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/1yab.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1yab/1yab.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 { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1yab/1yab.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1yab/1yab.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1yab.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1yab.pdb" } refinement { electron_density_maps { map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT mtz_label_phases = PH2FOFCWT fill_missing_f_obs = True } map_coefficients { map_type = 2mFo-DFc mtz_label_amplitudes = 2FOFCWT_no_fill mtz_label_phases = PH2FOFCWT_no_fill } map_coefficients { map_type = mFo-DFc mtz_label_amplitudes = FOFCWT mtz_label_phases = PHFOFCWT } map_coefficients { map_type = anomalous mtz_label_amplitudes = ANOM mtz_label_phases = PANOM } map { map_type = 2mFo-DFc fill_missing_f_obs = True } map { map_type = 2mFo-DFc } map { map_type = mFo-DFc } } refine { strategy = *individual_sites *individual_sites_real_space rigid_body \ *individual_adp group_adp tls occupancies group_anomalous \ den } 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: 2831 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1401 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 81} Chain: "B" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1430 Classifications: {'peptide': 87} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 82} Time building chain proxies: 0.54, per 1000 atoms: 0.19 Number of scatterers: 2831 At special positions: 0 Unit cell: (100.173, 100.173, 87.853, 90, 90, 120) Space group: P 31 2 1 (No. 152) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 4 16.00 O 257 8.00 N 229 7.00 C 865 6.00 H 1476 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: 0.67 Conformation dependent library (CDL) restraints added in 82.9 milliseconds 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 320 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 6 helices and 2 sheets defined 18.6% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 69 through 74 removed outlier: 4.330A pdb=" N LEU A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 69 through 74' Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'B' and resid 72 through 75 No H-bonds generated for 'chain 'B' and resid 72 through 75' Processing helix chain 'B' and resid 94 through 96 No H-bonds generated for 'chain 'B' and resid 94 through 96' Processing helix chain 'B' and resid 145 through 152 Processing sheet with id= A, first strand: chain 'A' and resid 81 through 84 removed outlier: 6.212A pdb=" N VAL A 118 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLU A 127 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ILE A 139 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL A 129 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL A 137 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N ILE A 131 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N PHE A 135 " --> pdb=" O ILE A 131 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 81 through 84 removed outlier: 3.630A pdb=" N ASP B 115 " --> pdb=" O GLU B 84 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 118 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLU B 127 " --> pdb=" O ILE B 139 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE B 139 " --> pdb=" O GLU B 127 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL B 129 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N VAL B 137 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ILE B 131 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE B 135 " --> pdb=" O ILE B 131 " (cutoff:3.500A) 26 hydrogen bonds defined for protein. 