Starting phenix.refine on Mon May 20 17:15:26 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u87.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u87/1u87.mtz Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- optimize_xyz=true optimize_adp=true main.number_of_mac=3 main.max_number_of_iterations=100 main.nproc=20 nonbonded_weight=100 modify_start_model.modify.selection=element H modify_start_model.modify.occupancies.set=1 strategy=individual_sites+individual_adp+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u87.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u87.pdb" miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u87/1u87.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u87/1u87.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 } main { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 3506 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3471 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 197} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'GSH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.78, per 1000 atoms: 0.22 Number of scatterers: 3506 At special positions: 0 Unit cell: (123.05, 123.05, 72.51, 90, 90, 120) Space group: P 63 2 2 (No. 182) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 316 8.00 N 282 7.00 C 1138 6.00 H 1756 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 - 3.50 Amino acid : False - 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: 0.71 Conformation dependent library (CDL) restraints added in 132.6 milliseconds 414 Ramachandran restraints generated. 207 Oldfield, 0 Emsley, 207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 8 helices and 1 sheets defined 56.0% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 15 through 24 Processing helix chain 'A' and resid 38 through 47 removed outlier: 4.093A pdb=" N ARG A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE A 46 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU A 47 " --> pdb=" O ASN A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 79 removed outlier: 4.265A pdb=" N HIS A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 110 removed outlier: 3.880A pdb=" N ILE A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 139 removed outlier: 4.783A pdb=" N VAL A 120 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) Proline residue: A 127 - end of helix removed outlier: 3.990A pdb=" N MET A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 133 " --> pdb=" O MET A 129 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N HIS A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 165 removed outlier: 4.289A pdb=" N TYR A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N MET A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.716A pdb=" N LYS A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 33 removed outlier: 3.849A pdb=" N TYR A 33 " --> pdb=" O PHE A 7 " (cutoff:3.500A) 73 hydrogen bonds defined for protein. 213 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.86 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 1751 1.15 - 1.33: 431 1.33 - 1.50: 638 1.50 - 1.68: 707 1.68 - 1.85: 23 Bond restraints: 3550 Sorted by residual: bond pdb=" N3 GSH A 500 " pdb=" HN3 GSH A 500 " ideal model delta sigma weight residual 0.860 1.020 -0.160 1.00e-02 1.00e+04 2.57e+02 bond pdb=" N2 GSH A 500 " pdb=" HN2 GSH A 500 " ideal model delta sigma weight residual 0.860 1.020 -0.160 1.10e-02 8.26e+03 2.12e+02 bond pdb=" CA2 GSH A 500 " pdb=" HA2 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.45e+02 bond pdb=" CB2 GSH A 500 " pdb="HB23 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.45e+02 bond pdb=" CA1 GSH A 500 " pdb=" HA1 GSH A 500 " ideal model delta sigma weight residual 0.970 1.090 -0.120 1.00e-02 1.00e+04 1.44e+02 ... (remaining 3545 not shown) Histogram of bond angle deviations from ideal: 99.31 - 107.06: 254 107.06 - 114.81: 