 2.450 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.805 2.450 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.835 2.100 nonbonded pdb=" H ALA A 6 " pdb=" O LYS A 32 " model vdw 1.844 2.450 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.849 2.100 ... (remaining 56626 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_6369642_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.00 - 49.25 A, n_refl.=5182 (all), 4.86 % free)-------------| | | | r_work= 0.3624 r_free= 0.1992 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.470828 | | target function (ml) not normalized (work): 22041.182468 | | target function (ml) not normalized (free): 1145.805985 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3803 0.2150 4.8474 4.91| | 2: 3.78 - 3.00 1.00 2430 110 0.3405 0.1724 4.0834 4.078| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.82 0.83 0.13 6605.50| | 2: 3.78 - 3.00 2430 110 0.93 11.56 1.48 0.26 458.58| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 393.60 max = 12066.60 mean = 3575.68| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.98 mean = 30.46| |phase err.(test): min = 0.00 max = 89.95 mean = 33.59| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.084 0.244 1557 Z= 5.707 Angle : 5.299 18.810 2118 Z= 3.727 Chirality : 0.381 1.110 243 Planarity : 0.029 0.139 284 Dihedral : 14.119 84.017 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.54 % Allowed : 1.08 % Favored : 98.38 % Rotamer: Outliers : 1.86 % Allowed : 3.11 % Favored : 95.03 % Cbeta Deviations : 29.73 % 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: -2.05 (0.47), residues: 224 helix: -2.31 (0.38), residues: 102 sheet: -0.68 (0.86), residues: 28 loop : -0.12 (0.56), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.108 0.030 ARG A 28 TYR 0.108 0.055 TYR A 141 PHE 0.140 0.044 PHE A 119 HIS 0.068 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= 0.3624 r_free= 0.1992 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.470828 | | target function (ml) not normalized (work): 22041.182468 | | target function (ml) not normalized (free): 1145.805985 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3577 0.3655 0.2075 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3577 0.3655 0.2075 n_refl.: 5182 remove outliers: r(all,work,free)=0.2528 0.2554 0.2075 n_refl.: 5178 overall B=-2.44 to atoms: r(all,work,free)=0.2433 0.2456 0.2036 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1566 0.1565 0.1578 n_refl.: 5178 remove outliers: r(all,work,free)=0.1562 0.1560 0.1578 n_refl.: 5176 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 98.94 88 5 0.3873 449.613 407.638 0.632 1.080 0.406 11.894-9.307 99.02 97 4 0.1845 714.247 691.966 0.893 1.076 0.397 9.237-7.194 100.00 213 7 0.2200 584.112 575.620 0.922 1.067 0.366 7.162-5.571 100.00 427 22 0.2279 438.305 424.386 0.898 1.052 0.301 5.546-4.326 100.00 867 58 0.1361 601.731 594.431 0.944 1.028 0.224 4.315-3.360 100.00 1859 96 0.1326 572.252 565.340 1.024 0.987 0.188 3.356-3.002 100.00 1373 60 0.1603 440.773 433.348 1.051 0.946 0.085 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9173 b_overall=-4.2318 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1560 r_free=0.1578 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1561 r_free=0.1575 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.802639 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.103428 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 0.1157 0.1821 0.0665 0.009 1.0 2.6 0.5 0.0 0 9.401 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 18.21 6.65 3.013 16.420 2.103 0.018 10.13 18.13 8.00 5.136 16.628 2.103 0.014 Individual atomic B min max mean iso aniso Overall: 