Starting phenix.refine on Mon May 20 17:17:37 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u9o.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u9o/1u9o.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 ramachandran_plot_restraints.enabled=False secondary_structure.enabled=True main.nqh_flips=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { miller_array { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u9o/1u9o.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/1u9o/1u9o.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u9o.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u9o.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 { nqh_flips = False max_number_of_iterations = 100 nproc = 20 } modify_start_model { modify { selection = element H occupancies { set = 1 } } } pdb_interpretation { secondary_structure { enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = true optimize_adp_weight = true } } Starting job =============================================================================== Symmetric amino acids flipped Residue "B GLU 180": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 5976 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Chain: "B" Number of atoms: 2988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2988 Classifications: {'peptide': 194} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 185} Time building chain proxies: 2.10, per 1000 atoms: 0.35 Number of scatterers: 5976 At special positions: 0 Unit cell: (140.5, 140.5, 76.69, 90, 90, 120) Space group: R 3 :H (No. 146) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 8 16.00 O 586 8.00 N 520 7.00 C 1908 6.00 H 2954 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: 4.39 Conformation dependent library (CDL) restraints added in 586.0 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 740 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 0 sheets defined 71.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 removed outlier: 3.669A pdb=" N LEU A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.704A pdb=" N TYR A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 90 removed outlier: 4.046A pdb=" N LEU A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.952A pdb=" N GLY A 106 " --> pdb=" O MET A 102 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 127 removed outlier: 3.545A pdb=" N ALA A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.679A pdb=" N LYS A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 157 " --> pdb=" O ILE A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 187 removed outlier: 3.650A pdb=" N ARG A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 211 Processing helix chain 'B' and resid 24 through 35 removed outlier: 3.595A pdb=" N ALA B 31 " --> pdb=" O ALA B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 54 removed outlier: 3.658A pdb=" N ALA B 51 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY B 53 " --> pdb=" O ASP B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 63 Processing helix chain 'B' and resid 68 through 92 removed outlier: 3.559A pdb=" N THR B 74 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 114 removed outlier: 3.545A pdb=" N TRP B 103 " --> pdb=" O ARG B 99 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLY B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL B 109 " --> pdb=" O THR B 105 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.719A pdb=" N ALA B 127 " --> pdb=" O ALA B 123 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 154 removed outlier: 3.752A pdb=" N PHE B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLN B 143 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 187 removed outlier: 3.582A pdb=" N PHE B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.667A pdb=" N ILE B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 210 " --> pdb=" O ILE B 206 " (cutoff:3.500A) 176 hydrogen bonds defined for protein. 