Starting phenix.refine on Mon May 20 17:17:36 2024 by afonine =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/3fm7.pdb Found miller_array, /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.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/3fm7/3fm7.mtz" } default_miller_array = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/original/3fm7/3fm7.mtz" model { file = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/3fm7.pdb" } default_model = "/net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/finalised/3fm7.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 None Time to flip residues: 0.00s Monomer Library directory: "/net/anaconda/raid1/afonine/phenix3/modules/chem_data/mon_lib" Total number of atoms: 6838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1598 Classifications: {'peptide': 103} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "B" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1609 Classifications: {'peptide': 104} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain: "C" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 23} Chain: "D" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 435 Classifications: {'peptide': 27} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 24} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1381 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "F" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1380 Classifications: {'peptide': 85} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 82} Time building chain proxies: 2.45, per 1000 atoms: 0.36 Number of scatterers: 6838 At special positions: 0 Unit cell: (115.79, 115.79, 90.5004, 90, 90, 120) Space group: P 62 (No. 171) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 22 16.00 O 666 8.00 N 569 7.00 C 2187 6.00 H 3394 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: 6.44 Conformation dependent library (CDL) restraints added in 860.3 milliseconds Adding C-beta torsion restraints... Number of C-beta restraints generated: 818 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 8 helices and 4 sheets defined 28.5% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 12 through 22 removed outlier: 3.750A pdb=" N LYS A 17 " --> pdb=" O ASP A 13 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 19 " --> pdb=" O VAL A 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 53 removed outlier: 5.803A pdb=" N ASN A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR A 41 " --> pdb=" O ASN A 38 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 42 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN A 47 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N CYS A 48 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL A 51 " --> pdb=" O CYS A 48 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 53 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 26 removed outlier: 4.854A pdb=" N THR B 18 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 48 removed outlier: 4.661A pdb=" N ASN B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ASN B 39 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 31 removed outlier: 3.637A pdb=" N GLU E 30 " --> pdb=" O THR E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 50 Processing helix chain 'F' and resid 16 through 31 removed outlier: 3.603A pdb=" N GLN F 27 " --> pdb=" O ASP F 23 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 49 Processing sheet with id= A, first strand: chain 'A' and resid 60 through 69 removed outlier: 3.531A pdb=" N MET A 68 " --> pdb=" O TYR A 101 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR A 101 " --> pdb=" O MET A 68 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 59 through 69 Processing sheet with id= C, first strand: chain 'E' and resid 54 through 59 removed outlier: 6.114A pdb=" N TYR E 77 " --> pdb=" O ILE E 8 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N ILE E 8 " --> pdb=" O TYR E 77 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 54 through 59 removed outlier: 6.889A pdb=" N TYR F 77 " --> pdb=" O ILE F 8 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE F 8 " --> pdb=" O TYR F 77 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 366 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: 4.74 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.15: 3382 1.15 - 1.31: 591 1.31 - 1.48: 1393 1.48 - 1.64: 1508 1.64 - 1.81: 32 Bond restraints: 6906 Sorted by residual: bond pdb=" NE2 GLN A 33 " pdb="HE21 GLN A 33 " 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 E 82 " pdb=" H ALA E 82 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" NE2 GLN F 27 " pdb="HE21 GLN F 27 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" NE2 GLN D 116 " pdb="HE21 GLN D 116 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" N PHE F 86 " pdb=" H PHE F 86 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 6901 not shown) Histogram of bond angle deviations from ideal: 100.88 - 107.50: 230 107.50 - 114.12: 8500 114.12 - 120.73: 1545 120.73 - 127.35: 2144 127.35 - 133.97: 26 Bond angle restraints: 12445 Sorted by residual: angle pdb=" C ASN F 51 " pdb=" N PRO F 52 " pdb=" CA PRO F 52 " ideal model delta sigma weight residual 119.89 122.75 -2.86 1.02e+00 9.61e-01 7.84e+00 angle pdb=" N VAL E 7 " pdb=" CA VAL E 7 " pdb=" C VAL E 7 " ideal model delta sigma weight residual 106.72 111.14 -4.42 1.59e+00 3.96e-01 7.74e+00 angle pdb=" N ASN C 119 " pdb=" CA ASN C 119 " pdb=" C ASN C 119 " ideal model delta sigma weight residual 107.61 112.16 -4.55 1.74e+00 3.30e-01 6.84e+00 angle pdb=" N ASN E 10 " pdb=" CA ASN E 10 " pdb=" C ASN E 10 " ideal model delta sigma weight residual 107.93 112.20 -4.27 1.65e+00 3.67e-01 6.71e+00 angle pdb=" CA GLY A 72 " pdb=" C GLY A 72 " pdb=" N ALA A 73 " ideal model delta sigma weight residual 118.67 116.19 2.48 9.80e-01 1.04e+00 6.40e+00 ... (remaining 12440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.78: 2904 26.78 - 53.56: 289 53.56 - 80.34: 53 80.34 - 107.12: 5 107.12 - 133.91: 2 Dihedral angle restraints: 3253 sinusoidal: 1731 harmonic: 1522 Sorted by residual: dihedral pdb=" CA MET F 13 " pdb=" C MET F 13 " pdb=" N SER F 14 " pdb=" CA SER F 14 " ideal model delta harmonic sigma weight residual 180.00 46.09 133.91 0 5.00e+00 4.00e-02 7.17e+02 dihedral pdb=" CA ASN C 114 " pdb=" C ASN C 114 " pdb=" N VAL C 115 " pdb=" CA VAL C 115 " ideal model delta harmonic sigma weight residual 180.00 52.83 127.17 0 5.00e+00 4.00e-02 6.47e+02 dihedral pdb=" CA MET E 13 " pdb=" C MET E 13 " pdb=" N SER E 14 " pdb=" CA SER E 14 " ideal model delta harmonic sigma weight residual -180.00 -75.18 -104.82 0 5.00e+00 4.00e-02 4.39e+02 ... (remaining 3250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.022: 437 0.022 - 0.043: 11 0.043 - 0.065: 19 0.065 - 0.087: 59 0.087 - 0.108: 13 Chirality restraints: 539 Sorted by residual: chirality pdb=" CA ASN D 114 " pdb=" N ASN D 114 " pdb=" C ASN D 114 " pdb=" CB ASN D 114 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 2.93e-01 chirality pdb=" CA ILE B 103 " pdb=" N ILE B 103 " pdb=" C ILE B 103 " pdb=" CB ILE B 103 " both_signs ideal model delta sigma weight residual False 2.43 2.53 -0.09 2.00e-01 2.50e+01 2.10e-01 chirality pdb=" CA ILE B 23 " pdb=" N ILE B 23 " pdb=" C ILE B 23 " pdb=" CB ILE B 23 " both_signs ideal model delta sigma weight residual False 2.43 2.52 -0.09 2.00e-01 2.50e+01 2.04e-01 ... (remaining 536 not shown) Planarity restraints: 1018 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 40 " -0.000 2.00e-02 2.50e+03 7.01e-04 1.97e-02 pdb=" CG TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 40 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP B 40 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP B 40 " -0.001 2.00e-02 2.50e+03 pdb=" HE3 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 40 " 0.001 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 40 " -0.002 2.00e-02 2.50e+03 pdb=" HH2 TRP B 40 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 46 " 0.000 2.00e-02 2.50e+03 7.99e-04 1.91e-02 pdb=" CG PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE F 46 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 46 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 46 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE F 46 " -0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE F 46 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE F 46 " 0.001 2.00e-02 2.50e+03 pdb=" HZ PHE F 46 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 54 " -0.000 2.00e-02 2.50e+03 6.55e-04 1.72e-02 pdb=" CG TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CD1 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" HD1 TRP E 54 " -0.000 2.00e-02 2.50e+03 pdb=" HE1 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" HE3 TRP E 54 " 0.002 2.00e-02 2.50e+03 pdb=" HZ2 TRP E 54 " 0.000 2.00e-02 2.50e+03 pdb=" HZ3 TRP E 54 " -0.001 2.00e-02 2.50e+03 pdb=" HH2 TRP E 54 " 0.000 2.00e-02 2.50e+03 ... (remaining 1015 not shown) Histogram of nonbonded interaction distances: 0.75 - 1.52: 46 1.52 - 2.29: 1632 2.29 - 3.06: 20346 3.06 - 3.83: 29944 3.83 - 4.60: 47504 Warning: very small nonbonded interaction distances. Nonbonded interactions: 99472 Sorted by model distance: nonbonded pdb=" HA ASN C 114 " pdb="HG23 VAL C 115 " model vdw 0.746 2.440 nonbonded pdb=" HG3 GLN C 133 " pdb=" HB3 LYS F 36 " model vdw 0.848 2.440 nonbonded pdb=" HA GLN C 116 " pdb=" HB2 ALA C 117 " model vdw 0.871 2.440 nonbonded pdb=" HG2 ARG B 94 " pdb="HH11 ARG B 94 " model vdw 0.985 2.270 nonbonded pdb=" HA MET F 13 " pdb=" HB2 SER F 14 " model vdw 1.040 2.440 ... (remaining 99467 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 22 15.91 1 O 666 7.97 1 N 569 6.97 1 C 2187 5.97 1 H 3394 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: 3394 of 6838 ******************************************************************************* Automatic adjustment: hydrogens.refine=riding ******************************************************************************* n_use = 6838 n_use_u_iso = 6838 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 = 6838 ================== Extract refinement strategy and selections ================= Refinement flags and selection counts: individual_sites = True (6838 atoms) torsion_angles = False (0 atoms) rigid_body = False (0 atoms in 0 groups) individual_adp = True (iso = 6838 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 12 through 22 } helix { serial_number = "2" helix_identifier = "2" selection = chain 'A' and resid 34 through 53 helix_type = alpha pi *3_10 unknown } helix { serial_number = "3" helix_identifier = "3" selection = chain 'B' and resid 13 through 26 } helix { serial_number = "4" helix_identifier = "4" selection = chain 'B' and resid 34 through 48 } helix { serial_number = "5" helix_identifier = "5" selection = chain 'E' and resid 16 through 31 } helix { serial_number = "6" helix_identifier = "6" selection = chain 'E' and resid 35 through 50 } helix { serial_number = "7" helix_identifier = "7" selection = chain 'F' and resid 16 through 31 } helix { serial_number = "8" helix_identifier = "8" selection = chain 'F' and resid 35 through 49 } sheet { first_strand = chain 'A' and resid 60 through 69 sheet_id = " A" strand { selection = chain 'A' and resid 100 through 109 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 109 and name N bond_start_previous = chain 'A' and resid 60 and name O } strand { selection = chain 'A' and resid 89 through 96 sense = parallel *antiparallel unknown bond_start_current = chain 'A' and resid 95 and name N bond_start_previous = chain 'A' and resid 102 and name O } } sheet { first_strand = chain 'B' and resid 59 through 69 sheet_id = " B" strand { selection = chain 'B' and resid 100 through 110 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 109 and name N bond_start_previous = chain 'B' and resid 60 and name O } strand { selection = chain 'B' and resid 89 through 94 sense = parallel *antiparallel unknown bond_start_current = chain 'B' and resid 93 and name N bond_start_previous = chain 'B' and resid 104 and name O } } sheet { first_strand = chain 'E' and resid 54 through 59 sheet_id = " C" strand { selection = chain 'E' and resid 81 through 87 sense = parallel *antiparallel unknown bond_start_current = chain 'E' and resid 86 and name N bond_start_previous = chain 'E' and resid 55 and name O } strand { selection = chain 'E' and resid 73 through 78 sense = parallel *antiparallel unknown bond_start_current = chain 'E' and resid 78 and name N bond_start_previous = chain 'E' and resid 81 and name O } strand { selection = chain 'E' and resid 6 through 12 sense = parallel *antiparallel unknown bond_start_current = chain 'E' and resid 12 and name N bond_start_previous = chain 'E' and resid 73 and name O } } sheet { first_strand = chain 'F' and resid 54 through 59 sheet_id = " D" strand { selection = chain 'F' and resid 81 through 87 sense = parallel *antiparallel unknown bond_start_current = chain 'F' and resid 86 and name N bond_start_previous = chain 'F' and resid 55 and name O } strand { selection = chain 'F' and resid 73 through 78 sense = parallel *antiparallel unknown bond_start_current = chain 'F' and resid 78 and name N bond_start_previous = chain 'F' and resid 81 and name O } strand { selection = chain 'F' and resid 6 through 12 sense = parallel *antiparallel unknown bond_start_current = chain 'F' and resid 12 and name N bond_start_previous = chain 'F' and resid 73 and name O } } } enabled = True } nonbonded_weight = 100 } target_weights { optimize_xyz_weight = True optimize_adp_weight = True } } output { prefix = "3fm7_refine" serial = 1 target_output_format = None *pdb mmcif } #phil __OFF__ ================================== Hydrogens ================================== Total: count: 3394 occupancy sum: 3394.00 (% of total atoms 49.68) Rotatable: count: 1005 occupancy sum: 1005.00 (% of total atoms 14.71) ----------structure factors based statistics (before refinement)---------- ----------X-ray data---------- |--(resolution: 3.50 - 35.65 A, n_refl.