72 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: 0.67 Time building geometry restraints manager: 0.77 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: 1476 1.15 - 1.32: 248 1.32 - 1.49: 442 1.49 - 1.66: 665 1.66 - 1.83: 8 Bond restraints: 2839 Sorted by residual: bond pdb=" NH1 ARG B 87 " pdb="HH12 ARG B 87 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N VAL A 114 " pdb=" H VAL A 114 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N HIS A 100 " pdb=" H HIS A 100 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N LYS B 108 " pdb=" H LYS B 108 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 bond pdb=" N LEU A 75 " pdb=" H LEU A 75 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.44e+01 ... (remaining 2834 not shown) Histogram of bond angle deviations from ideal: 97.32 - 104.19: 59 104.19 - 111.07: 3254 111.07 - 117.94: 912 117.94 - 124.81: 926 124.81 - 131.69: 70 Bond angle restraints: 5221 Sorted by residual: angle pdb=" N LYS B 70 " pdb=" CA LYS B 70 " pdb=" C LYS B 70 " ideal model delta sigma weight residual 112.92 102.67 10.25 1.23e+00 6.61e-01 6.95e+01 angle pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N PHE B 135 " ideal model delta sigma weight residual 115.55 123.69 -8.14 1.33e+00 5.65e-01 3.75e+01 angle pdb=" C ASN B 134 " pdb=" N PHE B 135 " pdb=" CA PHE B 135 " ideal model delta sigma weight residual 121.54 131.60 -10.06 1.91e+00 2.74e-01 2.77e+01 angle pdb=" C VAL A 81 " pdb=" CA VAL A 81 " pdb=" CB VAL A 81 " ideal model delta sigma weight residual 110.91 104.61 6.30 1.24e+00 6.50e-01 2.58e+01 angle pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" C ASP B 132 " ideal model delta sigma weight residual 110.80 120.70 -9.90 2.13e+00 2.20e-01 2.16e+01 ... (remaining 5216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.86: 1127 25.86 - 51.72: 116 51.72 - 77.58: 21 77.58 - 103.44: 5 103.44 - 129.30: 1 Dihedral angle restraints: 1270 sinusoidal: 764 harmonic: 506 Sorted by residual: dihedral pdb=" CA ASN B 134 " pdb=" C ASN B 134 " pdb=" N PHE B 135 " pdb=" CA PHE B 135 " ideal model delta harmonic sigma weight residual 180.00 50.70 129.30 0 5.00e+00 4.00e-02 6.69e+02 dihedral pdb=" C ASP B 132 " pdb=" N ASP B 132 " pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " ideal model delta harmonic sigma weight residual -122.60 -139.66 17.06 0 2.50e+00 1.60e-01 4.66e+01 dihedral pdb=" N ASP B 132 " pdb=" C ASP B 132 " pdb=" CA ASP B 132 " pdb=" CB ASP B 132 " ideal model delta harmonic sigma weight residual 122.80 139.34 -16.54 0 2.50e+00 1.60e-01 4.38e+01 ... (remaining 1267 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.134: 186 0.134 - 0.267: 45 0.267 - 0.401: 3 0.401 - 0.534: 2 0.534 - 0.667: 2 Chirality restraints: 238 Sorted by residual: chirality pdb=" CA PHE B 135 " pdb=" N PHE B 135 " pdb=" C PHE B 135 " pdb=" CB PHE B 135 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA ASP B 132 " pdb=" N ASP B 132 " pdb=" C ASP B 132 " pdb=" CB ASP B 132 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA ASP A 132 " pdb=" N ASP A 132 " pdb=" C ASP A 132 " pdb=" CB ASP A 132 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 235 not shown) Planarity restraints: 394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 134 " -0.004 2.00e-02 2.50e+03 1.16e-02 2.03e+00 pdb=" CG ASN A 134 " -0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN A 134 " 0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 134 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 134 " -0.009 2.00e-02 2.50e+03 pdb="HD22 ASN A 134 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 135 " 0.003 2.00e-02 2.50e+03 6.76e-03 1.37e+00 pdb=" CG PHE B 135 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 135 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 135 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 135 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 135 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 135 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE B 135 " -0.006 2.00e-02 2.50e+03 pdb=" HD2 PHE B 135 " 0.014 2.00e-02 2.50e+03 pdb=" HE1 PHE B 135 " 0.010 2.00e-02 2.50e+03 pdb=" HE2 PHE B 135 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE B 135 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 134 " -0.003 2.00e-02 2.50e+03 9.20e-03 1.27e+00 pdb=" CG ASN B 134 " -0.012 2.00e-02 2.50e+03 pdb=" OD1 ASN B 134 