501 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: 4.60 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.16: 2954 1.16 - 1.33: 935 1.33 - 1.51: 1032 1.51 - 1.69: 1101 1.69 - 1.86: 16 Bond restraints: 6038 Sorted by residual: bond pdb=" N SER A 131 " pdb=" H SER A 131 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NH1 ARG A 122 " pdb="HH11 ARG A 122 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" N ALA A 95 " pdb=" H ALA A 95 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NH2 ARG B 78 " pdb="HH22 ARG B 78 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N GLN A 191 " pdb=" H GLN A 191 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6033 not shown) Histogram of bond angle deviations from ideal: 100.03 - 106.85: 324 106.85 - 113.67: 6801 113.67 - 120.49: 2030 120.49 - 127.31: 1705 127.31 - 134.13: 30 Bond angle restraints: 10890 Sorted by residual: angle pdb=" N LEU B 36 " pdb=" CA LEU B 36 " pdb=" C LEU B 36 " ideal model delta sigma weight residual 114.56 103.25 11.31 1.27e+00 6.20e-01 7.92e+01 angle pdb=" N VAL B 109 " pdb=" CA VAL B 109 " pdb=" C VAL B 109 " ideal model delta sigma weight residual 110.30 103.58 6.72 9.70e-01 1.06e+00 4.81e+01 angle pdb=" N ARG B 159 " pdb=" CA ARG B 159 " pdb=" C ARG B 159 " ideal model delta sigma weight residual 112.92 104.87 8.05 1.23e+00 6.61e-01 4.29e+01 angle pdb=" N VAL A 47 " pdb=" CA VAL A 47 " pdb=" C VAL A 47 " ideal model delta sigma weight residual 111.05 103.32 7.73 1.25e+00 6.40e-01 3.83e+01 angle pdb=" N LEU A 90 " pdb=" CA LEU A 90 " pdb=" C LEU A 90 " ideal model delta sigma weight residual 114.39 106.42 7.97 1.45e+00 4.76e-01 3.02e+01 ... (remaining 10885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 2583 18.01 - 36.02: 171 36.02 - 54.02: 65 54.02 - 72.03: 23 72.03 - 90.04: 4 Dihedral angle restraints: 2846 sinusoidal: 1524 harmonic: 1322 Sorted by residual: dihedral pdb=" CB GLU B 180 " pdb=" CG GLU B 180 " pdb=" CD GLU B 180 " pdb=" OE1 GLU B 180 " ideal model delta sinusoidal sigma weight residual 0.00 90.04 -90.04 1 3.00e+01 1.11e-03 1.07e+01 dihedral pdb=" CB GLU B 26 " pdb=" CG GLU B 26 " pdb=" CD GLU B 26 " pdb=" OE1 GLU B 26 " ideal model delta sinusoidal sigma weight residual 0.00 -88.21 88.21 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" N ASP B 96 " pdb=" CA ASP B 96 " pdb=" CB ASP B 96 " pdb=" CG ASP B 96 " ideal model delta sinusoidal sigma weight residual -180.00 -120.07 -59.93 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 283 0.065 - 0.129: 133 0.129 - 0.194: 50 0.194 - 0.258: 13 0.258 - 0.323: 5 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA VAL B 109 " pdb=" N VAL B 109 " pdb=" C VAL B 109 " pdb=" CB VAL B 109 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA VAL A 47 " pdb=" N VAL A 47 " pdb=" C VAL A 47 " pdb=" CB VAL A 47 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA TYR B 62 " pdb=" N TYR B 62 " pdb=" C TYR B 62 " pdb=" CB TYR B 62 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 481 not shown) Planarity restraints: 922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 148 " 0.157 2.00e-02 2.50e+03 6.20e-02 1.15e+02 pdb=" CG TYR A 148 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR A 148 " -0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A 148 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR A 148 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A 148 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR A 148 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 148 " 0.109 2.00e-02 2.50e+03 pdb=" HD1 TYR A 148 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 TYR A 148 " -0.052 2.00e-02 2.50e+03 pdb=" HE1 