=8745 (all), 9.95 % free)-------------| | | | r_work= 0.3573 r_free= 0.3825 coordinate error (max.-lik. estimate): 0.14 A | | | | normalized target function (ml) (work): 6.431057 | | target function (ml) not normalized (work): 50644.571594 | | target function (ml) not normalized (free): 5712.019596 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 35.65 - 6.35 1.00 1358 142 0.4105 0.4302 7.4385 7.4058| | 2: 6.35 - 5.05 1.00 1326 136 0.3185 0.3402 6.6863 6.7637| | 3: 5.04 - 4.41 1.00 1320 143 0.3188 0.3218 6.3284 6.4613| | 4: 4.41 - 4.01 0.99 1291 153 0.3401 0.3699 6.1277 6.4141| | 5: 4.01 - 3.72 0.99 1285 148 0.3360 0.4071 5.9732 6.2399| | 6: 3.72 - 3.50 0.99 1295 148 0.3851 0.4177 5.9746 6.1601| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 35.65 - 6.35 1358 142 0.52 50.23 0.82 0.72 437329.23| | 2: 6.35 - 5.05 1326 136 0.56 47.21 1.23 0.89 198795.77| | 3: 5.04 - 4.41 1320 143 0.78 29.03 1.38 1.01 71014.34| | 4: 4.41 - 4.01 1291 153 0.71 34.61 1.41 1.00 52577.48| | 5: 4.01 - 3.72 1285 148 0.62 42.28 1.34 0.96 45018.50| | 6: 3.72 - 3.50 1295 148 0.64 41.10 1.46 0.94 40633.46| |alpha: min = 0.72 max = 1.01 mean = 0.92| |beta: min = 40633.46 max = 437329.23 mean = 143438.96| |figures of merit: min = 0.00 max = 1.00 mean = 0.64| |phase err.(work): min = 0.00 max = 89.98 mean = 40.81| |phase err.(test): min = 0.00 max = 89.61 mean = 40.40| |-----------------------------------------------------------------------------| ----------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 : 0.003 0.016 3512 Z= 0.194 Angle : 0.846 4.753 4762 Z= 0.586 Chirality : 0.032 0.108 539 Planarity : 0.000 0.001 601 Dihedral : 23.554 133.906 1264 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 44.73 Ramachandran Plot: Outliers : 4.77 % Allowed : 13.60 % Favored : 81.62 % Rotamer: Outliers : 25.33 % Allowed : 17.15 % Favored : 57.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.48 % Twisted Proline : 0.00 % Twisted General : 2.64 % 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: -5.75 (0.30), residues: 419 helix: -4.63 (0.19), residues: 131 sheet: -1.47 (0.57), residues: 92 loop : -4.46 (0.27), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 60 TYR 0.001 0.000 TYR F 65 PHE 0.001 0.000 PHE F 46 TRP 0.001 0.000 TRP B 40 HIS 0.000 0.000 HIS A 76 Individual atomic B min max mean iso aniso Overall: 2.00 500.00 94.66 89.80 3444 0 Protein: 2.00 500.00 94.66 89.80 3444 0 Chain A: 2.00 500.00 114.65 N/A 807 0 Chain B: 2.00 458.88 97.81 N/A 813 0 Chain C: 2.00 495.15 104.99 N/A 215 0 Chain D: 2.00 500.00 119.77 N/A 215 0 Chain E: 2.00 478.28 71.82 N/A 697 0 Chain F: 2.00 403.25 79.76 N/A 697 0 Histogram: Values Number of atoms 2.00 - 51.80 934 51.80 - 101.60 1312 101.60 - 151.40 657 151.40 - 201.20 310 201.20 - 251.00 111 251.00 - 300.80 57 300.80 - 350.60 34 350.60 - 400.40 17 400.40 - 450.20 6 450.20 - 500.00 6 |-Occupancies statistics------------------------------------------------------| | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1 = 0 | |-----------------------------------------------------------------------------| =================== Write initial parameters into .eff file =================== *********************** REFINEMENT MACRO_CYCLE 1 OF 3 ************************* |--(resolution: 3.50 - 35.65 A, n_refl.=8745 (all), 9.95 % free)-------------| | | | r_work= 0.3573 r_free= 0.3825 coordinate error (max.