4243 114.81 - 122.56: 1410 122.56 - 130.32: 522 130.32 - 138.07: 15 Bond angle restraints: 6444 Sorted by residual: angle pdb=" N TYR A 164 " pdb=" CA TYR A 164 " pdb=" C TYR A 164 " ideal model delta sigma weight residual 114.31 102.34 11.97 1.29e+00 6.01e-01 8.61e+01 angle pdb="HN11 GSH A 500 " pdb=" N1 GSH A 500 " pdb="HN12 GSH A 500 " ideal model delta sigma weight residual 111.04 138.07 -27.03 3.00e+00 1.11e-01 8.12e+01 angle pdb=" N ASP A 62 " pdb=" CA ASP A 62 " pdb=" C ASP A 62 " ideal model delta sigma weight residual 114.04 103.69 10.35 1.24e+00 6.50e-01 6.97e+01 angle pdb=" CA2 GSH A 500 " pdb=" C2 GSH A 500 " pdb=" O2 GSH A 500 " ideal model delta sigma weight residual 120.61 109.21 11.40 1.39e+00 5.18e-01 6.72e+01 angle pdb=" N GLY A 61 " pdb=" CA GLY A 61 " pdb=" C GLY A 61 " ideal model delta sigma weight residual 115.47 104.89 10.58 1.31e+00 5.83e-01 6.53e+01 ... (remaining 6439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.48: 1414 13.48 - 26.97: 129 26.97 - 40.45: 71 40.45 - 53.94: 33 53.94 - 67.42: 25 Dihedral angle restraints: 1672 sinusoidal: 918 harmonic: 754 Sorted by residual: dihedral pdb=" CA ASP A 190 " pdb=" CB ASP A 190 " pdb=" CG ASP A 190 " pdb=" OD1 ASP A 190 " ideal model delta sinusoidal sigma weight residual -30.00 -89.11 59.11 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" N HIS A 150 " pdb=" C HIS A 150 " pdb=" CA HIS A 150 " pdb=" CB HIS A 150 " ideal model delta harmonic sigma weight residual 122.80 130.92 -8.12 0 2.50e+00 1.60e-01 1.06e+01 dihedral pdb=" CB MET A 132 " pdb=" CG MET A 132 " pdb=" SD MET A 132 " pdb=" CE MET A 132 " ideal model delta sinusoidal sigma weight residual 180.00 120.60 59.40 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1669 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 1.084: 254 1.084 - 2.167: 0 2.167 - 3.250: 0 3.250 - 4.334: 0 4.334 - 5.417: 1 Chirality restraints: 255 Sorted by residual: chirality pdb=" CA1 GSH A 500 " pdb=" CB1 GSH A 500 " pdb=" C1 GSH A 500 " pdb=" N1 GSH A 500 " both_signs ideal model delta sigma weight residual False -2.66 2.76 -5.42 2.00e-01 2.50e+01 7.34e+02 chirality pdb=" CA HIS A 150 " pdb=" N HIS A 150 " pdb=" C HIS A 150 " pdb=" CB HIS A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA ILE A 186 " pdb=" N ILE A 186 " pdb=" C ILE A 186 " pdb=" CB ILE A 186 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 252 not shown) Planarity restraints: 502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 GSH A 500 " 0.313 2.00e-02 2.50e+03 2.24e-01 7.49e+02 pdb=" CA2 GSH A 500 " 0.101 2.00e-02 2.50e+03 pdb=" CA3 GSH A 500 " 0.137 2.00e-02 2.50e+03 pdb=" N3 GSH A 500 " 0.034 2.00e-02 2.50e+03 pdb=" O2 GSH A 500 " -0.303 2.00e-02 2.50e+03 pdb=" HN3 GSH A 500 " -0.283 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 156 " -0.131 2.00e-02 2.50e+03 5.15e-02 7.95e+01 pdb=" CG TYR A 156 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 156 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A 156 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 TYR A 156 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 156 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A 156 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 156 " -0.089 2.00e-02 2.50e+03 pdb=" HD1 TYR A 156 " 0.040 2.00e-02 2.50e+03 pdb=" HD2 TYR A 156 " 0.047 2.00e-02 2.50e+03 pdb=" HE1 TYR A 156 " 0.015 2.00e-02 2.50e+03 pdb=" HE2 TYR A 156 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 201 " 0.100 2.00e-02 2.50e+03 3.02e-02 3.64e+01 pdb=" CG TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 201 " -0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP A 201 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP A 201 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 201 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 201 " 0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 201 