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_9171019.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 { 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_9171019.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/5SY6/shaken/shake_9171019.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } fmodel { xray_data { high_resolution = 2 } } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/5SY6/5SY6.mtz" } 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 =============================================================================== 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: 1.79, per 1000 atoms: 0.53 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: 0.30 Conformation dependent library (CDL) restraints added in 116.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 370 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.66 - 0.93: 574 0.93 - 1.20: 1102 1.20 - 1.46: 785 1.46 - 1.73: 677 1.73 - 2.00: 15 Bond restraints: 3153 Sorted by residual: bond pdb=" CA BLYS A 93 " pdb=" C BLYS A 93 " ideal model delta sigma weight residual 1.524 1.760 -0.236 1.27e-02 6.20e+03 3.45e+02 bond pdb=" N PRO A 184 " pdb=" CA PRO A 184 " ideal model delta sigma weight residual 1.470 1.246 0.224 1.22e-02 6.72e+03 3.36e+02 bond pdb=" ND1 HIS A 126 " pdb=" CE1 HIS A 126 " ideal model delta sigma weight residual 1.321 1.140 0.181 1.00e-02 1.00e+04 3.27e+02 bond pdb=" C VAL A 146 " pdb=" O VAL A 146 " ideal model delta sigma weight residual 1.236 1.411 -0.175 9.90e-03 1.02e+04 3.12e+02 bond pdb=" C GLU A 143 " pdb=" N ASN A 144 " ideal model delta sigma weight residual 1.331 1.557 -0.226 1.31e-02 5.83e+03 2.97e+02 ... (remaining 3148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.15: 3445 5.15 - 10.29: 1760 10.29 - 15.44: 505 15.44 - 20.58: 60 20.58 - 25.73: 7 Bond angle restraints: 5777 Sorted by residual: angle pdb=" CA GLU A 143 " pdb=" C GLU A 143 " pdb=" O GLU A 143 " ideal model delta sigma weight residual 119.32 137.03 -17.71 1.19e+00 7.06e-01 2.21e+02 angle pdb=" O VAL A 25 " pdb=" C VAL A 25 " pdb=" N MET A 26 " ideal model delta sigma weight residual 121.91 107.67 14.24 9.80e-01 1.04e+00 2.11e+02 angle pdb=" O VAL A 51 " pdb=" C VAL A 51 " pdb=" N ILE A 52 " ideal model delta sigma weight residual 123.20 137.97 -14.77 1.06e+00 8.90e-01 1.94e+02 angle pdb=" OD1 ASN A 81 " pdb=" CG ASN A 81 " pdb=" ND2 ASN A 81 " ideal model delta sigma weight residual 122.60 109.16 13.44 1.00e+00 1.00e+00 1.81e+02 angle pdb=" C BCYS A 53 " pdb=" N PRO A 54 " pdb=" CA PRO A 54 " ideal model delta sigma weight residual 119.85 133.37 -13.52 1.01e+00 9.80e-01 1.79e+02 ... (remaining 5772 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 1308 17.88 - 35.76: 128 35.76 - 53.64: 33 53.64 - 71.53: 11 71.53 - 89.41: 1 Dihedral angle restraints: 1481 sinusoidal: 852 harmonic: 629 Sorted by residual: dihedral pdb=" C THR A 110 " pdb=" N THR A 110 " pdb=" CA THR A 110 " pdb=" CB THR A 110 " ideal model delta harmonic sigma weight residual -122.00 -139.44 17.44 0 2.50e+00 1.60e-01 4.86e+01 dihedral pdb=" C ILE A 105 " pdb=" N ILE A 105 " pdb=" CA ILE A 105 " pdb=" CB ILE A 105 " ideal model delta harmonic sigma weight residual -122.00 -139.24 17.24 0 2.50e+00 1.60e-01 4.76e+01 dihedral pdb=" N GLU A 116 " pdb=" C GLU A 116 " pdb=" CA GLU A 116 " pdb=" CB GLU A 116 " ideal model delta harmonic sigma weight residual 122.80 139.77 -16.97 0 2.50e+00 1.60e-01 4.61e+01 ... (remaining 1478 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.192: 98 0.192 - 0.383: 67 0.383 - 0.573: 45 0.573 - 0.764: 23 0.764 - 0.954: 10 Chirality restraints: 243 Sorted by residual: chirality pdb=" CA THR A 34 " pdb=" N THR A 34 " pdb=" C THR A 34 " pdb=" CB THR A 34 " both_signs ideal model delta sigma weight residual False 2.53 3.48 -0.95 2.00e-01 2.50e+01 2.28e+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 1.61 0.90 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 1.55 0.90 2.00e-01 2.50e+01 2.01e+01 ... (remaining 240 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 119 " 0.113 2.00e-02 2.50e+03 6.52e-02 1.28e+02 pdb=" CG PHE A 119 " -0.179 2.00e-02 2.50e+03 pdb=" CD1 PHE A 119 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 