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN B 134 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 134 " -0.007 2.00e-02 2.50e+03 pdb="HD22 ASN B 134 " 0.012 2.00e-02 2.50e+03 ... (remaining 391 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.84: 89 1.84 - 2.53: 2657 2.53 - 3.22: 8856 3.22 - 3.91: 12184 3.91 - 4.60: 18186 Nonbonded interactions: 41972 Sorted by model distance: nonbonded pdb=" HG3 ARG A 89 " pdb="HH11 ARG A 89 " model vdw 1.154 2.270 nonbonded pdb=" HA GLU A 147 " pdb=" HB2 GLU A 150 " model vdw 1.325 2.440 nonbonded pdb="HH22 ARG A 94 " pdb="HD12 ILE A 104 " model vdw 1.340 2.270 nonbonded pdb=" O LEU A 74 " pdb=" H ASP A 76 " model vdw 1.363 1.850 nonbonded pdb=" HA2 GLY B 126 " pdb=" H THR B 140 " model vdw 1.423 2.270 ... (remaining 41967 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 4 15.91 1 O 257 7.97 1 N 229 6.97 1 C 865 5.97 1 H 1476 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: 1476 of 2831 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 2831 n_use_u_iso = 2831 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 = 2831 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (2831 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 2831 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 69 through 74 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 92 through 97 } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 147 through 151 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'B' and resid 72 through 75 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'B' and resid 94 through 96 helix_type = alpha pi *3_10 unknown } helix { serial_number = "6" helix_identifier = "6" selection = chain 'B' and resid 145 through 152 } sheet { first_strand = chain 'A' and resid 81 through 84 sheet_id = " A" strand { selection = chain 'A' and resid 114 through 118 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 117 and name N bond_start_previous = chain 'A' and resid 82 and name O } strand { selection = chain 'A' and resid 121 through 131 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 126 and name N bond_start_previous = chain 'A' and resid 114 and name O } strand { selection = chain 'A' and resid 134 through 142 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 141 and name N bond_start_previous = chain 'A' and resid 125 and name O } } sheet { first_strand = chain 'B' and resid 81 through 84 sheet_id = " B" strand { selection = chain 'B' and resid 114 through 118 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 117 and name N bond_start_previous = chain 'B' and resid 82 and name O } strand { selection = chain 'B' and resid 121 through 131 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 126 and name N bond_start_previous = chain 'B' and resid 114 and name O } strand { selection = chain 'B' and resid 134 through 142 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 141 and name N bond_start_previous = chain 'B' and resid 125 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 = "1yab_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 1476 occupancy sum: 1476.00 (% of total atoms 52.17) Rotatable: count: 514 occupancy sum: 514.00 (% of total atoms 18.17) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.40 - 19.90 A, n_refl.=7246 (all), 4.69 % free)-------------| | | | r_work= 0.4059 r_free= 0.4598 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 5.289039 | | target function (ml) not normalized (work): 36526.102154 | | target function (ml) not normalized (free): 1841.689129 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.90 - 4.27 1.00 3512 170 0.3818 0.4405 5.9303 6.0787| | 2: 4.27 - 3.40 1.00 3394 170 0.4725 0.5140 4.6255 4.7548| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.90 - 4.27 3512 170 0.47 53.91 0.97 0.49 32804.81| | 2: 4.27 - 3.40 3394 170 0.71 34.58 1.68 1.01 2345.12| |alpha: min = 0.49 max = 1.01 mean = 0.75| |beta: min = 2345.12 max = 32804.81 mean = 17835.19| |figures of merit: min = 0.00 max = 1.00 mean = 0.59| |phase err.(work): min = 0.00 max = 89.99 mean = 44.41| |phase err.