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 201 " 0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP A 201 " -0.029 2.00e-02 2.50e+03 pdb=" HE1 TRP A 201 " 0.002 2.00e-02 2.50e+03 pdb=" HE3 TRP A 201 " -0.032 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 201 " 0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 201 " -0.007 2.00e-02 2.50e+03 pdb=" HH2 TRP A 201 " 0.021 2.00e-02 2.50e+03 ... (remaining 499 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.87: 132 1.87 - 2.55: 3303 2.55 - 3.23: 10888 3.23 - 3.92: 14214 3.92 - 4.60: 22150 Nonbonded interactions: 50687 Sorted by model distance: nonbonded pdb="HG13 ILE A 109 " pdb=" H ALA A 110 " model vdw 1.183 2.270 nonbonded pdb="HH12 ARG A 103 " pdb="HE21 GLN A 204 " model vdw 1.249 2.100 nonbonded pdb=" HD2 PHE A 122 " pdb=" HE1 MET A 165 " model vdw 1.275 2.270 nonbonded pdb=" HA PHE A 7 " pdb="HD22 LEU A 55 " model vdw 1.279 2.440 nonbonded pdb=" HB3 GLU A 30 " pdb="HD11 LEU A 32 " model vdw 1.331 2.440 ... (remaining 50682 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: 5 Type Number sf(0) Gaussians S 14 15.91 1 O 316 7.97 1 N 282 6.97 1 C 1138 5.97 1 H 1756 1.00 1 sf(0) = scattering factor at diffraction angle 0. =========================== Regularize ADP if needed ========================== ========================== Anomalous scatterer groups ========================= All atoms refined with f_prime=0 and f_double_prime=0. ====================== Modifying start model if requested ===================== Setting occupancies to: 1.000: selected atoms: 1756 of 3506 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 3506 n_use_u_iso = 3506 n_use_u_aniso = 0 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 = 3506 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (3506 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 3506 aniso = 0) group_adp = False (0 atoms in 0 groups) tls = False (0 atoms in 0 groups) occupancies = False (0 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 } main { max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } hydrogens { refine = individual *riding Auto } pdb_interpretation { secondary_structure { protein { helix { serial_number = "1" helix_identifier = "1" selection = chain 'A' and resid 15 through 24 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 38 through 47 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 68 through 79 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 86 through 110 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 115 through 139 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 150 through 165 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 174 through 185 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 187 through 193 } sheet { first_strand = chain 'A' and resid 29 through 33 sheet_id = " A" strand { selection = chain 'A' and resid 4 through 8 sense = *parallel antiparallel unknown bond_start_current = chain 'A' and resid 5 and name N bond_start_previous = chain 'A' and resid 29 and name O } strand { selection = chain 'A' and resid 57 through 59 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 59 and name N bond_start_previous = chain 'A' and resid 4 and name O } } } enabled = True } ramachandran_plot_restraints { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1u87_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1756 occupancy sum: 1756.00 (% of total atoms 50.11) Rotatable: count: 466 occupancy sum: 466.00 (% of total atoms 13.30) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 29.97 A, n_refl.