TYR A 148 " -0.018 2.00e-02 2.50e+03 pdb=" HE2 TYR A 148 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 141 " 0.107 2.00e-02 2.50e+03 3.96e-02 4.70e+01 pdb=" CG PHE A 141 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 PHE A 141 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE A 141 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 141 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 141 " 0.014 2.00e-02 2.50e+03 pdb=" HD1 PHE A 141 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 PHE A 141 " -0.040 2.00e-02 2.50e+03 pdb=" HE1 PHE A 141 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE A 141 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 141 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 138 " -0.105 2.00e-02 2.50e+03 3.17e-02 4.02e+01 pdb=" CG TRP B 138 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP B 138 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 138 " 0.019 2.00e-02 2.50e+03 pdb=" NE1 TRP B 138 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 138 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 138 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 138 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 138 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 138 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP B 138 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 TRP B 138 " -0.004 2.00e-02 2.50e+03 pdb=" HE3 TRP B 138 " 0.031 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 138 " -0.021 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 138 " 0.010 2.00e-02 2.50e+03 pdb=" HH2 TRP B 138 " -0.021 2.00e-02 2.50e+03 ... (remaining 919 not shown) Histogram of nonbonded interaction distances: 1.20 - 1.88: 191 1.88 - 2.56: 5680 2.56 - 3.24: 19042 3.24 - 3.92: 24455 3.92 - 4.60: 37582 Nonbonded interactions: 86950 Sorted by model distance: nonbonded pdb=" HE3 MET B 178 " pdb="HD22 LEU B 203 " model vdw 1.201 2.440 nonbonded pdb=" H ALA B 127 " pdb=" H ARG B 128 " model vdw 1.227 2.100 nonbonded pdb=" O GLN B 125 " pdb=" H ALA B 127 " model vdw 1.252 1.850 nonbonded pdb=" H LEU B 36 " pdb=" H LEU B 37 " model vdw 1.342 2.100 nonbonded pdb=" HG3 ARG A 40 " pdb="HH11 ARG A 40 " model vdw 1.436 2.270 ... (remaining 86945 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 8 15.96 2 O 586 7.97 1 N 520 6.97 1 C 1908 5.97 2 H 2954 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: 2954 of 5976 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 5976 n_use_u_iso = 5976 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 = 5976 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (5976 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 5976 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 { nqh_flips = False 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 24 through 37 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 42 through 44 helix_type = alpha pi *3_10 unknown } helix { serial_number = "3" helix_identifier = "3" selection = chain 'A' and resid 47 through 54 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'A' and resid 58 through 64 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'A' and resid 68 through 90 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'A' and resid 101 through 116 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'A' and resid 118 through 127 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'A' and resid 132 through 158 } helix { serial_number = "9" helix_identifier = "9" selection = chain 'A' and resid 168 through 187 } helix { serial_number = "10" helix_identifier = "10" selection = chain 'A' and resid 199 through 211 } helix { serial_number = "11" helix_identifier = "11" selection = chain 'B' and resid 24 through 35 helix_type = alpha pi *3_10 unknown } helix { serial_number = "12" helix_identifier = "12" selection = chain 'B' and resid 47 through 54 } helix { serial_number = "13" helix_identifier = "13" selection = chain 'B' and resid 60 through 63 helix_type = alpha pi *3_10 unknown } helix { serial_number = "14" helix_identifier = "14" selection = chain 'B' and resid 68 through 92 } helix { serial_number = "15" helix_identifier = "15" selection = chain 'B' and resid 99 through 114 } helix { serial_number = "16" helix_identifier = "16" selection = chain 'B' and resid 118 through 130 } helix { serial_number = "17" helix_identifier = "17" selection = chain 'B' and resid 132 through 154 } helix { serial_number = "18" helix_identifier = "18" selection = chain 'B' and resid 168 through 187 } helix { serial_number = "19" helix_identifier = "19" selection = chain 'B' and resid 199 through 212 } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "1u9o_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 2954 occupancy sum: 2954.00 (% of total atoms 49.43) Rotatable: count: 874 occupancy sum: 874.00 (% of total atoms 14.63) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.3147 r_free= 0.3639 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ml) (work): 7.003758 | | target function (ml) not normalized (work): 54657.324350 | | target function (ml) not normalized (free): 2915.597919 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.48 - 4.76 0.96 2554 135 0.3296 0.3883 7.6147 7.643| | 2: 4.76 - 3.79 1.00 2644 139 0.3008 0.3414 7.0188 7.1475| | 3: 3.79 - 3.31 0.98 2606 137 0.3026 0.3485 6.3898 6.4985| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.48 - 4.76 2554 135 0.56 48.14 0.92 0.54 844097.77| | 2: 4.76 - 3.79 2644 139 0.62 43.00 1.24 0.73 373205.76| | 3: 3.79 - 3.31 2606 137 0.74 33.70 1.14 0.78 84339.63| |alpha: min = 0.54 max = 0.78 mean = 0.68| |beta: min = 84339.63 max = 844097.77 mean = 430852.23| |figures of merit: min = 0.01 max = 0.99 mean = 0.64| |phase err.(work): min = 6.22 max = 89.62 mean = 41.58| |phase err.(test): min = 8.18 max = 87.95 mean = 39.39| |-----------------------------------------------------------------------------| ----------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 : 0.010 0.071 3084 Z= 0.647 Angle : 1.426 11.305 4206 Z= 0.952 Chirality : 0.088 0.323 484 Planarity : 0.009 0.069 552 Dihedral : 15.917 90.038 1102 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 29.65 Ramachandran Plot: Outliers : 5.73 % Allowed : 20.83 % Favored : 73.44 % Rotamer: Outliers : 7.05 % Allowed : 6.41 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -7.23 (0.24), residues: 384 helix: -4.48 (0.16), residues: 286 sheet: None (None), residues: 0 loop : -4.93 (0.41), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A 181 TYR 0.129 0.017 TYR A 148 PHE 0.065 0.014 PHE A 141 TRP 0.072 0.010 TRP B 138 HIS 0.003 0.001 HIS B 169 Individual atomic B min max mean iso aniso Overall: 6.35 60.00 50.91 1.57 3022 0 Protein: 6.35 60.00 50.91 1.57 3022 0 Chain A: 6.35 60.00 49.62 N/A 1511 0 Chain B: 25.19 60.00 52.21 N/A 1511 0 Histogram: Values Number of atoms 6.35 - 11.71 1 11.71 - 17.08 1 17.08 - 22.45 0 22.45 - 27.81 5 27.81 - 33.18 12 33.18 - 38.54 109 38.54 - 43.91 375 43.91 - 49.27 750 49.27 - 54.64 743 54.64 - 60.00 1026 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.3147 r_free= 0.3639 coordinate error (max.