119 " 0.031 2.00e-02 2.50e+03 pdb=" CE1 PHE A 119 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 119 " 0.051 2.00e-02 2.50e+03 pdb=" CZ PHE A 119 " 0.020 2.00e-02 2.50e+03 pdb=" HD1 PHE A 119 " -0.020 2.00e-02 2.50e+03 pdb=" HD2 PHE A 119 " -0.018 2.00e-02 2.50e+03 pdb=" HE1 PHE A 119 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE A 119 " -0.035 2.00e-02 2.50e+03 pdb=" HZ PHE A 119 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 164 " -0.071 2.00e-02 2.50e+03 5.79e-02 1.01e+02 pdb=" CG PHE A 164 " 0.083 2.00e-02 2.50e+03 pdb=" CD1 PHE A 164 " -0.053 2.00e-02 2.50e+03 pdb=" CD2 PHE A 164 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 PHE A 164 " -0.035 2.00e-02 2.50e+03 pdb=" CE2 PHE A 164 " 0.121 2.00e-02 2.50e+03 pdb=" CZ PHE A 164 " -0.026 2.00e-02 2.50e+03 pdb=" HD1 PHE A 164 " 0.076 2.00e-02 2.50e+03 pdb=" HD2 PHE A 164 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 164 " -0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE A 164 " -0.033 2.00e-02 2.50e+03 pdb=" HZ PHE A 164 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 95 " -0.043 2.00e-02 2.50e+03 9.32e-02 8.69e+01 pdb=" C GLN A 95 " 0.161 2.00e-02 2.50e+03 pdb=" O GLN A 95 " -0.060 2.00e-02 2.50e+03 pdb=" N AGLU A 96 " -0.058 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 841 2.29 - 2.87: 7976 2.87 - 3.44: 10512 3.44 - 4.02: 15324 4.02 - 4.60: 21971 Nonbonded interactions: 56624 Sorted by model distance: nonbonded pdb=" HG SER A 155 " pdb=" H ARG A 156 " model vdw 1.712 2.100 nonbonded pdb=" H GLY A 157 " pdb=" HG1 THR A 160 " model vdw 1.765 2.100 nonbonded pdb=" H THR A 125 " pdb=" HH TYR A 141 " model vdw 1.795 2.100 nonbonded pdb=" H ALYS A 41 " pdb=" O HOH A 360 " model vdw 1.834 2.450 nonbonded pdb=" O GLU A 147 " pdb=" H ATHR A 154 " model vdw 1.855 2.450 ... (remaining 56619 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_9171019_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= 0.2789 r_free= 0.1834 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.399642 | | target function (ml) not normalized (work): 71463.390356 | | target function (ml) not normalized (free): 3256.752756 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.3192 0.2168 7.5314 5.0439| | 2: 3.63 - 2.88 1.00 2711 122 0.2646 0.1706 4.3307 4.3145| | 3: 2.88 - 2.52 1.00 2682 148 0.2559 0.1769 4.1858 4.1839| | 4: 2.52 - 2.29 1.00 2661 139 0.2565 0.1567 3.5005 3.5865| | 5: 2.29 - 2.13 1.00 2678 122 0.2618 0.1474 3.3768 3.4094| | 6: 2.13 - 2.00 1.00 2692 117 0.2777 0.1828 3.309 3.3736| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 17.55 0.77 0.23 1302.60| | 2: 3.63 - 2.88 2711 122 0.83 23.97 1.31 0.23 1302.60| | 3: 2.88 - 2.52 2682 148 0.73 32.81 1.29 0.23 1302.60| | 4: 2.52 - 2.29 2661 139 0.94 10.86 1.30 0.26 124.50| | 5: 2.29 - 2.13 2678 122 0.93 12.61 1.31 0.26 124.50| | 6: 2.13 - 2.00 2692 117 0.91 15.44 1.34 0.26 124.50| |alpha: min = 0.23 max = 0.26 mean = 0.25| |beta: min = 124.50 max = 1302.60 mean = 720.11| |figures of merit: min = 0.00 max = 1.00 mean = 0.87| |phase err.(work): min = 0.00 max = 89.90 mean = 18.88| |phase err.(test): min = 0.00 max = 88.93 mean = 19.19| |-----------------------------------------------------------------------------| ----------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 : 0.079 0.236 1557 Z= 5.337 Angle : 5.264 22.096 2118 Z= 3.767 Chirality : 0.373 0.954 243 Planarity : 0.033 0.166 284 Dihedral : 13.785 89.406 611 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.54 % Allowed : 3.78 % Favored : 95.68 % Rotamer: Outliers : 0.62 % Allowed : 3.73 % Favored : 95.65 % Cbeta Deviations : 26.49 % 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 (0.49), residues: 224 helix: -2.67 (0.40), residues: 102 sheet: -0.50 (0.82), residues: 38 loop : -0.62 (0.60), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.100 0.023 ARG A 28 TYR 0.090 0.032 TYR A 141 PHE 0.185 0.046 PHE A 119 HIS 0.090 0.040 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= 0.2789 r_free= 0.1834 coordinate error (max.