Starting phenix.refine on Sun Dec 29 09:24:42 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3081210.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz Found phil, /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff Adding command-line PHIL: ------------------------- xray_data.high_resolution=2 ordered_solvent.low_resolution=4 No user-defined map coefficients or files defined; will use default map outputs instead. Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" phil_files = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" default_phil = "/net/anaconda/raid1/afonine/work/ANI/5SY6/params_restrained_def.eff" model { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3081210.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_3081210.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous \ den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } Starting job =============================================================================== Symmetric amino acids flipped. Time to flip 3 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: 1.34, per 1000 atoms: 0.40 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: 0.34 Conformation dependent library (CDL) restraints added in 144.0 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: 0.65 - 0.91: 512 0.91 - 1.16: 1125 1.16 - 1.41: 641 1.41 - 1.67: 832 1.67 - 1.92: 43 Bond restraints: 3153 Sorted by residual: bond pdb=" CG HIS A 138 " pdb=" ND1 HIS A 138 " ideal model delta sigma weight residual 1.378 1.156 0.222 1.10e-02 8.26e+03 4.09e+02 bond pdb=" ND1 HIS A 115 " pdb=" CE1 HIS A 115 " ideal model delta sigma weight residual 1.321 1.511 -0.190 1.00e-02 1.00e+04 3.61e+02 bond pdb=" C BCYS A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 1.330 1.539 -0.209 1.22e-02 6.72e+03 2.94e+02 bond pdb=" CA LEU A 72 " pdb=" C LEU A 72 " ideal model delta sigma weight residual 1.521 1.741 -0.220 1.32e-02 5.74e+03 2.78e+02 bond pdb=" N VAL A 186 " pdb=" CA VAL A 186 " ideal model delta sigma weight residual 1.459 1.251 0.208 1.25e-02 6.40e+03 2.76e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.14: 3403 5.14 - 10.27: 1796 10.27 - 15.41: 522 15.41 - 20.54: 53 20.54 - 25.68: 3 Bond angle restraints: 5777 Sorted by residual: angle pdb=" O GLU A 163 " pdb=" C GLU A 163 " pdb=" N PHE A 164 " ideal model delta sigma weight residual 122.08 106.03 16.05 1.07e+00 8.73e-01 2.25e+02 angle pdb=" CA ALYS A 93 " pdb=" C ALYS A 93 " pdb=" O ALYS A 93 " ideal model delta sigma weight residual 120.63 136.22 -15.59 1.08e+00 8.57e-01 2.08e+02 angle pdb=" O VAL A 44 " pdb=" C VAL A 44 " pdb=" N GLN A 45 " ideal model delta sigma weight residual 123.10 139.29 -16.19 1.17e+00 7.31e-01 1.91e+02 angle pdb=" O LYS A 12 " pdb=" C LYS A 12 " pdb=" N GLY A 13 " ideal model delta sigma weight residual 122.87 139.41 -16.54 1.23e+00 6.61e-01 1.81e+02 angle pdb=" N SER A 47 " pdb=" CA SER A 47 " pdb=" C SER A 47 " ideal model delta sigma weight residual 111.33 127.40 -16.07 1.21e+00 6.83e-01 1.76e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.25: 1306 17.25 - 34.48: 120 34.48 - 51.72: 34 51.72 - 68.95: 17 68.95 - 86.19: 4 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C LEU A 151 " pdb=" N LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual -122.60 -145.57 22.97 0 2.50e+00 1.60e-01 8.44e+01 dihedral pdb=" N LEU A 151 " pdb=" C LEU A 151 " pdb=" CA LEU A 151 " pdb=" CB LEU A 151 " ideal model delta harmonic sigma weight residual 122.80 145.17 -22.37 0 2.50e+00 1.60e-01 8.00e+01 dihedral pdb=" C ARG A 98 " pdb=" N ARG A 98 " pdb=" CA ARG A 98 " pdb=" CB ARG A 98 " ideal model delta harmonic sigma weight residual -122.60 -144.13 21.53 0 2.50e+00 1.60e-01 7.42e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.227: 86 0.227 - 0.455: 74 0.455 - 0.682: 55 0.682 - 0.910: 20 0.910 - 1.137: 8 Chirality restraints: 243 Sorted by residual: chirality pdb=" CG LEU A 7 " pdb=" CB LEU A 7 " pdb=" CD1 LEU A 7 " pdb=" CD2 LEU A 7 " both_signs ideal model delta sigma weight residual False -2.59 -3.73 1.14 2.00e-01 2.50e+01 3.23e+01 chirality pdb=" CA ARG A 98 " pdb=" N ARG A 98 " pdb=" C ARG A 98 " pdb=" CB ARG A 98 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.96e+01 chirality pdb=" CA SER A 57 " pdb=" N SER A 57 " pdb=" C SER A 57 " pdb=" CB SER A 57 " both_signs ideal model delta sigma weight residual False 2.51 3.55 -1.04 2.00e-01 2.50e+01 2.69e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 139 " -0.076 2.00e-02 2.50e+03 6.41e-02 1.23e+02 pdb=" CG TYR A 139 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 139 " -0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR A 139 " 0.041 