Starting phenix.real_space_refine on Wed Feb 4 14:00:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tfs_25879/02_2026/7tfs_25879.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tfs_25879/02_2026/7tfs_25879.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tfs_25879/02_2026/7tfs_25879.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tfs_25879/02_2026/7tfs_25879.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tfs_25879/02_2026/7tfs_25879.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tfs_25879/02_2026/7tfs_25879.map" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 28 7.16 5 S 91 5.16 5 C 7168 2.51 5 N 1918 2.21 5 O 2177 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11382 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1454 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 190} Chain: "B" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 172 Unusual residues: {'HEC': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: C, D, A, E, F, G Time building chain proxies: 1.57, per 1000 atoms: 0.14 Number of scatterers: 11382 At special positions: 0 Unit cell: (72.36, 72.36, 267.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 28 26.01 S 91 16.00 O 2177 8.00 N 1918 7.00 C 7168 6.00 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 - 3.00 Amino acid : True - 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=96, symmetry=0 Number of additional bonds: simple=96, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 518.2 milliseconds 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 14 sheets defined 23.3% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 50 through 54 removed outlier: 3.937A pdb=" N PHE A 53 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 4.006A pdb=" N THR A 76 " --> pdb=" O THR A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.696A pdb=" N LYS A 91 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 107 removed outlier: 3.643A pdb=" N PHE A 102 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 132 removed outlier: 3.826A pdb=" N ASN A 132 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 223 through 230 removed outlier: 4.050A pdb=" N CYS A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 54 removed outlier: 3.937A pdb=" N PHE B 53 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 77 removed outlier: 4.006A pdb=" N THR B 76 " --> pdb=" O THR B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.696A pdb=" N LYS B 91 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 removed outlier: 3.644A pdb=" N PHE B 102 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N CYS B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.826A pdb=" N ASN B 132 " --> pdb=" O VAL B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 223 through 230 removed outlier: 4.050A pdb=" N CYS B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 54 removed outlier: 3.937A pdb=" N PHE C 53 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 removed outlier: 4.006A pdb=" N THR C 76 " --> pdb=" O THR C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.696A pdb=" N LYS C 91 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 107 removed outlier: 3.643A pdb=" N PHE C 102 " --> pdb=" O SER C 98 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N CYS C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.826A pdb=" N ASN C 132 " --> pdb=" O VAL C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 223 through 230 removed outlier: 4.050A pdb=" N CYS C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 54 removed outlier: 3.937A pdb=" N PHE D 53 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 removed outlier: 4.007A pdb=" N THR D 76 " --> pdb=" O THR D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.696A pdb=" N LYS D 91 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 107 removed outlier: 3.643A pdb=" N PHE D 102 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 132 removed outlier: 3.827A pdb=" N ASN D 132 " --> pdb=" O VAL D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 223 through 230 removed outlier: 4.050A pdb=" N CYS D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 54 removed outlier: 3.936A pdb=" N PHE E 53 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 77 removed outlier: 4.007A pdb=" N THR E 76 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.697A pdb=" N LYS E 91 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 107 removed outlier: 3.644A pdb=" N PHE E 102 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N CYS E 106 " --> pdb=" O PHE E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 132 removed outlier: 3.826A pdb=" N ASN E 132 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 164 Processing helix chain 'E' and resid 223 through 230 removed outlier: 4.051A pdb=" N CYS E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 