2.38 111.95 17.84 5.53 1785 0 Protein: 2.38 111.95 15.13 5.52 1519 0 Water: 4.43 111.86 33.59 N/A 258 0 Other: 16.85 37.84 24.69 N/A 8 0 Chain A: 2.38 111.95 17.84 N/A 1785 0 Histogram: Values Number of atoms 2.38 - 13.33 901 13.33 - 24.29 493 24.29 - 35.25 192 35.25 - 46.21 108 46.21 - 57.16 57 57.16 - 68.12 17 68.12 - 79.08 8 79.08 - 90.03 5 90.03 - 100.99 1 100.99 - 111.95 3 =========================== Idealize ADP of riding H ========================== r_work=0.1013 r_free=0.1813 r_work=0.1008 r_free=0.1819 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1008 r_free = 0.1819 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1006 r_free = 0.1814 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.1006 r_free= 0.1814 coordinate error (max.-lik. estimate): 0.33 A | | | | normalized target function (ls_wunit_k1) (work): 0.013736 | | target function (ls_wunit_k1) not normalized (work): 67.634642 | | target function (ls_wunit_k1) not normalized (free): 10.794844 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1046 0.1006 0.1814 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2106 0.2103 0.2266 n_refl.: 5176 remove outliers: r(all,work,free)=0.2106 0.2103 0.2266 n_refl.: 5176 overall B=-1.05 to atoms: r(all,work,free)=0.2061 0.2057 0.2254 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.1054 0.1014 0.1815 n_refl.: 5176 remove outliers: r(all,work,free)=0.1054 0.1014 0.1815 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 0.3252 318.106 311.722 0.707 1.001 0.381 11.894-9.307 99.02 97 4 0.1535 505.337 498.250 0.986 1.003 0.361 9.237-7.194 100.00 213 7 0.1743 413.265 411.990 1.029 1.003 0.341 7.162-5.571 100.00 427 22 0.1587 310.105 307.850 0.989 1.002 0.292 5.546-4.326 100.00 867 58 0.0906 425.731 422.363 1.000 1.001 0.202 4.315-3.360 100.00 1859 96 0.0774 404.874 404.840 1.048 0.999 0.194 3.356-3.002 100.00 1373 60 0.0990 311.851 309.957 1.020 0.997 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-3.7531 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1014 r_free=0.1815 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1014 r_free=0.1815 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1014 r_free=0.1815 | n_water=258 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.1045 r_free=0.1804 | n_water=248 | time (s): 20.640 (total time: 21.190) Filter (q & B) r_work=0.1045 r_free=0.1808 | n_water=245 | time (s): 1.620 (total time: 22.810) Compute maps r_work=0.1045 r_free=0.1808 | n_water=245 | time (s): 0.670 (total time: 23.480) Filter (map) r_work=0.1354 r_free=0.1854 | n_water=145 | time (s): 1.900 (total time: 25.380) Find peaks r_work=0.1354 r_free=0.1854 | n_water=145 | time (s): 0.410 (total time: 25.790) Add new water r_work=0.1719 r_free=0.2113 | n_water=238 | time (s): 1.460 (total time: 27.250) Refine new water occ: r_work=0.1155 r_free=0.1716 adp: r_work=0.1125 r_free=0.1716 occ: r_work=0.1122 r_free=0.1703 adp: r_work=0.1109 r_free=0.1710 occ: r_work=0.1108 r_free=0.1701 adp: r_work=0.1104 r_free=0.1704 ADP+occupancy (water only), MIN, final r_work=0.1104 r_free=0.1704 r_work=0.1104 r_free=0.1704 | n_water=238 | time (s): 3.410 (total time: 30.660) Filter (q & B) r_work=0.1104 r_free=0.1704 | n_water=238 | time (s): 1.260 (total time: 31.920) Filter (dist only) r_work=0.1114 r_free=0.1704 | n_water=234 | time (s): 19.220 (total time: 51.140) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 21.947439 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.628084 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 0.1006 0.1736 0.0730 0.009 0.9 3.2 0.5 0.6 0 10.974 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.06 17.36 7.30 4.835 17.195 2.628 0.014 9.48 