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_5155044.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=3 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 3 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5155044.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_5155044.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" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3381 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3105 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} Conformer: "B" Number of residues, atoms: 187, 2807 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 177} bond proxies already assigned to first conformer: 2512 Chain: "A" Number of atoms: 276 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 271 Unusual residues: {'DTT': 1} Classifications: {'undetermined': 1, 'water': 253} Link IDs: {None: 253} Conformer: "B" Number of residues, atoms: 253, 253 Classifications: {'water': 253} Link IDs: {None: 252} Residues with excluded nonbonded symmetry interactions: 32 residue: pdb=" N ALYS A 41 " occ=0.48 ... (42 atoms not shown) pdb=" HZ3BLYS A 41 " occ=0.52 residue: pdb=" N ACYS A 53 " occ=0.70 ... (20 atoms not shown) pdb=" HG BCYS A 53 " occ=0.30 residue: pdb=" N AGLU A 64 " occ=0.53 ... (28 atoms not shown) pdb=" HG3BGLU A 64 " occ=0.47 residue: pdb=" N AGLY A 65 " occ=0.53 ... (12 atoms not shown) pdb=" HA3BGLY A 65 " occ=0.47 residue: pdb=" N APRO A 66 " occ=0.53 ... (26 atoms not shown) pdb=" HD3BPRO A 66 " occ=0.47 residue: pdb=" N ATYR A 67 " occ=0.53 ... (40 atoms not shown) pdb=" HH BTYR A 67 " occ=0.47 residue: pdb=" N AASN A 76 " occ=0.75 ... (26 atoms not shown) pdb="HD22BASN A 76 " occ=0.25 residue: pdb=" N AGLN A 80 " occ=0.54 ... (32 atoms not shown) pdb="HE22BGLN A 80 " occ=0.46 residue: pdb=" N AGLU A 90 " occ=0.59 ... (28 atoms not shown) pdb=" HG3BGLU A 90 " occ=0.41 residue: pdb=" N ALYS A 93 " occ=0.57 ... (42 atoms not shown) pdb=" HZ3BLYS A 93 " occ=0.43 residue: pdb=" N AGLU A 94 " occ=0.48 ... (28 atoms not shown) pdb=" HG3BGLU A 94 " occ=0.52 residue: pdb=" N AGLU A 96 " occ=0.57 ... (28 atoms not shown) pdb=" HG3BGLU A 96 " occ=0.43 ... (remaining 20 not shown) Time building chain proxies: 1.39, per 1000 atoms: 0.41 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: 0.32 Conformation dependent library (CDL) restraints added in 103.9 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.46 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: 552 0.91 - 1.19: 1117 1.19 - 1.46: 769 1.46 - 1.74: 706 1.74 - 2.01: 9 Bond restraints: 3153 Sorted by residual: bond pdb=" C BLYS A 132 " pdb=" O BLYS A 132 " ideal model delta sigma weight residual 1.236 1.026 0.210 1.15e-02 7.56e+03 3.35e+02 bond pdb=" CE1 HIS A 138 " pdb=" NE2 HIS A 138 " ideal model delta sigma weight residual 1.321 1.143 0.178 1.00e-02 1.00e+04 3.16e+02 bond pdb=" C ILE A 102 " pdb=" O ILE A 102 " ideal model delta sigma weight residual 1.236 1.060 0.176 9.90e-03 1.02e+04 3.16e+02 bond pdb=" CZ ARG A 48 " pdb=" NH2 ARG A 48 " ideal model delta sigma weight residual 1.330 1.553 -0.223 1.30e-02 5.92e+03 2.95e+02 bond pdb=" C VAL A 71 " pdb=" O VAL A 71 " ideal model delta sigma weight residual 1.237 1.426 -0.189 1.11e-02 8.12e+03 2.89e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.49: 3108 4.49 - 8.99: 1818 8.99 - 13.48: 707 13.48 - 17.97: 124 17.97 - 22.46: 20 Bond angle restraints: 5777 Sorted by residual: angle pdb=" N VAL A 20 " pdb=" CA VAL A 20 " pdb=" C VAL A 20 " ideal model delta sigma weight residual 111.05 132.28 -21.23 1.25e+00 6.40e-01 2.89e+02 angle pdb=" O GLY A 118 " pdb=" C GLY A 118 " pdb=" N PHE A 119 " ideal model delta sigma weight residual 122.41 136.93 -14.52 1.08e+00 8.57e-01 1.81e+02 angle pdb=" CA GLY A 108 " pdb=" C GLY A 108 " pdb=" O GLY A 108 " ideal model delta sigma weight residual 119.69 111.84 7.85 6.30e-01 2.52e+00 1.55e+02 angle pdb=" CA ARG A 156 " pdb=" C ARG A 156 " pdb=" O ARG A 156 " ideal model delta sigma weight residual 119.41 105.48 13.93 1.13e+00 7.83e-01 1.52e+02 angle pdb=" O BASN A 76 " pdb=" C BASN A 76 " pdb=" N LEU A 77 " ideal model delta sigma weight residual 122.09 