54 removed outlier: 3.937A pdb=" N PHE F 53 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 77 removed outlier: 4.006A pdb=" N THR F 76 " --> pdb=" O THR F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.696A pdb=" N LYS F 91 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 107 removed outlier: 3.643A pdb=" N PHE F 102 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N CYS F 106 " --> pdb=" O PHE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 132 removed outlier: 3.826A pdb=" N ASN F 132 " --> pdb=" O VAL F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 164 Processing helix chain 'F' and resid 223 through 230 removed outlier: 4.050A pdb=" N CYS F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 54 removed outlier: 3.937A pdb=" N PHE G 53 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 77 removed outlier: 4.006A pdb=" N THR G 76 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.696A pdb=" N LYS G 91 " --> pdb=" O VAL G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 107 removed outlier: 3.643A pdb=" N PHE G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS G 106 " --> pdb=" O PHE G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 132 removed outlier: 3.826A pdb=" N ASN G 132 " --> pdb=" O VAL G 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 164 Processing helix chain 'G' and resid 223 through 230 removed outlier: 4.050A pdb=" N CYS G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 153 through 154 removed outlier: 3.844A pdb=" N PHE A 153 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 168 through 170 removed outlier: 3.788A pdb=" N LEU A 187 " --> pdb=" O MET A 178 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'B' and resid 153 through 154 removed outlier: 3.844A pdb=" N PHE B 153 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'B' and resid 168 through 170 removed outlier: 3.788A pdb=" N LEU B 187 " --> pdb=" O MET B 178 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'C' and resid 153 through 154 removed outlier: 3.844A pdb=" N PHE C 153 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'C' and resid 168 through 170 removed outlier: 3.788A pdb=" N LEU C 187 " --> pdb=" O MET C 178 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'D' and resid 153 through 154 removed outlier: 3.844A pdb=" N PHE D 153 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'D' and resid 168 through 170 removed outlier: 3.788A pdb=" N LEU D 187 " --> pdb=" O MET D 178 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'E' and resid 153 through 154 removed outlier: 3.844A pdb=" N PHE E 153 " --> pdb=" O LEU E 199 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'E' and resid 168 through 170 removed outlier: 3.789A pdb=" N LEU E 187 " --> pdb=" O MET E 178 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'F' and resid 153 through 154 removed outlier: 3.844A pdb=" N PHE F 153 " --> pdb=" O LEU F 199 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'F' and resid 168 through 170 removed outlier: 3.789A pdb=" N LEU F 187 " --> pdb=" O MET F 178 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'G' and resid 153 through 154 removed outlier: 3.843A pdb=" N PHE G 153 " --> pdb=" O LEU G 199 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'G' and resid 168 through 170 removed outlier: 3.788A pdb=" N LEU G 187 " --> pdb=" O MET G 178 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 336 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: 1.57 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 4802 1.40 - 1.58: 6748 1.58 - 1.75: 0 1.75 - 1.93: 126 1.93 - 2.10: 112 Bond restraints: 11788 Sorted by residual: bond pdb=" C3B HEC E 301 " pdb=" CAB HEC E 301 " ideal model delta sigma weight residual 1.544 1.562 -0.018 2.00e-02 2.50e+03 7.95e-01 bond pdb=" C3B HEC G 301 " pdb=" CAB HEC G 301 " ideal model delta sigma weight residual 1.544 1.562 -0.018 2.00e-02 2.50e+03 7.86e-01 bond pdb=" C3B HEC A 301 " pdb=" CAB HEC A 301 " ideal model delta sigma weight residual 1.544 1.562 -0.018 2.00e-02 2.50e+03 7.66e-01 bond pdb=" C3B HEC F 301 " pdb=" CAB HEC F 301 " ideal model delta sigma weight residual 1.544 1.561 -0.017 2.00e-02 2.50e+03 7.55e-01 bond pdb=" C3B HEC D 301 " pdb=" CAB HEC D 301 " ideal model delta sigma weight residual 1.544 1.561 -0.017 2.00e-02 2.50e+03 7.54e-01 ... (remaining 11783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.30: 16208 3.30 - 6.60: 207 6.60 - 9.90: 7 9.90 - 13.21: 14 13.21 - 16.51: 7 Bond angle restraints: 16443 Sorted by residual: angle pdb=" C ALA E 213 " pdb=" N PRO E 214 " pdb=" CD PRO E 214 " ideal model delta sigma weight residual 120.60 104.09 16.51 2.20e+00 2.07e-01 5.63e+01 angle pdb=" C ALA B 213 " pdb=" N PRO B 214 " pdb=" CD PRO B 214 " ideal model delta sigma weight residual 120.60 104.10 