-lik. estimate): 0.00 A | | | | normalized target function (ml) (work): 4.399642 | | target function (ml) not normalized (work): 71463.390356 | | target function (ml) not normalized (free): 3256.752756 | |-----------------------------------------------------------------------------| Tidying ADP resulted in r_work increase by 1.3033 percent. r_work = 0.2920 r_free = 0.2009 =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2866 0.2920 0.2009 n_refl.: 17050 re-set all scales: r(all,work,free)=0.2866 0.2920 0.2009 n_refl.: 17050 remove outliers: r(all,work,free)=0.2159 0.2170 0.2009 n_refl.: 17045 overall B=-0.41 to atoms: r(all,work,free)=0.2132 0.2143 0.1991 n_refl.: 17045 bulk-solvent and scaling: r(all,work,free)=0.1624 0.1621 0.1683 n_refl.: 17045 remove outliers: r(all,work,free)=0.1623 0.1620 0.1683 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 0.4152 394.961 360.634 0.651 1.018 0.399 11.894-9.307 99.02 97 4 0.1839 633.924 616.359 0.924 1.018 0.375 9.237-7.194 100.00 213 7 0.2175 518.486 511.673 0.951 1.017 0.345 7.162-5.571 100.00 427 22 0.2313 389.124 376.274 0.911 1.015 0.284 5.546-4.326 100.00 867 58 0.1400 534.205 528.338 0.962 1.012 0.215 4.315-3.360 100.00 1859 96 0.1331 508.034 503.426 1.011 1.008 0.134 3.356-2.611 100.00 3867 181 0.1641 333.750 329.311 1.016 0.999 0.039 2.608-2.000 99.99 8818 434 0.1655 217.547 213.702 1.035 0.985 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4645 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ================================== NQH flips ================================== r_work=0.1620 r_free=0.1683 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 144 ASN A 173 ASN A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1627 r_free=0.1705 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 22.730484 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.857251 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 0.1353 0.1657 0.0304 0.008 1.0 1.0 0.5 0.0 0 11.365 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 13.53 16.57 3.04 3.013 18.449 0.857 0.023 12.79 16.75 3.97 3.657 18.726 0.857 0.020 Individual atomic B min max mean iso aniso Overall: 6.36 113.89 20.00 4.12 1785 0 Protein: 6.36 112.87 17.22 4.12 1519 0 Water: 8.57 113.89 36.20 N/A 258 0 Other: 21.13 37.57 26.40 N/A 8 0 Chain A: 6.36 113.89 20.00 N/A 1785 0 Histogram: Values Number of atoms 6.36 - 17.12 1091 17.12 - 27.87 335 27.87 - 38.62 183 38.62 - 49.37 99 49.37 - 60.13 50 60.13 - 70.88 13 70.88 - 81.63 6 81.63 - 92.38 4 92.38 - 103.14 1 103.14 - 113.89 3 =========================== Idealize ADP of riding H ========================== r_work=0.1279 r_free=0.1675 r_work=0.1282 r_free=0.1683 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1282 r_free = 0.1683 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1276 r_free = 0.1679 target_work(ls_wunit_k1) = 0.020 | | occupancies: max = 1.00 min = 0.26 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= 0.1276 r_free= 0.1679 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.020013 | | target function (ls_wunit_k1) not normalized (work): 324.950842 | | target function (ls_wunit_k1) not normalized (free): 27.900955 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1296 0.1276 0.1679 n_refl.: 17044 re-set all scales: r(all,work,free)=0.1910 0.1908 0.2007 n_refl.: 17044 remove outliers: r(all,work,free)=0.1910 0.1908 0.2007 n_refl.: 17044 overall B=-0.39 to atoms: r(all,work,free)=0.1881 0.1879 0.1991 n_refl.: 17044 bulk-solvent and scaling: r(all,work,free)=0.1297 0.1278 0.1673 n_refl.: 17044 remove outliers: r(all,work,free)=0.1295 0.1276 0.1673 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 0.3543 303.592 280.816 0.625 1.009 0.368 11.894-9.307 99.02 97 4 0.1698 488.279 478.251 0.918 1.009 0.367 9.237-7.194 100.00 213 7 0.1815 399.363 397.086 0.959 1.009 0.341 7.162-5.571 100.00 427 22 0.1821 299.723 295.151 0.931 1.008 0.291 5.546-4.326 100.00 867 58 0.1022 411.471 409.478 0.960 1.007 0.200 4.315-3.360 100.00 1859 96 0.0917 391.313 391.001 1.016 1.004 0.134 3.356-2.611 100.00 3867 181 0.1306 257.070 255.752 1.018 0.999 0.091 2.608-2.000 99.99 8818 434 0.1362 167.566 166.025 1.024 0.991 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9551 b_overall=-1.3999 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1276 r_free=0.1673 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A A 144 ASN