Starting phenix.real_space_refine on Wed Mar 4 06:08:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e27_30953/03_2026/7e27_30953.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e27_30953/03_2026/7e27_30953.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e27_30953/03_2026/7e27_30953.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e27_30953/03_2026/7e27_30953.map" model { file = "/net/cci-nas-00/data/ceres_data/7e27_30953/03_2026/7e27_30953.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e27_30953/03_2026/7e27_30953.cif" } resolution = 2.29 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.005 sd= 0.129 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 S 70 5.16 5 C 7575 2.51 5 N 1765 2.21 5 O 2040 1.98 5 F 25 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11475 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2256 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 282} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HV6': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Restraints were copied for chains: B, C, D, E Time building chain proxies: 1.87, per 1000 atoms: 0.16 Number of scatterers: 11475 At special positions: 0 Unit cell: (96.4678, 95.7932, 81.6266, 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) S 70 16.00 F 25 9.00 O 2040 8.00 N 1765 7.00 C 7575 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=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 490.5 milliseconds 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2650 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 1 sheets defined 82.9% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 20 through 34 Processing helix chain 'A' and resid 35 through 38 removed outlier: 3.712A pdb=" N TYR A 38 " --> pdb=" O LYS A 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 35 through 38' Processing helix chain 'A' and resid 39 through 68 removed outlier: 3.842A pdb=" N PHE A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 removed outlier: 3.810A pdb=" N ILE A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 91 through 100 removed outlier: 4.328A pdb=" N MET A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 100 " --> pdb=" O CYS A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 118 removed outlier: 4.453A pdb=" N LEU A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 148 Processing helix chain 'A' and resid 164 through 177 Processing helix chain 'A' and resid 181 through 206 removed outlier: 3.688A pdb=" N PHE A 195 " --> pdb=" O GLY A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 226 removed outlier: 3.958A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 Processing helix chain 'A' and resid 249 through 256 Processing helix chain 'A' and resid 257 through 271 Processing helix chain 'A' and resid 273 through 291 removed outlier: 5.960A pdb=" N GLU A 283 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 34 Processing helix chain 'B' and resid 35 through 38 removed outlier: 3.712A pdb=" N TYR B 38 " --> pdb=" O LYS B 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 35 through 38' Processing helix chain 'B' and resid 39 through 68 removed outlier: 3.842A pdb=" N PHE B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 78 removed outlier: 3.810A pdb=" N ILE B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 91 through 100 removed outlier: 4.328A pdb=" N MET B 95 " --> pdb=" O PRO B 91 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR B 100 " --> pdb=" O CYS B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 118 removed outlier: 4.453A pdb=" N LEU B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 113 " --> pdb=" O THR B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 148 Processing helix chain 'B' and resid 164 through 177 Processing helix chain 'B' and resid 181 through 206 removed outlier: 3.688A pdb=" N PHE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 226 removed outlier: 3.957A pdb=" N VAL B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 244 Processing helix chain 'B' and resid 249 through 256 Processing helix chain 'B' and resid 257 through 271 Processing helix chain 'B' and resid 273 through 291 removed outlier: 5.959A pdb=" N GLU B 283 " --> pdb=" O PHE B 279 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS B 284 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 34 Processing helix chain 'C' and resid 35 through 38 removed outlier: 3.712A pdb=" N TYR C 38 " --> pdb=" O LYS C 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 35 through 38' Processing helix chain 'C' and resid 39 through 68 removed outlier: 3.842A pdb=" N PHE C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 78 removed outlier: 3.810A pdb=" N ILE C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 100 removed outlier: 4.328A pdb=" N MET C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR C 100 " --> pdb=" O CYS C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 118 removed outlier: 4.454A pdb=" N LEU C 110 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR C 113 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 148 Processing helix chain 'C' and resid 164 through 177 Processing helix