2.00e-02 2.50e+03 pdb=" CE1 TYR A 139 " 0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR A 139 " -0.113 2.00e-02 2.50e+03 pdb=" CZ TYR A 139 " -0.076 2.00e-02 2.50e+03 pdb=" OH TYR A 139 " -0.024 2.00e-02 2.50e+03 pdb=" HD1 TYR A 139 " 0.047 2.00e-02 2.50e+03 pdb=" HD2 TYR A 139 " 0.074 2.00e-02 2.50e+03 pdb=" HE1 TYR A 139 " 0.062 2.00e-02 2.50e+03 pdb=" HE2 TYR A 139 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ATYR A 67 " -0.031 2.00e-02 2.50e+03 5.29e-02 8.38e+01 pdb=" CG ATYR A 67 " 0.033 2.00e-02 2.50e+03 pdb=" CD1ATYR A 67 " 0.062 2.00e-02 2.50e+03 pdb=" CD2ATYR A 67 " 0.096 2.00e-02 2.50e+03 pdb=" CE1ATYR A 67 " -0.058 2.00e-02 2.50e+03 pdb=" CE2ATYR A 67 " -0.026 2.00e-02 2.50e+03 pdb=" CZ ATYR A 67 " -0.053 2.00e-02 2.50e+03 pdb=" OH ATYR A 67 " 0.029 2.00e-02 2.50e+03 pdb=" HD1ATYR A 67 " -0.072 2.00e-02 2.50e+03 pdb=" HD2ATYR A 67 " -0.009 2.00e-02 2.50e+03 pdb=" HE1ATYR A 67 " 0.064 2.00e-02 2.50e+03 pdb=" HE2ATYR A 67 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.007 2.00e-02 2.50e+03 5.28e-02 8.37e+01 pdb=" CG PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.044 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " 0.067 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " 0.099 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.027 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.020 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.042 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " -0.045 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.100 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.037 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " 0.028 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 643 2.25 - 2.84: 7583 2.84 - 3.43: 10714 3.43 - 4.01: 15390 4.01 - 4.60: 22239 Nonbonded interactions: 56569 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.663 2.100 nonbonded pdb=" O VAL A 169 " pdb=" H ASN A 173 " model vdw 1.772 2.450 nonbonded pdb=" OE1 GLU A 16 " pdb=" H GLU A 16 " model vdw 1.777 2.450 nonbonded pdb=" HE2 HIS A 126 " pdb=" O PRO A 184 " model vdw sym.op. 1.804 2.450 x-y,-y,-z-4/3 nonbonded pdb=" H LEU A 10 " pdb=" O ALA A 36 " model vdw 1.833 2.450 ... (remaining 56564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. ============================== Scattering factors ============================= ----------X-ray scattering dictionary---------- Number of scattering types: 6 Type Number sf(0) Gaussians S 10 15.96 2 O1- 2 8.97 2 O 551 7.97 2 N 265 6.97 2 C 957 5.97 2 H 1596 1.00 2 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3381 n_use_u_iso = 1596 n_use_u_aniso = 1785 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 3381 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3381 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 1596 aniso = 1785) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = True (876 atoms) group_anomalous = False ============================ Non-default parameters =========================== A complete record of all parameters was written to the .eff file above. Below are only the non-defaults. #phil __ON__ refinement { electron_density_maps { map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT" mtz_label_phases = "PH2FOFCWT" fill_missing_f_obs = True } map_coefficients { map_type = "2mFo-DFc" mtz_label_amplitudes = "2FOFCWT_no_fill" mtz_label_phases = "PH2FOFCWT_no_fill" } map_coefficients { map_type = "mFo-DFc" mtz_label_amplitudes = "FOFCWT" mtz_label_phases = "PHFOFCWT" } map_coefficients { map_type = "anomalous" mtz_label_amplitudes = "ANOM" mtz_label_phases = "PANOM" } map { map_type = "2mFo-DFc" fill_missing_f_obs = True } map { map_type = "2mFo-DFc" } map { map_type = "mFo-DFc" } } refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous den occupancies { individual = (chain A and resseq 15 and (name OE2 or name OE1)) or \ (chain A and resseq 24 and (name OD2 or name OD1)) } } main { ordered_solvent = True number_of_macro_cycles = 5 max_number_of_iterations = 100 } hydrogens { refine = individual *riding Auto } ordered_solvent { low_resolution = 4 mode = second_half filter_only every_macro_cycle \ *every_macro_cycle_after_first primary_map_cutoff = 2.5 secondary_map_and_map_cc_filter { poor_map_value_threshold = 0.7 } ignore_final_filtering_step = True correct_drifted_waters = False } } output { prefix = "shake_3081210_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1596 occupancy sum: 1438.50 (% of total atoms 46.85) Rotatable: count: 507 occupancy sum: 483.00 (% of total atoms 15.73) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2786 r_free= 0.1815 