Starting phenix.refine on Sun Dec 29 09:10:02 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9451893.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_9451893.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9451893.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 1 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: 1.44, per 1000 atoms: 0.43 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 127.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.64 - 0.91: 494 0.91 - 1.17: 1146 1.17 - 1.43: 671 1.43 - 1.69: 816 1.69 - 1.95: 26 Bond restraints: 3153 Sorted by residual: bond pdb=" C SER A 85 " pdb=" O SER A 85 " ideal model delta sigma weight residual 1.236 1.511 -0.275 1.24e-02 6.50e+03 4.91e+02 bond pdb=" C ARG A 5 " pdb=" O ARG A 5 " ideal model delta sigma weight residual 1.235 1.495 -0.260 1.28e-02 6.10e+03 4.13e+02 bond pdb=" C ALA A 183 " pdb=" O ALA A 183 " ideal model delta sigma weight residual 1.241 1.054 0.188 9.80e-03 1.04e+04 3.67e+02 bond pdb=" CA ATYR A 67 " pdb=" C ATYR A 67 " ideal model delta sigma weight residual 1.523 1.289 0.234 1.24e-02 6.50e+03 3.56e+02 bond pdb=" C VAL A 70 " pdb=" O VAL A 70 " ideal model delta sigma weight residual 1.237 1.430 -0.193 1.07e-02 8.73e+03 3.26e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.80: 3262 4.80 - 9.61: 1836 9.61 - 14.41: 578 14.41 - 19.21: 94 19.21 - 24.02: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" O VAL A 177 " ideal model delta sigma weight residual 120.85 105.49 15.36 1.06e+00 8.90e-01 2.10e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N BCYS A 53 " ideal model delta sigma weight residual 123.26 138.41 -15.15 1.08e+00 8.57e-01 1.97e+02 angle pdb=" O ILE A 168 " pdb=" C ILE A 168 " pdb=" N VAL A 169 " ideal model delta sigma weight residual 121.91 135.44 -13.53 9.80e-01 1.04e+00 1.91e+02 angle pdb=" O ILE A 52 " pdb=" C ILE A 52 " pdb=" N ACYS A 53 " ideal model delta sigma weight residual 123.26 137.20 -13.94 1.08e+00 8.57e-01 1.67e+02 angle pdb=" CA ILE A 52 " pdb=" C ILE A 52 " pdb=" O ILE A 52 " ideal model delta sigma weight residual 120.39 107.10 13.29 1.05e+00 9.07e-01 1.60e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.68: 1283 15.68 - 31.35: 129 31.35 - 47.03: 45 47.03 - 62.71: 20 62.71 - 78.38: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: 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 122.80 146.67 -23.87 0 2.50e+00 1.60e-01 9.11e+01 dihedral pdb=" C ASP A 49 " pdb=" N ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual -122.60 -145.18 22.58 0 2.50e+00 1.60e-01 8.16e+01 dihedral pdb=" N ALYS A 99 " pdb=" C ALYS A 99 " pdb=" CA ALYS A 99 " pdb=" CB ALYS A 99 " ideal model delta harmonic sigma weight residual 122.80 143.40 -20.60 0 2.50e+00 1.60e-01 6.79e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 110 0.234 - 0.469: 74 0.469 - 0.703: 40 0.703 - 0.937: 16 0.937 - 1.171: 3 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 1.34 1.17 2.00e-01 2.50e+01 3.43e+01 chirality pdb=" CA ALYS A 99 " pdb=" N ALYS A 99 " pdb=" C ALYS A 99 " pdb=" CB ALYS A 99 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CA ARG A 5 " pdb=" N ARG A 5 " pdb=" C ARG A 5 " pdb=" CB ARG A 5 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.26e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 138 " 0.030 2.00e-02 2.50e+03 7.08e-02 1.13e+02 pdb=" CG HIS A 138 " 0.036 2.00e-02 2.50e+03 pdb=" ND1 HIS A 138 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 HIS A 138 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS A 138 " 0.022 2.00e-02 2.50e+03 pdb=" NE2 HIS A 138 " 0.128 2.00e-02 2.50e+03 pdb=" HD1 HIS A 138 " -0.080 2.00e-02 2.50e+03 pdb=" HD2 HIS A 138 " -0.097 2.00e-02 2.50e+03 pdb=" HE1 HIS A 138 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB BTYR A 67 " 0.015 2.00e-02 