=4185 (all), 10.01 % free)-------------| | | | r_work= 0.3292 r_free= 0.3504 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 4.035015 | | target function (ml) not normalized (work): 15195.866676 | | target function (ml) not normalized (free): 1683.480726 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 29.97 - 5.04 0.97 1353 151 0.3689 0.3748 4.5706 4.5071| | 2: 5.04 - 4.01 0.96 1235 137 0.2801 0.3157 3.9206 3.9093| | 3: 4.00 - 3.50 0.92 1178 131 0.3184 0.3512 3.5398 3.5675| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 29.97 - 5.04 1353 151 0.58 43.57 0.90 0.05 1455.33| | 2: 5.04 - 4.01 1235 137 0.71 33.64 1.20 0.06 636.30| | 3: 4.00 - 3.50 1178 131 0.85 21.79 1.27 0.07 174.86| |alpha: min = 0.05 max = 0.07 mean = 0.06| |beta: min = 174.86 max = 1455.33 mean = 786.21| |figures of merit: min = 0.00 max = 1.00 mean = 0.71| |phase err.(work): min = 0.00 max = 89.84 mean = 33.50| |phase err.(test): min = 0.00 max = 88.64 mean = 34.34| |-----------------------------------------------------------------------------| ----------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 : 0.011 0.121 1794 Z= 0.655 Angle : 1.713 19.034 2419 Z= 1.088 Chirality : 0.354 5.417 255 Planarity : 0.012 0.154 305 Dihedral : 17.263 67.421 697 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 38.80 Ramachandran Plot: Outliers : 8.70 % Allowed : 20.29 % Favored : 71.01 % Rotamer: Outliers : 9.57 % Allowed : 6.91 % Favored : 83.51 % Cbeta Deviations : 0.00 % 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: -6.40 (0.37), residues: 207 helix: -4.33 (0.27), residues: 104 sheet: None (None), residues: 0 loop : -4.22 (0.45), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 103 TYR 0.107 0.013 TYR A 156 PHE 0.039 0.010 PHE A 179 TRP 0.068 0.013 TRP A 201 HIS 0.001 0.001 HIS A 139 Individual atomic B min max mean iso aniso Overall: 15.03 98.11 43.96 1.66 1750 0 Protein: 15.03 98.11 43.87 1.66 1730 0 Other: 41.47 63.03 52.15 N/A 20 0 Chain A: 15.03 98.11 43.96 N/A 1750 0 Histogram: Values Number of atoms 15.03 - 23.34 283 23.34 - 31.65 247 31.65 - 39.95 311 39.95 - 48.26 195 48.26 - 56.57 287 56.57 - 64.88 141 64.88 - 73.19 115 73.19 - 81.49 109 81.49 - 89.80 54 89.80 - 98.11 8 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4185 (all), 10.01 % free)-------------| | | | r_work= 0.3292 r_free= 0.3504 coordinate error (max.-lik. estimate): 0.32 A | | | | normalized target function (ml) (work): 4.035015 | | target function (ml) not normalized (work): 15195.866676 | | target function (ml) not normalized (free): 1683.480726 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3311 0.3292 0.3504 n_refl.: 4185 re-set all scales: r(all,work,free)=0.3311 0.3292 0.3504 n_refl.: 4185 remove outliers: r(all,work,free)=0.3322 0.3304 0.3504 n_refl.: 4182 overall B=13.94 to atoms: r(all,work,free)=0.3719 0.3690 0.3993 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.2220 0.2217 0.2255 n_refl.: 4182 remove outliers: r(all,work,free)=0.2220 0.2217 0.2255 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2919 1104.388 1001.047 1.273 0.998 0.352 12.881-10.207 97.06 88 11 0.2180 1533.577 1475.189 1.351 0.999 0.334 10.181-8.045 98.52 181 19 0.1853 1232.177 1220.067 1.249 0.998 0.325 8.023-6.324 96.77 350 40 0.2505 756.993 729.392 1.028 0.996 0.298 6.311-4.969 96.87 696 77 0.2091 690.006 669.251 0.952 0.990 0.241 4.967-3.908 95.56 1374 153 0.2087 652.071 626.849 1.012 0.981 0.158 3.907-3.500 91.76 983 109 0.2468 480.180 456.614 1.052 0.972 0.077 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=3.6244 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 414 Ramachandran restraints generated. 207 Oldfield, 0 Emsley, 207 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2217 r_free=0.2255 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2217 r_free=0.2255 ========================= Local real-space refinement ========================= Before: r_work=0.2217 r_free=0.2255 84 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 0.154 outliers start: 18 outliers final: 7 residues processed: 18 average time/residue: 0.0764 time to fit residues: 2.3361 After: r_work=0.2237 r_free=0.2283 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.886894 