134.79 -12.70 1.04e+00 9.25e-01 1.49e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.04: 1295 17.04 - 34.08: 135 34.08 - 51.12: 32 51.12 - 68.16: 16 68.16 - 85.20: 3 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CA PRO A 127 " pdb=" CB PRO A 127 " ideal model delta harmonic sigma weight residual 115.10 137.05 -21.95 0 2.50e+00 1.60e-01 7.71e+01 dihedral pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CA ASP A 49 " pdb=" CB ASP A 49 " ideal model delta harmonic sigma weight residual 122.80 142.70 -19.90 0 2.50e+00 1.60e-01 6.33e+01 dihedral pdb=" N HIS A 115 " pdb=" C HIS A 115 " pdb=" CA HIS A 115 " pdb=" CB HIS A 115 " ideal model delta harmonic sigma weight residual 122.80 141.89 -19.09 0 2.50e+00 1.60e-01 5.83e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.241: 99 0.241 - 0.481: 85 0.481 - 0.720: 38 0.720 - 0.960: 16 0.960 - 1.200: 5 Chirality restraints: 243 Sorted by residual: chirality pdb=" CB VAL A 69 " pdb=" CA VAL A 69 " pdb=" CG1 VAL A 69 " pdb=" CG2 VAL A 69 " both_signs ideal model delta sigma weight residual False -2.63 -1.43 -1.20 2.00e-01 2.50e+01 3.60e+01 chirality pdb=" CA PRO A 127 " pdb=" N PRO A 127 " pdb=" C PRO A 127 " pdb=" CB PRO A 127 " both_signs ideal model delta sigma weight residual False 2.72 1.57 1.14 2.00e-01 2.50e+01 3.27e+01 chirality pdb=" CA ASP A 49 " pdb=" N ASP A 49 " pdb=" C ASP A 49 " pdb=" CB ASP A 49 " both_signs ideal model delta sigma weight residual False 2.51 1.46 1.05 2.00e-01 2.50e+01 2.74e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 126 " 0.125 2.00e-02 2.50e+03 9.34e-02 1.96e+02 pdb=" CG HIS A 126 " -0.095 2.00e-02 2.50e+03 pdb=" ND1 HIS A 126 " -0.079 2.00e-02 2.50e+03 pdb=" CD2 HIS A 126 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 HIS A 126 " 0.104 2.00e-02 2.50e+03 pdb=" NE2 HIS A 126 " 0.103 2.00e-02 2.50e+03 pdb=" HD2 HIS A 126 " -0.131 2.00e-02 2.50e+03 pdb=" HE1 HIS A 126 " -0.085 2.00e-02 2.50e+03 pdb=" HE2 HIS A 126 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " 0.052 2.00e-02 2.50e+03 6.73e-02 1.36e+02 pdb=" CG TYR A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.122 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " -0.109 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.067 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " 0.124 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " 0.029 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.048 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.006 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.041 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " 0.029 2.00e-02 2.50e+03 5.51e-02 9.11e+01 pdb=" CG ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " -0.105 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.061 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " 0.015 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.087 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.089 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " 0.044 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.024 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " -0.030 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " 0.000 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 409 2.20 - 2.80: 7174 2.80 - 3.40: 10810 3.40 - 4.00: 15518 4.00 - 4.60: 22781 Nonbonded interactions: 56692 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.600 2.100 nonbonded pdb=" HB2BGLN A 80 " pdb="HE21BGLN A 80 " model vdw 1.786 2.270 nonbonded pdb=" H GLY A 159 " pdb=" O LEU A 185 " model vdw sym.op. 1.805 2.450 x-y,-y,-z-4/3 nonbonded pdb=" HG SER A 142 " pdb=" H ASN A 144 " model vdw 1.812 2.100 nonbonded pdb="HH22 ARG A 98 " pdb=" O HOH A 305 " model vdw 1.829 2.450 ... (remaining 56687 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_5155044_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= 0.3626 r_free= 0.2014 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464897 | | target function (ml) not normalized (work): 22011.943808 | | target function (ml) not normalized (free): 1152.681221 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3816 0.2219 4.8509 4.9171| | 2: 3.78 - 3.00 1.00 2430 110 0.3394 0.1667 4.0678 4.1314| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 48.77 0.83 0.13 6601.02| | 2: 3.78 - 3.00 2430 110 0.94 11.24 1.48 0.26 443.93| |alpha: min = 0.02 max = 0.26 mean = 0.19| |beta: min = 376.55 max = 12065.25 mean = 3566.18| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 90.00 mean = 30.27| |phase err.