chain 'C' and resid 181 through 206 removed outlier: 3.688A pdb=" N PHE C 195 " --> pdb=" O GLY C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 226 removed outlier: 3.958A pdb=" N VAL C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 244 Processing helix chain 'C' and resid 249 through 256 Processing helix chain 'C' and resid 257 through 271 Processing helix chain 'C' and resid 273 through 291 removed outlier: 5.960A pdb=" N GLU C 283 " --> pdb=" O PHE C 279 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 34 Processing helix chain 'D' and resid 35 through 38 removed outlier: 3.712A pdb=" N TYR D 38 " --> pdb=" O LYS D 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 35 through 38' Processing helix chain 'D' and resid 39 through 68 removed outlier: 3.841A pdb=" N PHE D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 78 removed outlier: 3.810A pdb=" N ILE D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 90 Processing helix chain 'D' and resid 91 through 100 removed outlier: 4.328A pdb=" N MET D 95 " --> pdb=" O PRO D 91 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR D 100 " --> pdb=" O CYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 118 removed outlier: 4.453A pdb=" N LEU D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA D 111 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR D 113 " --> pdb=" O THR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 148 Processing helix chain 'D' and resid 164 through 177 Processing helix chain 'D' and resid 181 through 206 removed outlier: 3.689A pdb=" N PHE D 195 " --> pdb=" O GLY D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 226 removed outlier: 3.957A pdb=" N VAL D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 Processing helix chain 'D' and resid 249 through 256 Processing helix chain 'D' and resid 257 through 271 Processing helix chain 'D' and resid 273 through 291 removed outlier: 5.959A pdb=" N GLU D 283 " --> pdb=" O PHE D 279 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS D 284 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 34 Processing helix chain 'E' and resid 35 through 38 removed outlier: 3.712A pdb=" N TYR E 38 " --> pdb=" O LYS E 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 35 through 38' Processing helix chain 'E' and resid 39 through 68 removed outlier: 3.841A pdb=" N PHE E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 78 removed outlier: 3.810A pdb=" N ILE E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 90 Processing helix chain 'E' and resid 91 through 100 removed outlier: 4.327A pdb=" N MET E 95 " --> pdb=" O PRO E 91 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR E 100 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 4.454A pdb=" N LEU E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA E 111 " --> pdb=" O GLY E 107 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR E 113 " --> pdb=" O THR E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 148 Processing helix chain 'E' and resid 164 through 177 Processing helix chain 'E' and resid 181 through 206 removed outlier: 3.688A pdb=" N PHE E 195 " --> pdb=" O GLY E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 226 removed outlier: 3.958A pdb=" N VAL E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 244 Processing helix chain 'E' and resid 249 through 256 Processing helix chain 'E' and resid 257 through 271 Processing helix chain 'E' and resid 273 through 291 removed outlier: 5.960A pdb=" N GLU E 283 " --> pdb=" O PHE E 279 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N HIS E 284 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 16 removed outlier: 7.170A pdb=" N SER B 14 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE D 15 " --> pdb=" O SER B 14 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS B 16 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL C 13 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N SER A 14 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE E 15 " --> pdb=" O SER A 14 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS A 16 " --> pdb=" O ILE E 15 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2517 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: 1.93 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1680 1.31 - 1.43: 3560 1.43 - 1.56: 6340 1.56 - 1.69: 0 1.69 - 1.82: 100 Bond restraints: 11680 Sorted by residual: bond pdb=" C12 HV6 B 401 " pdb=" O21 HV6 B 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C12 HV6 A 401 " pdb=" O21 HV6 A 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C12 HV6 C 401 " pdb=" O21 HV6 C 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.80e+01 bond pdb=" C12 HV6 D 401 " pdb=" O21 HV6 D 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C12 HV6 E 401 " pdb=" O21 HV6 E 401 " ideal model delta sigma weight residual 1.311 1.396 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 11675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 15210 2.06 - 4.12: 530 4.12 - 6.18: 75 6.18 - 8.25: 30 8.25 - 10.31: 5 Bond angle restraints: 15850 Sorted by residual: angle pdb=" N PHE D 90 " pdb=" CA PHE D 90 " pdb=" C PHE D 90 " ideal model delta