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.396742 | | target function (ml) not normalized (work): 71416.280442 | | target function (ml) not normalized (free): 3255.821571 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 49.25 - 3.64 1.00 2819 159 0.3195 0.2190 7.4838 5.0528| | 2: 3.63 - 2.88 1.00 2711 122 0.2648 0.1710 4.3365 4.334| | 3: 2.88 - 2.52 1.00 2682 148 0.2531 0.1700 4.1835 4.1978| | 4: 2.52 - 2.29 1.00 2661 139 0.2559 0.1561 3.5032 3.5954| | 5: 2.29 - 2.13 1.00 2678 122 0.2629 0.1370 3.3927 3.3749| | 6: 2.13 - 2.00 1.00 2692 117 0.2768 0.1776 3.3192 3.3412| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 49.25 - 3.64 2819 159 0.88 17.75 0.77 0.23 1319.13| | 2: 3.63 - 2.88 2711 122 0.82 24.08 1.31 0.23 1319.13| | 3: 2.88 - 2.52 2682 148 0.73 33.13 1.28 0.23 1319.13| | 4: 2.52 - 2.29 2661 139 0.93 11.07 1.30 0.26 128.30| | 5: 2.29 - 2.13 2678 122 0.92 13.00 1.31 0.26 128.30| | 6: 2.13 - 2.00 2692 117 0.90 15.95 1.34 0.26 128.30| |alpha: min = 0.23 max = 0.26 mean = 0.24| |beta: min = 128.30 max = 1319.13 mean = 730.35| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.87 mean = 19.17| |phase err.(test): min = 0.00 max = 89.43 mean = 19.30| |-----------------------------------------------------------------------------| ----------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 0.228 1557 Z= 5.393 Angle : 5.341 17.586 2118 Z= 3.715 Chirality : 0.444 1.137 243 Planarity : 0.031 0.085 284 Dihedral : 13.921 86.187 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.24 % Favored : 96.22 % Rotamer: Outliers : 1.86 % Allowed : 1.86 % Favored : 96.27 % Cbeta Deviations : 35.14 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.48), residues: 224 helix: -3.12 (0.36), residues: 109 sheet: -0.94 (0.83), residues: 38 loop : -0.82 (0.61), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.099 0.019 ARG A 5 TYR 0.086 0.039 TYR A 139 PHE 0.083 0.029 PHE A 164 HIS 0.076 0.030 HIS A 126 Individual atomic B min max mean iso aniso Overall: 8.85 119.30 19.89 3.90 1785 0 Protein: 8.85 115.78 16.79 3.90 1519 0 Water: 11.36 119.30 38.03 N/A 258 0 Other: 19.04 26.29 21.71 N/A 8 0 Chain A: 8.85 119.30 19.89 N/A 1785 0 Histogram: Values Number of atoms 8.85 - 19.89 1276 19.89 - 30.94 224 30.94 - 41.98 127 41.98 - 53.03 89 53.03 - 64.07 44 64.07 - 75.12 11 75.12 - 86.16 7 86.16 - 97.21 4 97.21 - 108.25 1 108.25 - 119.30 2 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 5 ************************* |--(resolution: 2.00 - 49.25 A, n_refl.=17050 (all), 4.73 % free)------------| | | | r_work= 0.2786 r_free= 0.1815 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.396742 | | target function (ml) not normalized (work): 71416.280442 | | target function (ml) not normalized (free): 3255.821571 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3048 percent. r_work = 0.2916 r_free = 0.1967 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2862 0.2916 0.1967 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2862 0.2916 0.1967 n_refl.: 17050 remove outliers: r(all,work,free)=0.2155 0.2167 0.1967 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2128 0.2140 0.1949 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1617 0.1614 0.1656 n_refl.: 17045 remove outliers: r(all,work,free)=0.1616 0.1613 0.1656 n_refl.: 17044 ======================== 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 0.4088 394.876 358.571 0.644 1.009 0.387 11.894-9.307 99.02 97 4 0.1940 633.788 614.868 0.925 1.011 0.370 9.237-7.194 100.00 213 7 0.2137 518.375 508.610 0.961 1.011 0.339 7.162-5.571 100.00 427 22 0.2335 389.041 376.492 0.927 1.010 0.290 5.546-4.326 100.00 867 58 0.1394 534.091 528.119 0.964 1.008 0.271 4.315-3.360 100.00 1859 96 0.1285 507.925 503.999 1.018 1.005 0.201 3.356-2.611 100.00 3867 181 0.1667 333.678 328.830 1.012 1.000 0.091 2.608-2.000 99.99 8818 434 0.1643 217.501 213.457 1.028 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4526 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1613 r_free=0.1656 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1613 r_free=0.1656 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.353065 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.925244 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1355 0.1640 0.0285 0.009 1.0 1.0 0.5 0.0 0 11.177 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.55 16.40 2.85 3.013 18.452 0.925 0.023 12.79 16.63 3.84 3.640 18.706 0.925 0.021 Individual atomic B min max mean iso aniso Overall: 6.21 113.89 19.96 4.09 1785 0 Protein: 6.21 112.81 17.20 4.09 1519 0 Water: 9.09 113.89 36.02 N/A 258 0 Other: 22.32 37.24 26.63 N/A 8 0 Chain A: 6.21 113.89 19.96 N/A 