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.256777 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1874 0.2469 0.0595 0.013 1.5 20.8 0.0 5.9 0 7.443 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1874 r_free=0.2469 70 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.156 outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0521 time to fit residues: 1.2140 After: r_work=0.1946 r_free=0.2484 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.46 24.84 5.38 1.179 57.497 0.257 0.044 19.46 24.81 5.36 2.560 57.665 0.008 0.044 19.18 24.76 5.58 2.455 57.665 0.032 0.043 18.48 24.67 6.19 3.226 57.782 0.128 0.040 17.76 24.62 6.86 5.555 58.185 0.257 0.038 17.50 24.59 7.09 6.380 58.367 0.385 0.037 17.36 24.59 7.24 6.960 58.504 0.514 0.036 17.15 24.54 7.38 7.992 58.832 0.642 0.035 17.08 24.55 7.48 8.450 58.956 0.770 0.035 17.02 24.56 7.53 8.811 59.054 0.899 0.035 16.97 24.56 7.58 9.133 59.144 1.027 0.035 16.92 24.56 7.64 9.542 59.263 1.155 0.035 16.86 24.56 7.70 10.025 59.410 1.284 0.034 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.032 Accepted refinement result: 19.18 24.76 5.58 2.455 57.665 0.032 0.043 Individual atomic B min max mean iso aniso Overall: 29.81 111.69 58.24 1.89 1750 0 Protein: 29.81 111.69 58.18 1.89 1730 0 Other: 50.41 74.77 63.03 N/A 20 0 Chain A: 29.81 111.69 58.24 N/A 1750 0 Histogram: Values Number of atoms 29.81 - 38.00 236 38.00 - 46.19 272 46.19 - 54.37 351 54.37 - 62.56 235 62.56 - 70.75 239 70.75 - 78.94 144 78.94 - 87.12 120 87.12 - 95.31 97 95.31 - 103.50 50 103.50 - 111.69 6 =========================== Idealize ADP of riding H ========================== r_work=0.1918 r_free=0.2476 r_work=0.1914 r_free=0.2470 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1914 r_free= 0.2470 coordinate error (max.-lik. estimate): 0.37 A | | | | normalized target function (ls_wunit_k1) (work): 0.043029 | | target function (ls_wunit_k1) not normalized (work): 161.918487 | | target function (ls_wunit_k1) not normalized (free): 30.904980 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1970 0.1914 0.2470 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3615 0.3559 0.4102 n_refl.: 4182 remove outliers: r(all,work,free)=0.3615 0.3559 0.4102 n_refl.: 4182 overall B=0.00 to atoms: r(all,work,free)=0.3615 0.3559 0.4102 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1957 0.1900 0.2459 n_refl.: 4182 remove outliers: r(all,work,free)=0.1957 0.1900 0.2459 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2322 688.321 658.634 1.264 1.017 0.353 12.881-10.207 97.06 88 11 0.1554 955.818 936.150 1.382 1.015 0.340 10.181-8.045 98.52 181 19 0.1515 767.967 770.349 1.251 1.012 0.320 8.023-6.324 96.77 350 40 0.2161 471.804 466.500 1.069 1.005 0.310 6.311-4.969 96.87 696 77 0.1891 430.053 419.171 0.966 0.991 0.240 4.967-3.908 95.56 1374 153 0.1765 406.410 395.736 1.025 0.968 0.150 3.907-3.500 91.76 983 109 0.2209 299.277 283.582 1.079 0.946 0.072 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.0775 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 414 Ramachandran restraints generated. 207 Oldfield, 0 Emsley, 207 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.1900 r_free=0.2459 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 r_work=0.1900 r_free=0.2459 ========================= Local real-space refinement ========================= Before: r_work=0.1900 r_free=0.2459 61 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.163 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2344 After: r_work=0.1900 r_free=0.2459 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.288610 wxc_scale = 0.083 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.049686 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2156 0.2441 0.0285 0.003 0.8 4.0 0.0 0.0 0 0.027 0.2084 0.2423 0.0339 0.003 0.8 5.4 0.0 0.0 0 0.082 0.2029 0.2400 0.0371 0.003 0.8 5.7 0.0 0.5 0 0.164 0.1983 0.2392 0.0408 0.004 0.9 7.1 