A 173 ASN A 180 GLN Total number of N/Q/H flips: 4 r_work=0.1283 r_free=0.1680 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1283 r_free=0.1680 | n_water=258 | time (s): 0.610 (total time: 0.610) Filter (dist) r_work=0.1293 r_free=0.1670 | n_water=253 | time (s): 19.130 (total time: 19.740) Filter (q & B) r_work=0.1293 r_free=0.1670 | n_water=251 | time (s): 1.580 (total time: 21.320) Compute maps r_work=0.1293 r_free=0.1670 | n_water=251 | time (s): 0.680 (total time: 22.000) Filter (map) r_work=0.1327 r_free=0.1663 | n_water=211 | time (s): 2.200 (total time: 24.200) Find peaks r_work=0.1327 r_free=0.1663 | n_water=211 | time (s): 0.560 (total time: 24.760) Add new water r_work=0.1534 r_free=0.1887 | n_water=368 | time (s): 1.660 (total time: 26.420) Refine new water occ: r_work=0.1333 r_free=0.1614 adp: r_work=0.1276 r_free=0.1609 occ: r_work=0.1282 r_free=0.1580 adp: r_work=0.1250 r_free=0.1586 occ: r_work=0.1253 r_free=0.1578 adp: r_work=0.1240 r_free=0.1577 ADP+occupancy (water only), MIN, final r_work=0.1240 r_free=0.1577 r_work=0.1240 r_free=0.1577 | n_water=368 | time (s): 14.480 (total time: 40.900) Filter (q & B) r_work=0.1243 r_free=0.1592 | n_water=359 | time (s): 1.710 (total time: 42.610) Filter (dist only) r_work=0.1243 r_free=0.1592 | n_water=359 | time (s): 24.270 (total time: 66.880) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 24.253524 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.984819 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 0.1213 0.1609 0.0396 0.008 0.9 2.2 0.5 0.0 0 12.127 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 12.13 16.09 3.96 4.193 21.058 0.985 0.018 11.95 16.27 4.32 4.270 21.321 0.985 0.018 Individual atomic B min max mean iso aniso Overall: 6.69 107.48 21.35 4.35 1886 0 Protein: 6.69 107.48 17.74 4.34 1519 0 Water: 8.41 66.21 36.33 N/A 359 0 Other: 25.10 44.21 34.44 N/A 8 0 Chain A: 6.69 107.48 19.46 N/A 1738 0 Chain S: 18.89 66.21 43.53 N/A 148 0 Histogram: Values Number of atoms 6.69 - 16.77 1026 16.77 - 26.84 372 26.84 - 36.92 229 36.92 - 47.00 152 47.00 - 57.08 66 57.08 - 67.16 30 67.16 - 77.24 3 77.24 - 87.32 5 87.32 - 97.40 1 97.40 - 107.48 2 =========================== Idealize ADP of riding H ========================== r_work=0.1195 r_free=0.1627 r_work=0.1196 r_free=0.1628 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1196 r_free = 0.1628 target_work(ls_wunit_k1) = 0.018 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1192 r_free = 0.1624 target_work(ls_wunit_k1) = 0.017 | | occupancies: max = 1.00 min = 0.19 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= 0.1192 r_free= 0.1624 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ls_wunit_k1) (work): 0.016987 | | target function (ls_wunit_k1) not normalized (work): 275.785262 | | target function (ls_wunit_k1) not normalized (free): 25.934466 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1212 0.1192 0.1624 n_refl.: 17042 re-set all scales: r(all,work,free)=0.1751 0.1743 0.1943 n_refl.: 17042 remove outliers: r(all,work,free)=0.1751 0.1743 0.1943 n_refl.: 17042 overall B=-0.39 to atoms: r(all,work,free)=0.1726 0.1717 0.1925 n_refl.: 17042 bulk-solvent and scaling: r(all,work,free)=0.1205 0.1185 0.1609 n_refl.: 17042 remove outliers: r(all,work,free)=0.1204 0.1183 0.1609 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 0.3258 300.428 284.801 0.600 1.003 0.350 11.894-9.307 99.02 97 4 0.1491 488.279 484.895 0.915 1.003 0.337 9.237-7.194 100.00 213 7 0.1642 399.363 400.697 0.976 1.003 0.310 7.162-5.571 100.00 427 22 0.1550 299.723 295.555 0.939 1.003 0.271 5.546-4.326 100.00 867 58 0.0859 411.471 408.249 0.962 1.003 0.205 4.315-3.360 100.00 1859 96 0.0821 391.313 390.082 1.016 1.002 0.191 3.356-2.611 100.00 3867 181 0.1189 257.070 256.097 1.014 1.001 0.121 2.608-2.000 99.99 8818 434 0.1332 167.566 166.986 1.017 0.999 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.4090 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1183 r_free=0.1609 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1183 r_free=0.1609 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1183 r_free=0.1609 | n_water=359 | time (s): 0.710 (total time: 0.710) Filter (dist) r_work=0.1183 