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/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+individual_sites_real_space ramachandran_plot_restraints.enabled=True secondary_structure.enabled=True main.nqh_flips=True Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u9o.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/1u9o.pdb" 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" } 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 Residue "B GLU 180": "OE1" <-> "OE2" Time to flip residues: 0.00s 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: 1.13, per 1000 atoms: 0.19 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: 1.35 Conformation dependent library (CDL) restraints added in 196.7 milliseconds 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. 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: 0.43 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: 1.46 Time building geometry restraints manager: 1.56 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 { 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 } ramachandran_plot_restraints { 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 ============================ Update phi&psi targets =========================== 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ================================== NQH flips ================================== r_work=0.2218 r_free=0.2725 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.2218 r_free=0.2725 ========================= Local real-space refinement ========================= Before: r_work=0.2218 r_free=0.2725 113 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 91 time to evaluate : 0.245 outliers start: 22 outliers final: 13 residues processed: 22 average time/residue: 0.1421 time to fit residues: 4.6525 After: r_work=0.2221 r_free=0.2754 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 18.267900 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.258141 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 0.2307 0.2715 0.0408 0.005 0.9 10.2 0.5 5.1 0 0.125 0.2301 0.2718 0.0417 0.005 0.9 10.1 0.5 5.1 0 0.250 0.2287 0.2712 0.0424 0.006 0.9 10.9 0.5 5.4 0 0.500 0.2257 0.2709 0.0452 0.006 0.9 12.4 0.5 5.4 0 1.000 0.2213 0.2704 0.0491 0.007 1.0 12.7 0.5 5.8 0 2.000 0.2164 0.2699 0.0535 0.008 1.0 12.4 0.5 5.8 0 3.000 0.2139 0.2720 0.0581 0.009 1.1 12.9 0.5 5.8 0 4.000 0.2109 0.2727 0.0618 0.011 1.1 14.7 0.5 5.8 0 5.000 0.2086 0.2730 0.0643 0.012 1.2 16.1 0.8 6.1 0 6.000 0.2070 0.2720 0.0649 0.014 1.3 16.8 0.8 6.1 0 7.000 0.2041 0.2736 0.0696 0.014 1.3 17.6 0.8 6.1 0 8.000 0.2024 0.2738 0.0714 0.015 1.4 19.1 0.8 6.1 0 9.000 0.2007 0.2730 0.0723 0.015 1.5 18.4 0.8 6.1 0 10.000 0.2021 0.2734 0.0713 0.015 1.4 18.9 0.8 6.1 0 9.134 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2301 0.2718 0.0417 0.005 0.9 10.1 0.5 5.1 0 0.250 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2301 r_free=0.2718 116 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.411 outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1220 time to fit residues: 3.3992 After: r_work=0.2334 r_free=0.2746 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.34 27.46 4.12 1.120 69.771 0.258 0.060 23.41 27.50 4.09 1.782 69.842 0.008 0.060 23.00 27.48 4.48 1.843 69.897 0.032 0.058 22.00 27.38 5.38 3.468 70.207 0.129 0.053 20.83 27.35 6.52 7.479 71.165 0.258 0.048 20.51 27.41 6.90 8.931 71.612 0.387 0.047 20.15 27.41 7.26 10.673 72.283 0.516 0.045 20.01 27.45 7.44 11.592 72.585 0.645 0.045 19.90 27.49 7.59 12.315 72.823 0.774 0.044 19.82 27.52 7.69 12.903 73.015 0.903 0.044 19.76 27.55 7.79 13.398 73.176 1.033 0.044 19.65 27.56 7.92 14.227 73.471 1.162 0.043 19.57 27.58 8.01 14.862 73.691 1.291 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: 