16.50 2.20e+00 2.07e-01 5.63e+01 angle pdb=" C ALA A 213 " pdb=" N PRO A 214 " pdb=" CD PRO A 214 " ideal model delta sigma weight residual 120.60 104.12 16.48 2.20e+00 2.07e-01 5.61e+01 angle pdb=" C ALA C 213 " pdb=" N PRO C 214 " pdb=" CD PRO C 214 " ideal model delta sigma weight residual 120.60 104.13 16.47 2.20e+00 2.07e-01 5.61e+01 angle pdb=" C ALA F 213 " pdb=" N PRO F 214 " pdb=" CD PRO F 214 " ideal model delta sigma weight residual 120.60 104.14 16.46 2.20e+00 2.07e-01 5.60e+01 ... (remaining 16438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 5733 17.11 - 34.23: 392 34.23 - 51.34: 84 51.34 - 68.46: 84 68.46 - 85.57: 42 Dihedral angle restraints: 6335 sinusoidal: 2415 harmonic: 3920 Sorted by residual: dihedral pdb=" CA ILE B 64 " pdb=" C ILE B 64 " pdb=" N PRO B 65 " pdb=" CA PRO B 65 " ideal model delta harmonic sigma weight residual -180.00 -143.17 -36.83 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" CA ILE E 64 " pdb=" C ILE E 64 " pdb=" N PRO E 65 " pdb=" CA PRO E 65 " ideal model delta harmonic sigma weight residual -180.00 -143.17 -36.83 0 5.00e+00 4.00e-02 5.43e+01 dihedral pdb=" CA ILE A 64 " pdb=" C ILE A 64 " pdb=" N PRO A 65 " pdb=" CA PRO A 65 " ideal model delta harmonic sigma weight residual 180.00 -143.18 -36.82 0 5.00e+00 4.00e-02 5.42e+01 ... (remaining 6332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1170 0.044 - 0.087: 388 0.087 - 0.131: 59 0.131 - 0.174: 7 0.174 - 0.218: 7 Chirality restraints: 1631 Sorted by residual: chirality pdb=" CA ILE D 64 " pdb=" N ILE D 64 " pdb=" C ILE D 64 " pdb=" CB ILE D 64 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ILE B 64 " pdb=" N ILE B 64 " pdb=" C ILE B 64 " pdb=" CB ILE B 64 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE A 64 " pdb=" N ILE A 64 " pdb=" C ILE A 64 " pdb=" CB ILE A 64 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1628 not shown) Planarity restraints: 2065 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA F 213 " -0.084 5.00e-02 4.00e+02 1.26e-01 2.52e+01 pdb=" N PRO F 214 " 0.217 5.00e-02 4.00e+02 pdb=" CA PRO F 214 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO F 214 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 213 " 0.083 5.00e-02 4.00e+02 1.26e-01 2.52e+01 pdb=" N PRO B 214 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO B 214 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO B 214 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 213 " -0.084 5.00e-02 4.00e+02 1.25e-01 2.52e+01 pdb=" N PRO G 214 " 0.216 5.00e-02 4.00e+02 pdb=" CA PRO G 214 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO G 214 " -0.054 5.00e-02 4.00e+02 ... (remaining 2062 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 193 2.58 - 3.16: 9797 3.16 - 3.74: 17907 3.74 - 4.32: 23836 4.32 - 4.90: 37309 Nonbonded interactions: 89042 Sorted by model distance: nonbonded pdb=" NE2 HIS F 55 " pdb="FE HEC F 301 " model vdw 2.001 3.080 nonbonded pdb=" NE2 HIS B 55 " pdb="FE HEC B 301 " model vdw 2.001 3.080 nonbonded pdb=" NE2 HIS A 55 " pdb="FE HEC A 301 " model vdw 2.001 3.080 nonbonded pdb=" NE2 HIS D 55 " pdb="FE HEC D 301 " model vdw 2.001 3.080 nonbonded pdb=" NE2 HIS C 55 " pdb="FE HEC C 301 " model vdw 2.001 3.080 ... (remaining 89037 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'A' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.820 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 0.343 11884 Z= 1.475 Angle : 0.957 16.507 16443 Z= 0.415 Chirality : 0.043 0.218 1631 Planarity : 0.010 0.126 2065 Dihedral : 16.802 85.571 3829 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 34.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.20), residues: 1400 helix: 0.45 (0.39), residues: 154 sheet: -1.68 (0.45), residues: 70 loop : -1.77 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 69 TYR 0.002 0.001 TYR F 80 PHE 0.005 0.001 PHE D 215 TRP 0.004 0.001 TRP B 67 HIS 0.012 0.002 HIS D 230 Details of bonding type rmsd covalent geometry : bond 0.00397 (11788) covalent geometry : angle 0.95684 (16443) hydrogen bonds : bond 0.27741 ( 154) hydrogen bonds : angle 8.13248 ( 336) Misc. bond : bond 0.18545 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 PHE cc_start: 0.7028 (m-10) cc_final: 0.6749 (m-10) REVERT: B 83 SER cc_start: 0.8053 (p) cc_final: 0.7791 (p) REVERT: B 148 ASP cc_start: 0.6455 (t70) cc_final: 0.6246 (t70) REVERT: B 174 ASN cc_start: 0.7817 (m-40) cc_final: 0.7554 (m-40) REVERT: C 83 SER cc_start: 0.7995 (p) cc_final: 0.7629 (p) REVERT: C 200 GLU cc_start: 0.8440 (tp30) cc_final: 0.8230 (tp30) REVERT: D 77 PHE cc_start: 0.7182 (m-10) cc_final: 0.6692 (m-10) REVERT: D 104 MET cc_start: 0.7908 (mtt) cc_final: 0.7665 (mtt) REVERT: D 174 ASN cc_start: 0.7892 (m-40) cc_final: 0.7548 (m-40) REVERT: D 231 LYS cc_start: 0.7641 (pptt) cc_final: 0.6609 (ttmt) REVERT: A 77 PHE cc_start: 