r_free=0.1611 | n_water=357 | time (s): 27.990 (total time: 28.700) Filter (q & B) r_work=0.1183 r_free=0.1613 | n_water=356 | time (s): 1.470 (total time: 30.170) Compute maps r_work=0.1183 r_free=0.1613 | n_water=356 | time (s): 0.560 (total time: 30.730) Filter (map) r_work=0.1243 r_free=0.1645 | n_water=269 | time (s): 1.740 (total time: 32.470) Find peaks r_work=0.1243 r_free=0.1645 | n_water=269 | time (s): 0.650 (total time: 33.120) Add new water r_work=0.1433 r_free=0.1821 | n_water=415 | time (s): 1.920 (total time: 35.040) Refine new water occ: r_work=0.1249 r_free=0.1621 adp: r_work=0.1242 r_free=0.1616 occ: r_work=0.1224 r_free=0.1591 adp: r_work=0.1213 r_free=0.1588 occ: r_work=0.1206 r_free=0.1572 adp: r_work=0.1196 r_free=0.1565 ADP+occupancy (water only), MIN, final r_work=0.1196 r_free=0.1565 r_work=0.1196 r_free=0.1565 | n_water=415 | time (s): 30.090 (total time: 65.130) Filter (q & B) r_work=0.1200 r_free=0.1566 | n_water=406 | time (s): 1.520 (total time: 66.650) Filter (dist only) r_work=0.1200 r_free=0.1566 | n_water=406 | time (s): 29.900 (total time: 96.550) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.942597 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.145431 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 0.1170 0.1571 0.0401 0.009 1.0 4.2 0.5 0.0 0 0.971 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.70 15.71 4.01 4.380 21.532 0.145 4.998 11.51 15.82 4.32 4.893 21.467 0.145 4.978 Individual atomic B min max mean iso aniso Overall: 6.50 104.41 20.92 4.64 1933 0 Protein: 6.50 104.41 17.01 4.63 1519 0 Water: 8.73 62.52 35.28 N/A 406 0 Other: 26.96 45.96 35.07 N/A 8 0 Chain A: 6.50 104.41 18.76 N/A 1734 0 Chain S: 14.57 62.52 39.80 N/A 199 0 Histogram: Values Number of atoms 6.50 - 16.29 1069 16.29 - 26.08 346 26.08 - 35.87 221 35.87 - 45.66 179 45.66 - 55.45 72 55.45 - 65.25 33 65.25 - 75.04 4 75.04 - 84.83 4 84.83 - 94.62 3 94.62 - 104.41 2 =========================== Idealize ADP of riding H ========================== r_work=0.1151 r_free=0.1582 r_work=0.1151 r_free=0.1583 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1151 r_free = 0.1583 target_work(ml) = 4.978 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1142 r_free = 0.1578 target_work(ml) = 4.972 | | occupancies: max = 1.00 min = 0.20 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= 0.1142 r_free= 0.1578 coordinate error (max.-lik. estimate): 0.09 A | | | | normalized target function (ml) (work): 4.971705 | | target function (ml) not normalized (work): 80710.662097 | | target function (ml) not normalized (free): 4197.664773 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1163 0.1142 0.1578 n_refl.: 17041 re-set all scales: r(all,work,free)=0.1671 0.1663 0.1885 n_refl.: 17041 remove outliers: r(all,work,free)=0.1671 0.1663 0.1885 n_refl.: 17041 overall B=-0.38 to atoms: r(all,work,free)=0.1645 0.1636 0.1876 n_refl.: 17041 bulk-solvent and scaling: r(all,work,free)=0.1160 0.1139 0.1578 n_refl.: 17041 remove outliers: r(all,work,free)=0.1159 0.1138 0.1578 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 0.3495 296.861 277.552 0.568 1.008 0.350 11.894-9.307 99.02 97 4 0.1738 488.279 480.599 0.906 1.008 0.342 9.237-7.194 100.00 213 7 0.1797 399.363 399.037 0.980 1.008 0.290 7.162-5.571 100.00 427 22 0.1643 299.723 294.508 0.941 1.007 0.221 5.546-4.326 100.00 867 58 0.0947 411.471 407.885 0.965 1.006 0.211 4.315-3.360 100.00 1859 96 0.0874 391.313 389.461 1.010 1.004 0.201 3.356-2.611 100.00 3867 181 0.1278 257.070 254.751 1.011 1.001 0.152 2.608-2.000 99.99 8818 434 0.1078 167.566 166.129 1.019 0.995 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9550 b_overall=-1.3568 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1138 r_free=0.1578 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1138 r_free=0.1578 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1138 r_free=0.1578 | n_water=406 | time (s): 0.830 (total time: 0.830) Filter (dist) r_work=0.1138 r_free=0.1578 | n_water=406 | time (s): 29.870 (total time: 30.700) Filter (q & B) r_work=0.1138 r_free=0.1578 | n_water=406 | time (s): 0.800 (total time: 31.500) Compute maps r_work=0.1138 r_free=0.1578 | n_water=406 | time (s): 