0.0 1.6 0 0.246 0.1954 0.2408 0.0454 0.005 0.9 8.8 0.0 1.1 0 0.329 0.1927 0.2397 0.0470 0.005 1.0 9.7 0.0 1.6 0 0.411 0.1903 0.2387 0.0483 0.006 1.0 10.6 0.0 3.2 0 0.493 0.1888 0.2389 0.0502 0.007 1.1 11.1 0.0 3.7 0 0.575 0.1967 0.2392 0.0425 0.004 0.9 7.4 0.0 1.6 0 0.274 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2156 0.2441 0.0285 0.003 0.8 4.0 0.0 0.0 0 0.027 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2156 r_free=0.2441 66 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 0.564 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5468 After: r_work=0.2156 r_free=0.2441 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.56 24.41 2.85 8.591 63.659 0.050 6.107 22.31 25.41 3.10 9.328 64.652 0.001 6.130 21.40 24.94 3.54 9.126 64.434 0.006 6.099 19.91 24.17 4.26 9.560 64.608 0.025 6.046 19.47 23.95 4.48 10.178 64.764 0.050 6.032 19.30 23.89 4.59 10.664 64.916 0.075 6.027 19.17 23.87 4.70 11.148 65.094 0.099 6.023 19.05 23.86 4.82 11.733 65.318 0.124 6.020 18.98 23.85 4.87 12.103 65.444 0.149 6.018 18.93 23.87 4.94 12.403 65.546 0.174 6.017 18.88 23.88 5.00 12.725 65.657 0.199 6.016 18.84 23.88 5.05 13.067 65.771 0.224 6.014 18.81 23.88 5.07 13.262 65.836 0.248 6.014 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.149 Accepted refinement result: 18.98 23.85 4.87 12.103 65.444 0.149 6.018 Individual atomic B min max mean iso aniso Overall: 24.81 133.53 61.81 10.96 1750 0 Protein: 24.81 133.53 61.80 10.97 1730 0 Other: 45.41 87.62 62.95 N/A 20 0 Chain A: 24.81 133.53 61.81 N/A 1750 0 Histogram: Values Number of atoms 24.81 - 35.68 158 35.68 - 46.55 323 46.55 - 57.43 344 57.43 - 68.30 313 68.30 - 79.17 217 79.17 - 90.04 188 90.04 - 100.91 119 100.91 - 111.78 60 111.78 - 122.65 26 122.65 - 133.53 2 =========================== Idealize ADP of riding H ========================== r_work=0.1898 r_free=0.2385 r_work=0.1878 r_free=0.2389 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1878 r_free= 0.2389 coordinate error (max.-lik. estimate): 0.34 A | | | | normalized target function (ml) (work): 6.012944 | | target function (ml) not normalized (work): 22626.708574 | | target function (ml) not normalized (free): 2586.406992 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.1930 0.1878 0.2389 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3672 0.3618 0.4125 n_refl.: 4182 remove outliers: r(all,work,free)=0.3672 0.3618 0.4125 n_refl.: 4182 overall B=3.00 to atoms: r(all,work,free)=0.3774 0.3720 0.4231 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1917 0.1867 0.2365 n_refl.: 4182 remove outliers: r(all,work,free)=0.1917 0.1867 0.2365 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2586 688.321 630.756 1.221 1.059 0.363 12.881-10.207 97.06 88 11 0.1623 955.818 937.993 1.331 1.052 0.358 10.181-8.045 98.52 181 19 0.1634 767.967 764.974 1.197 1.041 0.327 8.023-6.324 96.77 350 40 0.2222 471.804 463.772 1.073 1.023 0.305 6.311-4.969 96.87 696 77 0.1948 430.053 417.113 0.971 0.993 0.244 4.967-3.908 95.56 1374 153 0.1669 406.410 393.030 1.053 0.945 0.144 3.907-3.500 91.76 983 109 0.1984 299.277 285.186 1.164 0.899 0.091 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.2521 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 414 Ramachandran restraints generated. 207 Oldfield, 0 Emsley, 207 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1867 r_free=0.2365 After: r_work=0.1867 r_free=0.2364 ================================== NQH flips ================================== r_work=0.1867 r_free=0.2364 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 r_work=0.1867 r_free=0.2364 ========================= Local real-space refinement ========================= Before: r_work=0.1867 r_free=0.2364 70 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.739 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7741 After: r_work=0.1867 r_free=0.2364 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 