0.7113 (m-10) cc_final: 0.6603 (m-10) REVERT: A 148 ASP cc_start: 0.6994 (t70) cc_final: 0.6753 (t70) REVERT: A 174 ASN cc_start: 0.7974 (m-40) cc_final: 0.7692 (m-40) REVERT: A 200 GLU cc_start: 0.8474 (tp30) cc_final: 0.8171 (tp30) REVERT: E 77 PHE cc_start: 0.7213 (m-10) cc_final: 0.6993 (m-10) REVERT: E 83 SER cc_start: 0.7852 (p) cc_final: 0.7632 (p) REVERT: E 150 PRO cc_start: 0.8905 (Cg_exo) cc_final: 0.8674 (Cg_endo) REVERT: F 67 TRP cc_start: 0.7281 (t-100) cc_final: 0.6095 (t-100) REVERT: F 77 PHE cc_start: 0.7228 (m-10) cc_final: 0.6963 (m-10) REVERT: F 102 PHE cc_start: 0.7364 (m-10) cc_final: 0.7147 (m-10) REVERT: F 104 MET cc_start: 0.8001 (mtt) cc_final: 0.7740 (mtt) REVERT: F 174 ASN cc_start: 0.7917 (m-40) cc_final: 0.7636 (m-40) REVERT: F 231 LYS cc_start: 0.7545 (pptt) cc_final: 0.6789 (ttmt) REVERT: G 67 TRP cc_start: 0.7501 (t-100) cc_final: 0.6966 (t-100) REVERT: G 83 SER cc_start: 0.7925 (p) cc_final: 0.7633 (p) REVERT: G 141 LEU cc_start: 0.8267 (tp) cc_final: 0.7986 (tp) REVERT: G 174 ASN cc_start: 0.8111 (m-40) cc_final: 0.7838 (m-40) REVERT: G 200 GLU cc_start: 0.8451 (tp30) cc_final: 0.8224 (tp30) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.0940 time to fit residues: 36.8323 Evaluate side-chains 215 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 ASN C 152 ASN D 152 ASN A 152 ASN E 152 ASN F 152 ASN G 152 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.175876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.138355 restraints weight = 18528.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.143284 restraints weight = 13311.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.147136 restraints weight = 10436.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.150112 restraints weight = 8599.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.152070 restraints weight = 7378.823| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.442 11884 Z= 0.248 Angle : 1.074 14.966 16443 Z= 0.390 Chirality : 0.046 0.222 1631 Planarity : 0.007 0.069 2065 Dihedral : 15.006 89.972 1659 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.20), residues: 1400 helix: 0.06 (0.37), residues: 154 sheet: -1.90 (0.47), residues: 70 loop : -1.71 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 217 TYR 0.014 0.002 TYR G 80 PHE 0.014 0.001 PHE E 215 TRP 0.009 0.002 TRP B 67 HIS 0.007 0.002 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00710 (11788) covalent geometry : angle 1.07371 (16443) hydrogen bonds : bond 0.05012 ( 154) hydrogen bonds : angle 7.92051 ( 336) Misc. bond : bond 0.13990 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: B 102 PHE cc_start: 0.7889 (m-10) cc_final: 0.7610 (m-10) REVERT: B 231 LYS cc_start: 0.7240 (pptt) cc_final: 0.6753 (ttmt) REVERT: C 83 SER cc_start: 0.8166 (p) cc_final: 0.7746 (p) REVERT: C 191 LYS cc_start: 0.8626 (tptp) cc_final: 0.8265 (tptp) REVERT: D 77 PHE cc_start: 0.7800 (m-10) cc_final: 0.7490 (m-10) REVERT: D 104 MET cc_start: 0.8501 (mtt) cc_final: 0.8266 (mtt) REVERT: D 148 ASP cc_start: 0.7568 (t70) cc_final: 0.7300 (t70) REVERT: D 174 ASN cc_start: 0.8153 (m-40) cc_final: 0.7870 (m-40) REVERT: D 231 LYS cc_start: 0.7782 (pptt) cc_final: 0.6829 (ttmt) REVERT: A 56 THR cc_start: 0.9289 (t) cc_final: 0.9044 (p) REVERT: A 83 SER cc_start: 0.8145 (p) cc_final: 0.7881 (p) REVERT: A 102 PHE cc_start: 0.7727 (m-10) cc_final: 0.7344 (m-10) REVERT: A 174 ASN cc_start: 0.8206 (m-40) cc_final: 0.7990 (m-40) REVERT: A 206 LYS cc_start: 0.7752 (tttt) cc_final: 0.7403 (tptt) REVERT: E 206 LYS cc_start: 0.7966 (tttt) cc_final: 0.7632 (tptp) REVERT: F 174 ASN cc_start: 0.8197 (m-40) cc_final: 0.7988 (m-40) REVERT: F 206 LYS cc_start: 0.7824 (tttt) cc_final: 0.7506 (tptt) REVERT: F 231 LYS cc_start: 0.7641 (pptt) cc_final: 0.6887 (tttt) REVERT: G 67 TRP cc_start: 0.7724 (t-100) cc_final: 0.7122 (t-100) REVERT: G 206 LYS cc_start: 0.7857 (tttt) cc_final: 0.7503 (tptt) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.0956 time to fit residues: 37.5281 Evaluate side-chains 220 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 220 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 106 optimal weight: 0.2980 chunk 115 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 113 optimal weight: 20.0000 chunk 109 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 ASN A 152 ASN E 152 ASN G 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.176682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.139003 restraints weight = 18489.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.143983 restraints weight = 13226.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.147952 restraints weight = 10331.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.150957 restraints weight = 8508.