sigma weight residual 109.81 120.12 -10.31 2.21e+00 2.05e-01 2.18e+01 angle pdb=" N PHE A 90 " pdb=" CA PHE A 90 " pdb=" C PHE A 90 " ideal model delta sigma weight residual 109.81 120.11 -10.30 2.21e+00 2.05e-01 2.17e+01 angle pdb=" N PHE B 90 " pdb=" CA PHE B 90 " pdb=" C PHE B 90 " ideal model delta sigma weight residual 109.81 120.07 -10.26 2.21e+00 2.05e-01 2.16e+01 angle pdb=" N PHE E 90 " pdb=" CA PHE E 90 " pdb=" C PHE E 90 " ideal model delta sigma weight residual 109.81 120.07 -10.26 2.21e+00 2.05e-01 2.16e+01 angle pdb=" N PHE C 90 " pdb=" CA PHE C 90 " pdb=" C PHE C 90 " ideal model delta sigma weight residual 109.81 120.07 -10.26 2.21e+00 2.05e-01 2.16e+01 ... (remaining 15845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 5857 16.42 - 32.84: 608 32.84 - 49.27: 95 49.27 - 65.69: 40 65.69 - 82.11: 15 Dihedral angle restraints: 6615 sinusoidal: 2420 harmonic: 4195 Sorted by residual: dihedral pdb=" CA TYR E 70 " pdb=" C TYR E 70 " pdb=" N HIS E 71 " pdb=" CA HIS E 71 " ideal model delta harmonic sigma weight residual -180.00 -161.21 -18.79 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR C 70 " pdb=" C TYR C 70 " pdb=" N HIS C 71 " pdb=" CA HIS C 71 " ideal model delta harmonic sigma weight residual -180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TYR B 70 " pdb=" C TYR B 70 " pdb=" N HIS B 71 " pdb=" CA HIS B 71 " ideal model delta harmonic sigma weight residual 180.00 -161.25 -18.75 0 5.00e+00 4.00e-02 1.41e+01 ... (remaining 6612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1508 0.068 - 0.137: 209 0.137 - 0.205: 38 0.205 - 0.273: 20 0.273 - 0.341: 15 Chirality restraints: 1790 Sorted by residual: chirality pdb=" CB VAL E 142 " pdb=" CA VAL E 142 " pdb=" CG1 VAL E 142 " pdb=" CG2 VAL E 142 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CB VAL C 142 " pdb=" CA VAL C 142 " pdb=" CG1 VAL C 142 " pdb=" CG2 VAL C 142 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB VAL A 142 " pdb=" CA VAL A 142 " pdb=" CG1 VAL A 142 " pdb=" CG2 VAL A 142 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 1787 not shown) Planarity restraints: 1930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 212 " 0.023 2.00e-02 2.50e+03 2.06e-02 8.46e+00 pdb=" CG TYR D 212 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR D 212 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR D 212 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 212 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 212 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 212 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 212 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 212 " 0.023 2.00e-02 2.50e+03 2.06e-02 8.46e+00 pdb=" CG TYR E 212 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR E 212 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR E 212 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 212 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR E 212 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR E 212 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 212 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 212 " -0.023 2.00e-02 2.50e+03 2.06e-02 8.46e+00 pdb=" CG TYR B 212 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 212 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 212 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 212 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR B 212 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 212 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 212 " -0.002 2.00e-02 2.50e+03 ... (remaining 1927 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 3927 2.84 - 3.35: 10752 3.35 - 3.87: 21475 3.87 - 4.38: 25395 4.38 - 4.90: 42009 Nonbonded interactions: 103558 Sorted by model distance: nonbonded pdb=" O ALA E 226 " pdb=" O HOH E 501 " model vdw 2.322 3.040 nonbonded pdb=" N ASP E 208 " pdb=" OD1 ASP E 208 " model vdw 2.331 3.120 nonbonded pdb=" N ASP B 208 " pdb=" OD1 ASP B 208 " model vdw 2.331 3.120 nonbonded pdb=" N ASP A 208 " pdb=" OD1 ASP A 208 " model vdw 2.331 3.120 nonbonded pdb=" N ASP D 208 " pdb=" OD1 ASP D 208 " model vdw 2.332 3.120 ... (remaining 103553 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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 individual isotropic 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: 4.160 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.600 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:8.