17.47 7.99 5.440 17.578 2.628 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 108.94 16.95 6.43 1761 0 Protein: 0.00 108.94 15.32 6.41 1519 0 Water: 0.00 64.20 27.25 N/A 234 0 Other: 12.38 41.34 24.86 N/A 8 0 Chain A: 0.00 108.94 16.08 N/A 1669 0 Chain S: 2.92 58.66 32.68 N/A 92 0 Histogram: Values Number of atoms 0.00 - 10.89 656 10.89 - 21.79 694 21.79 - 32.68 215 32.68 - 43.58 114 43.58 - 54.47 40 54.47 - 65.37 31 65.37 - 76.26 4 76.26 - 87.16 2 87.16 - 98.05 4 98.05 - 108.94 1 =========================== Idealize ADP of riding H ========================== r_work=0.0948 r_free=0.1747 r_work=0.0945 r_free=0.1747 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0945 r_free = 0.1747 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0939 r_free = 0.1716 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.27 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= 0.0939 r_free= 0.1716 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ls_wunit_k1) (work): 0.011841 | | target function (ls_wunit_k1) not normalized (work): 58.305485 | | target function (ls_wunit_k1) not normalized (free): 9.440257 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0978 0.0939 0.1716 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2125 0.2130 0.2188 n_refl.: 5176 remove outliers: r(all,work,free)=0.2125 0.2130 0.2188 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2125 0.2130 0.2188 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0977 0.0937 0.1717 n_refl.: 5176 remove outliers: r(all,work,free)=0.0977 0.0937 0.1717 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 0.3175 318.106 304.424 0.710 1.009 0.381 11.894-9.307 99.02 97 4 0.1466 505.337 499.045 0.981 1.011 0.350 9.237-7.194 100.00 213 7 0.1459 413.265 411.209 1.017 1.010 0.340 7.162-5.571 100.00 427 22 0.1372 310.105 308.619 0.986 1.008 0.280 5.546-4.326 100.00 867 58 0.0796 425.731 422.890 1.005 1.004 0.217 4.315-3.360 100.00 1859 96 0.0718 404.874 404.873 1.060 0.998 0.200 3.356-3.002 100.00 1373 60 0.0992 311.851 310.671 1.039 0.992 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.3099 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0937 r_free=0.1717 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 3 r_work=0.0942 r_free=0.1722 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0942 r_free=0.1722 | n_water=234 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.0951 r_free=0.1702 | n_water=230 | time (s): 18.400 (total time: 18.980) Filter (q & B) r_work=0.1031 r_free=0.1679 | n_water=227 | time (s): 1.500 (total time: 20.480) Compute maps r_work=0.1031 r_free=0.1679 | n_water=227 | time (s): 0.600 (total time: 21.080) Filter (map) r_work=0.1274 r_free=0.1765 | n_water=152 | time (s): 1.290 (total time: 22.370) Find peaks r_work=0.1274 r_free=0.1765 | n_water=152 | time (s): 0.400 (total time: 22.770) Add new water r_work=0.1660 r_free=0.2107 | n_water=237 | time (s): 1.680 (total time: 24.450) Refine new water occ: r_work=0.1062 r_free=0.1675 adp: r_work=0.1058 r_free=0.1686 occ: r_work=0.1047 r_free=0.1679 adp: r_work=0.1047 r_free=0.1678 occ: r_work=0.1038 r_free=0.1676 adp: r_work=0.1038 r_free=0.1672 ADP+occupancy (water only), MIN, final r_work=0.1038 r_free=0.1672 r_work=0.1038 r_free=0.1672 | n_water=237 | time (s): 7.460 (total time: 31.910) Filter (q & B) r_work=0.1038 r_free=0.1672 | n_water=237 | time (s): 0.830 (total time: 32.740) Filter (dist only) r_work=0.1059 r_free=0.1674 | n_water=233 | time (s): 18.060 (total time: 50.800) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.170390 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.229327 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 0.0951 0.1737 