1785 0 Histogram: Values Number of atoms 6.21 - 16.98 1093 16.98 - 27.75 334 27.75 - 38.52 184 38.52 - 49.29 100 49.29 - 60.05 47 60.05 - 70.82 13 70.82 - 81.59 6 81.59 - 92.36 4 92.36 - 103.12 1 103.12 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1663 r_work=0.1282 r_free=0.1670 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1670 target_work(ls_wunit_k1) = 0.021 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1278 r_free = 0.1661 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 2 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17044 (all), 4.73 % free)------------| | | | r_work= 0.1278 r_free= 0.1661 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020118 | | target function (ls_wunit_k1) not normalized (work): 326.657597 | | target function (ls_wunit_k1) not normalized (free): 27.341829 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1278 0.1661 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1910 0.1909 0.1979 n_refl.: 17044 remove outliers: r(all,work,free)=0.1910 0.1909 0.1979 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1882 0.1881 0.1963 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1295 0.1278 0.1649 n_refl.: 17044 remove outliers: r(all,work,free)=0.1294 0.1276 0.1649 n_refl.: 17042 ======================== 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 0.3578 303.472 279.074 0.622 1.009 0.370 11.894-9.307 99.02 97 4 0.1708 488.086 477.706 0.915 1.010 0.367 9.237-7.194 100.00 213 7 0.1833 399.205 396.720 0.958 1.010 0.325 7.162-5.571 100.00 427 22 0.1829 299.604 294.585 0.932 1.009 0.301 5.546-4.326 100.00 867 58 0.1048 411.308 409.087 0.960 1.008 0.241 4.315-3.360 100.00 1859 96 0.0920 391.158 390.773 1.017 1.005 0.191 3.356-2.611 100.00 3867 181 0.1302 256.969 255.755 1.014 1.000 0.101 2.608-2.000 99.99 8818 434 0.1354 167.500 166.038 1.022 0.992 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3782 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1649 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1276 r_free=0.1649 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1276 r_free=0.1649 | n_water=258 | time (s): 0.840 (total time: 0.840) Filter (dist) r_work=0.1286 r_free=0.1639 | n_water=252 | time (s): 21.200 (total time: 22.040) Filter (q & B) r_work=0.1286 r_free=0.1638 | n_water=250 | time (s): 1.390 (total time: 23.430) Compute maps r_work=0.1286 r_free=0.1638 | n_water=250 | time (s): 0.520 (total time: 23.950) Filter (map) r_work=0.1314 r_free=0.1627 | n_water=212 | time (s): 1.660 (total time: 25.610) Find peaks r_work=0.1314 r_free=0.1627 | n_water=212 | time (s): 0.650 (total time: 26.260) Add new water r_work=0.1538 r_free=0.1884 | n_water=366 | time (s): 2.180 (total time: 28.440) Refine new water occ: r_work=0.1333 r_free=0.1584 adp: r_work=0.1277 r_free=0.1580 occ: r_work=0.1280 r_free=0.1548 adp: r_work=0.1250 r_free=0.1555 occ: r_work=0.1250 r_free=0.1549 adp: r_work=0.1238 r_free=0.1547 ADP+occupancy (water only), MIN, final r_work=0.1238 r_free=0.1547 r_work=0.1238 r_free=0.1547 | n_water=366 | time (s): 21.330 (total time: 49.770) Filter (q & B) r_work=0.1240 r_free=0.1554 | n_water=357 | time (s): 1.850 (total time: 51.620) Filter (dist only) r_work=0.1240 r_free=0.1555 | n_water=356 | time (s): 27.570 (total time: 79.190) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.713228 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.990191 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1211 0.1590 0.0379 0.008 0.9 1.6 0.5 0.0 0 12.357 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.11 15.90 3.79 4.180 21.068 0.990 0.018 11.99 16.23 4.24 4.218 21.348 0.990 0.018 Individual atomic B min max mean iso aniso Overall: 6.48 107.42 21.37 4.26 1883 0 Protein: 6.48 107.42 17.76 4.24 1519 0 Water: 9.11 65.79 36.43 N/A 356 0 Other: 24.54 47.17 36.41 N/A 8 0 Chain A: 6.48 107.42 19.51 N/A 1739 0 Chain S: 16.89 65.77 43.86 N/A 144 0 Histogram: Values Number of atoms 6.48 - 16.57 1013 16.57 - 26.67 385 26.67 - 36.76 208 36.76 - 46.86 164 46.86 - 56.95 76 56.95 - 67.05 26 67.05 - 77.14 4 77.14 - 87.24 3 87.24 - 97.33 2 97.33 - 107.42 2 =========================== Idealize ADP of riding H ========================== r_work=0.1199 r_free=0.1623 r_work=0.1200 r_free=0.1624 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1200 r_free = 0.1624 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1198 r_free = 0.1626 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 3 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17042 (all), 4.74 % free)------------| | | | r_work= 0.1198 r_free= 0.1626 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ls_wunit_k1) (work): 