22.00 27.38 5.38 3.468 70.207 0.129 0.053 Individual atomic B min max mean iso aniso Overall: 44.85 97.13 70.83 3.15 3022 0 Protein: 44.85 97.13 70.83 3.15 3022 0 Chain A: 44.85 92.76 69.31 N/A 1511 0 Chain B: 51.08 97.13 72.36 N/A 1511 0 Histogram: Values Number of atoms 44.85 - 50.08 7 50.08 - 55.31 55 55.31 - 60.53 281 60.53 - 65.76 580 65.76 - 70.99 704 70.99 - 76.22 579 76.22 - 81.45 394 81.45 - 86.67 304 86.67 - 91.90 108 91.90 - 97.13 10 =========================== Idealize ADP of riding H ========================== r_work=0.2200 r_free=0.2738 r_work=0.2183 r_free=0.2738 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.2183 r_free= 0.2738 coordinate error (max.-lik. estimate): 0.55 A | | | | normalized target function (ls_wunit_k1) (work): 0.052539 | | target function (ls_wunit_k1) not normalized (work): 410.012527 | | target function (ls_wunit_k1) not normalized (free): 34.311206 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2213 0.2183 0.2738 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3666 0.3642 0.4083 n_refl.: 8215 remove outliers: r(all,work,free)=0.3666 0.3642 0.4083 n_refl.: 8215 overall B=0.00 to atoms: r(all,work,free)=0.3666 0.3642 0.4083 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2205 0.2175 0.2728 n_refl.: 8215 remove outliers: r(all,work,free)=0.2205 0.2175 0.2728 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 0.2131 1234.728 1167.003 1.053 1.023 0.360 12.667-10.628 93.40 94 5 0.1459 1644.178 1624.780 1.139 1.019 0.357 10.620-8.919 89.94 153 8 0.1316 1642.171 1614.655 1.136 1.017 0.348 8.899-7.465 94.10 272 15 0.1646 1190.706 1171.311 1.145 1.011 0.340 7.459-6.262 96.09 468 24 0.2318 790.810 753.393 1.081 1.005 0.330 6.257-5.249 97.47 805 43 0.2229 658.378 634.798 0.962 0.995 0.280 5.246-4.401 98.85 1382 73 0.1947 734.356 702.586 0.998 0.981 0.250 4.399-3.690 99.80 2346 123 0.2255 550.550 524.442 1.074 0.962 0.120 3.688-3.311 97.83 2189 115 0.2928 332.515 302.190 1.025 0.943 0.020 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.5781 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ================================== NQH flips ================================== r_work=0.2175 r_free=0.2728 Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS B 108 ASN B 125 GLN Total number of N/Q/H flips: 3 r_work=0.2177 r_free=0.2720 ========================= Local real-space refinement ========================= Before: r_work=0.2177 r_free=0.2720 96 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.879 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9226 After: r_work=0.2177 r_free=0.2720 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.013580 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.054539 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 0.2161 0.2628 0.0467 0.003 0.5 4.7 0.3 0.3 0 0.125 0.2110 0.2624 0.0514 0.004 0.6 6.5 0.3 1.3 0 0.250 0.2053 0.2606 0.0553 0.005 0.7 7.0 0.3 2.6 0 0.500 0.1997 0.2633 0.0636 0.009 0.9 9.9 0.3 4.2 0 1.000 0.1940 0.2643 0.0703 0.014 1.2 12.9 0.3 6.7 0 2.000 0.1907 0.2646 0.0739 0.019 1.5 18.3 0.3 10.9 0 3.000 0.1885 0.2655 0.0770 0.023 1.7 20.3 0.8 11.9 0 4.000 0.1866 0.2662 0.0796 0.026 1.9 21.9 0.8 12.8 0 5.000 0.1850 0.2669 0.0819 0.030 2.1 26.6 1.0 14.4 0 6.000 0.1837 0.2689 0.0852 0.033 2.3 28.3 1.0 16.0 0 7.000 0.1830 0.2692 0.0863 0.036 2.5 29.5 1.0 17.0 0 8.000 0.1818 0.2702 0.0884 0.039 2.6 30.2 1.3 17.6 0 9.000 0.1808 0.2717 0.0909 0.042 2.8 32.2 1.6 17.6 0 10.000 0.1942 0.2648 0.0706 0.014 1.2 12.7 0.3 6.7 0 2.007 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2161 0.2628 0.0467 0.003 0.5 4.7 0.3 0.3 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.2161 r_free=0.2628 106 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.466 outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3793 time to fit residues: 2.2269 After: r_work=0.2162 r_free=0.2621 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 21.62 26.21 4.59 10.211 77.761 0.055 6.448 23.03 26.49 3.47 8.702 79.964 0.002 6.480 21.87 26.07 4.20 10.379 77.645 0.007 6.448 21.55 26.19 4.64 10.287 77.711 0.027 6.445 20.23 25.76 5.54 12.004 77.817 0.055 6.397 19.91 25.70 5.79 12.633 78.443 0.082 6.388 19.86 25.84 5.98 12.878 78.577 0.109 6.388 19.77 25.87 6.10 13.305 78.829 0.136 6.386 19.70 25.91 6.21 13.678 79.031 0.164 6.385 19.65 25.97 6.32 14.021 79.198 0.191 6.384 19.61 25.99 6.38 14.324 79.337 0.218 6.384 19.59 26.01 6.42 14.578 79.447 0.245 6.383 19.56 26.03 6.47 14.815 79.549 0.273 6.383 max suggested for this run: 20.00 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.082 Accepted refinement result: 19.91 25.70 5.79 12.633 78.443 0.082 6.388 Individual atomic B min max mean iso aniso Overall: 44.15 141.65 72.18 9.90 3022 0 Protein: 44.15 141.65 72.18 9.90 3022 0 Chain A: 44.15 126.25 70.23 N/A 1511 0 Chain B: 46.08 141.65 74.13 N/A 1511 0 Histogram: Values Number of atoms 44.15 - 53.90 194 53.90 - 63.65 852 63.65 - 73.40 888 73.40 - 83.15 452 83.15 - 92.90 288 92.90 - 102.65 163 102.65 - 112.40 91 112.40 - 122.15 76 122.15 - 131.90 15 131.90 - 141.65 3 =========================== Idealize ADP of riding H ========================== r_work=0.1991 r_free=0.2570 r_work=0.1982 r_free=0.2566 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.1982 r_free= 0.2566 coordinate error (max.-lik. estimate): 0.49 A | | | | normalized target function (ml) (work): 6.384385 | | target function (ml) not normalized (work): 49823.741913 | | target function (ml) not normalized (free): 2696.573094 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2012 0.1982 0.2566 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3574 0.3548 0.4014 n_refl.: 8215 remove outliers: r(all,work,free)=0.3574 0.3548 0.4014 n_refl.: 8215 overall B=0.00 to atoms: r(all,work,free)=0.3574 0.3548 0.4014 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2009 0.1978 0.2575 n_refl.: 8215 remove outliers: r(all,work,free)=0.2009 0.1978 0.2575 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 0.2037 1234.728 1173.255 1.139 1.013 0.370 12.667-10.628 93.40 94 5 0.1399 1644.178 1630.040 1.165 1.010 0.363 10.620-8.919 89.94 153 8 0.1177 1642.171 1625.659 1.154 1.009 0.351 8.899-7.465 94.10 272 15 0.1477 1190.706 1169.732 1.173 1.006 0.346 7.459-6.262 96.09 468 24 0.2143 790.810 755.012 1.099 1.002 0.323 6.257-5.249 97.47 805 43 0.2154 658.378 633.669 1.015 0.996 0.290 5.246-4.401 98.85 1382 73 0.1784 734.356 703.344 1.001 0.988 0.240 4.399-3.690 99.80 2346 123 0.2008 550.550 525.543 1.059 0.977 0.120 3.688-3.311 97.83 2189 115 0.2595 332.515 305.890 0.994 0.965 0.030 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.8163 ============================ Set refinement target ============================ using refinement target ml ============================ Update phi&psi targets =========================== 768 Ramachandran restraints generated. 384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2. ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.1978 r_free=0.2575 After: r_work=0.1978 r_free=0.2575 ================================== NQH flips ================================== r_work=0.1978 r_free=0.2575 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle r_work=0.1978 r_free=0.2575 ========================= Local real-space refinement ========================= Before: r_work=0.1978 r_free=0.2575 115 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.191 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1042 After: r_work=0.1978 r_free=0.2575 