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.007 0.094 11680 Z= 0.341 Angle : 0.911 10.307 15850 Z= 0.513 Chirality : 0.061 0.341 1790 Planarity : 0.006 0.033 1930 Dihedral : 14.587 82.111 3965 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.42 % Allowed : 5.08 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.60 (0.17), residues: 1425 helix: -1.34 (0.12), residues: 1145 sheet: None (None), residues: 0 loop : -2.57 (0.26), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 74 TYR 0.050 0.003 TYR B 212 PHE 0.042 0.004 PHE C 223 HIS 0.010 0.002 HIS A 59 Details of bonding type rmsd covalent geometry : bond 0.00739 (11680) covalent geometry : angle 0.91057 (15850) hydrogen bonds : bond 0.12179 ( 841) hydrogen bonds : angle 6.18439 ( 2517) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 169 time to evaluate : 0.348 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 169 average time/residue: 0.6754 time to fit residues: 122.2845 Evaluate side-chains 133 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 208 ASP Chi-restraints excluded: chain E residue 208 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 71 HIS A 265 ASN B 71 HIS B 265 ASN C 71 HIS C 265 ASN D 71 HIS D 265 ASN E 71 HIS E 265 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.091077 restraints weight = 12404.994| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 1.21 r_work: 0.2911 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11680 Z= 0.121 Angle : 0.521 7.048 15850 Z= 0.290 Chirality : 0.039 0.144 1790 Planarity : 0.004 0.028 1930 Dihedral : 4.868 35.909 1599 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.03 % Allowed : 9.83 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.33 (0.21), residues: 1425 helix: 0.75 (0.14), residues: 1130 sheet: None (None), residues: 0 loop : -1.61 (0.31), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 290 TYR 0.017 0.002 TYR A 236 PHE 0.025 0.002 PHE B 223 HIS 0.004 0.001 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00245 (11680) covalent geometry : angle 0.52059 (15850) hydrogen bonds : bond 0.04486 ( 841) hydrogen bonds : angle 4.38539 ( 2517) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.418 Fit side-chains REVERT: A 201 TYR cc_start: 0.8572 (OUTLIER) cc_final: 0.7913 (m-80) REVERT: A 283 GLU cc_start: 0.7495 (mm-30) cc_final: 0.6560 (pm20) REVERT: B 201 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7903 (m-80) REVERT: B 283 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6506 (pm20) REVERT: C 283 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6559 (pm20) REVERT: D 201 TYR cc_start: 0.8603 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: E 201 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.7949 (m-80) REVERT: E 283 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6647 (pm20) outliers start: 24 outliers final: 6 residues processed: 163 average time/residue: 0.6386 time to fit residues: 111.8905 Evaluate side-chains 144 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 134 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 74 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 127 optimal weight: 9.9990 chunk 54 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 0.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 179 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.098516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.086404 restraints weight = 12583.211| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.22 r_work: 0.2838 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11680 Z= 0.151 Angle : 0.569 7.382 15850 Z= 0.317 Chirality : 0.042 0.154 1790 Planarity : 0.003 0.025 1930 Dihedral : 4.757 26.089 1595 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.63 % Allowed : 10.25 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.08 (0.22), residues: 1425 helix: 1.34 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.76 (0.30), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 128 TYR 0.017 0.002 TYR A 236 PHE 0.024 0.002 PHE D 223 HIS 0.005 0.002 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00325 (11680) covalent geometry : angle 0.56882 (15850) hydrogen bonds : bond 0.05291 ( 841) hydrogen bonds : angle 4.39164 ( 2517) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.352 Fit side-chains REVERT: A 201 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.7929 (m-80) REVERT: A 283 GLU cc_start: 0.7494 (mm-30) cc_final: 0.6502 (pm20) REVERT: B 201 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: B 283 GLU cc_start: 0.7504 (mm-30) cc_final: 0.6504 (pm20) REVERT: C 283 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6572 (pm20) REVERT: D 201 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.7792 (m-80) REVERT: D 223 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.7268 (p90) REVERT: E 201 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: E 283 GLU cc_start: 0.7578 (mm-30) cc_final: 0.6638 (pm20) outliers start: 31 outliers final: 16 residues processed: 161 average time/residue: 0.6166 time to fit residues: 107.0639 Evaluate side-chains 156 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LYS Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 126 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 35 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS E 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.100846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.088795 restraints weight = 12542.418| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.22 r_work: 0.2874 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11680 Z= 0.124 Angle : 0.519 7.101 15850 Z= 0.289 Chirality : 0.040 0.152 1790 Planarity : 0.003 0.023 1930 Dihedral : 4.519 26.270 1595 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.37 % Allowed : 11.61 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.52 (0.22), residues: 1425 