0.017126 | | target function (ls_wunit_k1) not normalized (work): 278.042931 | | target function (ls_wunit_k1) not normalized (free): 25.132965 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1218 0.1198 0.1626 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1764 0.1755 0.1964 n_refl.: 17042 remove outliers: r(all,work,free)=0.1764 0.1755 0.1964 n_refl.: 17042 overall B=-0.38 to atoms: r(all,work,free)=0.1740 0.1730 0.1946 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1212 0.1192 0.1616 n_refl.: 17042 remove outliers: r(all,work,free)=0.1211 0.1191 0.1616 n_refl.: 17041 ======================== Statistics in resolution bins ======================== Total model structure factor: F_model = k_total * (F_calc + k_mask * F_mask) k_total = k_isotropic * k_anisotropic Resolution Compl Nwork Nfree R_work kiso kani kmask 32.574-12.150 94.79 86 5 0.3210 300.309 285.476 0.607 1.004 0.350 11.894-9.307 99.02 97 4 0.1543 488.086 486.583 0.912 1.005 0.335 9.237-7.194 100.00 213 7 0.1678 399.205 400.658 0.975 1.005 0.290 7.162-5.571 100.00 427 22 0.1552 299.604 296.307 0.934 1.005 0.281 5.546-4.326 100.00 867 58 0.0868 411.308 408.626 0.959 1.004 0.220 4.315-3.360 100.00 1859 96 0.0834 391.158 390.197 1.015 1.003 0.201 3.356-2.611 100.00 3867 181 0.1205 256.969 255.954 1.012 1.001 0.058 2.608-2.000 99.99 8818 434 0.1329 167.500 166.411 1.017 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3426 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1191 r_free=0.1616 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1191 r_free=0.1616 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1191 r_free=0.1616 | n_water=356 | time (s): 0.680 (total time: 0.680) Filter (dist) r_work=0.1191 r_free=0.1620 | n_water=355 | time (s): 28.680 (total time: 29.360) Filter (q & B) r_work=0.1191 r_free=0.1620 | n_water=355 | time (s): 0.890 (total time: 30.250) Compute maps r_work=0.1191 r_free=0.1620 | n_water=355 | time (s): 0.590 (total time: 30.840) Filter (map) r_work=0.1253 r_free=0.1637 | n_water=261 | time (s): 1.590 (total time: 32.430) Find peaks r_work=0.1253 r_free=0.1637 | n_water=261 | time (s): 0.520 (total time: 32.950) Add new water r_work=0.1443 r_free=0.1791 | n_water=410 | time (s): 1.610 (total time: 34.560) Refine new water occ: r_work=0.1247 r_free=0.1575 adp: r_work=0.1235 r_free=0.1578 occ: r_work=0.1220 r_free=0.1554 adp: r_work=0.1206 r_free=0.1557 occ: r_work=0.1200 r_free=0.1544 adp: r_work=0.1189 r_free=0.1547 ADP+occupancy (water only), MIN, final r_work=0.1189 r_free=0.1547 r_work=0.1189 r_free=0.1547 | n_water=410 | time (s): 37.190 (total time: 71.750) Filter (q & B) r_work=0.1193 r_free=0.1554 | n_water=402 | time (s): 1.720 (total time: 73.470) Filter (dist only) r_work=0.1193 r_free=0.1554 | n_water=402 | time (s): 31.630 (total time: 105.100) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.797824 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.163161 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1176 0.1551 0.0375 0.009 0.9 3.2 0.5 0.0 0 0.899 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.76 15.51 3.75 4.336 21.564 0.163 4.993 11.53 15.52 3.99 4.905 21.536 0.163 4.971 Individual atomic B min max mean iso aniso Overall: 6.21 103.79 21.02 4.78 1929 0 Protein: 6.21 103.79 17.07 4.76 1519 0 Water: 9.06 68.27 35.66 N/A 402 0 Other: 27.39 50.63 37.10 N/A 8 0 Chain A: 6.21 103.79 18.81 N/A 1735 0 Chain S: 18.04 68.27 40.79 N/A 194 0 Histogram: Values Number of atoms 6.21 - 15.96 1044 15.96 - 25.72 355 25.72 - 35.48 229 35.48 - 45.24 167 45.24 - 55.00 85 55.00 - 64.75 34 64.75 - 74.51 6 74.51 - 84.27 4 84.27 - 94.03 3 94.03 - 103.79 2 =========================== Idealize ADP of riding H ========================== r_work=0.1153 r_free=0.1552 r_work=0.1153 r_free=0.1554 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1153 r_free = 0.1554 target_work(ml) = 4.971 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1146 r_free = 0.1548 target_work(ml) = 4.967 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 4 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17041 (all), 4.74 % free)------------| | | | r_work= 0.1146 r_free= 0.1548 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.966705 | | target function (ml) not normalized (work): 80629.482825 | | target function (ml) not normalized (free): 4181.770213 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1166 0.1146 0.1548 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1665 0.1655 0.1893 n_refl.: 17041 remove outliers: r(all,work,free)=0.1665 0.1655 0.1893 n_refl.: 17041 overall B=-0.37 to atoms: r(all,work,free)=0.1640 