(test): min = 0.00 max = 89.81 mean = 43.07| |-----------------------------------------------------------------------------| ----------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 : 0.014 0.080 1363 Z= 0.957 Angle : 1.971 12.009 1839 Z= 1.158 Chirality : 0.128 0.667 238 Planarity : 0.005 0.024 230 Dihedral : 23.170 129.301 543 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 23.72 Ramachandran Plot: Outliers : 8.33 % Allowed : 10.12 % Favored : 81.55 % Rotamer: Outliers : 24.68 % Allowed : 21.52 % Favored : 53.80 % Cbeta Deviations : 2.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.61 % Twisted Proline : 0.00 % Twisted General : 1.83 % 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: -4.61 (0.52), residues: 168 helix: -4.84 (0.42), residues: 40 sheet: -3.56 (1.49), residues: 10 loop : -2.51 (0.48), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 94 PHE 0.008 0.003 PHE B 135 HIS 0.002 0.001 HIS A 100 Individual atomic B min max mean iso aniso Overall: 93.69 154.06 112.45 1.19 1355 0 Protein: 93.69 154.06 112.45 1.19 1355 0 Chain A: 94.35 154.06 112.30 N/A 669 0 Chain B: 93.69 153.95 112.61 N/A 686 0 Histogram: Values Number of atoms 93.69 - 99.73 219 99.73 - 105.76 346 105.76 - 111.80 259 111.80 - 117.84 158 117.84 - 123.88 111 123.88 - 129.91 104 129.91 - 135.95 47 135.95 - 141.99 29 141.99 - 148.02 23 148.02 - 154.06 59 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7246 (all), 4.69 % free)-------------| | | | r_work= 0.4059 r_free= 0.4598 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ml) (work): 5.289039 | | target function (ml) not normalized (work): 36526.102154 | | target function (ml) not normalized (free): 1841.689129 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.4088 0.4059 0.4598 n_refl.: 7246 re-set all scales: r(all,work,free)=0.4088 0.4059 0.4598 n_refl.: 7246 remove outliers: r(all,work,free)=0.4086 0.4057 0.4598 n_refl.: 7245 overall B=-8.40 to atoms: r(all,work,free)=0.3843 0.3813 0.4380 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2258 0.2228 0.2845 n_refl.: 7245 remove outliers: r(all,work,free)=0.2258 0.2228 0.2845 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1925 763.916 733.811 1.338 0.999 0.338 12.965-10.793 93.40 95 4 0.1555 722.206 703.625 1.337 0.998 0.330 10.793-8.919 99.47 176 10 0.1458 676.649 670.817 1.301 0.998 0.327 8.905-7.374 99.69 313 12 0.2067 409.798 395.940 1.152 0.996 0.300 7.364-6.089 99.82 547 20 0.2513 296.258 285.152 1.064 0.993 0.273 6.087-5.031 100.00 938 48 0.2290 234.401 224.135 0.961 0.989 0.215 5.030-4.158 99.88 1640 78 0.1969 247.791 238.471 0.978 0.983 0.155 4.156-3.397 99.85 3105 159 0.2879 111.432 103.442 1.032 0.973 0.058 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.6281 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ============================ Update phi&psi targets =========================== 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2228 r_free=0.2845 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2228 r_free=0.2845 ========================= Local real-space refinement ========================= Before: r_work=0.2228 r_free=0.2845 148 residues out of total 158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 109 time to evaluate : 0.116 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 22 residues processed: 39 average time/residue: 0.1493 time to fit residues: 6.8086 After: r_work=0.2431 r_free=0.3051 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 14.810292 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.180382 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2512 0.2894 0.0382 0.003 0.8 8.1 1.2 15.2 0 0.125 0.2522 0.2886 0.0364 0.003 0.8 8.1 1.2 15.2 0 0.250 0.2486 0.2885 0.0399 0.004 0.8 8.1 1.2 15.2 0 0.500 0.2437 0.2903 0.0466 0.005 0.9 9.2 1.2 15.8 0 1.000 0.2367 0.2891 0.0523 0.006 1.0 14.2 1.2 17.7 0 2.000 0.2305 0.2860 0.0555 0.008 1.1 14.9 1.2 17.7 0 3.000 0.2285 0.2816 0.0531 0.010 1.2 16.6 1.2 19.0 0 4.000 0.2261 0.2852 0.0590 0.011 1.3 17.0 1.2 22.2 0 5.000 0.2245 0.2831 0.0586 0.013 1.4 