(test): min = 0.00 max = 89.98 mean = 33.38| |-----------------------------------------------------------------------------| ----------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 0.243 1557 Z= 5.592 Angle : 5.321 21.233 2118 Z= 3.749 Chirality : 0.416 1.200 243 Planarity : 0.032 0.094 284 Dihedral : 14.211 85.196 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 2.48 % Allowed : 3.73 % Favored : 93.79 % Cbeta Deviations : 32.97 % 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: -2.56 (0.46), residues: 224 helix: -2.56 (0.37), residues: 102 sheet: -0.71 (0.75), residues: 38 loop : -0.64 (0.57), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.140 0.030 ARG A 156 TYR 0.135 0.040 TYR A 139 PHE 0.117 0.033 PHE A 164 HIS 0.035 0.019 HIS A 115 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= 0.3626 r_free= 0.2014 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.464897 | | target function (ml) not normalized (work): 22011.943808 | | target function (ml) not normalized (free): 1152.681221 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3582 0.3658 0.2122 n_refl.: 5182 re-set all scales: r(all,work,free)=0.3582 0.3658 0.2122 n_refl.: 5182 remove outliers: r(all,work,free)=0.2524 0.2548 0.2122 n_refl.: 5178 overall B=-2.75 to atoms: r(all,work,free)=0.2419 0.2439 0.2079 n_refl.: 5178 bulk-solvent and scaling: r(all,work,free)=0.1551 0.1548 0.1611 n_refl.: 5178 remove outliers: r(all,work,free)=0.1549 0.1546 0.1611 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 0.4040 444.950 409.724 0.655 1.091 0.409 11.894-9.307 99.02 97 4 0.1808 714.313 694.260 0.922 1.085 0.402 9.237-7.194 100.00 213 7 0.2133 584.166 576.226 0.948 1.076 0.363 7.162-5.571 100.00 427 22 0.2321 438.346 424.195 0.919 1.059 0.299 5.546-4.326 100.00 867 58 0.1382 601.786 593.353 0.972 1.031 0.221 4.315-3.360 100.00 1859 96 0.1290 572.305 566.438 1.058 0.985 0.189 3.356-3.002 100.00 1373 60 0.1584 440.814 433.092 1.081 0.940 0.075 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.5386 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1546 r_free=0.1611 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1546 r_free=0.1611 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 19.266327 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 1.866528 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 0.1158 0.1779 0.0620 0.010 1.0 2.6 0.5 0.0 0 9.633 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.58 17.79 6.20 3.013 16.105 1.867 0.018 10.20 17.64 7.44 4.867 16.269 1.867 0.015 Individual atomic B min max mean iso aniso Overall: 1.97 111.55 17.44 5.24 1785 0 Protein: 1.97 110.99 14.74 5.23 1519 0 Water: 4.11 111.55 33.13 N/A 258 0 Other: 16.68 37.04 24.57 N/A 8 0 Chain A: 1.97 111.55 17.44 N/A 1785 0 Histogram: Values Number of atoms 1.97 - 12.93 905 12.93 - 23.89 489 23.89 - 34.84 197 34.84 - 45.80 105 45.80 - 56.76 55 56.76 - 67.72 17 67.72 - 78.67 8 78.67 - 89.63 5 89.63 - 100.59 1 100.59 - 111.55 3 =========================== Idealize ADP of riding H ========================== r_work=0.1020 r_free=0.1764 r_work=0.1013 r_free=0.1770 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1013 r_free = 0.1770 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 = 0.1023 r_free = 0.1771 target_work(ls_wunit_k1) = 0.014 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5177 (all), 4.87 % free)-------------| | | | r_work= 0.1023 r_free= 0.1771 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ls_wunit_k1) (work): 0.014355 | | target function (ls_wunit_k1) not normalized (work): 70.697665 | | target function (ls_wunit_k1) not normalized (free): 10.513895 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1061 0.1023 0.1771 n_refl.: 5177 re-set all scales: r(all,work,free)=0.2110 0.2110 0.2217 n_refl.: 5177 remove