0.590 (total time: 32.090) Filter (map) r_work=0.1193 r_free=0.1604 | n_water=309 | time (s): 1.690 (total time: 33.780) Find peaks r_work=0.1193 r_free=0.1604 | n_water=309 | time (s): 0.420 (total time: 34.200) Add new water r_work=0.1348 r_free=0.1744 | n_water=441 | time (s): 1.450 (total time: 35.650) Refine new water occ: r_work=0.1188 r_free=0.1580 adp: r_work=0.1181 r_free=0.1581 occ: r_work=0.1162 r_free=0.1549 adp: r_work=0.1152 r_free=0.1549 occ: r_work=0.1145 r_free=0.1531 adp: r_work=0.1135 r_free=0.1530 ADP+occupancy (water only), MIN, final r_work=0.1135 r_free=0.1530 r_work=0.1135 r_free=0.1530 | n_water=441 | time (s): 35.870 (total time: 71.520) Filter (q & B) r_work=0.1138 r_free=0.1542 | n_water=434 | time (s): 1.810 (total time: 73.330) Filter (dist only) r_work=0.1138 r_free=0.1542 | n_water=434 | time (s): 35.050 (total time: 108.380) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 2.070130 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.164151 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 0.1583 0.0463 0.010 1.0 4.2 0.5 0.0 0 1.035 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.20 15.83 4.63 4.469 21.091 0.164 4.967 11.13 15.81 4.68 4.677 21.050 0.164 4.961 Individual atomic B min max mean iso aniso Overall: 5.69 101.73 20.85 4.77 1961 0 Protein: 5.69 101.73 16.51 4.76 1519 0 Water: 8.44 64.27 35.79 N/A 434 0 Other: 25.14 44.72 32.93 N/A 8 0 Chain A: 5.69 101.73 18.21 N/A 1734 0 Chain S: 16.36 64.27 41.01 N/A 227 0 Histogram: Values Number of atoms 5.69 - 15.30 1019 15.30 - 24.90 379 24.90 - 34.51 218 34.51 - 44.11 203 44.11 - 53.71 88 53.71 - 63.32 39 63.32 - 72.92 5 72.92 - 82.53 5 82.53 - 92.13 3 92.13 - 101.73 2 =========================== Idealize ADP of riding H ========================== r_work=0.1113 r_free=0.1581 r_work=0.1113 r_free=0.1581 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1113 r_free = 0.1581 target_work(ml) = 4.961 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1107 r_free = 0.1579 target_work(ml) = 4.957 | | occupancies: max = 1.00 min = 0.15 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= 0.1107 r_free= 0.1579 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.956819 | | target function (ml) not normalized (work): 80464.038003 | | target function (ml) not normalized (free): 4194.756581 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1130 0.1107 0.1579 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1609 0.1598 0.1866 n_refl.: 17040 remove outliers: r(all,work,free)=0.1609 0.1598 0.1866 n_refl.: 17040 overall B=-0.30 to atoms: r(all,work,free)=0.1590 0.1578 0.1856 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1128 0.1106 0.1577 n_refl.: 17040 remove outliers: r(all,work,free)=0.1128 0.1106 0.1577 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 0.3590 296.861 275.347 0.558 1.004 0.340 11.894-9.307 99.02 97 4 0.1709 488.279 480.745 0.919 1.004 0.340 9.237-7.194 100.00 213 7 0.1728 399.363 400.643 0.985 1.004 0.260 7.162-5.571 100.00 427 22 0.1563 299.723 294.450 0.947 1.004 0.215 5.546-4.326 100.00 867 58 0.0920 411.471 407.599 0.966 1.003 0.200 4.315-3.360 100.00 1859 96 0.0847 391.313 389.162 1.006 1.002 0.191 3.356-2.611 100.00 3867 181 0.1249 257.070 254.673 1.004 1.001 0.161 2.608-2.000 99.99 8818 434 0.1044 167.566 166.324 1.003 0.998 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-1.0289 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1106 r_free=0.1577 After: r_work=0.1108 r_free=0.1575 ================================== NQH flips ================================== r_work=0.1108 r_free=0.1575 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1108 r_free=0.1575 ================== Update (add/remove/refine) ordered solvent ================= Start r_work=0.1108 r_free=0.1575 | n_water=434 | time (s): 0.780 (total time: 0.780) Filter (dist) r_work=0.1108 r_free=0.1575 | n_water=434 | time (s): 34.970 (total time: 35.750) Filter (q & B) r_work=0.1108 r_free=0.1575 | n_water=433 | time (s): 1.960 (total time: 37.710) Compute maps r_work=0.1108 r_free=0.1575 | n_water=433 | time (s): 0.580 (total time: 38.290) Filter (map) r_work=0.1176 r_free=0.1567 | n_water=330 | time (s): 1.820 (total time: 