17.0 1.8 23.4 0 6.000 0.2226 0.2848 0.0621 0.014 1.5 17.7 1.8 23.4 0 7.000 0.2218 0.2826 0.0608 0.015 1.6 18.8 2.4 24.7 0 8.000 0.2211 0.2850 0.0639 0.017 1.6 19.5 2.4 26.6 0 9.000 0.2207 0.2855 0.0648 0.018 1.7 19.5 2.4 27.8 0 10.000 0.2223 0.2828 0.0606 0.015 1.5 17.7 1.8 24.1 0 7.405 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2486 0.2885 0.0399 0.004 0.8 8.1 1.2 15.2 0 0.500 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2486 r_free=0.2885 139 residues out of total 158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 0.116 revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 2 residues processed: 24 average time/residue: 0.0600 time to fit residues: 2.1527 After: r_work=0.2669 r_free=0.2944 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 26.69 29.44 2.75 0.822 103.807 0.180 0.072 26.81 29.52 2.71 2.036 103.883 0.005 0.073 26.27 29.22 2.95 2.135 103.860 0.023 0.070 25.48 28.86 3.38 3.291 103.984 0.090 0.066 24.28 28.26 3.98 8.114 105.168 0.180 0.059 24.01 28.11 4.10 9.653 105.632 0.271 0.058 23.85 28.04 4.19 10.724 105.954 0.361 0.057 23.65 27.98 4.33 12.017 106.407 0.451 0.056 23.52 27.96 4.44 12.886 106.688 0.541 0.055 23.26 27.92 4.67 14.702 107.350 0.631 0.054 23.18 27.88 4.70 15.328 107.538 0.722 0.053 23.13 27.86 4.73 15.842 107.690 0.812 0.053 23.09 27.86 4.77 16.293 107.820 0.902 0.053 max suggested for this run: 20.76 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.902 Accepted refinement result: 23.09 27.86 4.77 16.293 107.820 0.902 0.053 Individual atomic B min max mean iso aniso Overall: 80.29 211.44 112.44 13.29 1355 0 Protein: 80.29 211.44 112.44 13.29 1355 0 Chain A: 81.33 189.26 113.25 N/A 669 0 Chain B: 80.29 211.44 111.64 N/A 686 0 Histogram: Values Number of atoms 80.29 - 93.40 338 93.40 - 106.52 296 106.52 - 119.63 274 119.63 - 132.75 184 132.75 - 145.86 134 145.86 - 158.98 75 158.98 - 172.09 41 172.09 - 185.21 10 185.21 - 198.32 2 198.32 - 211.44 1 =========================== Idealize ADP of riding H ========================== r_work=0.2309 r_free=0.2786 r_work=0.2282 r_free=0.2774 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.2282 r_free= 0.2774 coordinate error (max.-lik. estimate): 0.43 A | | | | normalized target function (ls_wunit_k1) (work): 0.051307 | | target function (ls_wunit_k1) not normalized (work): 354.276836 | | target function (ls_wunit_k1) not normalized (free): 31.665293 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2306 0.2282 0.2774 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3881 0.3857 0.4321 n_refl.: 7245 remove outliers: r(all,work,free)=0.3881 0.3857 0.4321 n_refl.: 7245 overall B=-1.12 to atoms: r(all,work,free)=0.3849 0.3824 0.4291 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2266 0.2239 0.2780 n_refl.: 7245 remove outliers: r(all,work,free)=0.2266 0.2239 0.2780 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1734 490.916 474.234 1.394 0.997 0.335 12.965-10.793 95.19 95 4 0.1458 464.112 457.739 1.347 0.996 0.331 10.793-8.919 99.47 176 10 0.1403 434.835 432.939 1.279 0.997 0.311 8.905-7.374 99.69 313 12 0.2071 263.349 254.663 1.113 0.995 0.281 7.364-6.089 99.82 547 20 0.2398 190.384 186.026 1.023 0.993 0.242 6.087-5.031 100.00 938 48 0.2385 150.633 144.654 0.951 0.989 0.182 5.030-4.158 99.88 1640 78 0.1933 159.238 153.597 0.989 0.984 0.122 4.156-3.397 99.85 3105 159 0.3039 71.609 66.244 1.057 0.976 0.051 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=0.3914 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2239 r_free=0.2780 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 r_work=0.2239 r_free=0.2780 ========================= Local real-space refinement ========================= Before: r_work=0.2239 r_free=0.2780 128 residues out of total 158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 0.178 outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.7801 time to fit residues: 1.8358 After: r_work=0.2243 r_free=0.2776 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.889338 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.040234 