2.50e+03 5.79e-02 1.01e+02 pdb=" CG BTYR A 67 " 0.018 2.00e-02 2.50e+03 pdb=" CD1BTYR A 67 " 0.016 2.00e-02 2.50e+03 pdb=" CD2BTYR A 67 " 0.105 2.00e-02 2.50e+03 pdb=" CE1BTYR A 67 " 0.010 2.00e-02 2.50e+03 pdb=" CE2BTYR A 67 " -0.084 2.00e-02 2.50e+03 pdb=" CZ BTYR A 67 " 0.021 2.00e-02 2.50e+03 pdb=" OH BTYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" HD1BTYR A 67 " -0.007 2.00e-02 2.50e+03 pdb=" HD2BTYR A 67 " -0.059 2.00e-02 2.50e+03 pdb=" HE1BTYR A 67 " -0.090 2.00e-02 2.50e+03 pdb=" HE2BTYR A 67 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.095 2.00e-02 2.50e+03 5.26e-02 8.29e+01 pdb=" CG PHE A 164 " -0.004 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " 0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.046 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " -0.008 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.051 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " 0.073 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " 0.007 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.104 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 897 2.29 - 2.87: 7938 2.87 - 3.45: 10599 3.45 - 4.02: 15296 4.02 - 4.60: 21855 Nonbonded interactions: 56585 Sorted by model distance: nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.718 2.100 nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.798 2.100 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.798 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.815 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H VAL A 44 " pdb=" O ILE A 52 " model vdw 1.843 2.450 ... (remaining 56580 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_9451893_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= 0.3625 r_free= 0.2074 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469636 | | target function (ml) not normalized (work): 22035.306382 | | target function (ml) not normalized (free): 1158.767486 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3812 0.2308 4.8533 4.9359| | 2: 3.78 - 3.00 1.00 2430 110 0.3396 0.1679 4.0749 4.1625| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.79 0.83 0.13 6606.56| | 2: 3.78 - 3.00 2430 110 0.94 11.29 1.48 0.26 448.13| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 378.87 max = 12056.70 mean = 3571.06| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.99 mean = 30.31| |phase err.(test): min = 0.00 max = 89.93 mean = 33.15| |-----------------------------------------------------------------------------| ----------Initial model statistics (before refinement)---------- Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.081 0.275 1557 Z= 5.352 Angle : 5.186 17.364 2118 Z= 3.623 Chirality : 0.393 1.171 243 Planarity : 0.028 0.076 284 Dihedral : 13.704 78.382 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.62 % Allowed : 2.48 % Favored : 96.89 % 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: -2.64 (0.46), residues: 224 helix: -2.29 (0.38), residues: 108 sheet: -1.39 (0.93), residues: 30 loop : -0.79 (0.56), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.097 0.018 ARG A 28 TYR 0.097 0.044 TYR A 139 PHE 0.113 0.031 PHE A 162 HIS 0.065 0.027 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= 0.3625 r_free= 0.2074 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.469636 | | target function (ml) not normalized (work): 22035.306382 | | target function (ml) not normalized (free): 1158.767486 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3578 0.3656 0.2171 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3578 0.3656 0.2171 n_refl.: 5182 remove outliers: r(all,work,free)=0.2526 0.2548 0.2171 n_refl.: 5178 overall B=-2.84 to atoms: r(all,work,free)=0.2417 0.2436 0.2124 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1556 0.1550 0.1675 n_refl.: 