-lik. estimate): 0.41 A | | | | normalized target function (ml) (work): 7.003758 | | target function (ml) not normalized (work): 54657.324350 | | target function (ml) not normalized (free): 2915.597919 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3173 0.3147 0.3639 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3173 0.3147 0.3639 n_refl.: 8215 remove outliers: r(all,work,free)=0.3173 0.3147 0.3639 n_refl.: 8215 overall B=19.06 to atoms: r(all,work,free)=0.3688 0.3662 0.4130 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2244 0.2218 0.2725 n_refl.: 8215 remove outliers: r(all,work,free)=0.2244 0.2218 0.2725 n_refl.: 8215 ======================== 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 19.484-12.760 91.74 95 5 0.2140 2101.007 1985.849 1.061 1.015 0.363 12.667-10.628 93.40 94 5 0.1444 2797.724 2757.347 1.135 1.012 0.357 10.620-8.919 89.94 153 8 0.1314 2794.309 2744.774 1.125 1.010 0.351 8.899-7.465 94.10 272 15 0.1747 2026.099 1969.520 1.129 1.007 0.343 7.459-6.262 96.09 468 24 0.2320 1345.638 1277.552 1.060 1.002 0.320 6.257-5.249 97.47 805 43 0.2137 1120.292 1077.800 0.933 0.996 0.267 5.246-4.401 98.85 1382 73 0.2029 1249.575 1192.160 0.988 0.986 0.235 4.399-3.690 99.80 2346 123 0.2350 936.813 886.466 1.076 0.973 0.119 3.688-3.311 97.83 2189 115 0.2945 565.805 509.627 1.024 0.960 0.041 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0231 b_overall=1.0130 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.321273 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.258016 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 0.2332 0.2705 0.0373 0.003 0.7 6.5 2.9 6.7 0 0.125 0.2313 0.2706 0.0393 0.004 0.7 6.4 3.1 6.7 0 0.250 0.2277 0.2705 0.0427 0.004 0.7 6.7 3.1 6.7 0 0.500 0.2233 0.2698 0.0465 0.004 0.7 7.5 3.1 6.7 0 1.000 0.2171 0.2717 0.0545 0.006 0.8 9.4 3.1 6.7 0 2.000 0.2134 0.2723 0.0589 0.007 0.9 11.6 3.4 7.1 0 3.000 0.2096 0.2720 0.0624 0.008 1.0 13.1 3.4 7.1 0 4.000 0.2069 0.2722 0.0654 0.009 1.1 14.7 3.4 7.1 0 5.000 0.2051 0.2730 0.0678 0.011 1.2 16.8 4.4 7.1 0 6.000 0.2026 0.2720 0.0693 0.012 1.2 16.8 5.2 7.4 0 7.000 0.2008 0.2719 0.0711 0.013 1.3 17.3 5.5 7.7 0 8.000 0.1991 0.2727 0.0735 0.013 1.3 18.3 6.0 7.7 0 9.000 0.1978 0.2727 0.0749 0.015 1.4 20.3 6.2 7.7 0 10.000 0.1990 0.2720 0.0731 0.014 1.3 19.6 5.7 8.0 0 9.161 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2332 0.2705 0.0373 0.003 0.7 6.5 2.9 6.7 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.32 27.05 3.73 1.120 69.771 0.258 0.060 23.39 27.17 3.78 1.759 69.844 0.008 0.060 22.98 27.12 4.14 1.827 69.904 0.032 0.058 21.99 26.97 4.98 3.416 70.207 0.129 0.054 20.81 26.96 6.15 7.469 71.186 0.258 0.048 20.40 27.01 6.61 9.279 71.813 0.387 0.046 20.14 27.10 6.96 10.658 72.296 0.516 0.045 20.00 27.19 7.19 11.575 72.595 0.645 0.045 19.90 27.25 7.35 12.288 72.828 0.774 0.044 19.80 27.31 7.50 12.941 73.046 0.903 0.044 19.69 27.36 7.66 13.746 73.329 1.032 0.043 19.64 27.40 7.76 14.214 73.482 1.161 0.043 19.56 27.45 7.88 14.853 73.704 1.290 0.043 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.129 Accepted refinement result: 21.99 26.97 4.98 3.416 70.207 0.129 0.054 Individual atomic B min max mean iso aniso Overall: 44.50 93.48 70.83 3.14 3022 0 Protein: 44.50 93.48 70.83 3.14 3022 0 Chain A: 44.50 92.20 69.32 N/A 1511 0 Chain B: 49.52 93.48 72.34 N/A 1511 0 Histogram: Values Number of atoms 44.50 - 49.40 3 49.40 - 54.30 43 54.30 - 59.19 186 59.19 - 64.09 459 64.09 - 68.99 656 68.99 - 73.89 627 73.89 - 78.79 455 78.79 - 83.68 334 83.68 - 88.58 207 88.58 - 93.48 52 =========================== Idealize ADP of riding H ========================== r_work=0.2199 r_free=0.2697 r_work=0.2182 r_free=0.2697 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.2182 r_free= 0.2697 coordinate error (max.