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2145 0.2710 0.0566 0.003 0.7 6.4 1.2 6.3 0 0.125 0.2090 0.2721 0.0631 0.003 0.7 7.1 1.2 7.6 0 0.250 0.2046 0.2721 0.0675 0.005 0.8 9.9 1.2 8.9 0 0.500 0.2007 0.2713 0.0706 0.007 1.0 11.3 1.8 12.0 0 1.000 0.1965 0.2681 0.0717 0.012 1.3 15.6 1.8 16.5 0 2.000 0.1945 0.2719 0.0774 0.016 1.5 17.3 2.4 15.8 0 3.000 0.1932 0.2713 0.0781 0.019 1.7 20.2 2.4 19.0 0 4.000 0.1919 0.2721 0.0802 0.023 1.9 22.3 2.4 18.4 0 5.000 0.1909 0.2722 0.0813 0.026 2.1 22.3 2.4 20.9 0 6.000 0.1901 0.2730 0.0828 0.029 2.3 25.5 2.4 22.2 0 7.000 0.1896 0.2733 0.0836 0.031 2.5 25.1 3.0 23.4 0 8.000 0.1896 0.2753 0.0857 0.033 2.6 26.9 3.0 27.2 0 9.000 0.1900 0.2775 0.0875 0.036 2.8 27.3 3.0 28.5 0 10.000 0.1955 0.2696 0.0742 0.014 1.4 17.3 1.8 16.5 0 2.445 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2145 0.2710 0.0566 0.003 0.7 6.4 1.2 6.3 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2145 r_free=0.2710 130 residues out of total 158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 0.396 revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 10 average time/residue: 0.0856 time to fit residues: 1.7397 After: r_work=0.2168 r_free=0.2695 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.68 26.95 5.26 18.957 123.258 0.040 4.994 26.98 31.04 4.06 14.270 132.695 0.001 5.082 25.03 29.45 4.42 14.252 130.829 0.005 5.045 22.43 27.41 4.98 16.622 127.349 0.020 4.983 21.58 27.03 5.45 17.684 125.823 0.040 4.961 21.27 26.93 5.66 18.208 125.648 0.060 4.953 21.09 26.80 5.72 18.756 125.966 0.080 4.946 20.81 26.51 5.70 18.664 125.533 0.101 4.939 20.72 26.48 5.76 18.955 125.735 0.121 4.936 20.65 26.46 5.81 19.235 125.906 0.141 4.934 20.61 26.43 5.83 19.519 126.075 0.161 4.933 20.54 26.38 5.84 19.875 126.296 0.181 4.931 20.51 26.37 5.86 20.134 126.442 0.201 4.930 max suggested for this run: 24.65 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.201 Accepted refinement result: 20.51 26.37 5.86 20.134 126.442 0.201 4.930 Individual atomic B min max mean iso aniso Overall: 74.17 227.91 117.97 19.34 1355 0 Protein: 74.17 227.91 117.97 19.34 1355 0 Chain A: 75.84 203.81 119.13 N/A 669 0 Chain B: 74.17 227.91 116.84 N/A 686 0 Histogram: Values Number of atoms 74.17 - 89.54 242 89.54 - 104.91 265 104.91 - 120.29 278 120.29 - 135.66 217 135.66 - 151.04 164 151.04 - 166.41 104 166.41 - 181.78 59 181.78 - 197.16 20 197.16 - 212.53 5 212.53 - 227.91 1 =========================== Idealize ADP of riding H ========================== r_work=0.2051 r_free=0.2637 r_work=0.2056 r_free=0.2630 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.2056 r_free= 0.2630 coordinate error (max.-lik. estimate): 0.30 A | | | | normalized target function (ml) (work): 4.929381 | | target function (ml) not normalized (work): 34037.378801 | | target function (ml) not normalized (free): 1741.603306 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2084 0.2056 0.2630 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3864 0.3840 0.4321 n_refl.: 7245 remove outliers: r(all,work,free)=0.3864 0.3840 0.4321 n_refl.: 7245 overall B=-5.82 to atoms: r(all,work,free)=0.3682 0.3657 0.4158 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2071 0.2043 0.2613 n_refl.: 7245 remove outliers: r(all,work,free)=0.2071 0.2043 0.2613 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1645 490.916 469.845 1.485 0.978 0.341 12.965-10.793 95.19 95 4 0.1243 464.112 456.843 1.422 0.979 0.334 10.793-8.919 99.47 176 10 0.1344 434.835 432.849 1.337 0.982 0.315 8.905-7.374 99.69 313 12 0.1910 263.349 255.974 1.146 0.984 0.276 7.364-6.089 99.82 547 20 0.2183 190.384 184.813 1.069 0.986 0.238 6.087-5.031 100.00 938 48 0.2317 150.633 143.960 0.969 0.989 0.178 5.030-4.158 99.88 1640 78 0.1816 159.238 154.124 0.985 0.994 0.107 4.156-3.397 99.85 3105 159 0.2599 71.609 66.791 1.025 1.002 0.044 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=2.6295 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2043 r_free=0.2613 After: r_work=0.2043 r_free=0.2613 ================================== NQH flips ================================== r_work=0.2043 