outliers: r(all,work,free)=0.2110 0.2110 0.2217 n_refl.: 5177 overall B=-0.98 to atoms: r(all,work,free)=0.2068 0.2067 0.2205 n_refl.: 5177 bulk-solvent and scaling: r(all,work,free)=0.1062 0.1024 0.1772 n_refl.: 5177 remove outliers: r(all,work,free)=0.1060 0.1022 0.1772 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 0.3402 323.575 306.198 0.644 1.029 0.365 11.894-9.307 99.02 97 4 0.1507 523.931 516.076 0.967 1.028 0.361 9.237-7.194 100.00 213 7 0.1722 428.472 427.621 1.008 1.025 0.315 7.162-5.571 100.00 427 22 0.1659 321.516 317.908 0.972 1.020 0.292 5.546-4.326 100.00 867 58 0.0932 441.396 438.457 0.991 1.011 0.192 4.315-3.360 100.00 1859 96 0.0769 419.772 419.593 1.049 0.995 0.183 3.356-3.002 100.00 1373 60 0.0997 323.326 321.793 1.029 0.980 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9552 b_overall=-3.4961 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1022 r_free=0.1772 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1022 r_free=0.1772 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1022 r_free=0.1772 | n_water=258 | time (s): 0.470 (total time: 0.470) Filter (dist) r_work=0.1057 r_free=0.1789 | n_water=247 | time (s): 22.330 (total time: 22.800) Filter (q & B) r_work=0.1058 r_free=0.1795 | n_water=244 | time (s): 1.730 (total time: 24.530) Compute maps r_work=0.1058 r_free=0.1795 | n_water=244 | time (s): 0.560 (total time: 25.090) Filter (map) r_work=0.1362 r_free=0.1897 | n_water=143 | time (s): 1.850 (total time: 26.940) Find peaks r_work=0.1362 r_free=0.1897 | n_water=143 | time (s): 0.450 (total time: 27.390) Add new water r_work=0.1696 r_free=0.2168 | n_water=230 | time (s): 1.510 (total time: 28.900) Refine new water occ: r_work=0.1158 r_free=0.1717 adp: r_work=0.1131 r_free=0.1713 occ: r_work=0.1131 r_free=0.1702 adp: r_work=0.1118 r_free=0.1706 occ: r_work=0.1120 r_free=0.1686 adp: r_work=0.1116 r_free=0.1691 ADP+occupancy (water only), MIN, final r_work=0.1116 r_free=0.1691 r_work=0.1116 r_free=0.1691 | n_water=230 | time (s): 3.550 (total time: 32.450) Filter (q & B) r_work=0.1116 r_free=0.1691 | n_water=230 | time (s): 0.860 (total time: 33.310) Filter (dist only) r_work=0.1121 r_free=0.1693 | n_water=228 | time (s): 19.240 (total time: 52.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.744230 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 2.771558 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 0.1012 0.1810 0.0798 0.009 1.0 4.5 0.5 0.6 0 11.372 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 10.12 18.10 7.98 4.636 16.794 2.772 0.014 9.45 18.36 8.91 5.456 17.147 2.772 0.012 Individual atomic B min max mean iso aniso Overall: 0.00 105.47 16.50 6.47 1755 0 Protein: 0.00 105.47 14.93 6.46 1519 0 Water: 0.00 63.49 26.69 N/A 228 0 Other: 10.70 38.34 24.75 N/A 8 0 Chain A: 0.00 105.47 15.65 N/A 1668 0 Chain S: 1.25 63.49 32.92 N/A 87 0 Histogram: Values Number of atoms 0.00 - 10.55 656 10.55 - 21.09 674 21.09 - 31.64 223 31.64 - 42.19 116 42.19 - 52.73 41 52.73 - 63.28 31 63.28 - 73.83 7 73.83 - 84.38 2 84.38 - 94.92 3 94.92 - 105.47 2 =========================== Idealize ADP of riding H ========================== r_work=0.0945 r_free=0.1836 r_work=0.0942 r_free=0.1833 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0942 r_free = 0.1833 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0938 r_free = 0.1822 target_work(ls_wunit_k1) = 0.012 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 3.00 - 32.57 A, n_refl.=5176 (all), 4.87 % free)-------------| | | | r_work= 0.0938 r_free= 0.1822 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ls_wunit_k1) (work): 0.011858 | | target function (ls_wunit_k1) not normalized (work): 58.386958 | | target function (ls_wunit_k1) not normalized (free): 10.011376 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0983 0.0938 0.1822 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2121 0.2124 0.2194 n_refl.: 5176 remove outliers: r(all,work,free)=0.2121 0.2124 0.2194 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2121 0.2124 0.2194 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0983 0.0937 0.1830 n_refl.: 5176 remove outliers: r(all,work,free)=0.0983 