-lik. estimate): 0.53 A | | | | normalized target function (ls_wunit_k1) (work): 0.052799 | | target function (ls_wunit_k1) not normalized (work): 412.039890 | | target function (ls_wunit_k1) not normalized (free): 32.875090 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2210 0.2182 0.2697 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3689 0.3671 0.4019 n_refl.: 8215 remove outliers: r(all,work,free)=0.3689 0.3671 0.4019 n_refl.: 8215 overall B=0.00 to atoms: r(all,work,free)=0.3689 0.3671 0.4019 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2196 0.2170 0.2671 n_refl.: 8215 remove outliers: r(all,work,free)=0.2196 0.2170 0.2671 n_refl.: 8215 ======================== 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 19.484-12.760 91.74 95 5 0.2080 1233.374 1174.252 1.123 1.034 0.370 12.667-10.628 93.40 94 5 0.1423 1642.375 1630.553 1.160 1.029 0.363 10.620-8.919 89.94 153 8 0.1296 1640.370 1616.218 1.157 1.026 0.352 8.899-7.465 94.10 272 15 0.1646 1189.400 1168.238 1.161 1.019 0.344 7.459-6.262 96.09 468 24 0.2235 789.943 755.693 1.105 1.010 0.340 6.257-5.249 97.47 805 43 0.2208 657.656 633.901 0.992 0.997 0.290 5.246-4.401 98.85 1382 73 0.1973 733.550 701.322 1.034 0.979 0.270 4.399-3.690 99.80 2346 123 0.2265 549.946 523.644 1.102 0.954 0.130 3.688-3.311 97.83 2189 115 0.2916 332.150 301.824 1.059 0.928 0.030 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=4.7430 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.042104 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.052661 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 0.2129 0.2598 0.0469 0.002 0.5 5.0 1.8 5.1 0 0.125 0.2074 0.2598 0.0523 0.003 0.6 5.9 2.9 5.4 0 0.250 0.2015 0.2599 0.0583 0.005 0.7 6.2 3.4 6.1 0 0.500 0.1972 0.2596 0.0623 0.008 0.8 8.7 3.9 6.4 0 1.000 0.1918 0.2596 0.0678 0.013 1.2 14.2 5.2 7.7 0 2.000 0.1891 0.2629 0.0738 0.019 1.5 16.9 5.7 10.3 0 3.000 0.1868 0.2643 0.0775 0.023 1.7 20.1 6.2 12.2 0 4.000 0.1854 0.2645 0.0791 0.026 1.9 20.3 6.0 13.1 0 5.000 0.1839 0.2656 0.0816 0.030 2.1 24.3 6.8 14.1 0 6.000 0.1827 0.2680 0.0853 0.033 2.4 27.6 8.1 16.3 0 7.000 0.1817 0.2686 0.0869 0.036 2.5 28.1 8.3 16.7 0 8.000 0.1807 0.2686 0.0879 0.039 2.7 29.3 7.8 17.3 0 9.000 0.1799 0.2711 0.0912 0.042 2.8 32.7 8.9 18.6 0 10.000 0.1920 0.2587 0.0667 0.014 1.2 14.6 5.5 7.7 0 2.021 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2129 0.2598 0.0469 0.002 0.5 5.0 1.8 5.1 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.29 25.98 4.69 10.206 77.750 0.053 6.436 22.75 26.31 3.56 8.703 79.803 0.002 6.470 21.57 25.83 4.26 10.351 77.651 0.007 6.437 21.24 25.95 4.71 10.271 77.709 0.026 6.434 19.94 25.48 5.54 11.995 77.998 0.053 6.383 19.67 25.52 5.85 12.540 78.485 0.079 6.377 19.54 25.59 6.06 12.994 78.764 0.105 6.375 19.54 25.69 6.15 13.090 78.779 0.132 6.376 19.47 25.70 6.23 13.424 78.971 0.158 6.375 19.42 25.73 6.30 13.720 79.129 0.184 6.374 19.38 25.75 6.37 13.983 79.259 0.211 6.374 19.35 25.79 6.43 14.225 79.375 0.237 6.374 19.33 25.81 6.48 14.446 79.477 0.263 6.374 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.053 Accepted refinement result: 19.94 25.48 5.54 11.995 77.998 0.053 6.383 Individual atomic B min max mean iso aniso Overall: 44.08 126.68 71.32 7.87 3022 0 Protein: 44.08 126.68 71.32 7.87 3022 0 Chain A: 44.08 123.05 69.32 N/A 1511 0 Chain B: 47.21 126.68 73.33 N/A 1511 0 Histogram: Values Number of atoms 44.08 - 52.34 115 52.34 - 60.60 600 60.60 - 68.86 908 68.86 - 77.12 578 77.12 - 85.38 344 85.38 - 93.64 202 93.64 - 101.90 121 101.90 - 110.16 78 110.16 - 118.42 57 118.42 - 126.68 19 =========================== Idealize ADP of riding H ========================== r_work=0.1994 r_free=0.2548 r_work=0.1988 r_free=0.2543 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.1988 r_free= 0.2543 coordinate error (max.