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.153363 restraints weight = 7303.665| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.328 11884 Z= 0.186 Angle : 0.964 16.075 16443 Z= 0.345 Chirality : 0.044 0.220 1631 Planarity : 0.005 0.053 2065 Dihedral : 14.865 89.083 1659 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.21), residues: 1400 helix: -0.93 (0.35), residues: 196 sheet: -1.99 (0.50), residues: 70 loop : -1.68 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 194 TYR 0.007 0.001 TYR B 80 PHE 0.012 0.001 PHE E 215 TRP 0.007 0.002 TRP B 67 HIS 0.017 0.002 HIS G 230 Details of bonding type rmsd covalent geometry : bond 0.00527 (11788) covalent geometry : angle 0.96447 (16443) hydrogen bonds : bond 0.03712 ( 154) hydrogen bonds : angle 7.76393 ( 336) Misc. bond : bond 0.11145 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.7652 (mtp) cc_final: 0.7338 (mpp) REVERT: B 102 PHE cc_start: 0.7917 (m-10) cc_final: 0.7270 (m-10) REVERT: B 170 ASP cc_start: 0.7397 (t0) cc_final: 0.6923 (t0) REVERT: C 83 SER cc_start: 0.8184 (p) cc_final: 0.7852 (p) REVERT: C 148 ASP cc_start: 0.7776 (t70) cc_final: 0.7535 (t70) REVERT: C 191 LYS cc_start: 0.8754 (tptp) cc_final: 0.8422 (tptp) REVERT: D 104 MET cc_start: 0.8534 (mtt) cc_final: 0.8232 (mtm) REVERT: D 170 ASP cc_start: 0.6741 (t0) cc_final: 0.6273 (t0) REVERT: D 174 ASN cc_start: 0.8186 (m-40) cc_final: 0.7869 (m-40) REVERT: D 231 LYS cc_start: 0.7301 (pptt) cc_final: 0.7085 (pttm) REVERT: A 83 SER cc_start: 0.8260 (p) cc_final: 0.8006 (p) REVERT: A 206 LYS cc_start: 0.7694 (tttt) cc_final: 0.7363 (tptt) REVERT: E 148 ASP cc_start: 0.7758 (t70) cc_final: 0.7542 (t70) REVERT: E 170 ASP cc_start: 0.7215 (t0) cc_final: 0.6880 (t0) REVERT: E 206 LYS cc_start: 0.7979 (tttt) cc_final: 0.7599 (tptp) REVERT: F 33 LEU cc_start: 0.9139 (mp) cc_final: 0.8934 (mp) REVERT: F 80 TYR cc_start: 0.8288 (t80) cc_final: 0.8035 (t80) REVERT: F 85 MET cc_start: 0.7824 (mtp) cc_final: 0.7377 (mpp) REVERT: F 150 PRO cc_start: 0.8957 (Cg_exo) cc_final: 0.8581 (Cg_endo) REVERT: F 174 ASN cc_start: 0.8200 (m-40) cc_final: 0.7968 (m-40) REVERT: F 206 LYS cc_start: 0.7834 (tttt) cc_final: 0.7497 (tptt) REVERT: F 231 LYS cc_start: 0.7518 (pptt) cc_final: 0.6772 (tttt) REVERT: G 67 TRP cc_start: 0.7963 (t-100) cc_final: 0.7400 (t-100) REVERT: G 85 MET cc_start: 0.7855 (mtm) cc_final: 0.7139 (mtm) REVERT: G 104 MET cc_start: 0.8521 (mtt) cc_final: 0.8230 (mtt) REVERT: G 170 ASP cc_start: 0.7358 (t0) cc_final: 0.6948 (t0) REVERT: G 206 LYS cc_start: 0.7793 (tttt) cc_final: 0.7474 (tptt) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.0965 time to fit residues: 37.3343 Evaluate side-chains 213 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 73 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 1 optimal weight: 0.0770 chunk 7 optimal weight: 9.9990 chunk 118 optimal weight: 0.0670 chunk 13 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 ASN G 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.181762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.144818 restraints weight = 18123.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.150250 restraints weight = 12669.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.154538 restraints weight = 9685.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.157754 restraints weight = 7810.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.159794 restraints weight = 6577.230| |-----------------------------------------------------------------------------| r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.256 11884 Z= 0.130 Angle : 0.883 13.658 16443 Z= 0.323 Chirality : 0.043 0.223 1631 Planarity : 0.005 0.051 2065 Dihedral : 14.977 89.970 1659 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.21), residues: 1400 helix: -0.90 (0.34), residues: 196 sheet: -1.97 (0.49), residues: 70 loop : -1.60 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 69 TYR 0.006 0.001 TYR B 80 PHE 0.006 0.001 PHE C 190 TRP 0.005 0.001 TRP F 67 HIS 0.015 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00352 (11788) covalent geometry : angle 0.88325 (16443) hydrogen bonds : bond 0.03167 ( 154) hydrogen bonds : angle 7.54913 ( 336) Misc. bond : bond 0.08006 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.7674 (mtp) cc_final: 0.7406 (mpp) REVERT: B 102 PHE cc_start: 0.7909 (m-10) cc_final: 0.7332 (m-10) REVERT: C 83 SER cc_start: 0.8023 (p) cc_final: 0.7743 (p) REVERT: C 148 ASP cc_start: 0.7635 (t70) cc_final: 0.7360 (t70) REVERT: C 191 LYS cc_start: 0.8762 (tptp) cc_final: 0.8459 (tptp) REVERT: D 104 MET cc_start: 0.8443 (mtt) cc_final: 0.8034 (mtt) REVERT: D 174 ASN cc_start: 0.8151 (m-40) cc_final: 0.7870 (m-40) REVERT: A 83 SER cc_start: 0.8186 (p) cc_final: 0.7965 (p) REVERT: A 206 LYS cc_start: 0.7684 (tttt) cc_final: 0.7344 (tptt) REVERT: E 104 MET cc_start: 0.8512 (mtt) cc_final: 0.8152 (mtm) REVERT: E 148 ASP cc_start: 