-lik. estimate): 0.14 A | | | | normalized target function (ml) (work): 6.431057 | | target function (ml) not normalized (work): 50644.571594 | | target function (ml) not normalized (free): 5712.019596 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.3589 0.3573 0.3825 n_refl.: 8745 re-set all scales: r(all,work,free)=0.3589 0.3573 0.3825 n_refl.: 8745 remove outliers: r(all,work,free)=0.3585 0.3571 0.3811 n_refl.: 8739 overall B=17.64 to atoms: r(all,work,free)=0.4218 0.4229 0.4187 n_refl.: 8739 bulk-solvent and scaling: r(all,work,free)=0.2240 0.2141 0.3139 n_refl.: 8739 remove outliers: r(all,work,free)=0.2235 0.2135 0.3139 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3558 1472.375 1342.545 1.239 0.973 0.325 15.490-12.512 99.01 89 11 0.2187 1306.036 1261.365 1.106 0.974 0.283 12.419-9.967 99.48 175 15 0.1814 1476.037 1437.608 1.169 0.977 0.280 9.933-7.985 99.73 337 34 0.1928 1108.226 1073.275 1.178 0.978 0.264 7.976-6.403 100.00 631 64 0.2456 609.809 575.118 1.094 0.979 0.229 6.399-5.132 99.93 1234 135 0.2161 578.066 550.281 0.973 0.981 0.174 5.129-4.115 99.81 2357 259 0.1739 559.520 545.409 0.991 0.984 0.113 4.114-3.501 98.83 2959 341 0.2478 337.971 323.299 1.036 0.987 0.037 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0046 b_overall=-0.2819 ============================ Set refinement target ============================ using refinement target ls_wunit_k1 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 17.692378 wxc_scale = 0.500 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.127326 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2308 0.3256 0.0948 0.003 0.6 6.7 3.8 15.3 0 0.125 0.2266 0.3249 0.0983 0.003 0.6 6.6 3.6 16.1 0 0.250 0.2218 0.3248 0.1030 0.003 0.6 6.3 3.8 16.6 0 0.500 0.2156 0.3248 0.1092 0.004 0.7 8.4 3.8 16.6 0 1.000 0.2076 0.3245 0.1168 0.005 0.7 10.4 4.3 18.5 0 2.000 0.2016 0.3236 0.1219 0.007 0.8 13.9 4.3 19.0 0 3.000 0.1986 0.3240 0.1255 0.008 0.9 16.1 4.3 19.8 0 4.000 0.1955 0.3243 0.1288 0.009 1.0 18.2 4.5 20.1 0 5.000 0.1934 0.3231 0.1297 0.010 1.0 21.3 4.3 20.1 0 6.000 0.1919 0.3225 0.1306 0.011 1.1 22.4 4.5 20.8 0 7.000 0.1903 0.3218 0.1315 0.012 1.2 24.9 4.3 21.4 0 8.000 0.1893 0.3227 0.1333 0.013 1.2 26.1 4.8 22.7 0 9.000 0.1882 0.3217 0.1335 0.014 1.3 27.7 4.8 22.4 0 10.000 0.1892 0.3218 0.1326 0.013 1.2 25.8 4.8 21.9 0 8.846 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.1882 0.3217 0.1335 0.014 1.3 27.7 4.8 22.4 0 10.000 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 18.82 32.17 13.35 64.040 110.958 0.127 0.043 24.97 32.43 7.45 46.624 120.196 0.004 0.069 24.64 32.29 7.65 46.711 120.014 0.016 0.067 23.52 31.84 8.32 47.106 119.381 0.064 0.062 22.45 31.44 8.99 47.604 118.847 0.127 0.057 21.73 31.22 9.49 47.989 118.622 0.191 0.054 21.08 31.05 9.97 48.530 118.168 0.255 0.052 20.56 30.90 10.34 49.052 117.778 0.318 0.049 20.16 30.82 10.66 49.517 117.490 0.382 0.048 19.79 30.70 10.91 50.028 117.142 0.446 0.046 19.53 30.65 11.11 50.364 117.059 0.509 0.045 19.91 30.91 11.00 50.193 118.346 0.573 0.047 19.62 30.84 11.21 50.618 117.970 0.637 0.046 max suggested for this run: 22.19 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.004 Accepted refinement result: 24.97 32.43 7.45 46.624 120.196 0.004 0.069 Individual atomic B min max mean iso aniso Overall: 65.10 512.64 130.65 57.58 3444 0 Protein: 65.10 512.64 130.65 57.58 3444 0 Chain A: 79.18 512.64 152.14 N/A 807 0 Chain B: 79.38 471.52 133.56 N/A 813 0 Chain C: 75.34 507.79 144.16 N/A 215 0 Chain D: 80.29 512.64 154.89 N/A 215 0 Chain E: 65.10 490.92 106.54 N/A 697 0 Chain F: 72.69 415.89 114.81 N/A 697 0 Histogram: Values Number of atoms 65.10 - 109.86 1506 109.86 - 154.61 1249 154.61 - 199.37 398 199.37 - 244.12 144 244.12 - 288.87 62 288.87 - 333.63 36 333.63 - 378.38 26 378.38 - 423.13 14 423.13 - 467.89 3 467.89 - 512.64 6 =========================== Idealize ADP of riding H ========================== r_work=0.2497 r_free=0.3243 r_work=0.2592 r_free=0.3243 *********************** REFINEMENT MACRO_CYCLE 2 OF 3 ************************* |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2592 r_free= 0.3243 coordinate error (max.-lik. estimate): 0.16 A | | | | normalized target function (ls_wunit_k1) (work): 0.073511 | | target function (ls_wunit_k1) not normalized (work): 578.458460 | | target function (ls_wunit_k1) not normalized (free): 106.159926 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2656 0.2592 0.3243 n_refl.: 8738 re-set all scales: r(all,work,free)=0.5144 0.5171 0.4913 n_refl.: 8738 remove outliers: r(all,work,free)=0.5144 0.5171 0.4913 n_refl.: 8738 overall B=-32.16 to atoms: r(all,work,free)=0.4002 0.4011 0.3981 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2301 0.2217 0.3075 n_refl.: 8738 remove outliers: r(all,work,free)=0.2301 0.2217 0.3075 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.2995 655.750 623.864 1.330 0.945 0.326 