-lik. estimate): 0.49 A | | | | normalized target function (ml) (work): 6.380052 | | target function (ml) not normalized (work): 49789.924637 | | target function (ml) not normalized (free): 2693.262933 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2016 0.1988 0.2543 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3572 0.3549 0.3971 n_refl.: 8215 remove outliers: r(all,work,free)=0.3572 0.3549 0.3971 n_refl.: 8215 overall B=1.20 to atoms: r(all,work,free)=0.3614 0.3591 0.4010 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2015 0.1986 0.2550 n_refl.: 8215 remove outliers: r(all,work,free)=0.2015 0.1986 0.2550 n_refl.: 8215 ======================== 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 19.484-12.760 91.74 95 5 0.1991 1233.374 1176.882 1.089 1.023 0.366 12.667-10.628 93.40 94 5 0.1383 1642.375 1627.963 1.147 1.019 0.363 10.620-8.919 89.94 153 8 0.1198 1640.370 1624.378 1.144 1.018 0.350 8.899-7.465 94.10 272 15 0.1511 1189.400 1169.257 1.164 1.012 0.342 7.459-6.262 96.09 468 24 0.2139 789.943 755.382 1.109 1.006 0.338 6.257-5.249 97.47 805 43 0.2151 657.656 632.992 1.010 0.997 0.287 5.246-4.401 98.85 1382 73 0.1806 733.550 702.072 1.020 0.983 0.257 4.399-3.690 99.80 2346 123 0.2032 549.946 524.201 1.073 0.965 0.118 3.688-3.311 97.83 2189 115 0.2562 332.150 306.226 1.024 0.946 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.3999 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1986 r_free=0.2550 After: r_work=0.1986 r_free=0.2550 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.249957 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.048578 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 0.1983 0.2547 0.0564 0.002 0.5 5.2 1.8 5.1 0 0.125 0.1976 0.2549 0.0573 0.003 0.5 5.5 1.8 5.1 0 0.250 0.1935 0.2535 0.0600 0.006 0.7 6.4 1.8 5.4 0 0.500 0.1858 0.2553 0.0695 0.009 1.0 8.2 2.6 4.8 0 1.000 0.1817 0.2560 0.0743 0.013 1.4 12.7 3.6 5.1 0 2.000 0.1791 0.2571 0.0780 0.016 1.7 14.6 4.2 5.8 0 3.000 0.1770 0.2577 0.0807 0.021 2.0 19.9 4.4 6.1 0 4.000 0.1750 0.2583 0.0832 0.024 2.3 22.3 5.5 7.1 0 5.000 0.1740 0.2588 0.0847 0.026 2.4 26.8 6.0 9.6 0 6.000 0.1729 0.2607 0.0879 0.029 2.7 27.6 6.0 10.3 0 7.000 0.1735 0.2596 0.0861 0.031 2.6 28.0 7.0 12.2 0 8.000 0.1716 0.2630 0.0914 0.033 2.8 30.8 6.5 12.5 0 9.000 0.1710 0.2648 0.0937 0.036 3.0 32.3 7.3 13.5 0 10.000 0.1815 0.2557 0.0742 0.013 1.4 13.1 3.6 5.1 0 2.125 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1983 0.2547 0.0564 0.002 0.5 5.2 1.8 5.1 0 0.125 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.83 25.47 5.64 11.573 79.371 0.049 6.381 22.28 26.31 4.03 7.771 85.157 0.001 6.429 21.68 25.39 3.71 10.027 82.973 0.006 6.422 19.92 25.35 5.43 11.569 79.127 0.024 6.382 19.83 25.47 5.64 11.573 79.371 0.049 6.381 19.77 25.47 5.71 11.686 79.295 0.073 6.379 19.54 25.51 5.97 12.203 79.047 0.097 6.374 18.89 25.52 6.63 13.601 79.710 0.121 6.363 18.89 25.61 6.73 13.766 79.648 0.146 6.362 18.83 25.66 6.83 14.041 79.801 0.170 6.362 18.79 25.69 6.91 14.286 79.931 0.194 6.362 18.75 25.72 6.97 14.508 80.046 0.219 6.362 18.72 25.75 7.03 14.721 80.157 0.243 6.362 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.024 Accepted refinement result: 19.92 25.35 5.43 11.569 79.127 0.024 6.382 Individual atomic B min max mean iso aniso Overall: 42.50 126.95 72.04 6.77 3022 0 Protein: 42.50 126.95 72.04 6.77 3022 0 Chain A: 42.50 123.52 69.95 N/A 1511 0 Chain B: 45.05 126.95 74.13 N/A 1511 0 Histogram: Values Number of atoms 42.50 - 50.94 56 50.94 - 59.39 460 59.39 - 67.84 895 67.84 - 76.28 688 76.28 - 84.73 412 84.73 - 93.17 217 93.17 - 101.62 132 101.62 - 110.06 69 110.06 - 118.51 73 118.51 - 126.95 20 =========================== Idealize ADP of riding H ========================== r_work=0.1992 r_free=0.2535 r_work=0.1994 r_free=0.2534 ----------X-ray data---------- |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.1994 r_free= 0.2534 coordinate error (max.