0.0786 0.011 1.1 5.4 0.5 0.0 0 0.585 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.51 17.37 7.86 5.397 18.106 0.229 5.132 9.06 17.75 8.69 7.233 18.113 0.229 5.030 Individual atomic B min max mean iso aniso Overall: 0.00 108.69 16.65 8.90 1760 0 Protein: 0.00 108.69 15.45 8.89 1519 0 Water: 0.00 59.77 24.17 N/A 233 0 Other: 13.70 42.49 26.14 N/A 8 0 Chain A: 0.00 108.69 16.07 N/A 1651 0 Chain S: 0.00 58.18 25.41 N/A 109 0 Histogram: Values Number of atoms 0.00 - 10.87 653 10.87 - 21.74 688 21.74 - 32.61 234 32.61 - 43.48 113 43.48 - 54.35 35 54.35 - 65.22 19 65.22 - 76.09 12 76.09 - 86.95 1 86.95 - 97.82 4 97.82 - 108.69 1 =========================== Idealize ADP of riding H ========================== r_work=0.0906 r_free=0.1775 r_work=0.0912 r_free=0.1791 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0912 r_free = 0.1791 target_work(ml) = 5.033 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0901 r_free = 0.1785 target_work(ml) = 5.027 | | occupancies: max = 1.00 min = 0.20 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= 0.0901 r_free= 0.1785 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.026638 | | target function (ml) not normalized (work): 24751.165905 | | target function (ml) not normalized (free): 1778.017554 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0945 0.0901 0.1785 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2146 0.2156 0.2110 n_refl.: 5176 remove outliers: r(all,work,free)=0.2146 0.2156 0.2110 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2146 0.2156 0.2110 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0937 0.0893 0.1773 n_refl.: 5176 remove outliers: r(all,work,free)=0.0933 0.0888 0.1773 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3633 317.525 287.860 0.617 0.994 0.350 11.894-9.307 99.02 97 4 0.1797 505.337 489.310 0.948 0.998 0.333 9.237-7.194 100.00 213 7 0.1889 413.265 406.886 1.005 0.999 0.320 7.162-5.571 100.00 427 22 0.1855 310.105 301.597 0.974 1.000 0.270 5.546-4.326 100.00 867 58 0.0918 425.731 421.235 1.002 1.001 0.220 4.315-3.360 100.00 1859 96 0.0578 404.874 404.703 1.061 1.002 0.210 3.356-3.002 100.00 1373 60 0.0624 311.851 311.668 1.040 1.004 0.069 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9175 b_overall=-6.6373 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0888 r_free=0.1773 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0888 r_free=0.1773 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0888 r_free=0.1773 | n_water=233 | time (s): 0.660 (total time: 0.660) Filter (dist) r_work=0.0894 r_free=0.1788 | n_water=231 | time (s): 17.350 (total time: 18.010) Filter (q & B) r_work=0.0971 r_free=0.1815 | n_water=227 | time (s): 1.200 (total time: 19.210) Compute maps r_work=0.0971 r_free=0.1815 | n_water=227 | time (s): 0.440 (total time: 19.650) Filter (map) r_work=0.1244 r_free=0.1934 | n_water=154 | time (s): 1.360 (total time: 21.010) Find peaks r_work=0.1244 r_free=0.1934 | n_water=154 | time (s): 0.490 (total time: 21.500) Add new water r_work=0.1564 r_free=0.2202 | n_water=232 | time (s): 1.350 (total time: 22.850) Refine new water occ: r_work=0.1013 r_free=0.1781 adp: r_work=0.1008 r_free=0.1789 occ: r_work=0.1001 r_free=0.1770 adp: r_work=0.0999 r_free=0.1779 occ: r_work=0.0992 r_free=0.1759 adp: r_work=0.0990 r_free=0.1770 ADP+occupancy (water only), MIN, final r_work=0.0990 r_free=0.1770 r_work=0.0990 r_free=0.1770 | n_water=232 | time (s): 10.040 (total time: 32.890) Filter (q & B) r_work=0.0991 r_free=0.1775 | n_water=229 | time (s): 1.620 (total time: 34.510) Filter (dist only) r_work=0.0991 r_free=0.1782 | n_water=228 | time (s): 17.020 (total time: 51.530) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.004999 