helix: 1.67 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.72 (0.29), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 290 TYR 0.014 0.001 TYR A 236 PHE 0.022 0.002 PHE D 223 HIS 0.004 0.002 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00251 (11680) covalent geometry : angle 0.51930 (15850) hydrogen bonds : bond 0.04516 ( 841) hydrogen bonds : angle 4.22839 ( 2517) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 0.457 Fit side-chains REVERT: A 201 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: A 283 GLU cc_start: 0.7451 (mm-30) cc_final: 0.6558 (pm20) REVERT: B 201 TYR cc_start: 0.8634 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: B 283 GLU cc_start: 0.7500 (mm-30) cc_final: 0.6494 (pm20) REVERT: C 283 GLU cc_start: 0.7508 (mm-30) cc_final: 0.6513 (pm20) REVERT: D 173 ILE cc_start: 0.8586 (mm) cc_final: 0.8385 (mm) REVERT: D 201 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.7990 (m-80) REVERT: D 247 LYS cc_start: 0.8136 (mttt) cc_final: 0.7931 (ttmm) REVERT: E 283 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6595 (pm20) outliers start: 28 outliers final: 13 residues processed: 162 average time/residue: 0.5929 time to fit residues: 103.8176 Evaluate side-chains 148 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain C residue 15 ILE Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 4 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 56 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.096974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.084924 restraints weight = 12472.469| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.22 r_work: 0.2814 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11680 Z= 0.171 Angle : 0.590 7.305 15850 Z= 0.329 Chirality : 0.044 0.162 1790 Planarity : 0.003 0.024 1930 Dihedral : 4.764 26.097 1595 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.39 % Allowed : 10.76 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.39 (0.22), residues: 1425 helix: 1.55 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.62 (0.29), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 128 TYR 0.017 0.002 TYR A 286 PHE 0.025 0.002 PHE D 223 HIS 0.005 0.002 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00381 (11680) covalent geometry : angle 0.58984 (15850) hydrogen bonds : bond 0.05570 ( 841) hydrogen bonds : angle 4.42252 ( 2517) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 132 time to evaluate : 0.372 Fit side-chains REVERT: A 201 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7886 (m-80) REVERT: A 283 GLU cc_start: 0.7464 (mm-30) cc_final: 0.6497 (pm20) REVERT: A 290 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7284 (ttm-80) REVERT: B 201 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: B 283 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6496 (pm20) REVERT: C 283 GLU cc_start: 0.7475 (mm-30) cc_final: 0.6476 (pm20) REVERT: D 173 ILE cc_start: 0.8610 (mm) cc_final: 0.8405 (mm) REVERT: D 201 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: D 247 LYS cc_start: 0.8256 (mttt) cc_final: 0.8046 (ttmm) REVERT: E 201 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8049 (m-80) REVERT: E 283 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6578 (pm20) outliers start: 40 outliers final: 18 residues processed: 163 average time/residue: 0.5495 time to fit residues: 97.4418 Evaluate side-chains 152 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 106 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 HIS C 179 HIS D 179 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.095530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.083476 restraints weight = 12527.910| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.22 r_work: 0.2792 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11680 Z= 0.199 Angle : 0.624 7.375 15850 Z= 0.349 Chirality : 0.046 0.175 1790 Planarity : 0.004 0.026 1930 Dihedral : 4.938 27.093 1595 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.88 % Allowed : 12.03 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.38 (0.22), residues: 1425 helix: 1.50 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.28 (0.31), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 128 TYR 0.019 0.002 TYR A 286 PHE 0.027 0.003 PHE D 223 HIS 0.006 0.002 HIS D 284 Details of bonding type rmsd covalent geometry : bond 0.00456 (11680) covalent geometry : angle 0.62434 (15850) hydrogen bonds : bond 0.05987 ( 841) hydrogen bonds : angle 4.52726 ( 2517) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 136 time to evaluate : 0.477 Fit side-chains REVERT: A 201 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: A 290 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7182 (ttm-80) REVERT: B 201 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: B 283 GLU cc_start: 0.7500 (mm-30) cc_final: 0.6516 (pm20) REVERT: C 283 GLU cc_start: 0.7529 (mm-30) cc_final: 0.6464 (pm20) REVERT: D 173 ILE cc_start: 0.8640 (mm) cc_final: 0.8422 (mm) REVERT: D 201 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.7959 (m-80) REVERT: D 247 LYS cc_start: 0.8270 (mttt) cc_final: 0.8066 (ttmm) REVERT: E 34 LYS cc_start: 0.7496 (mtmt) cc_final: 