-lik. estimate): 0.47 A | | | | normalized target function (ml) (work): 6.381762 | | target function (ml) not normalized (work): 49803.273790 | | target function (ml) not normalized (free): 2692.329136 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 19.48 - 4.76 0.96 2554 135 0.1848 0.2398 6.724 6.8593| | 2: 4.76 - 3.79 1.00 2644 139 0.1931 0.2397 6.4074 6.6287| | 3: 3.79 - 3.31 0.98 2606 137 0.2463 0.3115 6.0204 6.1675| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 19.48 - 4.76 2554 135 0.84 23.71 1.00 0.92 133510.76| | 2: 4.76 - 3.79 2644 139 0.83 25.13 1.00 0.91 83299.80| | 3: 3.79 - 3.31 2606 137 0.77 31.13 0.98 0.85 42043.20| |alpha: min = 0.85 max = 0.92 mean = 0.89| |beta: min = 42043.20 max = 133510.76 mean = 85955.37| |figures of merit: min = 0.02 max = 1.00 mean = 0.81| |phase err.(work): min = 0.00 max = 88.32 mean = 26.67| |phase err.(test): min = 0.00 max = 88.07 mean = 25.37| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2021 0.1994 0.2534 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3599 0.3577 0.3994 n_refl.: 8215 remove outliers: r(all,work,free)=0.3599 0.3577 0.3994 n_refl.: 8215 overall B=0.00 to atoms: r(all,work,free)=0.3599 0.3577 0.3994 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2023 0.1995 0.2535 n_refl.: 8215 remove outliers: r(all,work,free)=0.2023 0.1995 0.2535 n_refl.: 8215 ======================== 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 19.484-12.760 91.74 95 5 0.1983 1233.374 1177.200 1.104 1.010 0.366 12.667-10.628 93.40 94 5 0.1382 1642.375 1628.941 1.160 1.008 0.363 10.620-8.919 89.94 153 8 0.1196 1640.370 1624.446 1.155 1.007 0.351 8.899-7.465 94.10 272 15 0.1502 1189.400 1169.557 1.172 1.004 0.343 7.459-6.262 96.09 468 24 0.2153 789.943 755.065 1.113 1.000 0.340 6.257-5.249 97.47 805 43 0.2150 657.656 632.773 1.011 0.995 0.290 5.246-4.401 98.85 1382 73 0.1816 733.550 701.720 1.005 0.987 0.250 4.399-3.690 99.80 2346 123 0.2049 549.946 523.932 1.051 0.977 0.120 3.688-3.311 97.83 2189 115 0.2578 332.150 305.913 0.990 0.966 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=6.0402 ================= 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 : 0.3147 0.3639 0.010 1.426 6.3 60.0 50.9 0 0.000 1_bss: 0.2218 0.2725 0.010 1.426 25.4 79.1 70.0 0 0.000 1_settarget: 0.2218 0.2725 0.010 1.426 25.4 79.1 70.0 0 0.000 1_weight: 0.2218 0.2725 0.010 1.426 25.4 79.1 70.0 0 0.000 1_xyzrec: 0.2332 0.2705 0.003 0.668 25.4 79.1 70.0 0 0.182 1_adp: 0.2199 0.2697 0.003 0.668 44.5 93.5 70.8 0 0.182 1_regHadp: 0.2182 0.2697 0.003 0.668 44.5 93.5 70.8 0 0.182 2_bss: 0.2170 0.2671 0.003 0.668 44.5 93.5 70.8 0 0.182 2_settarget: 0.2170 0.2671 0.003 0.668 44.5 93.5 70.8 0 0.182 2_updatecdl: 0.2170 0.2671 0.004 0.741 44.5 93.5 70.8 0 0.182 2_weight: 0.2170 0.2671 0.004 0.741 44.5 93.5 70.8 0 0.182 2_xyzrec: 0.2129 0.2598 0.002 0.491 44.5 93.5 70.8 0 0.255 2_adp: 0.1994 0.2548 0.002 0.491 44.1 126.7 71.3 0 0.255 2_regHadp: 0.1988 0.2543 0.002 0.491 44.1 126.7 71.3 0 0.255 3_bss: 0.1986 0.2550 0.002 0.491 45.3 127.9 72.5 0 0.255 3_settarget: 0.1986 0.2550 0.002 0.491 45.3 127.9 72.5 0 0.255 3_updatecdl: 0.1986 0.2550 0.003 0.543 45.3 127.9 72.5 0 0.255 3_setrh: 0.1986 0.2550 0.003 0.543 45.3 127.9 72.5 0 0.255 3_weight: 0.1986 0.2550 0.003 0.543 45.3 127.9 72.5 0 0.255 3_xyzrec: 0.1983 0.2547 0.002 0.495 45.3 127.9 72.5 0 0.255 3_adp: 0.1992 0.2535 0.002 0.495 42.5 127.0 72.0 0 0.255 3_regHadp: 0.1994 0.2534 0.002 0.495 42.5 127.0 72.0 0 0.255 end: 0.1995 0.2535 0.002 0.495 42.5 127.0 72.0 0 0.255 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1u9o_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/1u9o_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 9.0800 Refinement macro-cycles (run) : 222.8700 Write final files (write_after_run_outputs) : 23.4700 Total : 255.4200 Total CPU time: 4.92 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:33:28 PDT -0700 (1716251608.31 s) Start R-work = 0.2218, R-free = 0.2725 Final R-work = 0.1995, R-free = 0.2535 =============================================================================== Job complete usr+sys time: 317.78 seconds wall clock time: 16 minutes 29.97 seconds (989.97 seconds total)