40.110) Find peaks r_work=0.1176 r_free=0.1567 | n_water=330 | time (s): 0.470 (total time: 40.580) Add new water r_work=0.1327 r_free=0.1717 | n_water=472 | time (s): 1.670 (total time: 42.250) Refine new water occ: r_work=0.1161 r_free=0.1554 adp: r_work=0.1152 r_free=0.1556 occ: r_work=0.1133 r_free=0.1527 adp: r_work=0.1123 r_free=0.1532 occ: r_work=0.1114 r_free=0.1509 adp: r_work=0.1105 r_free=0.1512 ADP+occupancy (water only), MIN, final r_work=0.1105 r_free=0.1512 r_work=0.1105 r_free=0.1512 | n_water=472 | time (s): 31.810 (total time: 74.060) Filter (q & B) r_work=0.1111 r_free=0.1518 | n_water=458 | time (s): 1.800 (total time: 75.860) Filter (dist only) r_work=0.1111 r_free=0.1518 | n_water=458 | time (s): 35.960 (total time: 111.820) ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 1.946155 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.150371 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.0000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1126 0.1527 0.0401 0.009 1.0 3.8 0.5 0.0 0 0.973 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 11.26 15.27 4.01 4.492 20.825 0.150 4.948 11.15 15.20 4.05 4.558 20.859 0.150 4.941 Individual atomic B min max mean iso aniso Overall: 5.33 100.05 20.95 4.84 1985 0 Protein: 5.33 100.05 16.19 4.83 1519 0 Water: 7.85 67.94 36.51 N/A 458 0 Other: 25.32 43.96 32.26 N/A 8 0 Chain A: 5.33 100.05 17.87 N/A 1734 0 Chain S: 18.29 67.94 42.22 N/A 251 0 Histogram: Values Number of atoms 5.33 - 14.80 1003 14.80 - 24.27 389 24.27 - 33.74 209 33.74 - 43.22 203 43.22 - 52.69 114 52.69 - 62.16 47 62.16 - 71.63 11 71.63 - 81.11 2 81.11 - 90.58 3 90.58 - 100.05 4 =========================== Idealize ADP of riding H ========================== r_work=0.1115 r_free=0.1520 r_work=0.1115 r_free=0.1520 ============================= Occupancy refinement ============================ |-occupancy refinement: start-------------------------------------------------| | r_work = 0.1115 r_free = 0.1520 target_work(ml) = 4.941 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.1109 r_free = 0.1516 target_work(ml) = 4.938 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| ----------X-ray data---------- |--(resolution: 2.00 - 32.57 A, n_refl.=17040 (all), 4.74 % free)------------| | | | r_work= 0.1109 r_free= 0.1516 coordinate error (max.-lik. estimate): 0.11 A | | | | normalized target function (ml) (work): 4.937811 | | target function (ml) not normalized (work): 80155.490839 | | target function (ml) not normalized (free): 4164.542745 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1113 0.1416 5.4605 5.6658| | 2: 3.63 - 2.88 1.00 2711 122 0.1102 0.1427 5.2247 5.3179| | 3: 2.88 - 2.52 1.00 2681 148 0.1370 0.1762 5.1325 5.2245| | 4: 2.52 - 2.29 1.00 2661 139 0.0930 0.1495 4.626 4.9571| | 5: 2.29 - 2.13 1.00 2678 122 0.0967 0.1415 4.5838 4.8473| | 6: 2.13 - 2.00 1.00 2692 117 0.1112 0.1807 4.5698 4.7971| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 8.92 1.00 0.96 6340.55| | 2: 3.63 - 2.88 2711 122 0.92 12.74 1.01 0.96 6340.55| | 3: 2.88 - 2.52 2681 148 0.88 18.94 0.99 0.96 6340.55| | 4: 2.52 - 2.29 2661 139 0.93 12.18 1.01 0.97 2135.70| | 5: 2.29 - 2.13 2678 122 0.91 14.23 1.00 0.97 2135.70| | 6: 2.13 - 2.00 2692 117 0.89 16.95 0.99 0.97 2135.70| |alpha: min = 0.96 max = 0.97 mean = 0.96| |beta: min = 2135.70 max = 6340.55 mean = 4260.28| |figures of merit: min = 0.00 max = 1.00 mean = 0.91| |phase err.(work): min = 0.00 max = 90.00 mean = 13.95| |phase err.(test): min = 0.00 max = 88.83 mean = 13.66| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1129 0.1109 0.1516 n_refl.: 17040 re-set all scales: r(all,work,free)=0.1572 0.1561 0.1810 n_refl.: 17040 remove outliers: r(all,work,free)=0.1572 0.1561 0.1810 n_refl.: 17040 overall B=-0.23 to atoms: r(all,work,free)=0.1558 0.1547 0.1801 n_refl.: 17040 bulk-solvent and scaling: r(all,work,free)=0.1128 0.1109 0.1513 n_refl.: 17040 remove outliers: r(all,work,free)=0.1128 0.1109 0.1513 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 0.3609 296.861 275.903 0.545 1.005 0.324 11.894-9.307 99.02 97 4 0.1678 488.279 484.312 0.924 1.005 0.320 9.237-7.194 100.00 213 7 0.1738 399.363 399.766 0.986 1.005 0.240 7.162-5.571 100.00 