r_free=0.2613 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 HIS B 153 ASN Total number of N/Q/H flips: 2 r_work=0.2046 r_free=0.2610 ========================= Local real-space refinement ========================= Before: r_work=0.2046 r_free=0.2610 125 residues out of total 158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 0.686 outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.2170 time to fit residues: 1.4298 After: r_work=0.2048 r_free=0.2603 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 5.302183 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.039377 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 6.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2037 0.2612 0.0576 0.006 0.7 8.5 1.2 1.3 0 0.125 0.2027 0.2610 0.0583 0.006 0.8 8.5 1.2 1.3 0 0.250 0.1995 0.2598 0.0603 0.007 0.8 8.8 1.2 1.9 0 0.500 0.1917 0.2603 0.0686 0.009 1.3 14.5 1.2 1.9 0 1.000 0.1874 0.2595 0.0721 0.012 1.5 23.0 1.2 6.3 0 2.000 0.1858 0.2590 0.0732 0.014 1.9 23.4 1.8 6.3 0 3.000 0.1844 0.2586 0.0743 0.017 2.1 25.5 1.8 7.0 0 4.000 0.1824 0.2564 0.0741 0.022 2.3 29.0 1.8 12.0 0 5.000 0.1821 0.2572 0.0751 0.023 2.5 27.3 1.8 10.1 0 6.000 0.1812 0.2565 0.0753 0.025 2.8 28.7 1.8 11.4 0 7.000 0.1808 0.2566 0.0758 0.027 2.9 29.7 1.8 12.7 0 8.000 0.1800 0.2559 0.0760 0.030 3.1 31.5 1.8 15.2 0 9.000 0.1796 0.2562 0.0767 0.031 3.2 29.0 1.8 13.9 0 10.000 0.1867 0.2601 0.0734 0.012 1.7 23.4 1.8 6.3 0 2.651 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2037 0.2612 0.0576 0.006 0.7 8.5 1.2 1.3 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2037 r_free=0.2612 124 residues out of total 158 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 0.522 revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.1088 time to fit residues: 0.7796 After: r_work=0.2037 r_free=0.2612 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 20.37 26.12 5.76 22.075 124.917 0.039 4.929 26.38 30.32 3.93 17.573 134.438 0.001 5.045 24.95 29.14 4.19 17.176 133.226 0.005 5.024 22.79 27.42 4.63 18.579 129.961 0.020 4.986 21.51 26.97 5.46 19.073 127.567 0.039 4.953 21.01 26.38 5.37 19.494 127.172 0.059 4.936 20.68 25.92 5.24 19.790 126.779 0.079 4.923 20.54 25.75 5.21 20.046 126.942 0.098 4.917 20.31 25.77 5.46 20.311 126.696 0.118 4.913 20.20 25.76 5.56 20.628 126.582 0.138 4.911 20.12 25.77 5.65 20.885 126.480 0.158 4.909 20.07 25.75 5.68 21.067 126.609 0.177 4.907 20.02 25.73 5.70 21.240 126.741 0.197 4.905 max suggested for this run: 24.98 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.197 Accepted refinement result: 20.02 25.73 5.70 21.240 126.741 0.197 4.905 Individual atomic B min max mean iso aniso Overall: 63.35 236.38 115.96 20.60 1355 0 Protein: 63.35 236.38 115.96 20.60 1355 0 Chain A: 66.55 207.31 117.51 N/A 669 0 Chain B: 63.35 236.38 114.45 N/A 686 0 Histogram: Values Number of atoms 63.35 - 80.65 123 80.65 - 97.95 274 97.95 - 115.26 356 115.26 - 132.56 244 132.56 - 149.86 175 149.86 - 167.17 113 167.17 - 184.47 47 184.47 - 201.77 18 201.77 - 219.08 4 219.08 - 236.38 1 =========================== Idealize ADP of riding H ========================== r_work=0.2002 r_free=0.2573 r_work=0.2003 r_free=0.2579 ----------X-ray data---------- |--(resolution: 3.40 - 19.90 A, n_refl.=7245 (all), 4.69 % free)-------------| | | | r_work= 0.2003 r_free= 0.2579 coordinate error (max.-lik. estimate): 0.19 A | | | | normalized target function (ml) (work): 4.905131 | | target function (ml) not normalized (work): 33869.930650 | | target function (ml) not normalized (free): 1732.453626 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.90 - 4.27 0.99 3511 170 0.1871 0.2428 5.3273 5.5597| | 2: 4.27 - 3.40 1.00 3394 170 0.2369 0.3004 4.4684 4.6312| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.90 - 4.27 3511 170 0.79 26.42 1.00 0.95 8893.83| | 2: 4.27 - 3.40 3394 170 0.78 28.93 1.03 0.97 1689.65| |alpha: min = 0.95 max = 0.97 mean = 0.96| |beta: min = 1689.65 max = 8893.83 mean = 5352.77| |figures of merit: min = 0.00 max = 1.00 mean = 0.78| |phase err.(work): min = 0.00 max = 90.00 mean = 27.65| |phase err.