0.7551 (t70) cc_final: 0.7232 (t70) REVERT: E 206 LYS cc_start: 0.7958 (tttt) cc_final: 0.7657 (tptp) REVERT: F 85 MET cc_start: 0.7782 (mtp) cc_final: 0.7454 (mpp) REVERT: F 174 ASN cc_start: 0.8237 (m-40) cc_final: 0.8006 (m-40) REVERT: F 191 LYS cc_start: 0.8696 (tmtt) cc_final: 0.8472 (tptp) REVERT: F 231 LYS cc_start: 0.7576 (pptt) cc_final: 0.6677 (tttt) REVERT: G 67 TRP cc_start: 0.8039 (t-100) cc_final: 0.7650 (t-100) REVERT: G 191 LYS cc_start: 0.8711 (tptp) cc_final: 0.8388 (tptp) REVERT: G 194 ARG cc_start: 0.8822 (mpt-90) cc_final: 0.8602 (mmt90) REVERT: G 206 LYS cc_start: 0.7728 (tttt) cc_final: 0.7421 (tptt) REVERT: G 231 LYS cc_start: 0.6443 (pttm) cc_final: 0.5835 (ttmt) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.0968 time to fit residues: 37.7439 Evaluate side-chains 218 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 129 optimal weight: 0.5980 chunk 73 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 115 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 31 HIS D 31 HIS A 152 ASN E 152 ASN F 31 HIS F 152 ASN G 31 HIS G 152 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.180164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.142914 restraints weight = 18279.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.147861 restraints weight = 13021.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.151884 restraints weight = 10127.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.155000 restraints weight = 8254.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.157004 restraints weight = 7038.009| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.352 11884 Z= 0.157 Angle : 0.933 16.200 16443 Z= 0.326 Chirality : 0.043 0.214 1631 Planarity : 0.006 0.064 2065 Dihedral : 15.005 86.812 1659 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.21), residues: 1400 helix: -0.76 (0.35), residues: 196 sheet: -1.96 (0.51), residues: 70 loop : -1.61 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 69 TYR 0.006 0.001 TYR G 80 PHE 0.014 0.001 PHE C 102 TRP 0.007 0.002 TRP A 67 HIS 0.020 0.001 HIS F 230 Details of bonding type rmsd covalent geometry : bond 0.00437 (11788) covalent geometry : angle 0.93286 (16443) hydrogen bonds : bond 0.03055 ( 154) hydrogen bonds : angle 7.48993 ( 336) Misc. bond : bond 0.09268 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.7789 (mtp) cc_final: 0.7509 (mpp) REVERT: B 102 PHE cc_start: 0.7964 (m-10) cc_final: 0.7327 (m-10) REVERT: C 85 MET cc_start: 0.7940 (mtp) cc_final: 0.7285 (mpp) REVERT: C 191 LYS cc_start: 0.8765 (tptp) cc_final: 0.8447 (tptp) REVERT: C 231 LYS cc_start: 0.7037 (pttm) cc_final: 0.5906 (ttmt) REVERT: D 104 MET cc_start: 0.8439 (mtt) cc_final: 0.8102 (mtt) REVERT: D 174 ASN cc_start: 0.8106 (m-40) cc_final: 0.7822 (m-40) REVERT: A 77 PHE cc_start: 0.7742 (m-10) cc_final: 0.7264 (m-10) REVERT: A 83 SER cc_start: 0.8209 (p) cc_final: 0.7999 (p) REVERT: A 206 LYS cc_start: 0.7754 (tttt) cc_final: 0.7364 (tptt) REVERT: E 148 ASP cc_start: 0.7642 (t70) cc_final: 0.7344 (t70) REVERT: E 170 ASP cc_start: 0.7173 (t0) cc_final: 0.6748 (t0) REVERT: F 80 TYR cc_start: 0.8098 (t80) cc_final: 0.7871 (t80) REVERT: F 85 MET cc_start: 0.7800 (mtp) cc_final: 0.7468 (mpp) REVERT: F 174 ASN cc_start: 0.8101 (m-40) cc_final: 0.7880 (m-40) REVERT: F 191 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8486 (tptp) REVERT: G 67 TRP cc_start: 0.8166 (t-100) cc_final: 0.7775 (t-100) REVERT: G 104 MET cc_start: 0.8289 (mtt) cc_final: 0.8053 (mtt) REVERT: G 191 LYS cc_start: 0.8734 (tptp) cc_final: 0.8400 (tptp) REVERT: G 206 LYS cc_start: 0.7731 (tttt) cc_final: 0.7430 (tptt) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.0909 time to fit residues: 34.7138 Evaluate side-chains 208 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 9 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 ASN D 31 HIS D 152 ASN E 31 HIS E 152 ASN F 31 HIS G 152 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.180100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.142273 restraints weight = 18449.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.147377 restraints weight = 13206.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.151344 restraints weight = 10254.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.154356 restraints weight = 8435.