0.7260 (ttmt) REVERT: E 201 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.8081 (m-80) outliers start: 34 outliers final: 18 residues processed: 160 average time/residue: 0.6047 time to fit residues: 104.7082 Evaluate side-chains 158 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 139 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 28 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.096967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.084903 restraints weight = 12527.699| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.22 r_work: 0.2814 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11680 Z= 0.162 Angle : 0.580 7.240 15850 Z= 0.324 Chirality : 0.043 0.162 1790 Planarity : 0.003 0.025 1930 Dihedral : 4.807 26.444 1595 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.54 % Allowed : 12.37 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.52 (0.22), residues: 1425 helix: 1.62 (0.15), residues: 1125 sheet: None (None), residues: 0 loop : -1.30 (0.30), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 128 TYR 0.020 0.002 TYR A 286 PHE 0.025 0.002 PHE D 223 HIS 0.004 0.002 HIS D 165 Details of bonding type rmsd covalent geometry : bond 0.00355 (11680) covalent geometry : angle 0.57975 (15850) hydrogen bonds : bond 0.05371 ( 841) hydrogen bonds : angle 4.42389 ( 2517) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 137 time to evaluate : 0.308 Fit side-chains REVERT: A 201 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.8012 (m-80) REVERT: A 290 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7218 (ttm-80) REVERT: B 201 TYR cc_start: 0.8692 (OUTLIER) cc_final: 0.8004 (m-80) REVERT: B 283 GLU cc_start: 0.7479 (mm-30) cc_final: 0.6493 (pm20) REVERT: D 173 ILE cc_start: 0.8609 (mm) cc_final: 0.8403 (mm) REVERT: D 201 TYR cc_start: 0.8697 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: D 247 LYS cc_start: 0.8305 (mttt) cc_final: 0.8086 (ttmm) REVERT: E 34 LYS cc_start: 0.7497 (mtmt) cc_final: 0.7286 (ttmt) REVERT: E 201 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8029 (m-80) outliers start: 30 outliers final: 20 residues processed: 161 average time/residue: 0.5745 time to fit residues: 100.3430 Evaluate side-chains 161 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain C residue 102 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 247 LYS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain E residue 114 MET Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 78 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS A 265 ASN B 265 ASN C 265 ASN D 265 ASN E 265 ASN E 284 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.093525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.081536 restraints weight = 12594.348| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.21 r_work: 0.2761 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 2.61 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 11680 Z= 0.278 Angle : 0.706 7.468 15850 Z= 0.394 Chirality : 0.053 0.245 1790 Planarity : 0.004 0.027 1930 Dihedral : 5.215 30.857 1595 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.71 % Allowed : 12.29 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.01 (0.21), residues: 1425 helix: 1.26 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.58 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 128 TYR 0.022 0.003 TYR D 221 PHE 0.029 0.003 PHE D 223 HIS 0.007 0.002 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00664 (11680) covalent geometry : angle 0.70611 (15850) hydrogen bonds : bond 0.06840 ( 841) hydrogen bonds : angle 4.69889 ( 2517) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 135 time to evaluate : 0.469 Fit side-chains REVERT: A 201 TYR cc_start: 0.8738 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: A 290 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7246 (ttm-80) REVERT: B 201 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7905 (m-80) REVERT: B 283 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6510 (pm20) REVERT: D 201 TYR cc_start: 0.8755 (OUTLIER) cc_final: 0.7922 (m-80) REVERT: D 247 LYS cc_start: 0.8396 (mttt) cc_final: 0.8161 (ttmm) REVERT: E 201 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.8039 (m-80) outliers start: 32 outliers final: 18 residues processed: 158 average time/residue: 0.6213 time to fit residues: 106.0166 Evaluate side-chains 153 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain A residue 290 ARG Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain B residue 223 PHE Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 247 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 138 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 112 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 284 HIS B 265 ASN C 265 ASN D 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.089128 restraints weight = 12408.228| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.21 r_work: 0.2861 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11680 Z= 0.117 Angle : 0.512 7.246 15850 Z= 0.284 Chirality : 0.039 0.156 1790 Planarity : 0.003 0.025 1930 Dihedral : 4.587 29.324 1595 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.78 % Allowed : 13.64 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.70 (0.22), residues: 1425 helix: 1.80 (0.15), residues: 1135 sheet: None (None), residues: 0 loop : -1.59 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 290 TYR 0.013 0.001 TYR A 236 PHE 0.020 0.001 PHE D 223 HIS 0.005 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00226 (11680) covalent geometry : angle 0.51247 (15850) hydrogen bonds : bond 0.04264 ( 841) hydrogen bonds : angle 4.23311 ( 2517) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.460 Fit side-chains REVERT: A 201 TYR cc_start: 0.8624 (OUTLIER) cc_final: 0.8130 (m-80) REVERT: B 201 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8133 (m-80) REVERT: B 283 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6489 (pm20) REVERT: C 283 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6448 (pm20) REVERT: D 201 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.8185 (m-80) REVERT: D 247 LYS cc_start: 0.8219 (mttt) cc_final: 0.7958 (ttmm) REVERT: E 283 GLU cc_start: 0.7607 (mm-30) cc_final: 0.6503 (pm20) outliers start: 21 outliers final: 14 residues processed: 162 average time/residue: 0.5908 time to fit residues: 103.6942 Evaluate side-chains 149 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 54 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 25 optimal weight: 0.0470 chunk 136 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 125 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS E 265 ASN E 284 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.104159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.092229 restraints weight = 12459.616| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 1.21 r_work: 0.2908 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11680 Z= 0.108 Angle : 0.489 6.809 15850 Z= 0.270 Chirality : 0.038 0.151 1790 Planarity : 0.003 0.025 1930 Dihedral : 4.258 25.959 1595 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.44 % Allowed : 14.24 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 2.04 (0.22), residues: 1425 helix: 2.02 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.48 (0.28), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 290 TYR 0.021 0.001 TYR E 286 PHE 0.020 0.001 PHE A 223 HIS 0.005 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00205 (11680) covalent geometry : angle 0.48930 (15850) hydrogen bonds : bond 0.03783 ( 841) hydrogen bonds : angle 4.07772 ( 2517) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2850 Ramachandran restraints generated. 1425 Oldfield, 0 Emsley, 1425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.382 Fit side-chains REVERT: A 201 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8044 (m-80) REVERT: A 283 GLU cc_start: 0.7496 (mm-30) cc_final: 0.6550 (pm20) REVERT: B 201 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.8064 (m-80) REVERT: B 283 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6474 (pm20) REVERT: C 34 LYS cc_start: 0.7292 (mtmt) cc_final: 0.7039 (ttmt) REVERT: C 283 GLU cc_start: 0.7543 (mm-30) cc_final: 0.6470 (pm20) REVERT: D 201 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.8091 (m-80) REVERT: D 247 LYS cc_start: 0.8152 (mttt) cc_final: 0.7905 (ttmm) REVERT: D 283 GLU cc_start: 0.7603 (mm-30) cc_final: 0.6491 (pm20) REVERT: E 283 GLU cc_start: 0.7596 (mm-30) cc_final: 0.6543 (pm20) outliers start: 17 outliers final: 12 residues processed: 160 average time/residue: 0.5681 time to fit residues: 98.5346 Evaluate side-chains 152 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 TYR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 201 TYR Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 201 TYR Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 223 PHE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 201 TYR Chi-restraints excluded: chain E residue 223 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 0 optimal weight: 10.0000 chunk 131 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 83 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 HIS E 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.103230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.091389 restraints weight = 12559.520| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.19 r_work: 0.2929 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11680 Z= 0.115 Angle : 0.505 7.109 15850 Z= 0.278 Chirality : 0.038 0.152 1790 Planarity : 0.003 0.025 1930 Dihedral : 4.307 25.404 1595 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.36 % Allowed : 14.15 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.99 (0.22), residues: 1425 helix: 1.98 (0.15), residues: 1140 sheet: None (None), residues: 0 loop : -1.46 (0.28), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 290 TYR 0.013 0.001 TYR D 286 PHE 0.020 0.001 PHE A 223 HIS 0.005 0.001 HIS D 59 Details of bonding type rmsd covalent geometry : bond 0.00223 (11680) covalent geometry : angle 0.50505 (15850) hydrogen bonds : bond 0.04113 ( 841) hydrogen bonds : angle 4.10332 ( 2517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3678.60 seconds wall clock time: 63 minutes 53.97 seconds (3833.97 seconds total)