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 4.337890 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.048438 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 0.1979 0.2577 0.0598 0.003 0.5 5.4 0.3 0.0 0 0.125 0.1973 0.2577 0.0604 0.003 0.5 5.7 0.3 0.0 0 0.250 0.1940 0.2578 0.0638 0.006 0.7 6.9 0.3 0.0 0 0.500 0.1862 0.2600 0.0737 0.010 1.2 9.4 0.3 0.0 0 1.000 0.1815 0.2619 0.0805 0.014 1.5 14.1 0.5 0.6 0 2.000 0.1802 0.2619 0.0817 0.016 1.6 15.9 1.0 1.6 0 3.000 0.1775 0.2631 0.0856 0.020 1.9 18.8 1.6 3.2 0 4.000 0.1760 0.2641 0.0881 0.024 2.2 21.6 1.8 3.8 0 5.000 0.1750 0.2655 0.0905 0.026 2.3 24.3 2.3 6.4 0 6.000 0.1740 0.2660 0.0921 0.029 2.5 26.0 2.3 8.7 0 7.000 0.1727 0.2662 0.0935 0.031 2.7 29.0 2.3 9.9 0 8.000 0.1716 0.2674 0.0958 0.034 2.8 30.2 2.9 10.9 0 9.000 0.1710 0.2683 0.0973 0.036 3.0 32.3 2.9 11.5 0 10.000 0.1811 0.2627 0.0817 0.015 1.5 14.7 0.5 0.6 0 2.169 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1979 0.2577 0.0598 0.003 0.5 5.4 0.3 0.0 0 0.125 ===================== Post-minimization rotamer correction ==================== Before: r_work=0.1979 r_free=0.2577 112 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.402 outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2363 After: r_work=0.1979 r_free=0.2577 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 19.79 25.77 5.98 12.484 79.203 0.048 6.387 23.16 26.63 3.47 9.620 85.712 0.001 6.453 22.28 26.06 3.79 11.058 84.021 0.006 6.439 19.99 25.59 5.61 12.258 78.888 0.024 6.388 19.76 25.75 6.00 12.505 79.131 0.048 6.386 19.60 25.76 6.16 12.843 78.895 0.073 6.382 19.54 25.78 6.24 13.012 78.858 0.097 6.381 19.17 25.53 6.36 13.716 79.264 0.121 6.371 19.11 25.64 6.53 14.026 79.256 0.145 6.371 19.04 25.66 6.62 14.285 79.401 0.170 6.370 18.99 25.68 6.69 14.523 79.522 0.194 6.369 18.95 25.69 6.74 14.738 79.627 0.218 6.369 18.92 25.71 6.79 14.927 79.714 0.242 6.369 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: 19.99 25.59 5.61 12.258 78.888 0.024 6.388 Individual atomic B min max mean iso aniso Overall: 41.17 140.76 71.56 7.70 3022 0 Protein: 41.17 140.76 71.56 7.70 3022 0 Chain A: 41.17 125.75 69.52 N/A 1511 0 Chain B: 46.08 140.76 73.60 N/A 1511 0 Histogram: Values Number of atoms 41.17 - 51.13 103 51.13 - 61.09 697 61.09 - 71.05 979 71.05 - 81.01 578 81.01 - 90.97 313 90.97 - 100.93 166 100.93 - 110.88 85 110.88 - 120.84 85 120.84 - 130.80 14 130.80 - 140.76 2 =========================== Idealize ADP of riding H ========================== r_work=0.1999 r_free=0.2559 r_work=0.2002 r_free=0.2559 ----------X-ray data---------- |--(resolution: 3.31 - 19.48 A, n_refl.=8215 (all), 5.00 % free)-------------| | | | r_work= 0.2002 r_free= 0.2559 coordinate error (max.-lik. estimate): 0.48 A | | | | normalized target function (ml) (work): 6.388277 | | target function (ml) not normalized (work): 49854.113955 | | target function (ml) not normalized (free): 2695.960113 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | 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 0.1851 0.2424 6.7314 6.8717| | 2: 4.76 - 3.79 1.00 2644 139 0.1921 0.2442 6.4131 6.6378| | 3: 3.79 - 3.31 0.98 2606 137 0.2517 0.3099 6.0268 6.1724| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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 0.83 24.03 1.00 0.91 137219.80| | 2: 4.76 - 3.79 2644 139 0.83 25.35 1.00 0.90 84799.31| | 3: 3.79 - 3.31 2606 137 0.77 31.18 0.98 0.84 41872.77| |alpha: min = 0.84 max = 0.91 mean = 0.88| |beta: min = 41872.77 max = 137219.80 mean = 87620.34| |figures of merit: min = 0.01 max = 1.00 mean = 0.81| |phase err.(work): min = 0.00 max = 89.06 mean = 26.86| |phase err.