15.490-12.512 99.01 89 11 0.1628 581.669 570.934 1.213 0.947 0.292 12.419-9.967 99.48 175 15 0.1375 657.382 644.349 1.258 0.953 0.278 9.933-7.985 99.73 337 34 0.1448 493.570 484.624 1.262 0.957 0.266 7.976-6.403 100.00 631 64 0.2185 271.590 262.312 1.118 0.964 0.224 6.399-5.132 99.93 1234 135 0.2097 257.453 248.076 1.010 0.975 0.193 5.129-4.115 99.81 2357 259 0.2008 249.193 243.662 0.993 0.992 0.119 4.114-3.501 98.83 2959 341 0.3058 150.522 142.921 0.992 1.012 0.053 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0577 b_overall=3.4462 ============================ 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 = 6.213445 wxc_scale = 0.046 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.039671 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2471 0.3132 0.0661 0.003 0.7 8.7 4.1 15.8 0 0.028 0.2425 0.3111 0.0686 0.004 0.7 8.5 3.8 15.6 0 0.085 0.2377 0.3092 0.0715 0.003 0.7 9.5 3.8 16.1 0 0.170 0.2339 0.3077 0.0738 0.004 0.7 10.3 3.8 16.6 0 0.256 0.2295 0.3060 0.0765 0.004 0.7 10.7 3.8 17.4 0 0.341 0.2271 0.3052 0.0781 0.004 0.7 11.7 4.1 17.9 0 0.426 0.2255 0.3050 0.0795 0.005 0.8 11.7 4.1 17.9 0 0.511 0.2229 0.3037 0.0807 0.005 0.8 12.9 4.3 18.5 0 0.596 0.2313 0.3070 0.0757 0.004 0.7 10.4 3.8 17.4 0 0.284 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2229 0.3037 0.0807 0.005 0.8 12.9 4.3 18.5 0 0.596 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 22.29 30.37 8.07 45.489 110.146 0.040 5.647 28.58 31.69 3.11 33.392 125.663 0.001 5.692 27.22 30.83 3.62 33.103 124.522 0.005 5.682 24.32 29.16 4.84 34.112 121.379 0.020 5.657 22.00 28.64 6.64 36.954 117.023 0.040 5.609 21.41 28.43 7.01 38.743 116.788 0.060 5.591 20.94 28.43 7.49 40.200 115.528 0.079 5.581 20.63 28.49 7.85 41.035 114.119 0.099 5.577 20.52 28.52 8.01 41.757 113.621 0.119 5.575 20.45 28.58 8.13 42.278 113.324 0.139 5.574 20.40 28.63 8.23 42.675 113.133 0.159 5.574 20.37 28.70 8.33 43.006 112.828 0.179 5.574 20.34 28.72 8.39 43.250 112.779 0.198 5.574 max suggested for this run: 22.03 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.020 Accepted refinement result: 24.32 29.16 4.84 34.112 121.379 0.020 5.657 Individual atomic B min max mean iso aniso Overall: 33.19 475.48 120.78 37.78 3444 0 Protein: 33.19 475.48 120.78 37.78 3444 0 Chain A: 75.49 475.48 150.51 N/A 807 0 Chain B: 51.90 434.36 125.80 N/A 813 0 Chain C: 40.93 470.63 136.10 N/A 215 0 Chain D: 55.11 475.48 150.23 N/A 215 0 Chain E: 33.19 453.76 88.41 N/A 697 0 Chain F: 37.84 378.73 99.08 N/A 697 0 Histogram: Values Number of atoms 33.19 - 77.41 591 77.41 - 121.64 1405 121.64 - 165.87 991 165.87 - 210.10 294 210.10 - 254.33 79 254.33 - 298.56 35 298.56 - 342.79 26 342.79 - 387.02 14 387.02 - 431.25 3 431.25 - 475.48 6 =========================== Idealize ADP of riding H ========================== r_work=0.2432 r_free=0.2916 r_work=0.2470 r_free=0.2919 *********************** REFINEMENT MACRO_CYCLE 3 OF 3 ************************* |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2470 r_free= 0.2919 coordinate error (max.-lik. estimate): 0.40 A | | | | normalized target function (ml) (work): 5.666304 | | target function (ml) not normalized (work): 44588.143680 | | target function (ml) not normalized (free): 5021.524664 | |-----------------------------------------------------------------------------| =========================== Bulk-solvent and scaling ========================== ============================= updating all scales ============================= start: r(all,work,free)=0.2514 0.2470 0.2919 n_refl.: 8738 re-set all scales: r(all,work,free)=0.4644 0.4680 0.4360 n_refl.: 8738 remove outliers: r(all,work,free)=0.4644 0.4680 0.4360 n_refl.: 8738 overall B=-11.48 to atoms: r(all,work,free)=0.4223 0.4252 0.4010 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2432 0.2378 0.2932 n_refl.: 8738 remove outliers: r(all,work,free)=0.2432 0.2378 0.2932 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3279 738.906 684.576 1.257 0.960 0.327 15.490-12.512 99.01 89 11 0.1753 655.430 641.283 1.128 0.962 0.278 12.419-9.967 99.48 175 15 0.1511 740.744 723.874 1.193 0.967 0.266 9.933-7.985 99.73 337 34 0.1609 556.160 543.116 1.242 0.969 0.260 7.976-6.403 100.00 631 64 0.2589 306.031 287.740 1.145 0.974 0.212 6.399-5.132 99.93 1234 135 0.2401 290.100 274.653 1.008 0.982 0.164 5.129-4.115 99.81 2357 259 0.2083 280.793 272.161 0.983 0.993 0.081 4.114-3.501 98.83 2959 341 0.3132 169.610 159.287 0.991 1.005 0.038 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=1.0610 