0.1629 0.1879 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1163 0.1144 0.1550 n_refl.: 17041 remove outliers: r(all,work,free)=0.1163 0.1143 0.1550 n_refl.: 17040 ======================== 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 93.75 85 5 0.3344 296.743 281.094 0.571 1.004 0.337 11.894-9.307 99.02 97 4 0.1724 488.086 483.040 0.909 1.006 0.335 9.237-7.194 100.00 213 7 0.1772 399.205 399.044 0.984 1.006 0.260 7.162-5.571 100.00 427 22 0.1618 299.604 293.834 0.935 1.006 0.230 5.546-4.326 100.00 867 58 0.0953 411.308 407.640 0.964 1.005 0.210 4.315-3.360 100.00 1859 96 0.0893 391.158 388.987 1.011 1.003 0.201 3.356-2.611 100.00 3867 181 0.1279 256.969 254.710 1.012 1.000 0.101 2.608-2.000 99.99 8818 434 0.1086 167.500 166.052 1.017 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3261 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1143 r_free=0.1550 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.1143 r_free=0.1550 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1143 r_free=0.1550 | n_water=402 | time (s): 0.910 (total time: 0.910) Filter (dist) r_work=0.1147 r_free=0.1547 | n_water=401 | time (s): 33.210 (total time: 34.120) Filter (q & B) r_work=0.1147 r_free=0.1547 | n_water=401 | time (s): 0.940 (total time: 35.060) Compute maps r_work=0.1147 r_free=0.1547 | n_water=401 | time (s): 0.660 (total time: 35.720) Filter (map) r_work=0.1207 r_free=0.1604 | n_water=314 | time (s): 2.020 (total time: 37.740) Find peaks r_work=0.1207 r_free=0.1604 | n_water=314 | time (s): 0.480 (total time: 38.220) Add new water r_work=0.1346 r_free=0.1721 | n_water=464 | time (s): 1.650 (total time: 39.870) Refine new water occ: r_work=0.1171 r_free=0.1547 adp: r_work=0.1163 r_free=0.1548 occ: r_work=0.1149 r_free=0.1530 adp: r_work=0.1140 r_free=0.1531 occ: r_work=0.1134 r_free=0.1522 adp: r_work=0.1126 r_free=0.1524 ADP+occupancy (water only), MIN, final r_work=0.1126 r_free=0.1524 r_work=0.1126 r_free=0.1524 | n_water=464 | time (s): 37.690 (total time: 77.560) Filter (q & B) r_work=0.1130 r_free=0.1538 | n_water=452 | time (s): 1.700 (total time: 79.260) Filter (dist only) r_work=0.1130 r_free=0.1538 | n_water=452 | time (s): 33.980 (total time: 113.240) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.936692 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.157745 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1120 0.1572 0.0452 0.009 1.0 4.2 0.5 0.0 0 0.968 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.20 15.72 4.52 4.556 21.256 0.158 4.962 11.11 15.73 4.62 4.741 21.269 0.158 4.954 Individual atomic B min max mean iso aniso Overall: 5.79 100.32 21.17 4.85 1979 0 Protein: 5.79 100.32 16.59 4.84 1519 0 Water: 8.72 65.03 36.30 N/A 452 0 Other: 27.29 48.43 35.78 N/A 8 0 Chain A: 5.79 100.32 18.27 N/A 1733 0 Chain S: 15.74 65.03 41.58 N/A 246 0 Histogram: Values Number of atoms 5.79 - 15.25 1007 15.25 - 24.70 392 24.70 - 34.15 208 34.15 - 43.61 194 43.61 - 53.06 115 53.06 - 62.51 42 62.51 - 71.96 10 71.96 - 81.42 5 81.42 - 90.87 3 90.87 - 100.32 3 =========================== Idealize ADP of riding H ========================== r_work=0.1111 r_free=0.1573 r_work=0.1111 r_free=0.1574 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1111 r_free = 0.1574 target_work(ml) = 4.955 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1100 r_free = 0.1581 target_work(ml) = 4.952 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| *********************** REFINEMENT MACRO_CYCLE 5 OF 5 ************************* |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1100 r_free= 0.1581 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.951523 | | target function (ml) not normalized (work): 80378.070490 | | target function (ml) not normalized (free): 4191.394075 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1123 0.1100 0.1581 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1597 0.1584 0.1880 n_refl.: 17040 remove outliers: r(all,work,free)=0.1597 0.1584 0.1880 n_refl.: 17040 overall B=-0.30 to atoms: r(all,work,free)=0.1578 0.1565 0.1868 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1120 0.1097 0.1575 n_refl.: 17040 remove outliers: r(all,work,free)=0.1120 0.1097 0.1575 n_refl.: 17040 ======================== 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 93.75 85 5 0.3570 296.743 277.381 0.551 1.000 0.324 11.894-9.307 99.02 97 4 0.1758 488.086 479.794 0.915 1.002 0.320 9.237-7.194 100.00 213 7 0.1711 399.205 400.797 0.995 1.002 0.230 7.162-5.571 100.00 427 22 0.1542 299.604 293.607 0.940 1.002 0.230 5.546-4.326 100.00 867 58 0.0916 411.308 408.190 0.965 1.002 0.181 4.315-3.360 100.00 