0.0937 0.1830 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 0.3473 323.575 306.553 0.649 1.015 0.354 11.894-9.307 99.02 97 4 0.1448 523.931 519.926 0.978 1.015 0.343 9.237-7.194 100.00 213 7 0.1457 428.472 426.988 1.015 1.014 0.336 7.162-5.571 100.00 427 22 0.1378 321.516 319.567 0.992 1.011 0.300 5.546-4.326 100.00 867 58 0.0800 441.396 438.909 1.004 1.006 0.230 4.315-3.360 100.00 1859 96 0.0722 419.772 419.724 1.056 0.998 0.200 3.356-3.002 100.00 1373 60 0.0964 323.326 321.720 1.032 0.990 0.060 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-4.0753 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0937 r_free=0.1830 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0937 r_free=0.1830 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0937 r_free=0.1830 | n_water=228 | time (s): 0.580 (total time: 0.580) Filter (dist) r_work=0.0965 r_free=0.1823 | n_water=221 | time (s): 19.280 (total time: 19.860) Filter (q & B) r_work=0.1070 r_free=0.1829 | n_water=217 | time (s): 1.740 (total time: 21.600) Compute maps r_work=0.1070 r_free=0.1829 | n_water=217 | time (s): 0.500 (total time: 22.100) Filter (map) r_work=0.1309 r_free=0.1855 | n_water=152 | time (s): 1.420 (total time: 23.520) Find peaks r_work=0.1309 r_free=0.1855 | n_water=152 | time (s): 0.470 (total time: 23.990) Add new water r_work=0.1684 r_free=0.2226 | n_water=235 | time (s): 1.690 (total time: 25.680) Refine new water occ: r_work=0.1071 r_free=0.1711 adp: r_work=0.1062 r_free=0.1726 occ: r_work=0.1050 r_free=0.1711 adp: r_work=0.1049 r_free=0.1719 occ: r_work=0.1038 r_free=0.1705 adp: r_work=0.1038 r_free=0.1714 ADP+occupancy (water only), MIN, final r_work=0.1038 r_free=0.1714 r_work=0.1038 r_free=0.1714 | n_water=235 | time (s): 10.480 (total time: 36.160) Filter (q & B) r_work=0.1038 r_free=0.1714 | n_water=235 | time (s): 0.740 (total time: 36.900) Filter (dist only) r_work=0.1039 r_free=0.1707 | n_water=233 | time (s): 18.490 (total time: 55.390) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.101737 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.243476 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 0.0924 0.1746 0.0822 0.011 1.1 3.8 0.5 1.2 0 0.551 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.24 17.46 8.22 5.406 17.758 0.243 5.140 8.82 17.67 8.85 7.313 17.730 0.243 5.044 Individual atomic B min max mean iso aniso Overall: 0.00 105.17 16.31 9.00 1760 0 Protein: 0.00 105.17 15.02 8.99 1519 0 Water: 0.00 57.85 24.44 N/A 233 0 Other: 10.14 39.91 24.57 N/A 8 0 Chain A: 0.00 105.17 15.68 N/A 1653 0 Chain S: 0.00 55.27 25.98 N/A 107 0 Histogram: Values Number of atoms 0.00 - 10.52 671 10.52 - 21.03 645 21.03 - 31.55 244 31.55 - 42.07 119 42.07 - 52.59 44 52.59 - 63.10 17 63.10 - 73.62 10 73.62 - 84.14 5 84.14 - 94.65 4 94.65 - 105.17 1 =========================== Idealize ADP of riding H ========================== r_work=0.0882 r_free=0.1767 r_work=0.0888 r_free=0.1781 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0888 r_free = 0.1781 target_work(ml) = 5.049 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0875 r_free = 0.1768 target_work(ml) = 5.040 | | occupancies: max = 1.00 min = 0.25 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= 0.0875 r_free= 0.1768 coordinate error (max.-lik. estimate): 0.28 A | | | | normalized target function (ml) (work): 5.039659 | | target function (ml) not normalized (work): 24815.282932 | | target function (ml) not normalized (free): 1836.607963 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0920 0.0875 0.1768 n_refl.: 5176 re-set all scales: r(all,work,free)=0.2134 0.2141 0.2164 n_refl.: 5176 remove outliers: r(all,work,free)=0.2134 0.2141 0.2164 n_refl.: 5176 overall B=-0.00 to atoms: r(all,work,free)=0.2134 0.2141 0.2164 n_refl.: 5176 bulk-solvent and scaling: r(all,work,free)=0.0912 0.0867 0.1774 n_refl.: 5176 remove outliers: r(all,work,free)=0.0910 0.0865 0.1774 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 0.3630 325.689 295.732 0.605 0.994 0.344 11.894-9.307 99.02 97 4 0.1800 523.931 509.172 0.950 0.998 0.325 9.237-7.194 100.00 213 7 0.1815 428.472 421.380 1.003 0.999 0.310 7.162-5.571 100.00 