3.833130 wxc_scale = 0.022 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.045456 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.008 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.025 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.050 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.075 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.100 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.125 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.151 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.176 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.084 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.008 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.025 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.050 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.075 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.100 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.125 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.151 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.176 0.1867 0.2364 0.0497 0.003 0.8 4.0 0.0 0.0 0 0.084 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1867 r_free=0.2364 69 residues out of total 188 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.805 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7900 After: r_work=0.1867 r_free=0.2364 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.67 23.64 4.97 12.048 70.977 0.045 6.010 21.53 24.85 3.32 10.687 74.863 0.001 6.082 20.79 24.53 3.75 10.461 73.988 0.006 6.064 19.33 23.87 4.54 11.228 71.781 0.023 6.024 18.73 23.85 5.12 11.706 71.068 0.045 6.009 18.50 23.94 5.44 12.073 71.127 0.068 6.005 18.33 23.90 5.57 12.354 71.066 0.091 6.003 18.21 23.96 5.76 12.705 71.261 0.114 6.001 18.11 24.03 5.92 13.053 71.409 0.136 6.000 18.05 24.07 6.02 13.308 71.466 0.159 6.000 18.01 24.09 6.08 13.522 71.514 0.182 5.999 17.96 24.13 6.17 13.778 71.608 0.205 5.999 17.92 24.19 6.27 14.061 71.725 0.227 5.999 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.045 Accepted refinement result: 18.73 23.85 5.12 11.706 71.068 0.045 6.009 Individual atomic B min max mean iso aniso Overall: 25.04 136.98 65.00 8.45 1750 0 Protein: 25.04 136.98 64.99 8.43 1730 0 Other: 45.29 85.62 65.14 N/A 20 0 Chain A: 25.04 136.98 65.00 N/A 1750 0 Histogram: Values Number of atoms 25.04 - 36.24 68 36.24 - 47.43 282 47.43 - 58.62 438 58.62 - 69.82 332 69.82 - 81.01 245 81.01 - 92.21 189 92.21 - 103.40 112 103.40 - 114.59 60 114.59 - 125.79 19 125.79 - 136.98 5 =========================== Idealize ADP of riding H ========================== r_work=0.1873 r_free=0.2385 r_work=0.1877 r_free=0.2389 ----------X-ray data---------- |--(resolution: 3.50 - 29.97 A, n_refl.=4182 (all), 10.02 % free)-------------| | | | r_work= 0.1877 r_free= 0.2389 coordinate error (max.-lik. estimate): 0.31 A | | | | normalized target function (ml) (work): 6.010142 | | target function (ml) not normalized (work): 22616.166168 | | target function (ml) not normalized (free): 2585.846738 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 29.97 - 5.04 0.97 1352 151 0.1965 0.2324 6.2802 6.4163| | 2: 5.04 - 4.01 0.96 1235 137 0.1692 0.2343 5.9608 6.1201| | 3: 4.00 - 3.50 0.92 1176 131 0.1962 0.2579 5.7515 5.943| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 29.97 - 5.04 1352 151 0.84 21.09 0.99 1.01 43768.07| | 2: 5.04 - 4.01 1235 137 0.85 20.64 1.00 1.02 30837.03| | 3: 4.00 - 3.50 1176 131 0.84 22.76 1.01 1.00 19961.25| |alpha: min = 1.00 max = 1.02 mean = 1.01| |beta: min = 19961.25 max = 43768.07 mean = 32084.13| |figures of merit: min = 0.00 max = 1.00 mean = 0.84| |phase err.(work): min = 0.00 max = 89.75 mean = 21.47| |phase err.