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.211629 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 0.0897 0.1848 0.0951 0.011 1.0 3.5 0.5 0.6 0 0.502 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.97 18.48 9.51 6.956 18.258 0.212 4.991 8.74 18.91 10.16 8.152 18.350 0.212 4.925 Individual atomic B min max mean iso aniso Overall: 0.00 108.34 16.86 10.58 1755 0 Protein: 0.00 108.34 15.83 10.57 1519 0 Water: 0.34 63.70 23.36 N/A 228 0 Other: 13.66 43.24 27.23 N/A 8 0 Chain A: 0.00 108.34 16.33 N/A 1640 0 Chain S: 0.34 56.49 24.50 N/A 115 0 Histogram: Values Number of atoms 0.00 - 10.83 645 10.83 - 21.67 656 21.67 - 32.50 261 32.50 - 43.34 112 43.34 - 54.17 43 54.17 - 65.00 20 65.00 - 75.84 11 75.84 - 86.67 3 86.67 - 97.51 2 97.51 - 108.34 2 =========================== Idealize ADP of riding H ========================== r_work=0.0874 r_free=0.1891 r_work=0.0878 r_free=0.1897 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0878 r_free = 0.1897 target_work(ml) = 4.930 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0867 r_free = 0.1872 target_work(ml) = 4.921 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0867 r_free= 0.1872 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 4.920953 | | target function (ml) not normalized (work): 24220.933074 | | target function (ml) not normalized (free): 2079.766805 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0918 0.0867 0.1872 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2087 0.2087 0.2197 n_refl.: 5174 remove outliers: r(all,work,free)=0.2087 0.2087 0.2197 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2087 0.2087 0.2197 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0916 0.0865 0.1865 n_refl.: 5174 remove outliers: r(all,work,free)=0.0916 0.0865 0.1865 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3827 317.525 288.835 0.585 0.989 0.320 11.894-9.307 99.02 97 4 0.1876 505.337 489.344 0.949 0.994 0.320 9.237-7.194 100.00 213 7 0.1998 413.265 404.807 1.011 0.996 0.320 7.162-5.571 100.00 427 22 0.1954 310.105 300.701 0.987 0.998 0.300 5.546-4.326 100.00 867 58 0.0971 425.731 420.862 1.012 1.000 0.240 4.315-3.360 100.00 1859 96 0.0553 404.874 404.425 1.072 1.003 0.210 3.356-3.002 100.00 1373 60 0.0450 311.851 311.844 1.052 1.006 0.071 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.2636 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0865 r_free=0.1865 After: r_work=0.0868 r_free=0.1864 ================================== NQH flips ================================== r_work=0.0868 r_free=0.1864 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=0.0869 r_free=0.1863 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0869 r_free=0.1863 | n_water=228 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.0880 r_free=0.1873 | n_water=224 | time (s): 18.410 (total time: 19.020) Filter (q & B) r_work=0.1023 r_free=0.1898 | n_water=220 | time (s): 1.820 (total time: 20.840) Compute maps r_work=0.1023 r_free=0.1898 | n_water=220 | time (s): 0.500 (total time: 21.340) Filter (map) r_work=0.1245 r_free=0.1950 | n_water=162 | time (s): 1.510 (total time: 22.850) Find peaks r_work=0.1245 r_free=0.1950 | n_water=162 | time (s): 0.420 (total time: 23.270) Add new water r_work=0.1547 r_free=0.2204 | n_water=231 | time (s): 1.240 (total time: 24.510) Refine new water occ: r_work=0.1003 r_free=0.1867 adp: r_work=0.0989 r_free=0.1881 occ: r_work=0.0982 r_free=0.1863 adp: r_work=0.0981 r_free=0.1872 occ: r_work=0.0975 r_free=0.1853 adp: r_work=0.0973 r_free=0.1860 ADP+occupancy (water only), MIN, final r_work=0.0973 r_free=0.1860 r_work=0.0973 r_free=0.1860 | n_water=231 | time (s): 11.800 (total