427 22 0.1715 321.516 313.315 0.978 1.000 0.290 5.546-4.326 100.00 867 58 0.0915 441.396 435.767 0.994 1.001 0.250 4.315-3.360 100.00 1859 96 0.0578 419.772 419.630 1.048 1.002 0.210 3.356-3.002 100.00 1373 60 0.0584 323.326 323.074 1.024 1.003 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9171 b_overall=-6.0060 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.0865 r_free=0.1774 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0865 r_free=0.1774 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0865 r_free=0.1774 | n_water=233 | time (s): 0.640 (total time: 0.640) Filter (dist) r_work=0.0875 r_free=0.1790 | n_water=230 | time (s): 18.510 (total time: 19.150) Filter (q & B) r_work=0.1001 r_free=0.1835 | n_water=224 | time (s): 1.440 (total time: 20.590) Compute maps r_work=0.1001 r_free=0.1835 | n_water=224 | time (s): 0.530 (total time: 21.120) Filter (map) r_work=0.1286 r_free=0.1932 | n_water=152 | time (s): 1.490 (total time: 22.610) Find peaks r_work=0.1286 r_free=0.1932 | n_water=152 | time (s): 0.490 (total time: 23.100) Add new water r_work=0.1609 r_free=0.2197 | n_water=231 | time (s): 1.400 (total time: 24.500) Refine new water occ: r_work=0.1005 r_free=0.1734 adp: r_work=0.0996 r_free=0.1742 occ: r_work=0.0987 r_free=0.1727 adp: r_work=0.0986 r_free=0.1732 occ: r_work=0.0978 r_free=0.1717 adp: r_work=0.0977 r_free=0.1723 ADP+occupancy (water only), MIN, final r_work=0.0977 r_free=0.1723 r_work=0.0977 r_free=0.1723 | n_water=231 | time (s): 12.310 (total time: 36.810) Filter (q & B) r_work=0.0978 r_free=0.1722 | n_water=229 | time (s): 1.920 (total time: 38.730) Filter (dist only) r_work=0.0987 r_free=0.1733 | n_water=227 | time (s): 16.290 (total time: 55.020) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.988364 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.228087 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 0.0890 0.1813 0.0923 0.011 1.0 4.5 0.5 0.6 0 0.494 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 8.90 18.13 9.23 7.001 17.813 0.228 5.031 8.65 18.52 9.86 7.911 17.883 0.228 4.964 Individual atomic B min max mean iso aniso Overall: 0.00 104.63 16.46 10.27 1754 0 Protein: 0.00 104.63 15.32 10.27 1519 0 Water: 0.00 55.00 23.79 N/A 227 0 Other: 12.54 39.85 25.40 N/A 8 0 Chain A: 0.00 104.63 15.92 N/A 1643 0 Chain S: 0.00 55.00 24.54 N/A 111 0 Histogram: Values Number of atoms 0.00 - 10.46 658 10.46 - 20.93 636 20.93 - 31.39 259 31.39 - 41.85 118 41.85 - 52.31 47 52.31 - 62.78 14 62.78 - 73.24 11 73.24 - 83.70 5 83.70 - 94.17 4 94.17 - 104.63 2 =========================== Idealize ADP of riding H ========================== r_work=0.0865 r_free=0.1852 r_work=0.0869 r_free=0.1853 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0869 r_free = 0.1853 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0862 r_free = 0.1851 target_work(ml) = 4.963 | | occupancies: max = 1.00 min = 0.25 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= 0.0862 r_free= 0.1851 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.962590 | | target function (ml) not normalized (work): 24430.832382 | | target function (ml) not normalized (free): 2195.673594 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.0913 0.0862 0.1851 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2112 0.2110 0.2257 n_refl.: 5175 remove outliers: r(all,work,free)=0.2112 0.2110 0.2257 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2112 0.2110 0.2257 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0911 0.0860 0.1855 n_refl.: 5175 remove outliers: r(all,work,free)=0.0911 0.0860 0.1855 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 0.3747 325.689 298.384 0.582 0.987 0.320 11.894-9.307 99.02 97 4 0.1918 523.931 506.323 0.955 0.993 0.320 9.237-7.194 100.00 213 7 0.1983 428.472 418.172 1.008 0.996 0.320 7.162-5.571 100.00 427 22 0.1904 321.516 312.484 0.998 0.997 0.290 5.546-4.326 100.00 867 58 0.0969 441.396 435.213 1.008 0.999 0.229 4.315-3.360 100.00 1859 96 0.0544 419.772 419.801 1.073 1.001 0.210 3.356-3.002 100.00 1373 60 0.0466 323.326 323.128 1.053 1.004 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9167 b_overall=-7.1917 