5178 remove outliers: r(all,work,free)=0.1554 0.1548 0.1675 n_refl.: 5177 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 100.00 89 5 0.3985 445.201 409.053 0.655 1.071 0.398 11.894-9.307 99.02 97 4 0.1816 714.715 694.376 0.929 1.067 0.383 9.237-7.194 100.00 213 7 0.2157 584.495 574.242 0.974 1.059 0.356 7.162-5.571 100.00 427 22 0.2304 438.592 424.840 0.940 1.046 0.303 5.546-4.326 100.00 867 58 0.1384 602.125 594.571 0.979 1.025 0.228 4.315-3.360 100.00 1859 96 0.1302 572.628 566.367 1.053 0.990 0.200 3.356-3.002 100.00 1373 60 0.1567 441.062 433.997 1.069 0.954 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.6479 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1548 r_free=0.1675 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 80 GLN A Total number of N/Q/H flips: 2 r_work=0.1550 r_free=0.1683 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.476309 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.785280 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 0.1810 0.0654 0.009 1.0 2.9 0.5 0.0 0 9.238 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.57 18.10 6.54 3.013 16.020 1.785 0.018 10.18 17.95 7.77 4.831 16.219 1.785 0.015 Individual atomic B min max mean iso aniso Overall: 2.24 111.46 17.42 5.19 1785 0 Protein: 2.24 110.95 14.74 5.18 1519 0 Water: 4.03 111.46 33.02 N/A 258 0 Other: 18.02 35.64 24.20 N/A 8 0 Chain A: 2.24 111.46 17.42 N/A 1785 0 Histogram: Values Number of atoms 2.24 - 13.16 919 13.16 - 24.09 482 24.09 - 35.01 187 35.01 - 45.93 109 45.93 - 56.85 53 56.85 - 67.77 18 67.77 - 78.69 8 78.69 - 89.62 5 89.62 - 100.54 1 100.54 - 111.46 3 =========================== Idealize ADP of riding H ========================== r_work=0.1018 r_free=0.1795 r_work=0.1012 r_free=0.1799 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1012 r_free = 0.1799 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 = 0.1016 r_free = 0.1806 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1016 r_free= 0.1806 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014241 | | target function (ls_wunit_k1) not normalized (work): 70.138094 | | target function (ls_wunit_k1) not normalized (free): 10.628349 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1056 0.1016 0.1806 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2105 0.2105 0.2225 n_refl.: 5177 remove outliers: r(all,work,free)=0.2105 0.2105 0.2225 n_refl.: 5177 overall B=-1.00 to atoms: r(all,work,free)=0.2063 0.2061 0.2215 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1059 0.1019 0.1805 n_refl.: 5177 remove outliers: r(all,work,free)=0.1057 0.1017 0.1805 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 0.3430 323.773 307.802 0.653 1.018 0.370 11.894-9.307 99.02 97 4 0.1524 524.251 515.991 0.975 1.018 0.348 9.237-7.194 100.00 213 7 0.1723 428.733 427.288 1.016 1.017 0.323 7.162-5.571 100.00 427 22 0.1638 321.712 318.037 0.983 1.013 0.302 5.546-4.326 100.00 867 58 0.0916 441.665 438.651 0.996 1.007 0.202 4.315-3.360 100.00 1859 96 0.0766 420.028 419.808 1.045 0.997 0.193 3.356-3.002 100.00 1373 60 0.0994 323.524 321.995 1.026 0.987 0.067 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.5463 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1017 r_free=0.1805 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A Total number of N/Q/H flips: 1 r_work=0.1017 r_free=0.1808 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1017 r_free=0.1808 | n_water=258 | time (s): 0.550 (total time: 0.550) Filter (dist) r_work=0.1040 r_free=0.1790 | n_water=249 | time (s): 18.560 (total time: 19.110) Filter (q & B) r_work=0.1040 r_free=0.1792 | n_water=246 | time (s): 1.190 (total time: 20.300) Compute maps r_work=0.1040 r_free=0.1792 | n_water=246 | time (s): 0.520 (total time: 20.820) Filter (map) r_work=0.1314 r_free=0.1865 | n_water=152 | time (s): 1.770 (total time: 22.590) Find peaks r_work=0.1314 r_free=0.1865 | n_water=152 | time (s): 0.590 (total time: 23.180) Add new water r_work=0.1678 r_free=0.2089 | n_water=242 | time (s): 1.510 (total time: 24.690) Refine new water occ: r_work=0.1146 r_free=0.1698 adp: r_work=0.1117 r_free=0.1697 occ: r_work=0.1116 r_free=0.1685 adp: r_work=0.1101 r_free=0.1690 occ: r_work=0.1101 r_free=0.1678 adp: r_work=0.1098 r_free=0.1679 ADP+occupancy (water only), MIN, final r_work=0.1098 r_free=0.1679 r_work=0.1098 r_free=0.1679 | n_water=242 | time (s): 3.410 (total time: 28.100) Filter (q & B) r_work=0.1098 r_free=0.1679 | n_water=242 | time (s): 0.840 (total time: 28.940) Filter (dist only) r_work=0.1108 r_free=0.1665 | n_water=237 | time (s): 17.030 (total time: 45.970) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.421665 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.711886 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 0.1016 0.1738 0.0723 0.009 0.9 5.4 0.5 0.6 0 11.211 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.16 17.38 7.23 4.608 16.845 2.712 0.014 9.52 17.23 7.71 5.430 17.084 2.712 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 107.52 16.41 6.36 1764 0 Protein: 0.00 107.52 14.66 6.36 1519 0 Water: 0.00 64.77 27.37 N/A 237 0 Other: 13.26 34.60 22.86 N/A 8 0 Chain A: 0.00 107.52 15.43 N/A 1676 0 Chain S: 2.26 64.77 34.98 N/A 88 0 Histogram: Values Number of atoms 0.00 - 10.75 699 10.75 - 21.50 657 21.50 - 32.26 208 32.26 - 43.01 113 43.01 - 53.76 46 53.76 - 64.51 29 64.51 - 75.27 6 75.27 - 86.02 1 86.02 - 96.77 3 96.77 - 107.52 2 =========================== Idealize ADP of riding H ========================== r_work=0.0952 r_free=0.1723 r_work=0.0950 r_free=0.1721 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0950 r_free = 0.1721 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0946 r_free = 0.1709 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0946 r_free= 0.1709 coordinate error (max.-lik. estimate): 0.29 A | | | | normalized target function (ls_wunit_k1) (work): 0.012079 | | target function (ls_wunit_k1) not normalized (work): 59.477386 | | target function (ls_wunit_k1) not normalized (free): 9.479305 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0984 0.0946 0.1709 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2138 0.2142 0.2201 n_refl.: 5176 remove outliers: r(all,work,free)=0.2138 0.2142 0.2201 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2138 0.2142 0.2201 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0984 0.0944 0.1722 n_refl.: 5176 remove outliers: r(all,work,free)=0.0984 0.0944 0.1722 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 0.3386 323.773 307.091 0.652 1.013 0.358 11.894-9.307 99.02 97 4 0.1429 524.251 519.087 0.977 1.015 0.335 9.237-7.194 100.00 213 7 0.1476 428.733 429.003 1.020 1.014 0.310 7.162-5.571 100.00 427 22 0.1429 321.712 319.629 0.993 1.011 0.300 5.546-4.326 100.00 867 58 0.0799 441.665 439.356 1.004 1.006 0.223 4.315-3.360 100.00 1859 96 0.0742 420.028 419.576 1.056 0.998 0.214 3.356-3.002 100.00 1373 60 0.0951 323.524 322.197 1.036 0.989 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.1279 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0944 r_free=0.1722 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=0.0945 r_free=0.1722 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0945 r_free=0.1722 | n_water=237 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.0956 r_free=0.1719 | n_water=233 | time (s): 17.880 (total time: 18.370) Filter (q & B) r_work=0.1032 r_free=0.1710 | n_water=230 | time (s): 1.490 (total time: 19.860) Compute maps r_work=0.1032 r_free=0.1710 | n_water=230 | time (s): 0.630 (total time: 20.490) Filter (map) r_work=0.1277 r_free=0.1819 | n_water=155 | time (s): 1.720 (total time: 22.210) Find peaks r_work=0.1277 r_free=0.1819 | n_water=155 | time (s): 0.520 (total time: 22.730) Add new water r_work=0.1652 r_free=0.2143 | n_water=234 | time (s): 1.600 (total time: 24.330) Refine new water occ: r_work=0.1066 r_free=0.1746 adp: r_work=0.1060 r_free=0.1764 occ: r_work=0.1050 r_free=0.1743 adp: r_work=0.1050 r_free=0.1743 occ: r_work=0.1050 r_free=0.1743 adp: r_work=0.1050 r_free=0.1743 ADP+occupancy (water only), MIN, final r_work=0.1050 r_free=0.1743 r_work=0.1050 r_free=0.1743 | n_water=234 | time (s): 7.160 (total time: 31.490) Filter (q & B) r_work=0.1050 r_free=0.1743 | n_water=234 | time (s): 0.760 (total time: 32.250) Filter (dist only) r_work=0.1058 r_free=0.1743 | n_water=233 | time (s): 16.590 (total time: 48.840) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.083501 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.243574 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 0.0950 0.1796 0.0845 0.011 1.0 5.1 0.5 0.6 0 0.542 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.50 17.96 8.45 5.316 17.292 0.244 5.158 9.11 18.00 8.89 7.286 17.341 0.244 5.060 Individual atomic B min max mean iso aniso Overall: 0.00 107.77 15.94 8.97 1760 0 Protein: 0.00 107.77 14.84 8.97 1519 0 Water: 0.00 57.75 22.86 N/A 233 0 Other: 11.20 39.03 23.39 N/A 8 0 Chain A: 0.00 107.77 15.53 N/A 1663 0 Chain S: 0.00 50.00 22.97 N/A 97 0 Histogram: Values Number of atoms 0.00 - 10.78 701 10.78 - 21.55 648 21.55 - 32.33 239 32.33 - 43.11 112 43.11 - 53.88 28 53.88 - 64.66 16 64.66 - 75.44 8 75.44 - 86.21 3 86.21 - 96.99 4 96.99 - 107.77 1 =========================== Idealize ADP of riding H ========================== r_work=0.0911 r_free=0.1800 r_work=0.0918 r_free=0.1808 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0918 r_free = 0.1808 target_work(ml) = 5.066 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0909 r_free = 0.1797 target_work(ml) = 5.061 | | 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= 0.0909 r_free= 0.1797 coordinate error (max.-lik. estimate): 0.27 A | | | | normalized target function (ml) (work): 5.060505 | | target function (ml) not normalized (work): 24917.924794 | | target function (ml) not normalized (free): 1805.051462 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0953 0.0909 0.1797 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2157 0.2168 0.2130 n_refl.: 5176 remove outliers: r(all,work,free)=0.2157 0.2168 0.2130 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2157 0.2168 0.2130 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0942 0.0898 0.1779 n_refl.: 5176 remove outliers: r(all,work,free)=0.0939 0.0896 0.1779 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3813 325.888 291.334 0.564 0.995 0.326 11.894-9.307 99.02 97 4 0.1904 524.251 507.445 0.950 0.998 0.323 9.237-7.194 100.00 213 7 0.1936 428.733 420.746 1.010 0.999 0.300 7.162-5.571 100.00 427 22 0.1931 321.712 312.171 0.986 1.000 0.300 5.546-4.326 100.00 867 58 0.0906 441.665 437.441 1.004 1.001 0.229 4.315-3.360 100.00 1859 96 0.0581 420.028 419.820 1.059 1.002 0.220 3.356-3.002 100.00 1373 60 0.0604 323.524 323.263 1.034 1.004 0.080 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9172 b_overall=-6.4950 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0896 r_free=0.1779 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0896 r_free=0.1779 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0896 r_free=0.1779 | n_water=233 | time (s): 0.560 (total time: 0.560) Filter (dist) r_work=0.0914 r_free=0.1793 | n_water=229 | time (s): 18.230 (total time: 18.790) Filter (q & B) r_work=0.1011 r_free=0.1832 | n_water=225 | time (s): 1.590 (total time: 20.380) Compute maps r_work=0.1011 r_free=0.1832 | n_water=225 | time (s): 0.620 (total time: 21.000) Filter (map) r_work=0.1277 r_free=0.1954 | n_water=156 | time (s): 1.300 (total time: 22.300) Find peaks r_work=0.1277 r_free=0.1954 | n_water=156 | time (s): 0.380 (total time: 22.680) Add new water r_work=0.1563 r_free=0.2230 | n_water=226 | time (s): 1.180 (total time: 23.860) Refine new water occ: r_work=0.1051 r_free=0.1816 adp: r_work=0.1045 r_free=0.1816 occ: r_work=0.1038 r_free=0.1804 adp: r_work=0.1038 r_free=0.1809 occ: r_work=0.1032 r_free=0.1796 adp: r_work=0.1032 r_free=0.1801 ADP+occupancy (water only), MIN, final r_work=0.1032 r_free=0.1801 r_work=0.1032 r_free=0.1801 | n_water=226 | time (s): 7.180 (total time: 31.040) Filter (q & B) r_work=0.1032 r_free=0.1805 | n_water=225 | time (s): 1.650 (total time: 32.690) Filter (dist only) r_work=0.1038 r_free=0.1823 | n_water=223 | time (s): 18.690 (total time: 51.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.027242 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.261970 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 0.0930 0.1900 0.0970 0.011 1.0 5.8 0.5 0.6 0 0.514 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.30 19.00 9.70 6.976 17.593 0.262 5.075 9.02 19.39 10.37 8.048 17.658 0.262 5.005 Individual atomic B min max mean iso aniso Overall: 0.00 107.58 16.24 10.41 1750 0 Protein: 0.00 107.58 15.15 10.40 1519 0 Water: 0.00 58.06 23.36 N/A 223 0 Other: 9.80 43.18 23.76 N/A 8 0 Chain A: 0.00 107.58 15.73 N/A 1646 0 Chain S: 0.00 58.06 24.25 N/A 104 0 Histogram: Values Number of atoms 0.00 - 10.76 691 10.76 - 21.52 637 21.52 - 32.28 240 32.28 - 43.03 106 43.03 - 53.79 40 53.79 - 64.55 17 64.55 - 75.31 11 75.31 - 86.07 4 86.07 - 96.83 3 96.83 - 107.58 1 =========================== Idealize ADP of riding H ========================== r_work=0.0902 r_free=0.1939 r_work=0.0906 r_free=0.1944 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0906 r_free = 0.1944 target_work(ml) = 5.010 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0892 r_free = 0.1919 target_work(ml) = 5.001 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0892 r_free= 0.1919 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 5.000557 | | target function (ml) not normalized (work): 24617.741867 | | target function (ml) not normalized (free): 2108.742777 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0944 0.0892 0.1919 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2117 0.2112 0.2279 n_refl.: 5175 remove outliers: r(all,work,free)=0.2117 0.2112 0.2279 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2117 0.2112 0.2279 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0941 0.0889 0.1922 n_refl.: 5175 remove outliers: r(all,work,free)=0.0941 0.0889 0.1922 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3838 325.888 296.112 0.578 0.989 0.320 11.894-9.307 99.02 97 4 0.1875 524.251 508.064 0.954 0.993 0.320 9.237-7.194 100.00 213 7 0.2071 428.733 419.435 1.012 0.996 0.290 7.162-5.571 100.00 427 22 0.2020 321.712 311.878 0.992 0.997 0.290 5.546-4.326 100.00 867 58 0.0986 441.665 435.867 1.013 0.999 0.234 4.315-3.360 100.00 1859 96 0.0568 420.028 419.951 1.072 1.001 0.220 3.356-3.002 100.00 1373 60 0.0480 323.524 323.610 1.054 1.003 0.070 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.2065 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0889 r_free=0.1922 After: r_work=0.0892 r_free=0.1922 ================================== NQH flips ================================== r_work=0.0892 r_free=0.1922 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0892 r_free=0.1922 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0892 r_free=0.1922 | n_water=223 | time (s): 0.490 (total time: 0.490) Filter (dist) r_work=0.0895 r_free=0.1922 | n_water=222 | time (s): 17.410 (total time: 17.900) Filter (q & B) r_work=0.0985 r_free=0.1951 | n_water=219 | time (s): 1.570 (total time: 19.470) Compute maps r_work=0.0985 r_free=0.1951 | n_water=219 | time (s): 0.480 (total time: 19.950) Filter (map) r_work=0.1263 r_free=0.1989 | n_water=157 | time (s): 1.510 (total time: 21.460) Find peaks r_work=0.1263 r_free=0.1989 | n_water=157 | time (s): 0.420 (total time: 21.880) Add new water r_work=0.1540 r_free=0.2236 | n_water=228 | time (s): 1.420 (total time: 23.300) Refine new water occ: r_work=0.1009 r_free=0.1899 adp: r_work=0.1003 r_free=0.1907 occ: r_work=0.0996 r_free=0.1884 adp: r_work=0.0995 r_free=0.1898 occ: r_work=0.0988 r_free=0.1872 adp: r_work=0.0986 r_free=0.1885 ADP+occupancy (water only), MIN, final r_work=0.0986 r_free=0.1885 r_work=0.0986 r_free=0.1885 | n_water=228 | time (s): 14.450 (total time: 37.750) Filter (q & B) r_work=0.0987 r_free=0.1890 | n_water=225 | time (s): 1.740 (total time: 39.490) Filter (dist only) r_work=0.0998 r_free=0.1881 | n_water=223 | time (s): 16.910 (total time: 56.400) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.993563 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.228459 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 0.0933 0.1898 0.0965 0.011 1.1 7.7 0.5 0.6 0 0.497 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.33 18.98 9.65 7.927 17.933 0.228 5.047 9.10 19.18 10.08 8.581 18.018 0.228 4.991 Individual atomic B min max mean iso aniso Overall: 0.00 107.35 16.60 11.23 1750 0 Protein: 0.00 107.35 15.50 11.23 1519 0 Water: 1.02 65.88 23.85 N/A 223 0 Other: 10.75 40.15 23.18 N/A 8 0 Chain A: 0.00 107.35 16.01 N/A 1636 0 Chain S: 1.02 65.88 25.09 N/A 114 0 Histogram: Values Number of atoms 0.00 - 10.74 672 10.74 - 21.47 636 21.47 - 32.21 251 32.21 - 42.94 105 42.94 - 53.68 47 53.68 - 64.41 19 64.41 - 75.15 10 75.15 - 85.88 5 85.88 - 96.62 3 96.62 - 107.35 2 =========================== Idealize ADP of riding H ========================== r_work=0.0910 r_free=0.1918 r_work=0.0913 r_free=0.1924 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0913 r_free = 0.1924 target_work(ml) = 4.995 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0903 r_free = 0.1902 target_work(ml) = 4.990 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0903 r_free= 0.1902 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 4.990182 | | target function (ml) not normalized (work): 24566.667686 | | target function (ml) not normalized (free): 2177.657609 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.79 1.00 2493 142 0.1269 0.1910 5.5335 6.2615| | 2: 3.78 - 3.00 1.00 2430 110 0.0458 0.1890 4.4328 11.714| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.92 12.16 1.00 0.98 13286.86| | 2: 3.78 - 3.00 2430 110 0.99 2.18 1.00 1.00 1045.01| |alpha: min = 0.97 max = 1.00 mean = 0.99| |beta: min = 690.64 max = 22231.56 mean = 7244.26| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.84 mean = 7.23| |phase err.(test): min = 0.00 max = 89.94 mean = 7.99| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0954 0.0903 0.1902 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2175 0.2171 0.2304 n_refl.: 5175 remove outliers: r(all,work,free)=0.2175 0.2171 0.2304 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2175 0.2171 0.2304 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0955 0.0904 0.1907 n_refl.: 5175 remove outliers: r(all,work,free)=0.0955 0.0904 0.1907 n_refl.: 5175 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 95.83 87 5 0.3832 325.888 287.046 0.584 0.986 0.330 11.894-9.307 99.02 97 4 0.1868 524.251 511.683 0.966 0.993 0.315 9.237-7.194 100.00 213 7 0.2164 428.733 420.926 1.013 0.996 0.300 7.162-5.571 100.00 427 22 0.2075 321.712 312.754 0.993 0.998 0.300 5.546-4.326 100.00 867 58 0.1027 441.665 434.324 1.017 0.999 0.230 4.315-3.360 100.00 1859 96 0.0584 420.028 420.404 1.088 1.001 0.230 3.356-3.002 100.00 1373 60 0.0441 