b_overall=4.0621 ============================ Set refinement target ============================ using refinement target ml ============================ Update CDL restraints ============================ ============================= Setup riding H model ============================ Before: r_work=0.2378 r_free=0.2932 After: r_work=0.2378 r_free=0.2932 ==================== Compute data/restraints target weights =================== |-----------------------------------------------------------------------------| | XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc | | wxc = 6.567702 wxc_scale = 0.057 wc = 1.000 | | | | ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp * wu | | wxu = 0.035435 wxu_scale = 1.000 wu = 1.000 | |-----------------------------------------------------------------------------| ====================== XYZ individual (reciprocal space) ====================== Weight selection criteria: R_free deviation: 1.5000 R_free-R_work gap: 5.0000 Bond RMSD: 0.0150 Angle RMSD: 2.0000 R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2396 0.2935 0.0539 0.004 0.8 14.2 4.1 18.7 0 0.037 0.2392 0.2934 0.0543 0.004 0.8 13.9 4.1 18.7 0 0.112 0.2384 0.2934 0.0550 0.004 0.8 13.2 4.1 18.7 0 0.223 0.2382 0.2935 0.0553 0.005 0.8 13.3 4.1 18.7 0 0.335 0.2379 0.2934 0.0555 0.005 0.8 13.3 4.1 18.7 0 0.446 0.2376 0.2934 0.0559 0.005 0.8 13.5 4.1 18.7 0 0.558 0.2373 0.2934 0.0561 0.005 0.8 13.9 4.1 18.7 0 0.669 0.2368 0.2933 0.0565 0.006 0.8 14.1 4.1 18.7 0 0.781 0.2381 0.2934 0.0554 0.005 0.8 13.3 4.1 18.7 0 0.372 Best weight: R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT work free delta bonds angl 0.2368 0.2933 0.0565 0.006 0.8 14.1 4.1 18.7 0 0.781 ====================== ADP refinement (reciprocal space) ====================== ----------Individual ADP refinement---------- R-FACTORS WEIGHT TARGETS work free delta data restr 23.68 29.33 5.65 32.683 121.499 0.035 5.785 29.05 31.53 2.48 27.656 130.256 0.001 5.841 28.42 31.15 2.74 27.017 130.639 0.004 5.825 25.08 29.42 4.34 29.297 126.878 0.018 5.768 22.73 28.61 5.88 31.668 122.907 0.035 5.740 22.38 28.75 6.37 32.238 122.206 0.053 5.737 22.23 28.81 6.58 32.501 122.047 0.071 5.735 22.15 28.84 6.69 32.677 121.983 0.089 5.734 22.22 28.85 6.63 32.732 121.693 0.106 5.738 22.19 28.87 6.68 32.815 121.674 0.124 5.737 22.17 28.88 6.71 32.884 121.671 0.142 5.737 22.16 28.90 6.74 32.940 121.676 0.159 5.737 22.14 28.90 6.76 32.988 121.685 0.177 5.737 max suggested for this run: 24.30 max allowed Rfree-Rwork gap: 6.0 range of equivalent Rfree: 1.5 Best ADP weight: 0.018 Accepted refinement result: 25.08 29.42 4.34 29.297 126.878 0.018 5.768 Individual atomic B min max mean iso aniso Overall: 49.05 459.00 119.98 33.48 3444 0 Protein: 49.05 459.00 119.98 33.48 3444 0 Chain A: 82.66 459.00 148.68 N/A 807 0 Chain B: 59.03 417.88 124.28 N/A 813 0 Chain C: 59.83 454.15 133.25 N/A 215 0 Chain D: 66.89 459.00 148.62 N/A 215 0 Chain E: 49.05 437.28 90.70 N/A 697 0 Chain F: 52.34 362.25 98.11 N/A 697 0 Histogram: Values Number of atoms 49.05 - 90.04 1022 90.04 - 131.04 1296 131.04 - 172.03 774 172.03 - 213.03 220 213.03 - 254.02 63 254.02 - 295.02 29 295.02 - 336.01 19 336.01 - 377.01 13 377.01 - 418.00 4 418.00 - 459.00 4 =========================== Idealize ADP of riding H ========================== r_work=0.2508 r_free=0.2942 r_work=0.2517 r_free=0.2947 ----------X-ray data---------- |--(resolution: 3.50 - 35.65 A, n_refl.=8738 (all), 9.95 % free)-------------| | | | r_work= 0.2517 r_free= 0.2947 coordinate error (max.-lik. estimate): 0.20 A | | | | normalized target function (ml) (work): 5.771753 | | target function (ml) not normalized (work): 45417.923789 | | target function (ml) not normalized (free): 5120.302260 | |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| | Bin Resolution Compl. No. Refl. R-factors Targets | |number range work test work test work test| | 1: 35.65 - 6.35 1.00 1354 141 0.2229 0.2669 6.3042 6.5413| | 2: 6.35 - 5.05 1.00 1326 136 0.2315 0.2827 5.917 6.0645| | 3: 5.04 - 4.41 1.00 1320 143 0.2132 0.2516 5.7393 5.8097| | 4: 4.41 - 4.01 0.99 1291 153 0.2645 0.3072 5.6133 5.8084| | 5: 4.01 - 3.72 0.99 1285 148 0.3175 0.3449 5.4897 5.5803| | 6: 3.72 - 3.50 0.99 1293 148 0.3643 0.3988 5.5369 5.5935| |-----------------------------------------------------------------------------| |-----------------------------------------------------------------------------| |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: 35.65 - 6.35 1354 141 0.72 32.88 0.92 0.93 67948.03| | 2: 6.35 - 5.05 1326 136 0.71 35.25 1.02 0.98 36312.57| | 3: 5.04 - 4.41 1320 143 0.82 24.48 1.12 1.04 18111.33| | 4: 4.41 - 4.01 1291 153 0.77 29.84 1.14 1.07 14334.18| | 5: 4.01 - 3.72 1285 148 0.67 38.39 1.18 1.04 13068.17| | 6: 3.72 - 3.50 1293 148 0.66 39.92 1.24 1.00 13425.26| |alpha: min = 0.93 max = 1.07 mean = 1.01| |beta: min = 13068.17 max = 67948.03 mean = 27540.47| |figures of merit: min = 0.00 max = 1.00 mean = 0.72| |phase err.