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.156739 restraints weight = 7226.524| |-----------------------------------------------------------------------------| r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.302 11884 Z= 0.150 Angle : 0.935 16.825 16443 Z= 0.325 Chirality : 0.043 0.217 1631 Planarity : 0.005 0.054 2065 Dihedral : 15.157 87.970 1659 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.22), residues: 1400 helix: -0.81 (0.35), residues: 196 sheet: -1.88 (0.51), residues: 70 loop : -1.62 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 69 TYR 0.011 0.001 TYR B 80 PHE 0.007 0.001 PHE G 102 TRP 0.013 0.002 TRP B 67 HIS 0.012 0.001 HIS F 230 Details of bonding type rmsd covalent geometry : bond 0.00409 (11788) covalent geometry : angle 0.93509 (16443) hydrogen bonds : bond 0.03037 ( 154) hydrogen bonds : angle 7.38545 ( 336) Misc. bond : bond 0.09429 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.8063 (mtp) cc_final: 0.7582 (mpp) REVERT: B 102 PHE cc_start: 0.8003 (m-10) cc_final: 0.7365 (m-10) REVERT: B 231 LYS cc_start: 0.6397 (pttm) cc_final: 0.6119 (tttt) REVERT: C 83 SER cc_start: 0.8079 (p) cc_final: 0.7776 (p) REVERT: C 148 ASP cc_start: 0.7816 (t70) cc_final: 0.7615 (t70) REVERT: C 191 LYS cc_start: 0.8803 (tptp) cc_final: 0.8502 (tptp) REVERT: C 231 LYS cc_start: 0.6722 (pttm) cc_final: 0.5697 (tttt) REVERT: D 104 MET cc_start: 0.8404 (mtt) cc_final: 0.8030 (mtt) REVERT: D 174 ASN cc_start: 0.8093 (m-40) cc_final: 0.7810 (m-40) REVERT: A 83 SER cc_start: 0.8160 (p) cc_final: 0.7918 (p) REVERT: A 206 LYS cc_start: 0.7792 (tttt) cc_final: 0.7384 (tptt) REVERT: E 148 ASP cc_start: 0.7621 (t70) cc_final: 0.7304 (t70) REVERT: F 174 ASN cc_start: 0.8074 (m-40) cc_final: 0.7865 (m-40) REVERT: F 191 LYS cc_start: 0.8654 (tmtt) cc_final: 0.8439 (tptp) REVERT: G 67 TRP cc_start: 0.8335 (t-100) cc_final: 0.7705 (t-100) REVERT: G 83 SER cc_start: 0.8150 (p) cc_final: 0.7947 (p) REVERT: G 104 MET cc_start: 0.8323 (mtt) cc_final: 0.8112 (mtm) REVERT: G 191 LYS cc_start: 0.8748 (tptp) cc_final: 0.8423 (tptp) REVERT: G 206 LYS cc_start: 0.7761 (tttt) cc_final: 0.7462 (tptt) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.0867 time to fit residues: 31.8966 Evaluate side-chains 203 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 chunk 54 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS C 152 ASN D 152 ASN A 31 HIS A 152 ASN E 31 HIS E 152 ASN F 31 HIS F 152 ASN G 31 HIS G 152 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.178438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.140380 restraints weight = 18568.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.145347 restraints weight = 13378.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.149135 restraints weight = 10465.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.152071 restraints weight = 8687.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153972 restraints weight = 7487.561| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.358 11884 Z= 0.160 Angle : 0.947 17.829 16443 Z= 0.327 Chirality : 0.043 0.221 1631 Planarity : 0.005 0.050 2065 Dihedral : 15.299 87.553 1659 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.22), residues: 1400 helix: -0.74 (0.36), residues: 196 sheet: -1.83 (0.53), residues: 70 loop : -1.63 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 69 TYR 0.008 0.001 TYR G 80 PHE 0.007 0.001 PHE C 190 TRP 0.012 0.002 TRP B 67 HIS 0.010 0.001 HIS F 230 Details of bonding type rmsd covalent geometry : bond 0.00438 (11788) covalent geometry : angle 0.94726 (16443) hydrogen bonds : bond 0.02962 ( 154) hydrogen bonds : angle 7.39261 ( 336) Misc. bond : bond 0.09951 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 85 MET cc_start: 0.7980 (mtp) cc_final: 0.7607 (mpp) REVERT: B 102 PHE cc_start: 0.8002 (m-10) cc_final: 0.7385 (m-10) REVERT: B 170 ASP cc_start: 0.7393 (t0) cc_final: 0.7049 (t0) REVERT: C 83 SER cc_start: 0.8062 (p) cc_final: 0.7809 (p) REVERT: C 191 LYS cc_start: 0.8795 (tptp) cc_final: 0.8491 (tptp) REVERT: C 231 LYS cc_start: 0.6644 (pttm) cc_final: 0.6374 (pttm) REVERT: D 104 MET cc_start: 0.8349 (mtt) cc_final: 0.7911 (mtt) REVERT: D 174 ASN cc_start: 0.8013 (m-40) cc_final: 0.7730 (m-40) REVERT: A 85 MET cc_start: 0.8003 (mtp) cc_final: 0.7409 (mpp) REVERT: A 177 THR cc_start: 0.8646 (t) cc_final: 0.8437 (t) REVERT: A 206 LYS cc_start: 0.7786 (tttt) cc_final: 0.7458 (tptt) REVERT: E 128 MET cc_start: 0.7236 (tpp) cc_final: 0.7007 (mmm) REVERT: E 148 ASP cc_start: 0.7693 (t70) cc_final: 0.7386 (t70) REVERT: E 170 ASP cc_start: 0.7070 (t0) cc_final: 0.6718 (t0) REVERT: F 80 TYR cc_start: 0.8310 (t80) cc_final: 0.8007 (t80) REVERT: F 85 MET cc_start: 0.7869 (mtp) cc_final: 0.7542 (mpp) REVERT: F 174 ASN cc_start: 0.7989 (m-40) cc_final: 0.7776 (m-40) REVERT: G 67 TRP cc_start: 0.8445 (t-100) cc_final: 0.7794 (t-100) REVERT: G 104 MET cc_start: 0.8283 (mtt) cc_final: 0.8065 (mtm) REVERT: G 191 LYS cc_start: 0.8719 (tptp) cc_final: 0.8419 (tptp) REVERT: G 206 LYS cc_start: 0.7896 (tttt) cc_final: 0.7613 (tptt) outliers start: 0 outliers final: 0 residues processed: 254 average time/residue: 0.0811 time to fit residues: 31.0209 Evaluate side-chains 206 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 84 optimal weight: 0.2980 chunk 40 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 HIS C 152 ASN D 152 ASN A 31 HIS A 152 ASN E 31 HIS E 152 ASN F 31 HIS G 31 HIS G 152 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.179428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.138733 restraints weight = 18357.