323.524 322.942 1.071 1.003 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.9049 ================= 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 : 0.3625 0.2074 0.081 5.186 8.8 119.3 19.9 258 0.000 1_bss: 0.1548 0.1675 0.081 5.186 6.0 116.5 17.0 258 0.000 1_settarget: 0.1548 0.1675 0.081 5.186 6.0 116.5 17.0 258 0.000 1_nqh: 0.1550 0.1683 0.081 5.186 6.0 116.5 17.0 258 0.007 1_weight: 0.1550 0.1683 0.081 5.186 6.0 116.5 17.0 258 0.007 1_xyzrec: 0.1157 0.1810 0.009 0.957 6.0 116.5 17.0 258 0.214 1_adp: 0.1018 0.1795 0.009 0.957 2.2 111.5 17.4 258 0.214 1_regHadp: 0.1012 0.1799 0.009 0.957 2.2 111.5 17.4 258 0.214 1_occ: 0.1016 0.1806 0.009 0.957 2.2 111.5 17.4 258 0.214 2_bss: 0.1017 0.1805 0.009 0.957 1.2 110.5 16.4 258 0.214 2_settarget: 0.1017 0.1805 0.009 0.957 1.2 110.5 16.4 258 0.214 2_updatecdl: 0.1017 0.1805 0.009 0.982 1.2 110.5 16.4 258 0.214 2_nqh: 0.1017 0.1808 0.009 0.982 1.2 110.5 16.4 258 0.211 2_sol: 0.1108 0.1665 0.009 0.982 1.1 110.0 16.0 237 n/a 2_weight: 0.1108 0.1665 0.009 0.982 1.1 110.0 16.0 237 n/a 2_xyzrec: 0.1016 0.1738 0.009 0.950 1.1 110.0 16.0 237 n/a 2_adp: 0.0952 0.1723 0.009 0.950 0.0 107.5 16.4 237 n/a 2_regHadp: 0.0950 0.1721 0.009 0.950 0.0 107.5 16.4 237 n/a 2_occ: 0.0946 0.1709 0.009 0.950 0.0 107.5 16.4 237 n/a 3_bss: 0.0944 0.1722 0.009 0.950 0.0 107.5 16.4 237 n/a 3_settarget: 0.0944 0.1722 0.009 0.950 0.0 107.5 16.4 237 n/a 3_updatecdl: 0.0944 0.1722 0.009 0.956 0.0 107.5 16.4 237 n/a 3_nqh: 0.0945 0.1722 0.009 0.956 0.0 107.5 16.4 237 n/a 3_sol: 0.1058 0.1743 0.009 0.956 0.0 107.5 15.8 233 n/a 3_weight: 0.1058 0.1743 0.009 0.956 0.0 107.5 15.8 233 n/a 3_xyzrec: 0.0950 0.1796 0.011 1.033 0.0 107.5 15.8 233 n/a 3_adp: 0.0911 0.1800 0.011 1.033 0.0 107.8 15.9 233 n/a 3_regHadp: 0.0918 0.1808 0.011 1.033 0.0 107.8 15.9 233 n/a 3_occ: 0.0909 0.1797 0.011 1.033 0.0 107.8 15.9 233 n/a 4_bss: 0.0896 0.1779 0.011 1.033 0.0 107.8 15.9 233 n/a 4_settarget: 0.0896 0.1779 0.011 1.033 0.0 107.8 15.9 233 n/a 4_updatecdl: 0.0896 0.1779 0.011 1.054 0.0 107.8 15.9 233 n/a 4_nqh: 0.0896 0.1779 0.011 1.054 0.0 107.8 15.9 233 n/a 4_sol: 0.1038 0.1823 0.011 1.054 0.0 107.8 16.1 223 n/a 4_weight: 0.1038 0.1823 0.011 1.054 0.0 107.8 16.1 223 n/a 4_xyzrec: 0.0930 0.1900 0.011 1.008 0.0 107.8 16.1 223 n/a 4_adp: 0.0902 0.1939 0.011 1.008 0.0 107.6 16.2 223 n/a 4_regHadp: 0.0906 0.1944 0.011 1.008 0.0 107.6 16.2 223 n/a 4_occ: 0.0892 0.1919 0.011 1.008 0.0 107.6 16.2 223 n/a 5_bss: 0.0889 0.1922 0.011 1.008 0.0 107.6 16.2 223 n/a 5_settarget: 0.0889 0.1922 0.011 1.008 0.0 107.6 16.2 223 n/a 5_updatecdl: 0.0889 0.1922 0.011 1.013 0.0 107.6 16.2 223 n/a 5_setrh: 0.0892 0.1922 0.011 1.013 0.0 107.6 16.2 223 n/a 5_nqh: 0.0892 0.1922 0.011 1.013 0.0 107.6 16.2 223 n/a 5_sol: 0.0998 0.1881 0.011 1.013 0.0 107.6 16.4 223 n/a 5_weight: 0.0998 0.1881 0.011 1.013 0.0 107.6 16.4 223 n/a 5_xyzrec: 0.0933 0.1898 0.011 1.089 0.0 107.6 16.4 223 n/a 5_adp: 0.0910 0.1918 0.011 1.089 0.0 107.4 16.6 223 n/a 5_regHadp: 0.0913 0.1924 0.011 1.089 0.0 107.4 16.6 223 n/a 5_occ: 0.0903 0.1902 0.011 1.089 0.0 107.4 16.6 223 n/a end: 0.0904 0.1907 0.011 1.089 0.0 107.4 16.6 223 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_9451893_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_9451893_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.7300 Refinement macro-cycles (run) : 475.6700 Write final files (write_after_run_outputs) : 11.5400 Total : 490.9400 Total CPU time: 8.51 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:18:51 PST -0800 (1735492731.38 s) Start R-work = 0.1548, R-free = 0.1675 Final R-work = 0.0904, R-free = 0.1907 =============================================================================== Job complete usr+sys time: 519.66 seconds wall clock time: 9 minutes 1.48 seconds (541.48 seconds total)