(work): min = 0.00 max = 89.61 mean = 33.43| |phase err.(test): min = 0.00 max = 89.30 mean = 33.01| |-----------------------------------------------------------------------------| ==================================== Final ==================================== ============================= updating all scales ============================= start: r(all,work,free)=0.2559 0.2517 0.2947 n_refl.: 8738 re-set all scales: r(all,work,free)=0.4847 0.4886 0.4537 n_refl.: 8738 remove outliers: r(all,work,free)=0.4847 0.4886 0.4537 n_refl.: 8738 overall B=-13.13 to atoms: r(all,work,free)=0.4367 0.4400 0.4130 n_refl.: 8738 bulk-solvent and scaling: r(all,work,free)=0.2397 0.2341 0.2904 n_refl.: 8738 remove outliers: r(all,work,free)=0.2397 0.2341 0.2904 n_refl.: 8738 ======================== 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 35.652-15.678 96.04 87 10 0.3275 738.906 683.583 1.156 0.976 0.327 15.490-12.512 99.01 89 11 0.1715 655.430 640.445 1.053 0.976 0.284 12.419-9.967 99.48 175 15 0.1544 740.744 722.220 1.128 0.979 0.277 9.933-7.985 99.73 337 34 0.1632 556.160 542.353 1.150 0.979 0.261 7.976-6.403 100.00 631 64 0.2497 306.031 287.982 1.087 0.979 0.224 6.399-5.132 99.93 1234 135 0.2381 290.100 274.856 0.977 0.979 0.177 5.129-4.115 99.81 2357 259 0.2035 280.793 273.853 1.002 0.978 0.094 4.114-3.501 98.83 2959 341 0.3074 169.610 160.187 1.038 0.977 0.050 Approximation of k_total with k_overall*exp(-b_overall*s**2/4) k_overall=0.9911 b_overall=-0.9607 ================= 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 : 0.3573 0.3825 0.003 0.846 2.0 500.0 94.7 0 0.000 1_bss: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_settarget: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_weight: 0.2135 0.3139 0.003 0.846 19.6 517.6 112.3 0 0.000 1_xyzrec: 0.1882 0.3217 0.014 1.263 19.6 517.6 112.3 0 0.331 1_adp: 0.2497 0.3243 0.014 1.263 65.1 512.6 130.6 0 0.331 1_regHadp: 0.2592 0.3243 0.014 1.263 65.1 512.6 130.6 0 0.331 2_bss: 0.2217 0.3075 0.014 1.263 32.9 480.5 98.5 0 0.331 2_settarget: 0.2217 0.3075 0.014 1.263 32.9 480.5 98.5 0 0.331 2_updatecdl: 0.2217 0.3075 0.014 1.302 32.9 480.5 98.5 0 0.331 2_weight: 0.2217 0.3075 0.014 1.302 32.9 480.5 98.5 0 0.331 2_xyzrec: 0.2229 0.3037 0.005 0.787 32.9 480.5 98.5 0 0.319 2_adp: 0.2432 0.2916 0.005 0.787 33.2 475.5 120.8 0 0.319 2_regHadp: 0.2470 0.2919 0.005 0.787 33.2 475.5 120.8 0 0.319 3_bss: 0.2378 0.2932 0.005 0.787 21.7 464.0 109.3 0 0.319 3_settarget: 0.2378 0.2932 0.005 0.787 21.7 464.0 109.3 0 0.319 3_updatecdl: 0.2378 0.2932 0.006 0.839 21.7 464.0 109.3 0 0.319 3_setrh: 0.2378 0.2932 0.006 0.839 21.7 464.0 109.3 0 0.319 3_weight: 0.2378 0.2932 0.006 0.839 21.7 464.0 109.3 0 0.319 3_xyzrec: 0.2368 0.2933 0.006 0.828 21.7 464.0 109.3 0 0.319 3_adp: 0.2508 0.2942 0.006 0.828 49.0 459.0 120.0 0 0.319 3_regHadp: 0.2517 0.2947 0.006 0.828 49.0 459.0 120.0 0 0.319 end: 0.2341 0.2904 0.006 0.828 35.9 445.9 106.8 0 0.319 ------------------------------------------------------------------------ ============================== Exporting results ============================== Writing refined structure to CIF file: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/3fm7_refine_001.cif Writing default parameters for subsequent refinement: /net/anaconda/raid1/afonine/work/ANI/result/xray/pairs/phenix_V3/3fm7_refine_002.def Timing summary: Write initial files (write_before_run_outputs): 10.2400 Refinement macro-cycles (run) : 250.3900 Write final files (write_after_run_outputs) : 22.8100 Total : 283.4400 Total CPU time: 5.45 minutes =========================== phenix.refine: finished =========================== # Date 2024-05-20 Time 17:34:43 PDT -0700 (1716251683.67 s) Start R-work = 0.2135, R-free = 0.3139 Final R-work = 0.2341, R-free = 0.2904 =============================================================================== Job complete usr+sys time: 349.33 seconds wall clock time: 17 minutes 33.61 seconds (1053.61 seconds total)