1859 96 0.0841 391.158 388.854 1.009 1.002 0.181 3.356-2.611 100.00 3867 181 0.1226 256.969 254.868 1.006 1.001 0.121 2.608-2.000 99.99 8818 434 0.1043 167.500 166.286 1.001 1.000 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0280 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1097 r_free=0.1575 After: r_work=0.1099 r_free=0.1573 ================================== NQH flips ================================== r_work=0.1099 r_free=0.1573 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1099 r_free=0.1573 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1099 r_free=0.1573 | n_water=452 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1102 r_free=0.1568 | n_water=450 | time (s): 41.990 (total time: 42.600) Filter (q & B) r_work=0.1102 r_free=0.1567 | n_water=449 | time (s): 2.170 (total time: 44.770) Compute maps r_work=0.1102 r_free=0.1567 | n_water=449 | time (s): 0.760 (total time: 45.530) Filter (map) r_work=0.1178 r_free=0.1577 | n_water=340 | time (s): 2.050 (total time: 47.580) Find peaks r_work=0.1178 r_free=0.1577 | n_water=340 | time (s): 0.650 (total time: 48.230) Add new water r_work=0.1294 r_free=0.1684 | n_water=477 | time (s): 1.990 (total time: 50.220) Refine new water occ: r_work=0.1139 r_free=0.1534 adp: r_work=0.1133 r_free=0.1535 occ: r_work=0.1116 r_free=0.1518 adp: r_work=0.1109 r_free=0.1516 occ: r_work=0.1101 r_free=0.1501 adp: r_work=0.1096 r_free=0.1503 ADP+occupancy (water only), MIN, final r_work=0.1096 r_free=0.1503 r_work=0.1096 r_free=0.1503 | n_water=477 | time (s): 30.580 (total time: 80.800) Filter (q & B) r_work=0.1100 r_free=0.1512 | n_water=464 | time (s): 2.000 (total time: 82.800) Filter (dist only) r_work=0.1100 r_free=0.1512 | n_water=464 | time (s): 37.910 (total time: 120.710) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.989858 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.164984 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1118 0.1531 0.0413 0.010 1.0 3.8 0.5 0.0 0 0.995 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.18 15.31 4.13 4.551 20.947 0.165 4.946 11.07 15.12 4.06 4.675 20.985 0.165 4.935 Individual atomic B min max mean iso aniso Overall: 5.04 99.56 21.08 5.02 1991 0 Protein: 5.04 99.56 16.25 5.00 1519 0 Water: 8.06 67.94 36.64 N/A 464 0 Other: 26.43 49.07 34.38 N/A 8 0 Chain A: 5.04 99.56 17.92 N/A 1733 0 Chain S: 17.48 67.94 42.32 N/A 258 0 Histogram: Values Number of atoms 5.04 - 14.49 970 14.49 - 23.94 425 23.94 - 33.39 202 33.39 - 42.84 189 42.84 - 52.30 136 52.30 - 61.75 43 61.75 - 71.20 16 71.20 - 80.65 2 80.65 - 90.11 4 90.11 - 99.56 4 =========================== Idealize ADP of riding H ========================== r_work=0.1107 r_free=0.1512 r_work=0.1106 r_free=0.1511 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1106 r_free = 0.1511 target_work(ml) = 4.935 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1101 r_free = 0.1512 target_work(ml) = 4.933 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1101 r_free= 0.1512 coordinate error (max.-lik. estimate): 0.10 A | | | | normalized target function (ml) (work): 4.933017 | | target function (ml) not normalized (work): 80077.671106 | | target function (ml) not normalized (free): 4165.392696 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 32.57 - 3.64 1.00 2810 159 0.1109 0.1351 5.4431 5.6257| | 2: 3.63 - 2.88 1.00 2711 122 0.1077 0.1577 5.2167 5.3942| | 3: 2.88 - 2.52 1.00 2681 148 0.1357 0.1694 5.1275 5.2127| | 4: 2.52 - 2.29 1.00 2661 139 0.0935 0.1510 4.6276 4.9468| | 5: 2.29 - 2.13 1.00 2678 122 0.0963 0.1503 4.5814 4.8944| | 6: 2.13 - 2.00 1.00 2692 117 0.1115 0.1681 4.5729 4.7573| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |R-free likelihood based estimates for figures of merit, absolute phase error,| |and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)| | | | Bin Resolution No. Refl. FOM Phase Scale Alpha Beta | | # range work test error factor | | 1: 32.57 - 3.64 2810 159 0.95 9.07 1.00 0.96 6375.64| | 2: 3.63 - 2.88 2711 122 0.92 12.75 1.01 0.96 6375.64| | 3: 2.88 - 2.52 2681 148 0.88 18.94 0.99 0.96 6375.64| | 4: 2.52 - 2.29 2661 139 0.93 12.16 1.01 0.97 2120.35| | 5: 2.29 - 2.13 2678 122 0.91 14.10 1.00 0.97 2120.35| | 6: 2.13 - 2.00 2692 117 0.89 16.90 0.99 0.97 2120.35| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2120.35 max = 6375.64 mean = 4270.41| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 89.98 mean = 13.95| |phase err.