(test): min = 0.00 max = 83.38 mean = 25.41| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2031 0.2002 0.2559 n_refl.: 8215 re-set all scales: r(all,work,free)=0.3568 0.3544 0.3990 n_refl.: 8215 remove outliers: r(all,work,free)=0.3568 0.3544 0.3990 n_refl.: 8215 overall B=1.23 to atoms: r(all,work,free)=0.3611 0.3587 0.4031 n_refl.: 8215 bulk-solvent and scaling: r(all,work,free)=0.2029 0.2001 0.2553 n_refl.: 8215 remove outliers: r(all,work,free)=0.2029 0.2001 0.2553 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 0.2032 1234.728 1173.504 1.123 1.018 0.369 12.667-10.628 93.40 94 5 0.1404 1644.178 1630.291 1.152 1.015 0.362 10.620-8.919 89.94 153 8 0.1174 1642.171 1625.277 1.145 1.013 0.350 8.899-7.465 94.10 272 15 0.1488 1190.706 1171.303 1.165 1.009 0.342 7.459-6.262 96.09 468 24 0.2159 790.810 755.707 1.110 1.003 0.338 6.257-5.249 97.47 805 43 0.2166 658.378 633.264 1.016 0.996 0.287 5.246-4.401 98.85 1382 73 0.1810 734.356 702.253 1.009 0.985 0.247 4.399-3.690 99.80 2346 123 0.2039 550.550 525.013 1.069 0.970 0.118 3.688-3.311 97.83 2189 115 0.2629 332.515 305.159 1.012 0.955 0.019 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.1000 b_overall=5.5405 ================= 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_updatephipsi: 0.2218 0.2725 0.010 1.426 25.4 79.1 70.0 0 0.000 1_nqh: 0.2218 0.2725 0.010 1.426 25.4 79.1 70.0 0 0.000 1_realsrl: 0.2221 0.2754 0.011 1.432 25.4 79.1 70.0 0 0.011 1_weight: 0.2221 0.2754 0.011 1.432 25.4 79.1 70.0 0 0.011 1_xyzrec: 0.2301 0.2718 0.005 0.881 25.4 79.1 70.0 0 0.142 1_realsrl2: 0.2334 0.2746 0.005 0.881 25.4 79.1 70.0 0 0.155 1_adp: 0.2200 0.2738 0.005 0.881 44.9 97.1 70.8 0 0.155 1_regHadp: 0.2183 0.2738 0.005 0.881 44.9 97.1 70.8 0 0.155 2_bss: 0.2175 0.2728 0.005 0.881 44.9 97.1 70.8 0 0.155 2_settarget: 0.2175 0.2728 0.005 0.881 44.9 97.1 70.8 0 0.155 2_updatephipsi: 0.2175 0.2728 0.005 0.881 44.9 97.1 70.8 0 0.155 2_updatecdl: 0.2175 0.2728 0.005 0.927 44.9 97.1 70.8 0 0.155 2_nqh: 0.2177 0.2720 0.005 0.927 44.9 97.1 70.8 0 0.161 2_realsrl: 0.2177 0.2720 0.005 0.927 44.9 97.1 70.8 0 0.161 2_weight: 0.2177 0.2720 0.005 0.927 44.9 97.1 70.8 0 0.161 2_xyzrec: 0.2161 0.2628 0.003 0.533 44.9 97.1 70.8 0 0.261 2_realsrl2: 0.2162 0.2621 0.003 0.533 44.9 97.1 70.8 0 0.261 2_adp: 0.1991 0.2570 0.003 0.533 44.2 141.6 72.2 0 0.261 2_regHadp: 0.1982 0.2566 0.003 0.533 44.2 141.6 72.2 0 0.261 3_bss: 0.1978 0.2575 0.003 0.533 44.2 141.6 72.2 0 0.261 3_settarget: 0.1978 0.2575 0.003 0.533 44.2 141.6 72.2 0 0.261 3_updatephipsi: 0.1978 0.2575 0.003 0.533 44.2 141.6 72.2 0 0.261 3_updatecdl: 0.1978 0.2575 0.003 0.577 44.2 141.6 72.2 0 0.261 3_setrh: 0.1978 0.2575 0.003 0.577 44.2 141.6 72.2 0 0.261 3_nqh: 0.1978 0.2575 0.003 0.577 44.2 141.6 72.2 0 0.261 3_realsrl: 0.1978 0.2575 0.003 0.577 44.2 141.6 72.2 0 0.261 3_weight: 0.1978 0.2575 0.003 0.577 44.2 141.6 72.2 0 0.261 3_xyzrec: 0.1979 0.2577 0.003 0.538 44.2 141.6 72.2 0 0.263 3_realsrl2: 0.1979 0.2577 0.003 0.538 44.2 141.6 72.2 0 0.263 3_adp: 0.1999 0.2559 0.003 0.538 41.2 140.8 71.6 0 0.263 3_regHadp: 0.2002 0.2559 0.003 0.538 41.2 140.8 71.6 0 0.263 end: 0.2001 0.2553 0.003 0.538 42.4 142.0 72.8 0 0.263 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1u9o_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V0/1u9o_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 4.5500 Refinement macro-cycles (run) : 280.4900 Write final files (write_after_run_outputs) : 23.8300 Total : 308.8700 Total CPU time: 5.52 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:31:28 PDT -0700 (1716251488.30 s) Start R-work = 0.2218, R-free = 0.2725 Final R-work = 0.2001, R-free = 0.2553 =============================================================================== Job complete usr+sys time: 354.31 seconds wall clock time: 16 minutes 39.07 seconds (999.07 seconds total)