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.0860 r_free=0.1855 After: r_work=0.0863 r_free=0.1856 ================================== NQH flips ================================== r_work=0.0863 r_free=0.1856 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.0863 r_free=0.1856 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.0863 r_free=0.1856 | n_water=227 | time (s): 0.720 (total time: 0.720) Filter (dist) r_work=0.0869 r_free=0.1856 | n_water=225 | time (s): 16.780 (total time: 17.500) Filter (q & B) r_work=0.0940 r_free=0.1893 | n_water=223 | time (s): 1.420 (total time: 18.920) Compute maps r_work=0.0940 r_free=0.1893 | n_water=223 | time (s): 0.500 (total time: 19.420) Filter (map) r_work=0.1246 r_free=0.1952 | n_water=153 | time (s): 1.710 (total time: 21.130) Find peaks r_work=0.1246 r_free=0.1952 | n_water=153 | time (s): 0.620 (total time: 21.750) Add new water r_work=0.1564 r_free=0.2269 | n_water=231 | time (s): 1.580 (total time: 23.330) Refine new water occ: r_work=0.0990 r_free=0.1844 adp: r_work=0.0986 r_free=0.1851 occ: r_work=0.0978 r_free=0.1832 adp: r_work=0.0977 r_free=0.1842 occ: r_work=0.0970 r_free=0.1824 adp: r_work=0.0969 r_free=0.1834 ADP+occupancy (water only), MIN, final r_work=0.0969 r_free=0.1834 r_work=0.0969 r_free=0.1834 | n_water=231 | time (s): 11.060 (total time: 34.390) Filter (q & B) r_work=0.0971 r_free=0.1837 | n_water=228 | time (s): 1.560 (total time: 35.950) Filter (dist only) r_work=0.0971 r_free=0.1837 | n_water=228 | time (s): 17.150 (total time: 53.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 0.927438 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.181977 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 0.0908 0.1861 0.0953 0.011 1.1 6.4 0.5 0.6 0 0.464 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 9.08 18.61 9.53 7.837 18.116 0.182 5.014 8.90 18.62 9.72 8.860 18.223 0.182 4.960 Individual atomic B min max mean iso aniso Overall: 0.00 106.89 16.82 11.60 1755 0 Protein: 0.00 106.89 15.73 11.61 1519 0 Water: 0.00 55.09 23.76 N/A 228 0 Other: 16.65 38.48 25.85 N/A 8 0 Chain A: 0.00 106.89 16.24 N/A 1633 0 Chain S: 0.00 55.09 24.55 N/A 122 0 Histogram: Values Number of atoms 0.00 - 10.69 660 10.69 - 21.38 623 21.38 - 32.07 275 32.07 - 42.76 110 42.76 - 53.45 53 53.45 - 64.14 11 64.14 - 74.83 12 74.83 - 85.51 6 85.51 - 96.20 3 96.20 - 106.89 2 =========================== Idealize ADP of riding H ========================== r_work=0.0890 r_free=0.1862 r_work=0.0893 r_free=0.1865 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.0893 r_free = 0.1865 target_work(ml) = 4.965 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.0884 r_free = 0.1848 target_work(ml) = 4.960 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 3.00 - 32.57 A, n_refl.=5175 (all), 4.87 % free)-------------| | | | r_work= 0.0884 r_free= 0.1848 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.959677 | | target function (ml) not normalized (work): 24416.490252 | | target function (ml) not normalized (free): 2181.711042 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1251 0.1821 5.5205 6.2103| | 2: 3.78 - 3.00 1.00 2430 110 0.0437 0.1894 4.3843 11.817| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.79 2493 142 0.91 12.19 1.00 0.98 13152.39| | 2: 3.78 - 3.00 2430 110 0.99 1.93 1.00 1.00 946.46| |alpha: min = 0.96 max = 1.00 mean = 0.99| |beta: min = 619.89 max = 22203.16 mean = 7127.53| |figures of merit: min = 0.00 max = 1.00 mean = 0.95| |phase err.(work): min = 0.00 max = 89.70 mean = 7.12| |phase err.