(test): min = 0.00 max = 89.87 mean = 13.42| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1121 0.1101 0.1512 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1571 0.1557 0.1858 n_refl.: 17040 remove outliers: r(all,work,free)=0.1571 0.1557 0.1858 n_refl.: 17040 overall B=-0.24 to atoms: r(all,work,free)=0.1557 0.1543 0.1848 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1121 0.1102 0.1512 n_refl.: 17040 remove outliers: r(all,work,free)=0.1121 0.1102 0.1512 n_refl.: 17040 ======================== 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 93.75 85 5 0.3514 296.743 279.398 0.551 1.001 0.324 11.894-9.307 99.02 97 4 0.1711 488.086 482.222 0.922 1.002 0.320 9.237-7.194 100.00 213 7 0.1656 399.205 401.665 0.996 1.003 0.230 7.162-5.571 100.00 427 22 0.1565 299.604 293.344 0.935 1.003 0.230 5.546-4.326 100.00 867 58 0.0939 411.308 408.538 0.964 1.003 0.190 4.315-3.360 100.00 1859 96 0.0861 391.158 388.961 1.005 1.002 0.171 3.356-2.611 100.00 3867 181 0.1230 256.969 254.918 1.001 1.001 0.111 2.608-2.000 99.99 8818 434 0.1040 167.500 166.161 0.991 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8243 ================= 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 : 0.2786 0.1815 0.081 5.341 8.8 119.3 19.9 258 0.000 1_bss: 0.1613 0.1656 0.081 5.341 8.4 118.9 19.5 258 0.000 1_settarget: 0.1613 0.1656 0.081 5.341 8.4 118.9 19.5 258 0.000 1_nqh: 0.1613 0.1656 0.081 5.341 8.4 118.9 19.5 258 0.000 1_weight: 0.1613 0.1656 0.081 5.341 8.4 118.9 19.5 258 0.000 1_xyzrec: 0.1355 0.1640 0.009 0.966 8.4 118.9 19.5 258 0.153 1_adp: 0.1279 0.1663 0.009 0.966 6.2 113.9 20.0 258 0.153 1_regHadp: 0.1282 0.1670 0.009 0.966 6.2 113.9 20.0 258 0.153 1_occ: 0.1278 0.1661 0.009 0.966 6.2 113.9 20.0 258 0.153 2_bss: 0.1276 0.1649 0.009 0.966 5.8 113.5 19.6 258 0.153 2_settarget: 0.1276 0.1649 0.009 0.966 5.8 113.5 19.6 258 0.153 2_updatecdl: 0.1276 0.1649 0.009 0.988 5.8 113.5 19.6 258 0.153 2_nqh: 0.1276 0.1649 0.009 0.988 5.8 113.5 19.6 258 0.153 2_sol: 0.1240 0.1555 0.009 0.988 5.8 112.4 20.9 356 n/a 2_weight: 0.1240 0.1555 0.009 0.988 5.8 112.4 20.9 356 n/a 2_xyzrec: 0.1211 0.1590 0.008 0.930 5.8 112.4 20.9 356 n/a 2_adp: 0.1199 0.1623 0.008 0.930 6.5 107.4 21.4 356 n/a 2_regHadp: 0.1200 0.1624 0.008 0.930 6.5 107.4 21.4 356 n/a 2_occ: 0.1198 0.1626 0.008 0.930 6.5 107.4 21.4 356 n/a 3_bss: 0.1191 0.1616 0.008 0.930 6.1 107.0 21.0 356 n/a 3_settarget: 0.1191 0.1616 0.008 0.930 6.1 107.0 21.0 356 n/a 3_updatecdl: 0.1191 0.1616 0.008 0.930 6.1 107.0 21.0 356 n/a 3_nqh: 0.1191 0.1616 0.008 0.930 6.1 107.0 21.0 356 n/a 3_sol: 0.1193 0.1554 0.008 0.930 6.1 107.0 21.1 402 n/a 3_weight: 0.1193 0.1554 0.008 0.930 6.1 107.0 21.1 402 n/a 3_xyzrec: 0.1176 0.1551 0.009 0.950 6.1 107.0 21.1 402 n/a 3_adp: 0.1153 0.1552 0.009 0.950 6.2 103.8 21.0 402 n/a 3_regHadp: 0.1153 0.1554 0.009 0.950 6.2 103.8 21.0 402 n/a 3_occ: 0.1146 0.1548 0.009 0.950 6.2 103.8 21.0 402 n/a 4_bss: 0.1143 0.1550 0.009 0.950 5.8 103.4 20.7 402 n/a 4_settarget: 0.1143 0.1550 0.009 0.950 5.8 103.4 20.7 402 n/a 4_updatecdl: 0.1143 0.1550 0.009 0.950 5.8 103.4 20.7 402 n/a 4_nqh: 0.1143 0.1550 0.009 0.950 5.8 103.4 20.7 402 n/a 4_sol: 0.1130 0.1538 0.009 0.950 5.8 103.4 21.1 452 n/a 4_weight: 0.1130 0.1538 0.009 0.950 5.8 103.4 21.1 452 n/a 4_xyzrec: 0.1120 0.1572 0.009 0.969 5.8 103.4 21.1 452 n/a 4_adp: 0.1111 0.1573 0.009 0.969 5.8 100.3 21.2 452 n/a 4_regHadp: 0.1111 0.1574 0.009 0.969 5.8 100.3 21.2 452 n/a 4_occ: 0.1100 0.1581 0.009 0.969 5.8 100.3 21.2 452 n/a 5_bss: 0.1097 0.1575 0.009 0.969 5.5 100.0 20.9 452 n/a 5_settarget: 0.1097 0.1575 0.009 0.969 5.5 100.0 20.9 452 n/a 5_updatecdl: 0.1097 0.1575 0.009 0.969 5.5 100.0 20.9 452 n/a 5_setrh: 0.1099 0.1573 0.009 0.969 5.5 100.0 20.9 452 n/a 5_nqh: 0.1099 0.1573 0.009 0.969 5.5 100.0 20.9 452 n/a 5_sol: 0.1100 0.1512 0.009 0.969 5.5 100.0 21.0 464 n/a 5_weight: 0.1100 0.1512 0.009 0.969 5.5 100.0 21.0 464 n/a 5_xyzrec: 0.1118 0.1531 0.010 1.033 5.5 100.0 21.0 464 n/a 5_adp: 0.1107 0.1512 0.010 1.033 5.0 99.6 21.1 464 n/a 5_regHadp: 0.1106 0.1511 0.010 1.033 5.0 99.6 21.1 464 n/a 5_occ: 0.1101 0.1512 0.010 1.033 5.0 99.6 21.1 464 n/a end: 0.1102 0.1512 0.010 1.033 4.8 99.3 20.8 464 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3081210_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_3081210_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.1100 Refinement macro-cycles (run) : 946.8800 Write final files (write_after_run_outputs) : 18.3300 Total : 969.3200 Total CPU time: 16.51 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:31 PST -0800 (1735494091.97 s) Start R-work = 0.1613, R-free = 0.1656 Final R-work = 0.1102, R-free = 0.1512 =============================================================================== Job complete usr+sys time: 1010.40 seconds wall clock time: 17 minutes 13.12 seconds (1033.12 seconds total)