(test): min = 0.00 max = 88.07 mean = 20.99| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.1928 0.1877 0.2389 n_refl.: 4182 re-set all scales: r(all,work,free)=0.3821 0.3770 0.4255 n_refl.: 4182 remove outliers: r(all,work,free)=0.3821 0.3770 0.4255 n_refl.: 4182 overall B=0.00 to atoms: r(all,work,free)=0.3821 0.3770 0.4255 n_refl.: 4182 bulk-solvent and scaling: r(all,work,free)=0.1924 0.1872 0.2391 n_refl.: 4182 remove outliers: r(all,work,free)=0.1924 0.1872 0.2391 n_refl.: 4182 ======================== 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 29.974-12.976 97.12 91 10 0.2556 688.321 632.823 1.133 1.075 0.359 12.881-10.207 97.06 88 11 0.1615 955.818 935.918 1.248 1.065 0.350 10.181-8.045 98.52 181 19 0.1620 767.967 763.910 1.144 1.052 0.330 8.023-6.324 96.77 350 40 0.2193 471.804 464.357 1.039 1.031 0.310 6.311-4.969 96.87 696 77 0.1951 430.053 417.193 0.939 0.994 0.240 4.967-3.908 95.56 1374 153 0.1686 406.410 393.456 1.036 0.935 0.150 3.907-3.500 91.76 983 109 0.2010 299.277 285.044 1.166 0.879 0.090 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=4.3052 ================= 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) ------------------------------------------------------------------------ stage r-work r-free bonds angles b_min b_max b_ave n_water shift 0 : 0.3292 0.3504 0.011 1.713 15.0 98.1 44.0 0 0.000 1_bss: 0.2217 0.2255 0.011 1.713 29.0 112.0 57.9 0 0.000 1_settarget: 0.2217 0.2255 0.011 1.713 29.0 112.0 57.9 0 0.000 1_updatephipsi: 0.2217 0.2255 0.011 1.713 29.0 112.0 57.9 0 0.000 1_nqh: 0.2217 0.2255 0.011 1.713 29.0 112.0 57.9 0 0.000 1_realsrl: 0.2237 0.2283 0.013 1.792 29.0 112.0 57.9 0 0.034 1_weight: 0.2237 0.2283 0.013 1.792 29.0 112.0 57.9 0 0.034 1_xyzrec: 0.1874 0.2469 0.013 1.475 29.0 112.0 57.9 0 0.333 1_realsrl2: 0.1946 0.2484 0.013 1.475 29.0 112.0 57.9 0 0.342 1_adp: 0.1918 0.2476 0.013 1.475 29.8 111.7 58.2 0 0.342 1_regHadp: 0.1914 0.2470 0.013 1.475 29.8 111.7 58.2 0 0.342 2_bss: 0.1900 0.2459 0.013 1.475 29.8 111.7 58.2 0 0.342 2_settarget: 0.1900 0.2459 0.013 1.475 29.8 111.7 58.2 0 0.342 2_updatephipsi: 0.1900 0.2459 0.013 1.475 29.8 111.7 58.2 0 0.342 2_updatecdl: 0.1900 0.2459 0.013 1.492 29.8 111.7 58.2 0 0.342 2_nqh: 0.1900 0.2459 0.013 1.492 29.8 111.7 58.2 0 0.342 2_realsrl: 0.1900 0.2459 0.013 1.492 29.8 111.7 58.2 0 0.342 2_weight: 0.1900 0.2459 0.013 1.492 29.8 111.7 58.2 0 0.342 2_xyzrec: 0.2156 0.2441 0.003 0.778 29.8 111.7 58.2 0 0.360 2_realsrl2: 0.2156 0.2441 0.003 0.778 29.8 111.7 58.2 0 0.360 2_adp: 0.1898 0.2385 0.003 0.778 24.8 133.5 61.8 0 0.360 2_regHadp: 0.1878 0.2389 0.003 0.778 24.8 133.5 61.8 0 0.360 3_bss: 0.1867 0.2365 0.003 0.778 27.8 136.5 64.8 0 0.360 3_settarget: 0.1867 0.2365 0.003 0.778 27.8 136.5 64.8 0 0.360 3_updatephipsi: 0.1867 0.2365 0.003 0.778 27.8 136.5 64.8 0 0.360 3_updatecdl: 0.1867 0.2365 0.003 0.819 27.8 136.5 64.8 0 0.360 3_setrh: 0.1867 0.2364 0.003 0.819 27.8 136.5 64.8 0 0.360 3_nqh: 0.1867 0.2364 0.003 0.819 27.8 136.5 64.8 0 0.362 3_realsrl: 0.1867 0.2364 0.003 0.819 27.8 136.5 64.8 0 0.362 3_weight: 0.1867 0.2364 0.003 0.819 27.8 136.5 64.8 0 0.362 3_xyzrec: 0.1867 0.2364 0.003 0.819 27.8 136.5 64.8 0 0.362 3_realsrl2: 0.1867 0.2364 0.003 0.819 27.8 136.5 64.8 0 0.362 3_adp: 0.1873 0.2385 0.003 0.819 25.0 137.0 65.0 0 0.362 3_regHadp: 0.1877 0.2389 0.003 0.819 25.0 137.0 65.0 0 0.362 end: 0.1872 0.2391 0.003 0.819 25.0 137.0 65.0 0 0.362 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1u87_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1u87_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.6900 Refinement macro-cycles (run) : 166.2700 Write final files (write_after_run_outputs) : 16.4900 Total : 185.4500 Total CPU time: 3.38 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:23:35 PDT -0700 (1716251015.62 s) Start R-work = 0.2217, R-free = 0.2255 Final R-work = 0.1872, R-free = 0.2391 =============================================================================== Job complete usr+sys time: 215.47 seconds wall clock time: 8 minutes 56.78 seconds (536.78 seconds total)