(test): min = 0.00 max = 81.27 mean = 7.75| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.0934 0.0884 0.1848 n_refl.: 5175 re-set all scales: r(all,work,free)=0.2140 0.2141 0.2220 n_refl.: 5175 remove outliers: r(all,work,free)=0.2140 0.2141 0.2220 n_refl.: 5175 overall B=-0.00 to atoms: r(all,work,free)=0.2140 0.2141 0.2220 n_refl.: 5175 bulk-solvent and scaling: r(all,work,free)=0.0933 0.0884 0.1850 n_refl.: 5175 remove outliers: r(all,work,free)=0.0933 0.0884 0.1850 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 0.3858 325.689 297.241 0.591 0.987 0.310 11.894-9.307 99.02 97 4 0.2010 523.931 505.201 1.004 0.993 0.310 9.237-7.194 100.00 213 7 0.2133 428.472 417.337 1.057 0.996 0.300 7.162-5.571 100.00 427 22 0.1993 321.516 310.708 1.044 0.998 0.290 5.546-4.326 100.00 867 58 0.1020 441.396 435.228 1.065 0.999 0.229 4.315-3.360 100.00 1859 96 0.0557 419.772 419.891 1.145 1.002 0.210 3.356-3.002 100.00 1373 60 0.0427 323.326 323.641 1.128 1.003 0.040 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9549 b_overall=-8.4008 ================= 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 : 0.3626 0.2014 0.084 5.321 8.8 119.3 19.9 258 0.000 1_bss: 0.1546 0.1611 0.084 5.321 6.1 116.5 17.1 258 0.000 1_settarget: 0.1546 0.1611 0.084 5.321 6.1 116.5 17.1 258 0.000 1_nqh: 0.1546 0.1611 0.084 5.321 6.1 116.5 17.1 258 0.000 1_weight: 0.1546 0.1611 0.084 5.321 6.1 116.5 17.1 258 0.000 1_xyzrec: 0.1158 0.1779 0.010 0.972 6.1 116.5 17.1 258 0.202 1_adp: 0.1020 0.1764 0.010 0.972 2.0 111.5 17.4 258 0.202 1_regHadp: 0.1013 0.1770 0.010 0.972 2.0 111.5 17.4 258 0.202 1_occ: 0.1023 0.1771 0.010 0.972 2.0 111.5 17.4 258 0.202 2_bss: 0.1022 0.1772 0.010 0.972 1.0 110.6 16.5 258 0.202 2_settarget: 0.1022 0.1772 0.010 0.972 1.0 110.6 16.5 258 0.202 2_updatecdl: 0.1022 0.1772 0.010 0.999 1.0 110.6 16.5 258 0.202 2_nqh: 0.1022 0.1772 0.010 0.999 1.0 110.6 16.5 258 0.202 2_sol: 0.1121 0.1693 0.010 0.999 1.0 110.0 15.8 228 n/a 2_weight: 0.1121 0.1693 0.010 0.999 1.0 110.0 15.8 228 n/a 2_xyzrec: 0.1012 0.1810 0.009 0.984 1.0 110.0 15.8 228 n/a 2_adp: 0.0945 0.1836 0.009 0.984 0.0 105.5 16.5 228 n/a 2_regHadp: 0.0942 0.1833 0.009 0.984 0.0 105.5 16.5 228 n/a 2_occ: 0.0938 0.1822 0.009 0.984 0.0 105.5 16.5 228 n/a 3_bss: 0.0937 0.1830 0.009 0.984 0.0 105.5 16.5 228 n/a 3_settarget: 0.0937 0.1830 0.009 0.984 0.0 105.5 16.5 228 n/a 3_updatecdl: 0.0937 0.1830 0.009 0.988 0.0 105.5 16.5 228 n/a 3_nqh: 0.0937 0.1830 0.009 0.988 0.0 105.5 16.5 228 n/a 3_sol: 0.1039 0.1707 0.009 0.988 0.0 105.5 16.4 233 n/a 3_weight: 0.1039 0.1707 0.009 0.988 0.0 105.5 16.4 233 n/a 3_xyzrec: 0.0924 0.1746 0.011 1.070 0.0 105.5 16.4 233 n/a 3_adp: 0.0882 0.1767 0.011 1.070 0.0 105.2 16.3 233 n/a 3_regHadp: 0.0888 0.1781 0.011 1.070 0.0 105.2 16.3 233 n/a 3_occ: 0.0875 0.1768 0.011 1.070 0.0 105.2 16.3 233 n/a 4_bss: 0.0865 0.1774 0.011 1.070 0.0 105.2 16.3 233 n/a 4_settarget: 0.0865 0.1774 0.011 1.070 0.0 105.2 16.3 233 n/a 4_updatecdl: 0.0865 0.1774 0.011 1.081 0.0 105.2 16.3 233 n/a 4_nqh: 0.0865 0.1774 0.011 1.081 0.0 105.2 16.3 233 n/a 4_sol: 0.0987 0.1733 0.011 1.081 0.0 105.2 16.3 227 n/a 4_weight: 0.0987 0.1733 0.011 1.081 0.0 105.2 16.3 227 n/a 4_xyzrec: 0.0890 0.1813 0.011 1.034 0.0 105.2 16.3 227 n/a 4_adp: 0.0865 0.1852 0.011 1.034 0.0 104.6 16.5 227 n/a 4_regHadp: 0.0869 0.1853 0.011 1.034 0.0 104.6 16.5 227 n/a 4_occ: 0.0862 0.1851 0.011 1.034 0.0 104.6 16.5 227 n/a 5_bss: 0.0860 0.1855 0.011 1.034 0.0 104.6 16.5 227 n/a 5_settarget: 0.0860 0.1855 0.011 1.034 0.0 104.6 16.5 227 n/a 5_updatecdl: 0.0860 0.1855 0.011 1.039 0.0 104.6 16.5 227 n/a 5_setrh: 0.0863 0.1856 0.011 1.039 0.0 104.6 16.5 227 n/a 5_nqh: 0.0863 0.1856 0.011 1.039 0.0 104.6 16.5 227 n/a 5_sol: 0.0971 0.1837 0.011 1.039 0.0 104.6 16.6 228 n/a 5_weight: 0.0971 0.1837 0.011 1.039 0.0 104.6 16.6 228 n/a 5_xyzrec: 0.0908 0.1861 0.011 1.076 0.0 104.6 16.6 228 n/a 5_adp: 0.0890 0.1862 0.011 1.076 0.0 106.9 16.8 228 n/a 5_regHadp: 0.0893 0.1865 0.011 1.076 0.0 106.9 16.8 228 n/a 5_occ: 0.0884 0.1848 0.011 1.076 0.0 106.9 16.8 228 n/a end: 0.0884 0.1850 0.011 1.076 0.0 106.9 16.8 228 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5155044_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut3/shake_5155044_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.1800 Refinement macro-cycles (run) : 492.7900 Write final files (write_after_run_outputs) : 9.6100 Total : 505.5800 Total CPU time: 8.75 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:19:06 PST -0800 (1735492746.98 s) Start R-work = 0.1546, R-free = 0.1611 Final R-work = 0.0884, R-free = 0.1850 =============================================================================== Job complete usr+sys time: 532.26 seconds wall clock time: 9 minutes 14.58 seconds (554.58 seconds total)