427 22 0.1569 299.723 295.263 0.938 1.005 0.210 5.546-4.326 100.00 867 58 0.0921 411.471 407.569 0.966 1.004 0.187 4.315-3.360 100.00 1859 96 0.0875 391.313 389.090 1.004 1.003 0.174 3.356-2.611 100.00 3867 181 0.1255 257.070 254.563 0.999 1.000 0.131 2.608-2.000 99.99 8818 434 0.1034 167.566 166.225 0.994 0.996 0.000 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9581 b_overall=-0.8117 ================= 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 : 0.2789 0.1834 0.079 5.264 8.8 119.3 19.9 258 0.000 1_bss: 0.1620 0.1683 0.079 5.264 8.4 118.9 19.5 258 0.000 1_settarget: 0.1620 0.1683 0.079 5.264 8.4 118.9 19.5 258 0.000 1_nqh: 0.1627 0.1705 0.079 5.264 8.4 118.9 19.5 258 0.013 1_weight: 0.1627 0.1705 0.079 5.264 8.4 118.9 19.5 258 0.013 1_xyzrec: 0.1353 0.1657 0.008 0.960 8.4 118.9 19.5 258 0.165 1_adp: 0.1279 0.1675 0.008 0.960 6.4 113.9 20.0 258 0.165 1_regHadp: 0.1282 0.1683 0.008 0.960 6.4 113.9 20.0 258 0.165 1_occ: 0.1276 0.1679 0.008 0.960 6.4 113.9 20.0 258 0.165 2_bss: 0.1276 0.1673 0.008 0.960 6.0 113.5 19.6 258 0.165 2_settarget: 0.1276 0.1673 0.008 0.960 6.0 113.5 19.6 258 0.165 2_updatecdl: 0.1276 0.1673 0.009 0.988 6.0 113.5 19.6 258 0.165 2_nqh: 0.1283 0.1680 0.009 0.988 6.0 113.5 19.6 258 0.153 2_sol: 0.1243 0.1592 0.009 0.988 6.0 112.5 20.9 359 n/a 2_weight: 0.1243 0.1592 0.009 0.988 6.0 112.5 20.9 359 n/a 2_xyzrec: 0.1213 0.1609 0.008 0.924 6.0 112.5 20.9 359 n/a 2_adp: 0.1195 0.1627 0.008 0.924 6.7 107.5 21.3 359 n/a 2_regHadp: 0.1196 0.1628 0.008 0.924 6.7 107.5 21.3 359 n/a 2_occ: 0.1192 0.1624 0.008 0.924 6.7 107.5 21.3 359 n/a 3_bss: 0.1183 0.1609 0.008 0.924 6.3 107.1 21.0 359 n/a 3_settarget: 0.1183 0.1609 0.008 0.924 6.3 107.1 21.0 359 n/a 3_updatecdl: 0.1183 0.1609 0.008 0.921 6.3 107.1 21.0 359 n/a 3_nqh: 0.1183 0.1609 0.008 0.921 6.3 107.1 21.0 359 n/a 3_sol: 0.1200 0.1566 0.008 0.921 6.3 107.1 21.0 406 n/a 3_weight: 0.1200 0.1566 0.008 0.921 6.3 107.1 21.0 406 n/a 3_xyzrec: 0.1170 0.1571 0.009 0.974 6.3 107.1 21.0 406 n/a 3_adp: 0.1151 0.1582 0.009 0.974 6.5 104.4 20.9 406 n/a 3_regHadp: 0.1151 0.1583 0.009 0.974 6.5 104.4 20.9 406 n/a 3_occ: 0.1142 0.1578 0.009 0.974 6.5 104.4 20.9 406 n/a 4_bss: 0.1138 0.1578 0.009 0.974 6.1 104.0 20.5 406 n/a 4_settarget: 0.1138 0.1578 0.009 0.974 6.1 104.0 20.5 406 n/a 4_updatecdl: 0.1138 0.1578 0.009 0.975 6.1 104.0 20.5 406 n/a 4_nqh: 0.1138 0.1578 0.009 0.975 6.1 104.0 20.5 406 n/a 4_sol: 0.1138 0.1542 0.009 0.975 6.1 104.0 20.9 434 n/a 4_weight: 0.1138 0.1542 0.009 0.975 6.1 104.0 20.9 434 n/a 4_xyzrec: 0.1120 0.1583 0.010 0.993 6.1 104.0 20.9 434 n/a 4_adp: 0.1113 0.1581 0.010 0.993 5.7 101.7 20.8 434 n/a 4_regHadp: 0.1113 0.1581 0.010 0.993 5.7 101.7 20.8 434 n/a 4_occ: 0.1107 0.1579 0.010 0.993 5.7 101.7 20.8 434 n/a 5_bss: 0.1106 0.1577 0.010 0.993 5.4 101.4 20.5 434 n/a 5_settarget: 0.1106 0.1577 0.010 0.993 5.4 101.4 20.5 434 n/a 5_updatecdl: 0.1106 0.1577 0.010 0.994 5.4 101.4 20.5 434 n/a 5_setrh: 0.1108 0.1575 0.010 0.994 5.4 101.4 20.5 434 n/a 5_nqh: 0.1108 0.1575 0.010 0.994 5.4 101.4 20.5 434 n/a 5_sol: 0.1111 0.1518 0.010 0.994 5.4 101.4 20.9 458 n/a 5_weight: 0.1111 0.1518 0.010 0.994 5.4 101.4 20.9 458 n/a 5_xyzrec: 0.1126 0.1527 0.009 1.019 5.4 101.4 20.9 458 n/a 5_adp: 0.1115 0.1520 0.009 1.019 5.3 100.1 20.9 458 n/a 5_regHadp: 0.1115 0.1520 0.009 1.019 5.3 100.1 20.9 458 n/a 5_occ: 0.1109 0.1516 0.009 1.019 5.3 100.1 20.9 458 n/a end: 0.1109 0.1513 0.009 1.019 5.1 99.8 20.7 458 n/a ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_9171019_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/5SY6/restrained_cut2/shake_9171019_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 3.0700 Refinement macro-cycles (run) : 914.2500 Write final files (write_after_run_outputs) : 20.6500 Total : 937.9700 Total CPU time: 16.02 minutes =========================== phenix.refine: finished =========================== # Date 2024-12-29 Time 09:41:02 PST -0800 (1735494062.65 s) Start R-work = 0.1620, R-free = 0.1683 Final R-work = 0.1109, R-free = 0.1513 =============================================================================== Job complete usr+sys time: 984.00 seconds wall clock time: 16 minutes 47.21 seconds (1007.21 seconds total)