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144259 restraints weight = 12844.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.148545 restraints weight = 9879.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.151769 restraints weight = 8064.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.153925 restraints weight = 6890.967| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.343 11884 Z= 0.164 Angle : 0.954 17.915 16443 Z= 0.332 Chirality : 0.043 0.223 1631 Planarity : 0.005 0.051 2065 Dihedral : 15.275 87.673 1659 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 0.09 % Allowed : 1.25 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 9.09 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.22), residues: 1400 helix: 0.45 (0.39), residues: 154 sheet: -1.92 (0.53), residues: 70 loop : -1.47 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 69 TYR 0.008 0.001 TYR G 80 PHE 0.008 0.001 PHE F 190 TRP 0.014 0.001 TRP B 67 HIS 0.008 0.001 HIS F 230 Details of bonding type rmsd covalent geometry : bond 0.00455 (11788) covalent geometry : angle 0.95434 (16443) hydrogen bonds : bond 0.03220 ( 154) hydrogen bonds : angle 7.40671 ( 336) Misc. bond : bond 0.09786 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2800 Ramachandran restraints generated. 1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 102 PHE cc_start: 0.7985 (m-10) cc_final: 0.7357 (m-10) REVERT: C 83 SER cc_start: 0.8252 (p) cc_final: 0.7925 (p) REVERT: C 191 LYS cc_start: 0.8849 (tptp) cc_final: 0.8578 (tptp) REVERT: C 231 LYS cc_start: 0.6531 (pttm) cc_final: 0.6216 (pttm) REVERT: D 170 ASP cc_start: 0.7011 (t0) cc_final: 0.6396 (t0) REVERT: D 174 ASN cc_start: 0.8179 (m-40) cc_final: 0.7906 (m-40) REVERT: D 191 LYS cc_start: 0.8949 (tmtt) cc_final: 0.8678 (tptp) REVERT: A 77 PHE cc_start: 0.7983 (m-10) cc_final: 0.7679 (m-10) REVERT: A 83 SER cc_start: 0.8286 (p) cc_final: 0.8078 (p) REVERT: A 206 LYS cc_start: 0.7758 (tttt) cc_final: 0.7376 (tptt) REVERT: E 148 ASP cc_start: 0.7801 (t70) cc_final: 0.7505 (t70) REVERT: E 206 LYS cc_start: 0.7688 (tttt) cc_final: 0.7349 (tptp) REVERT: F 80 TYR cc_start: 0.8376 (t80) cc_final: 0.8172 (t80) REVERT: F 191 LYS cc_start: 0.8830 (tmtt) cc_final: 0.8600 (tptp) REVERT: G 67 TRP cc_start: 0.8558 (t-100) cc_final: 0.7808 (t-100) REVERT: G 191 LYS cc_start: 0.8797 (tptp) cc_final: 0.8472 (tptp) REVERT: G 194 ARG cc_start: 0.8584 (mmt90) cc_final: 0.8253 (mmt90) REVERT: G 206 LYS cc_start: 0.7886 (tttt) cc_final: 0.7535 (tptt) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.0905 time to fit residues: 33.5104 Evaluate side-chains 206 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9287 > 50: distance: 5 - 37: 33.698 distance: 8 - 34: 28.110 distance: 28 - 91: 31.545 distance: 30 - 34: 25.409 distance: 34 - 35: 38.179 distance: 35 - 36: 45.879 distance: 35 - 38: 13.228 distance: 36 - 37: 39.339 distance: 36 - 43: 57.133 distance: 38 - 39: 67.948 distance: 39 - 40: 14.851 distance: 40 - 41: 58.362 distance: 41 - 42: 39.689 distance: 43 - 44: 32.570 distance: 44 - 45: 40.095 distance: 44 - 47: 18.612 distance: 45 - 46: 48.707 distance: 45 - 50: 34.346 distance: 47 - 48: 48.946 distance: 47 - 49: 70.332 distance: 50 - 51: 25.036 distance: 51 - 52: 35.827 distance: 52 - 53: 34.231 distance: 52 - 54: 33.697 distance: 54 - 55: 30.219 distance: 55 - 56: 35.542 distance: 55 - 58: 21.280 distance: 56 - 57: 28.997 distance: 56 - 62: 23.100 distance: 58 - 59: 33.346 distance: 59 - 60: 19.340 distance: 59 - 61: 14.596 distance: 62 - 63: 29.348 distance: 63 - 64: 57.633 distance: 63 - 66: 29.963 distance: 64 - 65: 57.328 distance: 64 - 69: 53.871 distance: 66 - 67: 36.996 distance: 66 - 68: 23.718 distance: 69 - 70: 50.844 distance: 70 - 71: 43.393 distance: 70 - 73: 38.198 distance: 71 - 72: 24.326 distance: 71 - 76: 44.281 distance: 73 - 74: 34.726 distance: 73 - 75: 27.210 distance: 76 - 77: 18.429 distance: 77 - 78: 25.307 distance: 77 - 80: 29.422 distance: 78 - 79: 27.162 distance: 78 - 84: 41.264 distance: 80 - 81: 27.567 distance: 81 - 82: 6.159 distance: 81 - 83: 15.381 distance: 84 - 85: 25.442 distance: 85 - 86: 23.998 distance: 86 - 87: 25.244 distance: 86 - 88: 33.463 distance: 88 - 89: 3.641 distance: 89 - 90: 39.514 distance: 89 - 92: 29.130 distance: 90 - 91: 34.562 distance: 90 - 96: 51.961 distance: 92 - 93: 24.759 distance: 93 - 94: 54.657 distance: 93 - 95: 43.130 distance: 96 - 97: 13.534 distance: 96 - 102: 49.487 distance: 97 - 98: 30.446 distance: 97 - 100: 39.589 distance: 98 - 99: 29.785 distance: 98 - 103: 31.105 distance: 100 - 101: 17.327 distance: 101 - 102: 12.766