(test): min = 0.00 max = 89.55 mean = 28.23| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2032 0.2003 0.2579 n_refl.: 7245 re-set all scales: r(all,work,free)=0.3788 0.3765 0.4224 n_refl.: 7245 remove outliers: r(all,work,free)=0.3788 0.3765 0.4224 n_refl.: 7245 overall B=-1.86 to atoms: r(all,work,free)=0.3729 0.3706 0.4172 n_refl.: 7245 bulk-solvent and scaling: r(all,work,free)=0.2020 0.1992 0.2553 n_refl.: 7245 remove outliers: r(all,work,free)=0.2020 0.1992 0.2553 n_refl.: 7245 ======================== 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 19.902-13.063 90.91 91 9 0.1643 490.916 469.732 1.462 0.996 0.350 12.965-10.793 95.19 95 4 0.1175 464.112 458.727 1.395 0.996 0.341 10.793-8.919 99.47 176 10 0.1366 434.835 431.956 1.272 0.997 0.312 8.905-7.374 99.69 313 12 0.1920 263.349 256.304 1.089 0.997 0.272 7.364-6.089 99.82 547 20 0.2141 190.384 185.233 1.038 0.996 0.243 6.087-5.031 100.00 938 48 0.2281 150.633 144.326 0.947 0.995 0.183 5.030-4.158 99.88 1640 78 0.1781 159.238 154.108 0.964 0.994 0.102 4.156-3.397 99.85 3105 159 0.2461 71.609 67.079 1.036 0.993 0.041 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0265 b_overall=0.9328 ================= 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 : 0.4059 0.4598 0.014 1.971 93.7 154.1 112.5 0 0.000 1_bss: 0.2228 0.2845 0.014 1.971 85.3 145.7 104.1 0 0.000 1_settarget: 0.2228 0.2845 0.014 1.971 85.3 145.7 104.1 0 0.000 1_updatephipsi: 0.2228 0.2845 0.014 1.971 85.3 145.7 104.1 0 0.000 1_nqh: 0.2228 0.2845 0.014 1.971 85.3 145.7 104.1 0 0.000 1_realsrl: 0.2431 0.3051 0.014 1.971 85.3 145.7 104.1 0 0.079 1_weight: 0.2431 0.3051 0.014 1.971 85.3 145.7 104.1 0 0.079 1_xyzrec: 0.2486 0.2885 0.004 0.810 85.3 145.7 104.1 0 0.310 1_realsrl2: 0.2669 0.2944 0.004 0.810 85.3 145.7 104.1 0 0.350 1_adp: 0.2309 0.2786 0.004 0.810 80.3 211.4 112.4 0 0.350 1_regHadp: 0.2282 0.2774 0.004 0.810 80.3 211.4 112.4 0 0.350 2_bss: 0.2239 0.2780 0.004 0.810 79.2 210.3 111.3 0 0.350 2_settarget: 0.2239 0.2780 0.004 0.810 79.2 210.3 111.3 0 0.350 2_updatephipsi: 0.2239 0.2780 0.004 0.810 79.2 210.3 111.3 0 0.350 2_updatecdl: 0.2239 0.2780 0.004 0.859 79.2 210.3 111.3 0 0.350 2_nqh: 0.2239 0.2780 0.004 0.859 79.2 210.3 111.3 0 0.350 2_realsrl: 0.2243 0.2776 0.004 0.859 79.2 210.3 111.3 0 0.358 2_weight: 0.2243 0.2776 0.004 0.859 79.2 210.3 111.3 0 0.358 2_xyzrec: 0.2145 0.2710 0.003 0.662 79.2 210.3 111.3 0 0.409 2_realsrl2: 0.2168 0.2695 0.003 0.662 79.2 210.3 111.3 0 0.414 2_adp: 0.2051 0.2637 0.003 0.662 74.2 227.9 118.0 0 0.414 2_regHadp: 0.2056 0.2630 0.003 0.662 74.2 227.9 118.0 0 0.414 3_bss: 0.2043 0.2613 0.003 0.662 68.3 222.1 112.1 0 0.414 3_settarget: 0.2043 0.2613 0.003 0.662 68.3 222.1 112.1 0 0.414 3_updatephipsi: 0.2043 0.2613 0.003 0.662 68.3 222.1 112.1 0 0.414 3_updatecdl: 0.2043 0.2613 0.003 0.683 68.3 222.1 112.1 0 0.414 3_setrh: 0.2043 0.2613 0.003 0.683 68.3 222.1 112.1 0 0.414 3_nqh: 0.2046 0.2610 0.003 0.683 68.3 222.1 112.1 0 0.419 3_realsrl: 0.2048 0.2603 0.003 0.683 68.3 222.1 112.1 0 0.419 3_weight: 0.2048 0.2603 0.003 0.683 68.3 222.1 112.1 0 0.419 3_xyzrec: 0.2037 0.2612 0.006 0.738 68.3 222.1 112.1 0 0.420 3_realsrl2: 0.2037 0.2612 0.006 0.738 68.3 222.1 112.1 0 0.420 3_adp: 0.2002 0.2573 0.006 0.738 63.3 236.4 116.0 0 0.420 3_regHadp: 0.2003 0.2579 0.006 0.738 63.3 236.4 116.0 0 0.420 end: 0.1992 0.2553 0.006 0.738 61.5 234.5 114.1 0 0.420 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1yab_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1yab_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 2.2100 Refinement macro-cycles (run) : 168.8800 Write final files (write_after_run_outputs) : 18.1500 Total : 189.2400 Total CPU time: 3.41 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:24:21 PDT -0700 (1716251061.96 s) Start R-work = 0.2228, R-free = 0.2845 Final R-work = 0.1992, R-free = 0.2553 =============================================================================== Job complete usr+sys time: 221.50 seconds wall clock time: 9 minutes 51.15 seconds (591.15 seconds total)