time: 36.310) Filter (q & B) r_work=0.0973 r_free=0.1862 | n_water=228 | time (s): 1.730 (total time: 38.040) Filter (dist only) r_work=0.0970 r_free=0.1862 | n_water=227 | time (s): 17.830 (total time: 55.870) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.010882 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.209576 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 0.0912 0.1863 0.0951 0.011 1.1 6.1 0.5 0.6 0 0.505 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.12 18.63 9.51 8.068 18.658 0.210 4.964 8.96 18.59 9.63 8.755 18.715 0.210 4.914 Individual atomic B min max mean iso aniso Overall: 0.00 106.53 17.11 11.51 1754 0 Protein: 0.00 106.53 16.10 11.49 1519 0 Water: 0.98 66.80 23.57 N/A 227 0 Other: 11.89 43.48 27.08 N/A 8 0 Chain A: 0.00 106.53 16.56 N/A 1636 0 Chain S: 0.98 65.89 24.85 N/A 118 0 Histogram: Values Number of atoms 0.00 - 10.65 633 10.65 - 21.31 645 21.31 - 31.96 274 31.96 - 42.61 118 42.61 - 53.27 42 53.27 - 63.92 20 63.92 - 74.57 11 74.57 - 85.22 7 85.22 - 95.88 1 95.88 - 106.53 3 =========================== Idealize ADP of riding H ========================== r_work=0.0896 r_free=0.1859 r_work=0.0898 r_free=0.1860 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0898 r_free = 0.1860 target_work(ml) = 4.917 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0892 r_free = 0.1845 target_work(ml) = 4.913 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5174 (all), 4.87 % free)-------------| | | | r_work= 0.0892 r_free= 0.1845 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 4.913140 | | target function (ml) not normalized (work): 24182.472949 | | target function (ml) not normalized (free): 2144.415736 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2492 142 0.1277 0.1817 5.4993 6.1623| | 2: 3.78 - 3.00 1.00 2430 110 0.0422 0.1893 4.312 11.54| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2492 142 0.91 12.57 1.00 0.94 12815.72| | 2: 3.78 - 3.00 2430 110 0.99 1.82 1.00 0.97 835.92| |alpha: min = 0.93 max = 0.97 mean = 0.96| |beta: min = 533.23 max = 21650.97 mean = 6901.27| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.96 mean = 7.27| |phase err.(test): min = 0.00 max = 81.98 mean = 7.44| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0940 0.0892 0.1845 n_refl.: 5174 re-set all scales: r(all,work,free)=0.2155 0.2157 0.2243 n_refl.: 5174 remove outliers: r(all,work,free)=0.2155 0.2157 0.2243 n_refl.: 5174 overall B=-0.00 to atoms: r(all,work,free)=0.2155 0.2157 0.2243 n_refl.: 5174 bulk-solvent and scaling: r(all,work,free)=0.0938 0.0890 0.1844 n_refl.: 5174 remove outliers: r(all,work,free)=0.0938 0.0890 0.1844 n_refl.: 5174 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3782 317.525 289.553 0.583 0.989 0.320 11.894-9.307 99.02 97 4 0.2070 505.337 487.448 0.953 0.995 0.319 9.237-7.194 100.00 213 7 0.2198 413.265 401.646 1.014 0.997 0.318 7.162-5.571 100.00 427 22 0.2075 310.105 300.048 0.985 0.999 0.280 5.546-4.326 100.00 867 58 0.1021 425.731 420.210 1.024 1.000 0.250 4.315-3.360 100.00 1859 96 0.0562 404.874 404.717 1.093 1.002 0.220 3.356-3.002 100.00 1373 60 0.0403 311.851 311.934 1.076 1.004 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-8.1707 ================= overall refinement statistics: step by step ================= ****************** REFINEMENT STATISTICS STEP BY STEP ****************** leading digit, like 1_, means number of macro-cycle 0 : statistics at the very beginning when nothing is done yet 1_bss: bulk solvent correction and/or (anisotropic) scaling 1_xyz: refinement of coordinates 1_adp: refinement of ADPs (Atomic Displacement Parameters) 1_wat: ordered solvent update (add / remove) 1_occ: refinement of occupancies ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3624 0.1992 0.084 5.299 8.8 119.3 19.9 258 0.000 1_bss: 0.1560 0.1578 0.084 5.299 6.4 116.9 17.4 258 0.000 1_settarget: 0.1560 0.1578 0.084 5.299 6.4 116.9 17.4 258 0.000 1_nqh: 0.1561 0.1575 0.084 5.299 6.4 116.9 17.4 258 0.006 1_weight: 0.1561 0.1575 0.084 5.299 6.4 116.9 17.4 258 0.006 1_xyzrec: 0.1157 0.1821 0.009 0.965 6.4 116.9 17.4 258 0.215 1_adp: 0.1013 0.1813 0.009 0.965 2.4 111.9 17.8 258 0.215 1_regHadp: 0.1008 0.1819 0.009 0.965 2.4 111.9 17.8 258 0.215 1_occ: 0.1006 0.1814 0.009 0.965 2.4 111.9 17.8 258 0.215 2_bss: 0.1014 0.1815 0.009 0.965 1.3 110.9 16.8 258 0.215 2_settarget: 0.1014 0.1815 0.009 0.965 1.3 110.9 16.8 258 0.215 2_updatecdl: 0.1014 0.1815 0.009 0.988 1.3 110.9 16.8 258 0.215 2_nqh: 0.1014 0.1815 0.009 0.988 1.3 110.9 16.8 258 0.215 2_sol: 0.1114 0.1704 0.009 0.988 1.0 110.9 16.2 234 n/a 2_weight: 0.1114 0.1704 0.009 0.988 1.0 110.9 16.2 234 n/a 2_xyzrec: 0.1006 0.1736 0.009 0.949 1.0 110.9 16.2 234 n/a 2_adp: 0.0948 0.1747 0.009 0.949 0.0 108.9 16.9 234 n/a 2_regHadp: 0.0945 0.1747 0.009 0.949 0.0 108.9 16.9 234 n/a 2_occ: 0.0939 0.1716 0.009 0.949 0.0 108.9 16.9 234 n/a 3_bss: 0.0937 0.1717 0.009 0.949 0.0 108.9 16.9 234 n/a 3_settarget: 0.0937 0.1717 0.009 0.949 0.0 108.9 16.9 234 n/a 3_updatecdl: 0.0937 0.1717 0.009 0.964 0.0 108.9 16.9 234 n/a 3_nqh: 0.0942 0.1722 0.009 0.964 0.0 108.9 16.9 234 n/a 3_sol: 0.1059 0.1674 0.009 0.964 0.0 108.9 16.6 233 n/a 3_weight: 0.1059 0.1674 0.009 0.964 0.0 108.9 16.6 233 n/a 3_xyzrec: 0.0951 0.1737 0.011 1.095 0.0 108.9 16.6 233 n/a 3_adp: 0.0906 0.1775 0.011 1.095 0.0 108.7 16.7 233 n/a 3_regHadp: 0.0912 0.1791 0.011 1.095 0.0 108.7 16.7 233 n/a 3_occ: 0.0901 0.1785 0.011 1.095 0.0 108.7 16.7 233 n/a 4_bss: 0.0888 0.1773 0.011 1.095 0.0 108.7 16.7 233 n/a 4_settarget: 0.0888 0.1773 0.011 1.095 0.0 108.7 16.7 233 n/a 4_updatecdl: 0.0888 0.1773 0.011 1.107 0.0 108.7 16.7 233 n/a 4_nqh: 0.0888 0.1773 0.011 1.107 0.0 108.7 16.7 233 n/a 4_sol: 0.0991 0.1782 0.011 1.107 0.0 108.7 16.7 228 n/a 4_weight: 0.0991 0.1782 0.011 1.107 0.0 108.7 16.7 228 n/a 4_xyzrec: 0.0897 0.1848 0.011 1.042 0.0 108.7 16.7 228 n/a 4_adp: 0.0874 0.1891 0.011 1.042 0.0 108.3 16.9 228 n/a 4_regHadp: 0.0878 0.1897 0.011 1.042 0.0 108.3 16.9 228 n/a 4_occ: 0.0867 0.1872 0.011 1.042 0.0 108.3 16.9 228 n/a 5_bss: 0.0865 0.1865 0.011 1.042 0.0 108.3 16.9 228 n/a 5_settarget: 0.0865 0.1865 0.011 1.042 0.0 108.3 16.9 228 n/a 5_updatecdl: 0.0865 0.1865 0.011 1.048 0.0 108.3 16.9 228 n/a 5_setrh: 0.0868 0.1864 0.011 1.048 0.0 108.3 16.9 228 n/a 5_nqh: 0.0869 0.1863 0.011 1.048 0.0 108.3 16.9 228 n/a 5_sol: 0.0970 0.1862 0.011 1.048 0.0 108.3 17.0 227 n/a 5_weight: 0.0970 0.1862 0.011 1.048 0.0 108.3 17.0 227 n/a 5_xyzrec: 0.0912 0.1863 0.011 1.138 0.0 108.3 17.0 227 n/a 5_adp: 0.0896 0.1859 0.011 1.138 0.0 106.5 17.1 227 n/a 5_regHadp: 0.0898 0.1860 0.011 1.138 0.0 106.5 17.1 227 n/a 5_occ: 0.0892 0.1845 0.011 1.138 0.0 106.5 17.1 227 n/a end: 0.0890 0.1844 0.011 1.138 0.0 106.5 17.1 227 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6369642_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_6369642_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.9600 Refinement macro-cycles (run) : 480.3500 Write final files (write_after_run_outputs) : 11.1400 Total : 495.4500 Total CPU time: 8.64 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:00 PST -0800 (1735492740.70 s) Start R-work = 0.1560, R-free = 0.1578 Final R-work = 0.0890, R-free = 0.1844 =============================================================================== Job complete usr+sys time: 526.03 seconds wall clock time: 9 minutes 9.61 seconds (549.61 seconds total)